Single-particle spectral density of the unitary Fermi gas: Novel approach based on the operator product expansion, sum rules and the maximum entropy method

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

Gubler, Philipp, E-mail: pgubler@riken.jp; RIKEN Nishina Center, Wako, Saitama 351-0198; Yamamoto, Naoki

2015-05-15

Making use of the operator product expansion, we derive a general class of sum rules for the imaginary part of the single-particle self-energy of the unitary Fermi gas. The sum rules are analyzed numerically with the help of the maximum entropy method, which allows us to extract the single-particle spectral density as a function of both energy and momentum. These spectral densities contain basic information on the properties of the unitary Fermi gas, such as the dispersion relation and the superfluid pairing gap, for which we obtain reasonable agreement with the available results based on quantum Monte-Carlo simulations.

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

PubMed

Mallik, Saurav; Zhao, Zhongming

2017-12-28

For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm-RANWAR-was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

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

Egli, Martin; Pallan, Pradeep S.; Pattanayek, Rekha

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4{prime} {yields} 6{prime})-linked oligo(2{prime},3{prime}-dideoxy-{beta}-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4{prime} {yields} 6{prime})more » family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.« less

Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides

NASA Technical Reports Server (NTRS)

Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

2001-01-01

The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

Study on Incompatibility of Traditional Chinese Medicine: Evidence from Formula Network, Chemical Space, and Metabolism Room

PubMed Central

Zhang, Xiao-Dong; Wu, Hong-Ying; Jin, Jin; Yu, Guang-Yun; He, Xin; Wang, Hao; Shen, Xiu; Zhou, Ze-Wei; Liu, Pei-Xun; Fan, Sai-Jun

2013-01-01

A traditional Chinese medicine (TCM) formula network including 362 TCM formulas was built by using complex network methodologies. The properties of this network were analyzed including network diameter, average distance, clustering coefficient, and average degree. Meanwhile, we built a TCM chemical space and a TCM metabolism room under the theory of chemical space. The properties of chemical space and metabolism room were calculated and analyzed. The properties of the medicine pairs in “eighteen antagonisms and nineteen mutual inhibitors,” an ancient rule for TCM incompatibility, were studied based on the TCM formula network, chemical space, and metabolism room. The results showed that the properties of these incompatible medicine pairs are different from those of the other TCM based on the analysis of the TCM formula network, chemical space, and metabolism room. The lines of evidence derived from our work demonstrated that the ancient rule of TCM incompatibility, “eighteen antagonisms and nineteen mutual inhibitors,” is probably scientifically based. PMID:24369478

The segment polarity network is a robust developmental module

NASA Astrophysics Data System (ADS)

von Dassow, George; Meir, Eli; Munro, Edwin M.; Odell, Garrett M.

2000-07-01

All insects possess homologous segments, but segment specification differs radically among insect orders. In Drosophila, maternal morphogens control the patterned activation of gap genes, which encode transcriptional regulators that shape the patterned expression of pair-rule genes. This patterning cascade takes place before cellularization. Pair-rule gene products subsequently `imprint' segment polarity genes with reiterated patterns, thus defining the primordial segments. This mechanism must be greatly modified in insect groups in which many segments emerge only after cellularization. In beetles and parasitic wasps, for instance, pair-rule homologues are expressed in patterns consistent with roles during segmentation, but these patterns emerge within cellular fields. In contrast, although in locusts pair-rule homologues may not control segmentation, some segment polarity genes and their interactions are conserved. Perhaps segmentation is modular, with each module autonomously expressing a characteristic intrinsic behaviour in response to transient stimuli. If so, evolution could rearrange inputs to modules without changing their intrinsic behaviours. Here we suggest, using computer simulations, that the Drosophila segment polarity genes constitute such a module, and that this module is resistant to variations in the kinetic constants that govern its behaviour.

Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes

PubMed Central

Rosenberg, Miriam I; Brent, Ava E; Payre, François; Desplan, Claude

2014-01-01

Embryonic anterior–posterior patterning is well understood in Drosophila, which uses ‘long germ’ embryogenesis, in which all segments are patterned before cellularization. In contrast, most insects use ‘short germ’ embryogenesis, wherein only head and thorax are patterned in a syncytial environment while the remainder of the embryo is generated after cellularization. We use the wasp Nasonia (Nv) to address how the transition from short to long germ embryogenesis occurred. Maternal and gap gene expression in Nasonia suggest long germ embryogenesis. However, the Nasonia pair-rule genes even-skipped, odd-skipped, runt and hairy are all expressed as early blastoderm pair-rule stripes and late-forming posterior stripes. Knockdown of Nv eve, odd or h causes loss of alternate segments at the anterior and complete loss of abdominal segments. We propose that Nasonia uses a mixed mode of segmentation wherein pair-rule genes pattern the embryo in a manner resembling Drosophila at the anterior and ancestral Tribolium at the posterior. DOI: http://dx.doi.org/10.7554/eLife.01440.001 PMID:24599282

Light-dependent magnetoreception in birds: the crucial step occurs in the dark.

PubMed

Wiltschko, Roswitha; Ahmad, Margaret; Nießner, Christine; Gehring, Dennis; Wiltschko, Wolfgang

2016-05-01

The Radical Pair Model proposes that the avian magnetic compass is based on spin-chemical processes: since the ratio between the two spin states singlet and triplet of radical pairs depends on their alignment in the magnetic field, it can provide information on magnetic directions. Cryptochromes, blue light-absorbing flavoproteins, with flavin adenine dinucleotide as chromophore, are suggested as molecules forming the radical pairs underlying magnetoreception. When activated by light, cryptochromes undergo a redox cycle, in the course of which radical pairs are generated during photo-reduction as well as during light-independent re-oxidation. This raised the question as to which radical pair is crucial for mediating magnetic directions. Here, we present the results from behavioural experiments with intermittent light and magnetic field pulses that clearly show that magnetoreception is possible in the dark interval, pointing to the radical pair formed during flavin re-oxidation. This differs from the mechanism considered for cryptochrome signalling the presence of light and rules out most current models of an avian magnetic compass based on the radical pair generated during photo-reduction. Using the radical pair formed during re-oxidation may represent a specific adaptation of the avian magnetic compass. © 2016 The Authors.

Structural and Functional Basis of the Fidelity of Nucleotide Selection by Flavivirus RNA-Dependent RNA Polymerases

PubMed Central

Canard, Bruno

2018-01-01

Viral RNA-dependent RNA polymerases (RdRps) play a central role not only in viral replication, but also in the genetic evolution of viral RNAs. After binding to an RNA template and selecting 5′-triphosphate ribonucleosides, viral RdRps synthesize an RNA copy according to Watson-Crick base-pairing rules. The copy process sometimes deviates from both the base-pairing rules specified by the template and the natural ribose selectivity and, thus, the process is error-prone due to the intrinsic (in)fidelity of viral RdRps. These enzymes share a number of conserved amino-acid sequence strings, called motifs A–G, which can be defined from a structural and functional point-of-view. A co-relation is gradually emerging between mutations in these motifs and viral genome evolution or observed mutation rates. Here, we review our current knowledge on these motifs and their role on the structural and mechanistic basis of the fidelity of nucleotide selection and RNA synthesis by Flavivirus RdRps. PMID:29385764

Shaping tRNA

ERIC Educational Resources Information Center

Priano, Christine

2013-01-01

This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

National Rules for Drug–Drug Interactions: Are They Appropriate for Tertiary Hospitals?

PubMed Central

2016-01-01

The application of appropriate rules for drug–drug interactions (DDIs) could substantially reduce the number of adverse drug events. However, current implementations of such rules in tertiary hospitals are problematic as physicians are receiving too many alerts, causing high override rates and alert fatigue. We investigated the potential impact of Korean national DDI rules in a drug utilization review program in terms of their severity coverage and the clinical efficiency of how physicians respond to them. Using lists of high-priority DDIs developed with the support of the U.S. government, we evaluated 706 contraindicated DDI pairs released in May 2015. We evaluated clinical log data from one tertiary hospital and prescription data from two other tertiary hospitals. The measured parameters were national DDI rule coverage for high-priority DDIs, alert override rate, and number of prescription pairs. The coverage rates of national DDI rules were 80% and 3.0% at the class and drug levels, respectively. The analysis of the system log data showed an overall override rate of 79.6%. Only 0.3% of all of the alerts (n = 66) were high-priority DDI rules. These showed a lower override rate of 51.5%, which was much lower than for the overall DDI rules. We also found 342 and 80 unmatched high-priority DDI pairs which were absent in national rules in inpatient orders from the other two hospitals. The national DDI rules are not complete in terms of their coverage of severe DDIs. They also lack clinical efficiency in tertiary settings, suggesting improved systematic approaches are needed. PMID:27822925

Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation.

PubMed

De Zoysa, Meemanage D; Wu, Guowei; Katz, Raviv; Yu, Yi-Tao

2018-06-05

Box H/ACA RNAs are a group of small RNAs found in abundance in eukaryotes (as well as in archaea). Although their sequences differ, eukaryotic box H/ACA RNAs all share the same unique hairpin-hinge-hairpin-tail structure. Almost all of them function as guides that primarily direct pseudouridylation of rRNAs and spliceosomal snRNAs at specific sites. Although box H/ACA RNA-guided pseudouridylation has been extensively studied, the detailed rules governing this reaction, especially those concerning the guide RNA-substrate RNA base-pairing interactions that determine the specificity and efficiency of pseudouridylation, are still not exactly clear. This is particularly relevant given that the lengths of the guide sequences involved in base-pairing vary from one box H/ACA RNA to another. Here, we carry out a detailed investigation into guide-substrate base-pairing interactions, and identify the minimum number of base-pairs (8), required for RNA-guided pseudouridylation. In addition, we find that the pseudouridylation pocket, present in each hairpin of box H/ACA RNA, exhibits flexibility in fitting slightly different substrate sequences. Our results are consistent across three independent pseudouridylation pockets tested, suggesting that our findings are generally applicable to box H/ACA RNA-guided RNA pseudouridylation. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Two Interpretive Systems for Natural Language?

ERIC Educational Resources Information Center

Frazier, Lyn

2015-01-01

It is proposed that humans have available to them two systems for interpreting natural language. One system is familiar from formal semantics. It is a type based system that pairs a syntactic form with its interpretation using grammatical rules of composition. This system delivers both plausible and implausible meanings. The other proposed system…

Multiple approaches to fine-grained indexing of the biomedical literature.

PubMed

Neveol, Aurelie; Shooshan, Sonya E; Humphrey, Susanne M; Rindflesh, Thomas C; Aronson, Alan R

2007-01-01

The number of articles in the MEDLINE database is expected to increase tremendously in the coming years. To ensure that all these documents are indexed with continuing high quality, it is necessary to develop tools and methods that help the indexers in their daily task. We present three methods addressing a novel aspect of automatic indexing of the biomedical literature, namely producing MeSH main heading/subheading pair recommendations. The methods, (dictionary-based, post- processing rules and Natural Language Processing rules) are described and evaluated on a genetics-related corpus. The best overall performance is obtained for the subheading genetics (70% precision and 17% recall with post-processing rules, 48% precision and 37% recall with the dictionary-based method). Future work will address extending this work to all MeSH subheadings and a more thorough study of method combination.

Likelihood Ratio, Optimal Decision Rules, and Relationship between Proportion Correct and d' in the Dual-Pair AB vs BA identification Paradigm

PubMed Central

Micheyl, Christophe; Dai, Huanping

2010-01-01

The equal-variance Gaussian signal-detection-theory (SDT) decision model for the dual-pair change-detection (or “4IAX”) paradigm has been described in earlier publications. In this note, we consider the equal-variance Gaussian SDT model for the related dual-pair AB vs BA identification paradigm. The likelihood ratios, optimal decision rules, receiver operating characteristics (ROCs), and relationships between d' and proportion-correct (PC) are analyzed for two special cases: that of statistically independent observations, which is likely to apply in constant-stimuli experiments, and that of highly correlated observations, which is likely to apply in experiments where stimuli are roved widely across trials or pairs. A surprising outcome of this analysis is that although these two situations lead to different optimal decision rules, the predicted ROCs and proportions of correct responses (PCs) for these two cases are not substantially different, and are either identical or similar to those observed in the basic Yes-No paradigm. PMID:19633356

Mimic expert judgement through automated procedure for selecting rainfall events responsible for shallow landslide: A statistical approach to validation

NASA Astrophysics Data System (ADS)

Giovanna, Vessia; Luca, Pisano; Carmela, Vennari; Mauro, Rossi; Mario, Parise

2016-01-01

This paper proposes an automated method for the selection of rainfall data (duration, D, and cumulated, E), responsible for shallow landslide initiation. The method mimics an expert person identifying D and E from rainfall records through a manual procedure whose rules are applied according to her/his judgement. The comparison between the two methods is based on 300 D-E pairs drawn from temporal rainfall data series recorded in a 30 days time-lag before the landslide occurrence. Statistical tests, employed on D and E samples considered both paired and independent values to verify whether they belong to the same population, show that the automated procedure is able to replicate the expert pairs drawn by the expert judgment. Furthermore, a criterion based on cumulated distribution functions (CDFs) is proposed to select the most related D-E pairs to the expert one among the 6 drawn from the coded procedure for tracing the empirical rainfall threshold line.

Line segment confidence region-based string matching method for map conflation

NASA Astrophysics Data System (ADS)

Huh, Yong; Yang, Sungchul; Ga, Chillo; Yu, Kiyun; Shi, Wenzhong

2013-04-01

In this paper, a method to detect corresponding point pairs between polygon object pairs with a string matching method based on a confidence region model of a line segment is proposed. The optimal point edit sequence to convert the contour of a target object into that of a reference object was found by the string matching method which minimizes its total error cost, and the corresponding point pairs were derived from the edit sequence. Because a significant amount of apparent positional discrepancies between corresponding objects are caused by spatial uncertainty and their confidence region models of line segments are therefore used in the above matching process, the proposed method obtained a high F-measure for finding matching pairs. We applied this method for built-up area polygon objects in a cadastral map and a topographical map. Regardless of their different mapping and representation rules and spatial uncertainties, the proposed method with a confidence level at 0.95 showed a matching result with an F-measure of 0.894.

[Study on anti-hyperlipidemia mechanism of high frequency herb pairs by molecular docking method].

PubMed

Jiang, Lu-di; He, Yu-su; Chen, Xi; Tao, Ou; Li, Gong-Yu; Zhang, Yan-ling

2015-06-01

Traditional Chinese medicine (TCM) has definitely clinical effect in treating hyperlipidemia, but the action mechanism still need to be explored. Based on consulting Chinese Pharmacopoeia (2010), all the lipid-lowering Chinese patent medicines were analyzed by associated rules data mining method to explore high frequency herb pairs. The top three couplet medicines with high support degree were Puerariae Lobatae Radix-Crataegi Fructus, Salviae Miltiorrhizae Radix et Rhizoma-Crataegi Fructus, and Polygoni Multiflori Radix-Crataegi Fructus. The 20 main ingredients were selected from the herb pairs and docked with 3 key hyperlipidemia targets, namely 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase), peroxisome proliferator activated receptor-α (PPAR-α ) and niemann-pick C1 like 1 (NPC1L1) to further discuss the molecular mechanism of the high frequency herb pairs, by using the docking program, LibDock. To construct evaluation rules for the ingredients of herb pairs, the root-mean-square deviation (RMSD) value between computed and initial complexes was first calculated to validate the fitness of LibDock models. Then, the key residues were also confirmed by analyzing the interactions of those 3 proteins and corresponding marketed drugs. The docking results showed that hyperin, puerarin, salvianolic acid A and polydatin can interact with two targets, and the other five compounds may be potent for at least one of the three targets. In this study, the multi-target effect of high frequency herb pairs for lipid-lowering was discussed on the molecular level, which can help further researching new multi-target anti-hyperlipidemia drug.

[Prescription rules of preparations containing Crataegi Fructus in Chinese patent drug].

PubMed

Geng, Ya; Ma, Yue-Xiang; Xu, Hai-Yu; Li, Jun-Fang; Tang, Shi-Huan; Yang, Hong-Jun

2016-08-01

To analyze the prescription rules of preparations containing Crataegi Fructus in the drug standards of the People's Republic of China Ministry of Public Health-Chinese Patent Drug(hereinafter referred to as Chinese patent drug), and provide some references for clinical application and the research and development of new medicines. Based on TCMISS(V2.5), the prescriptions containing Crataegi Fructus in Chinese patent drug were collected to build the database; association rules, frequency statistics and other data mining methods were used to analyze the disease syndrome, common drug compatibility and prescription rules. There were a total of 308 prescriptions containing Crataegi Fructus, involving 499 kinds of Chinese medicines, 34 commonly used drug combinations, and mainly for 18 kinds of diseases. Drug combination analysis was done with "Crataegi Fructus-Citri Reticulatae Pericarpium" and "Crataegi Fructus-Poria" as the high-frequency herb pairs and with "stagnation" and "diarrhea" as the high-frequency diseases. The results indicated that the Crataegi Fructus in different herb pairs had a roughly same function, and its therapy effect was different in different diseases. The prescriptions containing Crataegi Fructus in Chinese patent drug had the effect of digestion, and they were widely used in clinical application, often used together with spleen-strengthening medicines to achieve different treatment effects; the prescription rules reflected the prescription characteristics of Crataegi Fructus for different diseases, providing a basis for its clinically scientific application and the research and development of new medicines. Copyright© by the Chinese Pharmaceutical Association.

Layout optimization with assist features placement by model based rule tables for 2x node random contact

NASA Astrophysics Data System (ADS)

Jun, Jinhyuck; Park, Minwoo; Park, Chanha; Yang, Hyunjo; Yim, Donggyu; Do, Munhoe; Lee, Dongchan; Kim, Taehoon; Choi, Junghoe; Luk-Pat, Gerard; Miloslavsky, Alex

2015-03-01

As the industry pushes to ever more complex illumination schemes to increase resolution for next generation memory and logic circuits, sub-resolution assist feature (SRAF) placement requirements become increasingly severe. Therefore device manufacturers are evaluating improvements in SRAF placement algorithms which do not sacrifice main feature (MF) patterning capability. There are known-well several methods to generate SRAF such as Rule based Assist Features (RBAF), Model Based Assist Features (MBAF) and Hybrid Assisted Features combining features of the different algorithms using both RBAF and MBAF. Rule Based Assist Features (RBAF) continue to be deployed, even with the availability of Model Based Assist Features (MBAF) and Inverse Lithography Technology (ILT). Certainly for the 3x nm node, and even at the 2x nm nodes and lower, RBAF is used because it demands less run time and provides better consistency. Since RBAF is needed now and in the future, what is also needed is a faster method to create the AF rule tables. The current method typically involves making masks and printing wafers that contain several experiments, varying the main feature configurations, AF configurations, dose conditions, and defocus conditions - this is a time consuming and expensive process. In addition, as the technology node shrinks, wafer process changes and source shape redesigns occur more frequently, escalating the cost of rule table creation. Furthermore, as the demand on process margin escalates, there is a greater need for multiple rule tables: each tailored to a specific set of main-feature configurations. Model Assisted Rule Tables(MART) creates a set of test patterns, and evaluates the simulated CD at nominal conditions, defocused conditions and off-dose conditions. It also uses lithographic simulation to evaluate the likelihood of AF printing. It then analyzes the simulation data to automatically create AF rule tables. It means that analysis results display the cost of different AF configurations as the space grows between a pair of main features. In summary, model based rule tables method is able to make it much easier to create rule tables, leading to faster rule-table creation and a lower barrier to the creation of more rule tables.

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

Using SAR Interferograms and Coherence Images for Object-Based Delineation of Unstable Slopes

NASA Astrophysics Data System (ADS)

Friedl, Barbara; Holbling, Daniel

2015-05-01

This study uses synthetic aperture radar (SAR) interferometric products for the semi-automated identification and delineation of unstable slopes and active landslides. Single-pair interferograms and coherence images are therefore segmented and classified in an object-based image analysis (OBIA) framework. The rule-based classification approach has been applied to landslide-prone areas located in Taiwan and Southern Germany. The semi-automatically obtained results were validated against landslide polygons derived from manual interpretation.

A quantitative quantum chemical model of the Dewar-Knott color rule for cationic diarylmethanes

NASA Astrophysics Data System (ADS)

Olsen, Seth

2012-04-01

We document the quantitative manifestation of the Dewar-Knott color rule in a four-electron, three-orbital state-averaged complete active space self-consistent field (SA-CASSCF) model of a series of bridge-substituted cationic diarylmethanes. We show that the lowest excitation energies calculated using multireference perturbation theory based on the model are linearly correlated with the development of hole density in an orbital localized on the bridge, and the depletion of pair density in the same orbital. We quantitatively express the correlation in the form of a generalized Hammett equation.

77 FR 33972 - Channel Spacing and Bandwidth Limitations for Certain Economic Area (EA)-based 800 MHz...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-08

... Nextel reports it will incorporate its 800 MHz SMR spectrum into its CDMA network and forthcoming LTE... LTE because of the channel spacing and bandwidth limitation in Sec. 90.209 of the Commission's rules... other wireless carriers are deploying LTE using 10 megahertz or 20 megahertz channel pairs. Specifically...

Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

PubMed

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Drug side effect extraction from clinical narratives of psychiatry and psychology patients

PubMed Central

Kocher, Jean-Pierre A; Chute, Christopher G; Savova, Guergana K

2011-01-01

Objective To extract physician-asserted drug side effects from electronic medical record clinical narratives. Materials and methods Pattern matching rules were manually developed through examining keywords and expression patterns of side effects to discover an individual side effect and causative drug relationship. A combination of machine learning (C4.5) using side effect keyword features and pattern matching rules was used to extract sentences that contain side effect and causative drug pairs, enabling the system to discover most side effect occurrences. Our system was implemented as a module within the clinical Text Analysis and Knowledge Extraction System. Results The system was tested in the domain of psychiatry and psychology. The rule-based system extracting side effects and causative drugs produced an F score of 0.80 (0.55 excluding allergy section). The hybrid system identifying side effect sentences had an F score of 0.75 (0.56 excluding allergy section) but covered more side effect and causative drug pairs than individual side effect extraction. Discussion The rule-based system was able to identify most side effects expressed by clear indication words. More sophisticated semantic processing is required to handle complex side effect descriptions in the narrative. We demonstrated that our system can be trained to identify sentences with complex side effect descriptions that can be submitted to a human expert for further abstraction. Conclusion Our system was able to extract most physician-asserted drug side effects. It can be used in either an automated mode for side effect extraction or semi-automated mode to identify side effect sentences that can significantly simplify abstraction by a human expert. PMID:21946242

TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries.

PubMed

Chang, Yung-Chun; Dai, Hong-Jie; Wu, Johnny Chi-Yang; Chen, Jian-Ming; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2013-12-01

Patient discharge summaries provide detailed medical information about individuals who have been hospitalized. To make a precise and legitimate assessment of the abundant data, a proper time layout of the sequence of relevant events should be compiled and used to drive a patient-specific timeline, which could further assist medical personnel in making clinical decisions. The process of identifying the chronological order of entities is called temporal relation extraction. In this paper, we propose a hybrid method to identify appropriate temporal links between a pair of entities. The method combines two approaches: one is rule-based and the other is based on the maximum entropy model. We develop an integration algorithm to fuse the results of the two approaches. All rules and the integration algorithm are formally stated so that one can easily reproduce the system and results. To optimize the system's configuration, we used the 2012 i2b2 challenge TLINK track dataset and applied threefold cross validation to the training set. Then, we evaluated its performance on the training and test datasets. The experiment results show that the proposed TEMPTING (TEMPoral relaTion extractING) system (ranked seventh) achieved an F-score of 0.563, which was at least 30% better than that of the baseline system, which randomly selects TLINK candidates from all pairs and assigns the TLINK types. The TEMPTING system using the hybrid method also outperformed the stage-based TEMPTING system. Its F-scores were 3.51% and 0.97% better than those of the stage-based system on the training set and test set, respectively. Copyright © 2013 Elsevier Inc. All rights reserved.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

EM Transition Sum Rules Within the Framework of sdg Proton-Neutron Interacting Boson Model, Nuclear Pair Shell Model and Fermion Dynamical Symmetry Model

NASA Astrophysics Data System (ADS)

Zhao, Yumin

1997-07-01

By the techniques of the Wick theorem for coupled clusters, the no-energy-weighted electromagnetic sum-rule calculations are presented in the sdg neutron-proton interacting boson model, the nuclear pair shell model and the fermion-dynamical symmetry model. The project supported by Development Project Foundation of China, National Natural Science Foundation of China, Doctoral Education Fund of National Education Committee, Fundamental Research Fund of Southeast University

Pair Identity and Smooth Variation Rules Applicable for the Spectroscopic Parameters of H2O Transitions Involving High-J States

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

2010-01-01

Two basic rules (i.e. the pair identity and the smooth variation) applicable for H2O transitions involving high-J states have been discovered. The origins of these rules are the properties of the energy levels and wavefunctions of H2O states with the quantum number J above certain boundaries. As a result, for lines involving high-J states in individually defined groups, all their spectroscopic parameters (i.e. the transition wavenumber, intensity, pressure-broadened half-width, pressure-induced shift, and temperature exponent) must follow these rules. One can use these rules to screen spectroscopic data provided by databases and to identify possible errors. In addition, by using extrapolation methods within the individual groups, one is able to predict the spectroscopic parameters for lines in this group involving very high-J states. The latter are required in developing high-temperature molecular spectroscopic databases such as HITEMP.

Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation

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

Zhang, Qiang; Department of Chemistry, Bohai University, Jinzhou 121000; Zhang, Ruiting

2014-05-14

We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significantmore » deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.« less

Does syntax contribute to the function of duets in a parrot, Amazona auropalliata?

PubMed

Dahlin, Christine R; Wright, Timothy F

2012-07-01

Complex acoustic signals in many animal species are characterized by a syntax that governs how different notes are combined, but the importance of syntax to the communicative function of signals is not well understood. Mated pairs of yellow-naped amazons, Amazona auropalliata, produce coordinated vocal duets that are used for territory maintenance and defense. These duets follow rules that specify the ordering of notes within duets, such as a strict alternation of sex-specific notes and a defined progression of note types through each duet. These syntactical rules may function to define sex-specific roles, improve coordination, and allow individuals to combine calls into meaningful sequences. As a first step toward understanding the functional significance of syntax, we conducted two separate audio playback experiments in which we presented nesting pairs with normal duets and duets with broken syntax (i.e., one of the syntactic rules was broken). In Experiment One, we reversed the order of female and male notes within note pairs while retaining the typical progression of note types through a duet. In Experiment Two we reversed the order of note types across a whole duet while retaining the typical female-male ordering within note pairs. We hypothesized that duets with broken syntax would be less-effective signals than duets with normal syntax and predicted that pairs would respond less to broken syntax than to normal duets. Contrary to predictions, we did not observe differences in response between treatments for any variables except latency to approach the speaker. After we combined data across experiments post hoc, we observed longer latencies to approach the speakers after playbacks of broken syntax duets, suggesting that pairs could differentiate between playbacks. These responses suggest that breaking one rule of duet syntax at a time does not result in detectable loss of signal efficacy in the context of territorial intrusions.

Aggregation and folding phase transitions of RNA molecules

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf

2007-03-01

RNA is a biomolecule that is involved in nearly all aspects of cellular functions. In order to perform many of these functions, RNA molecules have to fold into specific secondary structures. This folding is driven by the tendency of the bases to form Watson-Crick base pairs. Beyond the biological importance of RNA, the relatively simple rules for structure formation of RNA make it a very interesting system from the statistical physics point of view. We will present examples of phase transitions in RNA secondary structure formation that are amenable to analytical descriptions. A special focus will be on aggregation between several RNA molecules which is important for some regulatory circuits based on RNA structure, triplet repeat diseases like Huntington's, and as a model for prion diseases. We show that depending on the relative strength of the intramolecular and the intermolecular base pairing, RNA molecules undergo a transition into an aggregated phase and quantitatively characterize this transition.

Collaborative Brain-Computer Interface for Aiding Decision-Making

PubMed Central

Poli, Riccardo; Valeriani, Davide; Cinel, Caterina

2014-01-01

We look at the possibility of integrating the percepts from multiple non-communicating observers as a means of achieving better joint perception and better group decisions. Our approach involves the combination of a brain-computer interface with human behavioural responses. To test ideas in controlled conditions, we asked observers to perform a simple matching task involving the rapid sequential presentation of pairs of visual patterns and the subsequent decision as whether the two patterns in a pair were the same or different. We recorded the response times of observers as well as a neural feature which predicts incorrect decisions and, thus, indirectly indicates the confidence of the decisions made by the observers. We then built a composite neuro-behavioural feature which optimally combines the two measures. For group decisions, we uses a majority rule and three rules which weigh the decisions of each observer based on response times and our neural and neuro-behavioural features. Results indicate that the integration of behavioural responses and neural features can significantly improve accuracy when compared with the majority rule. An analysis of event-related potentials indicates that substantial differences are present in the proximity of the response for correct and incorrect trials, further corroborating the idea of using hybrids of brain-computer interfaces and traditional strategies for improving decision making. PMID:25072739

CONSTRAINTS ON THE INTERGALACTIC MAGNETIC FIELD WITH GAMMA-RAY OBSERVATIONS OF BLAZARS

DOE PAGES

Finke, Justin D.; Reyes, Luis C.; Georganopoulos, Markos; ...

2015-11-12

Distant BL Lacertae objects emit γ rays which interact with the extragalactic background light (EBL), creating electron-positron pairs, and reducing the flux measured by ground-based imaging atmospheric Cherenkov telescopes (IACTs) at very-high energies (VHE). These pairs can Comptonscatter the cosmic microwave background, creating a γ-ray signature at slightly lower energies observable by the Fermi Large Area Telescope (LAT). This signal is strongly dependent on the intergalactic magnetic field (IGMF) strength (B) and its coherence length (LB). We use IACT spectra taken from the literature for 5 VHE-detected BL Lac objects, and combine it with LAT spectra for these sources tomore » constrain these IGMF parameters. Low B values can be ruled out by the constraint that the cascade flux cannot exceed that observed by the LAT. High values of B can be ruled out from the constraint that the EBL-deabsorbed IACT spectrum cannot be greater than the LAT spectrum extrapolated into the VHE band, unless the cascade spectrum contributes a sizable fraction of the LAT flux. We rule out low B values (B . 10 -19 G for LB ≥ 1 Mpc) at > 5σ in all trials with different EBL models and data selection, except when« less

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

Heaney, Libby; Jaksch, Dieter; Centre for Quantum Technologies, National University of Singapore

Proposals for Bell-inequality tests on systems restricted by the particle-number-superselection rule often require operations that are difficult to implement in practice. In this article, we derive a Bell inequality, where measurements on pairs of states are used as a method to bypass this superselection rule. In particular, we focus on mode entanglement of an arbitrary number of massive particles and show that our Bell inequality detects the entanglement in an identical pair of states when other inequalities fail. However, as the number of particles in the system increases, the violation of our Bell inequality decreases due to the restriction inmore » the measurement space caused by the superselection rule. This Bell test can be implemented using techniques that are routinely used in current experiments.« less

Toward rules relating zinc finger protein sequences and DNA binding site preferences.

PubMed

Desjarlais, J R; Berg, J M

1992-08-15

Zinc finger proteins of the Cys2-His2 type consist of tandem arrays of domains, where each domain appears to contact three adjacent base pairs of DNA through three key residues. We have designed and prepared a series of variants of the central zinc finger within the DNA binding domain of Sp1 by using information from an analysis of a large data base of zinc finger protein sequences. Through systematic variations at two of the three contact positions (underlined), relatively specific recognition of sequences of the form 5'-GGGGN(G or T)GGG-3' has been achieved. These results provide the basis for rules that may develop into a code that will allow the design of zinc finger proteins with preselected DNA site specificity.

Experiments on individual strategy updating in iterated snowdrift game under random rematching.

PubMed

Qi, Hang; Ma, Shoufeng; Jia, Ning; Wang, Guangchao

2015-03-07

How do people actually play the iterated snowdrift games, particularly under random rematching protocol is far from well explored. Two sets of laboratory experiments on snowdrift game were conducted to investigate human strategy updating rules. Four groups of subjects were modeled by experience-weighted attraction learning theory at individual-level. Three out of the four groups (75%) passed model validation. Substantial heterogeneity is observed among the players who update their strategies in four typical types, whereas rare people behave like belief-based learners even under fixed pairing. Most subjects (63.9%) adopt the reinforcement learning (or alike) rules; but, interestingly, the performance of averaged reinforcement learners suffered. It is observed that two factors seem to benefit players in competition, i.e., the sensitivity to their recent experiences and the overall consideration of forgone payoffs. Moreover, subjects with changing opponents tend to learn faster based on their own recent experience, and display more diverse strategy updating rules than they do with fixed opponent. These findings suggest that most of subjects do apply reinforcement learning alike updating rules even under random rematching, although these rules may not improve their performance. The findings help evolutionary biology researchers to understand sophisticated human behavioral strategies in social dilemmas. Copyright © 2015 Elsevier Ltd. All rights reserved.

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.

PubMed

Mukherjee, Sanchita; Kailasam, Senthilkumar; Bansal, Manju; Bhattacharyya, Dhananjay

2014-01-01

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3'-endo sugars and this demands C1'-C1' distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1'-C1' distance from the mean value, to the recent DFT-D functionals, specifically ωB97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014. Copyright © 2013 Wiley Periodicals, Inc.

Theoretical Studies of N2-broadened Half-widths of H2O Lines Involving High j States

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

2012-01-01

Based on the properties of the energy levels and wave functions of H2O states, one can categorize H2O lines into individually defined groups such that within the same group, the energy levels and the wave functions associated with two paired lines have an identity property while those associated with different pairs have a similarity property. Meanwhile, by thoroughly analyzing processes used to calculate N2-broadened half-widths, it was found that the 'Fourier series' of W(sup a)(sub L(sub 1))(sub K(sub 1))(sub K(sub 1)) (t; j(sub f) T(sub f) and W(sup a)(sub L(sub 1))(sub K(sub 1))(sub K(sub 1)) (t; j(sub i) T(sub i), and a factor P(sub 222) (j(sub f) T(sub f) j(sub i) T(sub i)) are the key items in the Robert-Bonamy formalism to distinguish contributions to ReS2(r(sub c)) among different transitions of j(sub f) T(sub f) - j(sub i). However, these items are completely determined by the energy levels and the wave functions associated with their initial and final states and they must bear the latter's features as well. Thus, it becomes obvious that for two paired lines in the same group, their calculated half-widths must be almost identical and the values associated with different pairs must vary smoothly as their ji values vary. Thus, the pair identity and the smooth variation rules are established within individual groups of lines. One can use these rules to screen half-width data listed in HITRAN and to improve the data accuracies.

Termination of String Rewriting Rules that have One Pair of Overlaps

NASA Technical Reports Server (NTRS)

Geser, Alfons; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper presents a partial solution to the long standing open problem of termination of one-rule string rewriting. Overlaps between the two sides of the rule play a central role in existing termination criteria. We characterize termination of all one-rule string rewriting systems that have one such overlap at either end. This both completes a result of Kurth and generalizes a result of Shikishima-Tsuji et al.

First comparative approach to touchscreen-based visual object-location paired-associates learning in humans (Homo sapiens) and a nonhuman primate (Microcebus murinus).

PubMed

Schmidtke, Daniel; Ammersdörfer, Sandra; Joly, Marine; Zimmermann, Elke

2018-05-10

A recent study suggests that a specific, touchscreen-based task on visual object-location paired-associates learning (PAL), the so-called Different PAL (dPAL) task, allows effective translation from animal models to humans. Here, we adapted the task to a nonhuman primate (NHP), the gray mouse lemur, and provide first evidence for the successful comparative application of the task to humans and NHPs. Young human adults reach the learning criterion after considerably less sessions (one order of magnitude) than young, adult NHPs, which is likely due to faster and voluntary rejection of ineffective learning strategies in humans and almost immediate rule generalization. At criterion, however, all human subjects solved the task by either applying a visuospatial rule or, more rarely, by memorizing all possible stimulus combinations and responding correctly based on global visual information. An error-profile analysis in humans and NHPs suggests that successful learning in NHPs is comparably based either on the formation of visuospatial associative links or on more reflexive, visually guided stimulus-response learning. The classification in the NHPs is further supported by an analysis of the individual response latencies, which are considerably higher in NHPs classified as spatial learners. Our results, therefore, support the high translational potential of the standardized, touchscreen-based dPAL task by providing first empirical and comparable evidence for two different cognitive processes underlying dPAL performance in primates. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

PubMed Central

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits. PMID:25097891

Is the Factor-of-2 Rule Broadly Applicable for Evaluating the Prediction Accuracy of Metal-Toxicity Models?

PubMed

Meyer, Joseph S; Traudt, Elizabeth M; Ranville, James F

2018-01-01

In aquatic toxicology, a toxicity-prediction model is generally deemed acceptable if its predicted median lethal concentrations (LC50 values) or median effect concentrations (EC50 values) are within a factor of 2 of their paired, observed LC50 or EC50 values. However, that rule of thumb is based on results from only two studies: multiple LC50 values for the fathead minnow (Pimephales promelas) exposed to Cu in one type of exposure water, and multiple EC50 values for Daphnia magna exposed to Zn in another type of exposure water. We tested whether the factor-of-2 rule of thumb also is supported in a different dataset in which D. magna were exposed separately to Cd, Cu, Ni, or Zn. Overall, the factor-of-2 rule of thumb appeared to be a good guide to evaluating the acceptability of a toxicity model's underprediction or overprediction of observed LC50 or EC50 values in these acute toxicity tests.

Constraints on the Intergalactic Magnetic Field with Gamma-Ray Observations of Blazars

NASA Astrophysics Data System (ADS)

Finke, Justin D.; Reyes, Luis C.; Georganopoulos, Markos; Reynolds, Kaeleigh; Ajello, Marco; Fegan, Stephen J.; McCann, Kevin

2015-11-01

Distant BL Lacertae objects emit γ-rays that interact with the extragalactic background light (EBL), creating electron-positron pairs, and reducing the flux measured by ground-based imaging atmospheric Cherenkov telescopes (IACTs) at very-high energies (VHE). These pairs can Compton-scatter the cosmic microwave background, creating a γ-ray signature at slightly lower energies that is observable by the Fermi Large Area Telescope (LAT). This signal is strongly dependent on the intergalactic magnetic field (IGMF) strength (B) and its coherence length (LB). We use IACT spectra taken from the literature for 5 VHE-detected BL Lac objects and combine them with LAT spectra for these sources to constrain these IGMF parameters. Low B values can be ruled out by the constraint that the cascade flux cannot exceed that observed by the LAT. High values of B can be ruled out from the constraint that the EBL-deabsorbed IACT spectrum cannot be greater than the LAT spectrum extrapolated into the VHE band, unless the cascade spectrum contributes a sizable fraction of the LAT flux. We rule out low B values (B ≲ 10-19 G for LB ≥ 1 Mpc) at >5σ in all trials with different EBL models and data selection, except when using >1 GeV spectra and the lowest EBL models. We were not able to constrain high values of B.

Trajectory selection for the Mariner Jupiter/Saturn 1977 project

NASA Technical Reports Server (NTRS)

Dyer, J. S.; Miles, R. F., Jr.

1974-01-01

The use of decision analysis to facilitate a group decision-making problem in the selection of trajectories for the two spacecraft of the Mariner Jupiter/Saturn 1977 Project. A set of 32 candidate trajectory pairs was developed. Cardinal utility function values were assigned to the trajectory pairs, and the data and statistics derived from collective choice rules were used in selecting the science-preferred trajectory pair.

Expression of the pair-rule gene homologs runt, Pax3/7, even-skipped-1 and even-skipped-2 during larval and juvenile development of the polychaete annelid Capitella teleta does not support a role in segmentation

PubMed Central

2012-01-01

Background Annelids and arthropods each possess a segmented body. Whether this similarity represents an evolutionary convergence or inheritance from a common segmented ancestor is the subject of ongoing investigation. Methods To investigate whether annelids and arthropods share molecular components that control segmentation, we isolated orthologs of the Drosophila melanogaster pair-rule genes, runt, paired (Pax3/7) and eve, from the polychaete annelid Capitella teleta and used whole mount in situ hybridization to characterize their expression patterns. Results When segments first appear, expression of the single C. teleta runt ortholog is only detected in the brain. Later, Ct-runt is expressed in the ventral nerve cord, foregut and hindgut. Analysis of Pax genes in the C. teleta genome reveals the presence of a single Pax3/7 ortholog. Ct-Pax3/7 is initially detected in the mid-body prior to segmentation, but is restricted to two longitudinal bands in the ventral ectoderm. Each of the two C. teleta eve orthologs has a unique and complex expression pattern, although there is partial overlap in several tissues. Prior to and during segment formation, Ct-eve1 and Ct-eve2 are both expressed in the bilaterial pair of mesoteloblasts, while Ct-eve1 is expressed in the descendant mesodermal band cells. At later stages, Ct-eve2 is expressed in the central and peripheral nervous system, and in mesoderm along the dorsal midline. In late stage larvae and adults, Ct-eve1 and Ct-eve2 are expressed in the posterior growth zone. Conclusions C. teleta eve, Pax3/7 and runt homologs all have distinct expression patterns and share expression domains with homologs from other bilaterians. None of the pair-rule orthologs examined in C. teleta exhibit segmental or pair-rule stripes of expression in the ectoderm or mesoderm, consistent with an independent origin of segmentation between annelids and arthropods. PMID:22510249

Knowledge Acquisition from Structural Descriptions.

ERIC Educational Resources Information Center

Hayes-Roth, Frederick; McDermott, John

The learning machine described in this paper acquires concepts representable as conjunctive forms of the predicate calculus and behaviors representable as productions (antecedent-consequent pairs of such conjunctive forms): these concepts and behavior rules are inferred from sequentially presented pairs of examples by an algorithm that is probably…

Emergence of a coherent and cohesive swarm based on mutual anticipation

PubMed Central

Murakami, Hisashi; Niizato, Takayuki; Gunji, Yukio-Pegio

2017-01-01

Collective behavior emerging out of self-organization is one of the most striking properties of an animal group. Typically, it is hypothesized that each individual in an animal group tends to align its direction of motion with those of its neighbors. Most previous models for collective behavior assume an explicit alignment rule, by which an agent matches its velocity with that of neighbors in a certain neighborhood, to reproduce a collective order pattern by simple interactions. Recent empirical studies, however, suggest that there is no evidence for explicit matching of velocity, and that collective polarization arises from interactions other than those that follow the explicit alignment rule. We here propose a new lattice-based computational model that does not incorporate the explicit alignment rule but is based instead on mutual anticipation and asynchronous updating. Moreover, we show that this model can realize densely collective motion with high polarity. Furthermore, we focus on the behavior of a pair of individuals, and find that the turning response is drastically changed depending on the distance between two individuals rather than the relative heading, and is consistent with the empirical observations. Therefore, the present results suggest that our approach provides an alternative model for collective behavior. PMID:28406173

IOTA Simple Rules in Differentiating between Benign and Malignant Adnexal Masses by Non-expert Examiners.

PubMed

Tinnangwattana, Dangcheewan; Vichak-Ururote, Linlada; Tontivuthikul, Paponrad; Charoenratana, Cholaros; Lerthiranwong, Thitikarn; Tongsong, Theera

2015-01-01

To evaluate the diagnostic performance of IOTA simple rules in predicting malignant adnexal tumors by non-expert examiners. Five obstetric/gynecologic residents, who had never performed gynecologic ultrasound examination by themselves before, were trained for IOTA simple rules by an experienced examiner. One trained resident performed ultrasound examinations including IOTA simple rules on 100 women, who were scheduled for surgery due to ovarian masses, within 24 hours of surgery. The gold standard diagnosis was based on pathological or operative findings. The five-trained residents performed IOTA simple rules on 30 patients for evaluation of inter-observer variability. A total of 100 patients underwent ultrasound examination for the IOTA simple rules. Of them, IOTA simple rules could be applied in 94 (94%) masses including 71 (71.0%) benign masses and 29 (29.0%) malignant masses. The diagnostic performance of IOTA simple rules showed sensitivity of 89.3% (95%CI, 77.8%; 100.7%), specificity 83.3% (95%CI, 74.3%; 92.3%). Inter-observer variability was analyzed using Cohen's kappa coefficient. Kappa indices of the four pairs of raters are 0.713-0.884 (0.722, 0.827, 0.713, and 0.884). IOTA simple rules have high diagnostic performance in discriminating adnexal masses even when are applied by non-expert sonographers, though a training course may be required. Nevertheless, they should be further tested by a greater number of general practitioners before widely use.

How Best to Remove the Snare from the Pair: Construction and Cognitive Load Hypotheses

ERIC Educational Resources Information Center

Igo, L. Brent; Kiewra, Kenneth A.; Zumbrunn, Sharon K.; Kirschbaum, Allison L.

2007-01-01

Students (N = 124) viewed 14 timed Web pages that distinguished 14 confusing word pairs. In a 2 x 2 factorial design, the authors gave all of the students matrices containing representational pictures for each pair of words, as well as examples of each word in use. One factor in the design was the absence or presence of rules of usage for each…

Flexible Computing Architecture for Real Time Skin Detection

DTIC Science & Technology

2010-03-01

Figure 6. Spectra of Light and Dark Skin Compared with Spectra of Other Materials .............. 2-5 Figure 7(a.) Joint Distribution of (NDSI/ NDVI ...Vegetation Index ( NDVI ). In Eqn. 2, and are the estimated reflectances of the 660 and 750 nm wavelengths, respectively. As can be seen from Eqn...values, while the rules based detectors use a rectangular bound on either (NDSI, NDVI ) or (NDSI, NDGRI) pairs. The last detection algorithm is the

AUCTSP: an improved biomarker gene pair class predictor.

PubMed

Kagaris, Dimitri; Khamesipour, Alireza; Yiannoutsos, Constantin T

2018-06-26

The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule for classification and class prediction of gene expression profiles. The idea that differences in gene expression ranking are associated with presence or absence of disease is compelling and has strong biological plausibility. Nevertheless, the TSP formulation ignores significant available information which can improve classification accuracy and is vulnerable to selecting genes which do not have differential expression in the two conditions ("pivot" genes). We introduce the AUCTSP classifier as an alternative rank-based estimator of the magnitude of the ranking reversals involved in the original TSP. The proposed estimator is based on the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) and as such, takes into account the separation of the entire distribution of gene expression levels in gene pairs under the conditions considered, as opposed to comparing gene rankings within individual subjects as in the original TSP formulation. Through extensive simulations and case studies involving classification in ovarian, leukemia, colon, breast and prostate cancers and diffuse large b-cell lymphoma, we show the superiority of the proposed approach in terms of improving classification accuracy, avoiding overfitting and being less prone to selecting non-informative (pivot) genes. The proposed AUCTSP is a simple yet reliable and robust rank-based classifier for gene expression classification. While the AUCTSP works by the same principle as TSP, its ability to determine the top scoring gene pair based on the relative rankings of two marker genes across all subjects as opposed to each individual subject results in significant performance gains in classification accuracy. In addition, the proposed method tends to avoid selection of non-informative (pivot) genes as members of the top-scoring pair.

Classified one-step high-radix signed-digit arithmetic units

NASA Astrophysics Data System (ADS)

Cherri, Abdallah K.

1998-08-01

High-radix number systems enable higher information storage density, less complexity, fewer system components, and fewer cascaded gates and operations. A simple one-step fully parallel high-radix signed-digit arithmetic is proposed for parallel optical computing based on new joint spatial encodings. This reduces hardware requirements and improves throughput by reducing the space-bandwidth produce needed. The high-radix signed-digit arithmetic operations are based on classifying the neighboring input digit pairs into various groups to reduce the computation rules. A new joint spatial encoding technique is developed to present both the operands and the computation rules. This technique increases the spatial bandwidth product of the spatial light modulators of the system. An optical implementation of the proposed high-radix signed-digit arithmetic operations is also presented. It is shown that our one-step trinary signed-digit and quaternary signed-digit arithmetic units are much simpler and better than all previously reported high-radix signed-digit techniques.

Microarray-based cancer prediction using soft computing approach.

PubMed

Wang, Xiaosheng; Gotoh, Osamu

2009-05-26

One of the difficulties in using gene expression profiles to predict cancer is how to effectively select a few informative genes to construct accurate prediction models from thousands or ten thousands of genes. We screen highly discriminative genes and gene pairs to create simple prediction models involved in single genes or gene pairs on the basis of soft computing approach and rough set theory. Accurate cancerous prediction is obtained when we apply the simple prediction models for four cancerous gene expression datasets: CNS tumor, colon tumor, lung cancer and DLBCL. Some genes closely correlated with the pathogenesis of specific or general cancers are identified. In contrast with other models, our models are simple, effective and robust. Meanwhile, our models are interpretable for they are based on decision rules. Our results demonstrate that very simple models may perform well on cancerous molecular prediction and important gene markers of cancer can be detected if the gene selection approach is chosen reasonably.

Building v/s Exploring Models: Comparing Learning of Evolutionary Processes through Agent-based Modeling

NASA Astrophysics Data System (ADS)

Wagh, Aditi

Two strands of work motivate the three studies in this dissertation. Evolutionary change can be viewed as a computational complex system in which a small set of rules operating at the individual level result in different population level outcomes under different conditions. Extensive research has documented students' difficulties with learning about evolutionary change (Rosengren et al., 2012), particularly in terms of levels slippage (Wilensky & Resnick, 1999). Second, though building and using computational models is becoming increasingly common in K-12 science education, we know little about how these two modalities compare. This dissertation adopts agent-based modeling as a representational system to compare these modalities in the conceptual context of micro-evolutionary processes. Drawing on interviews, Study 1 examines middle-school students' productive ways of reasoning about micro-evolutionary processes to find that the specific framing of traits plays a key role in whether slippage explanations are cued. Study 2, which was conducted in 2 schools with about 150 students, forms the crux of the dissertation. It compares learning processes and outcomes when students build their own models or explore a pre-built model. Analysis of Camtasia videos of student pairs reveals that builders' and explorers' ways of accessing rules, and sense-making of observed trends are of a different character. Builders notice rules through available blocks-based primitives, often bypassing their enactment while explorers attend to rules primarily through the enactment. Moreover, builders' sense-making of observed trends is more rule-driven while explorers' is more enactment-driven. Pre and posttests reveal that builders manifest a greater facility with accessing rules, providing explanations manifesting targeted assembly. Explorers use rules to construct explanations manifesting non-targeted assembly. Interviews reveal varying degrees of shifts away from slippage in both modalities, with students who built models not incorporating slippage explanations in responses. Study 3 compares these modalities with a control using traditional activities. Pre and posttests reveal that the two modalities manifested greater facility with accessing and assembling rules than the control. The dissertation offers implications for the design of learning environments for evolutionary change, design of the two modalities based on their strengths and weaknesses, and teacher training for the same.

Integrating policy-based management and SLA performance monitoring

NASA Astrophysics Data System (ADS)

Liu, Tzong-Jye; Lin, Chin-Yi; Chang, Shu-Hsin; Yen, Meng-Tzu

2001-10-01

Policy-based management system provides the configuration capability for the system administrators to focus on the requirements of customers. The service level agreement performance monitoring mechanism helps system administrators to verify the correctness of policies. However, it is difficult for a device to process the policies directly because the policies are the management concept. This paper proposes a mechanism to decompose a policy into rules that can be efficiently processed by a device. Thus, the device may process the rule and collect the performance statistics information efficiently; and the policy-based management system may collect these performance statistics information and report the service-level agreement performance monitoring information to the system administrator. The proposed policy-based management system achieves both the policy configuration and service-level agreement performance monitoring requirements. A policy consists of a condition part and an action part. The condition part is a Boolean expression of a source host IP group, a destination host IP group, etc. The action part is the parameters of services. We say that an address group is compact if it only consists of a range of IP address that can be denoted by a pair of IP address and corresponding IP mask. If the condition part of a policy only consists of the compact address group, we say that the policy is a rule. Since a device can efficiently process a compact address and a system administrator prefers to define a range of IP address, the policy-based management system has to translate policy into rules and supplements the gaps between policy and rules. The proposed policy-based management system builds the relationships between VPN and policies, policy and rules. Since the system administrator wants to monitor the system performance information of VPNs and policies, the proposed policy-based management system downloads the relationships among VPNs, policies and rules to the SNMP agents. The SNMP agents build the management information base (MIB) of all VPNs, policies and rules according to the relationships obtained from the management server. Thus, the proposed policy-based management system may get all performance monitoring information of VPNs and policies from agents. The proposed policy-based manager achieves two goals: a) provide a management environment for the system administrator to configure their network only considering the policy requirement issues and b) let the device have only to process the packet and then collect the required performance information. These two things make the proposed management system satisfy both the user and device requirements.

Infant Learning Is Influenced by Local Spurious Generalizations

ERIC Educational Resources Information Center

Gerken, LouAnn; Quam, Carolyn

2017-01-01

In previous work, 11-month-old infants were able to learn rules about the relation of the consonants in CVCV words from just four examples. The rules involved phonetic feature relations (same voicing or same place of articulation), and infants' learning was impeded when pairs of words allowed alternative possible generalizations (e.g. two words…

Learning in the Absence of Experience-Dependent Regulation of NMDAR Composition

ERIC Educational Resources Information Center

Lebel, David; Sidhu, Nishchal; Barkai, Edi; Quinlan, Elizabeth M.

2006-01-01

Olfactory discrimination (OD) learning consists of two phases: an initial N-methyl-d-aspartate (NMDA) receptor--sensitive rule-learning phase, followed by an NMDA receptor (NMDAR)--insensitive pair-learning phase. The rule-learning phase is accompanied by changes in the composition and function of NMDARs at synapses in the piriform cortex,…

Storage-based Intrusion Detection: Watching storage activity for suspicious behavior

DTIC Science & Technology

2002-10-01

password management involves a pair of inter-related files (/etc/ passwd and /etc/shadow). The corresponding access pat- terns seen at the storage...example, consider a UNIX system password file (/etc/ passwd ), which con- sists of a set of well-defined records. Records are delimited by a line-break, and...etc/ passwd and verify that they conform to a set of basic integrity rules: 7-field records, non-empty password field, legal default shell, legal home

Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule.

PubMed

Rosandić, Marija; Vlahović, Ines; Glunčić, Matko; Paar, Vladimir

2016-07-01

For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson-Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson-Crick base pairing generates CSPR. We demonstrate quadruplet's symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These "landscapes" are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1-12, and X, Y the "landscapes" are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.

A three-state kinetic agent-based model to analyze tax evasion dynamics

NASA Astrophysics Data System (ADS)

Crokidakis, Nuno

2014-11-01

In this work we study the problem of tax evasion on a fully-connected population. For this purpose, we consider that the agents may be in three different states, namely honest tax payers, tax evaders and undecided, that are individuals in an intermediate class among honests and evaders. Every individual can change his/her state following a kinetic exchange opinion dynamics, where the agents interact by pairs with competitive negative (with probability q) and positive (with probability 1-q) couplings, representing agreement/disagreement between pairs of agents. In addition, we consider the punishment rules of the Zaklan econophysics model, for which there is a probability pa of an audit each agent is subject to in every period and a length of time k detected tax evaders remain honest. Our results suggest that below the critical point qc=1/4 of the opinion dynamics the compliance is high, and the punishment rules have a small effect in the population. On the other hand, for q>qc the tax evasion can be considerably reduced by the enforcement mechanism. We also discuss the impact of the presence of the undecided agents in the evolution of the system.

Unipolar distributions of junctional Myosin II identify cell stripe boundaries that drive cell intercalation throughout Drosophila axis extension

PubMed Central

Tetley, Robert J; Blanchard, Guy B; Fletcher, Alexander G; Adams, Richard J; Sanson, Bénédicte

2016-01-01

Convergence and extension movements elongate tissues during development. Drosophila germ-band extension (GBE) is one example, which requires active cell rearrangements driven by Myosin II planar polarisation. Here, we develop novel computational methods to analyse the spatiotemporal dynamics of Myosin II during GBE, at the scale of the tissue. We show that initial Myosin II bipolar cell polarization gives way to unipolar enrichment at parasegmental boundaries and two further boundaries within each parasegment, concomitant with a doubling of cell number as the tissue elongates. These boundaries are the primary sites of cell intercalation, behaving as mechanical barriers and providing a mechanism for how cells remain ordered during GBE. Enrichment at parasegment boundaries during GBE is independent of Wingless signaling, suggesting pair-rule gene control. Our results are consistent with recent work showing that a combinatorial code of Toll-like receptors downstream of pair-rule genes contributes to Myosin II polarization via local cell-cell interactions. We propose an updated cell-cell interaction model for Myosin II polarization that we tested in a vertex-based simulation. DOI: http://dx.doi.org/10.7554/eLife.12094.001 PMID:27183005

High sensitivity Troponin T: an audit of implementation of its protocol in a district general hospital.

PubMed

Kalim, Shahid; Nazir, Shaista; Khan, Zia Ullah

2013-01-01

Protocols based on newer high sensitivity Troponin T (hsTropT) assays can rule in a suspected Acute Myocardial Infarction (AMI) as early as 3 hours. We conducted this study to audit adherence to our Trust's newly introduced AMI diagnostic protocol based on paired hsTropT testing at 0 and 3 hours. We retrospectively reviewed data of all patients who had hsTropT test done between 1st and 7th May 2012. Patient's demographics, utility of single or paired samples, time interval between paired samples, patient's presenting symptoms and ECG findings were noted and their means, medians, Standard deviations and proportions were calculated. A total of 66 patients had hsTropT test done during this period. Mean age was 63.30 +/- 17.46 years and 38 (57.57%) were males. Twenty-four (36.36%) patients had only single, rather than protocol recommended paired hsTropT samples, taken. Among the 42 (63.63%) patients with paired samples, the mean time interval was found to be 4.41 +/- 5.7 hours. Contrary to the recommendations, 15 (22.73%) had a very long whereas 2 (3.03%) had a very short time interval between two samples. A subgroup analysis of patients with single samples, found only 2 (3.03%) patient with ST-segment elevation, appropriate for single testing. Our study confirmed that in a large number of patients the protocol for paired sampling or a recommended time interval of 3 hours between 2 samples was not being followed.

Learning the rules of the rock-paper-scissors game: chimpanzees versus children.

PubMed

Gao, Jie; Su, Yanjie; Tomonaga, Masaki; Matsuzawa, Tetsuro

2018-01-01

The present study aimed to investigate whether chimpanzees (Pan troglodytes) could learn a transverse pattern by being trained in the rules of the rock-paper-scissors game in which "paper" beats "rock," "rock" beats "scissors," and "scissors" beats "paper." Additionally, this study compared the learning processes between chimpanzees and children. Seven chimpanzees were tested using a computer-controlled task. They were trained to choose the stronger of two options according to the game rules. The chimpanzees first engaged in the paper-rock sessions until they reached the learning criterion. Subsequently, they engaged in the rock-scissors and scissors-paper sessions, before progressing to sessions with all three pairs mixed. Five of the seven chimpanzees completed training after a mean of 307 sessions, which indicates that they learned the circular pattern. The chimpanzees required more scissors-paper sessions (14.29 ± 6.89), the third learnt pair, than paper-rock (1.71 ± 0.18) and rock-scissors (3.14 ± 0.70) sessions, suggesting they had difficulty finalizing the circularity. The chimpanzees then received generalization tests using new stimuli, which they learned quickly. A similar procedure was performed with children (35-71 months, n = 38) who needed the same number of trials for all three pairs during single-paired sessions. Their accuracy during the mixed-pair sessions improved with age and was better than chance from 50 months of age, which indicates that the ability to solve the transverse patterning problem might develop at around 4 years of age. The present findings show that chimpanzees were able to learn the task but had difficulties with circularity, whereas children learned the task more easily and developed the relevant ability at approximately 4 years of age. Furthermore, the chimpanzees' performance during the mixed-pair sessions was similar to that of 4-year-old children during the corresponding stage of training.

Preparation of name and address data for record linkage using hidden Markov models

PubMed Central

Churches, Tim; Christen, Peter; Lim, Kim; Zhu, Justin Xi

2002-01-01

Background Record linkage refers to the process of joining records that relate to the same entity or event in one or more data collections. In the absence of a shared, unique key, record linkage involves the comparison of ensembles of partially-identifying, non-unique data items between pairs of records. Data items with variable formats, such as names and addresses, need to be transformed and normalised in order to validly carry out these comparisons. Traditionally, deterministic rule-based data processing systems have been used to carry out this pre-processing, which is commonly referred to as "standardisation". This paper describes an alternative approach to standardisation, using a combination of lexicon-based tokenisation and probabilistic hidden Markov models (HMMs). Methods HMMs were trained to standardise typical Australian name and address data drawn from a range of health data collections. The accuracy of the results was compared to that produced by rule-based systems. Results Training of HMMs was found to be quick and did not require any specialised skills. For addresses, HMMs produced equal or better standardisation accuracy than a widely-used rule-based system. However, acccuracy was worse when used with simpler name data. Possible reasons for this poorer performance are discussed. Conclusion Lexicon-based tokenisation and HMMs provide a viable and effort-effective alternative to rule-based systems for pre-processing more complex variably formatted data such as addresses. Further work is required to improve the performance of this approach with simpler data such as names. Software which implements the methods described in this paper is freely available under an open source license for other researchers to use and improve. PMID:12482326

Relative Stabilities and Reactivities of Isolated Versus Conjugated Alkenes: Reconciliation Via a Molecular Orbital Approach

NASA Astrophysics Data System (ADS)

Sotiriou-Leventis, Chariklia; Hanna, Samir B.; Leventis, Nicholas

1996-04-01

The well-accepted practice of generating a pair of molecular orbitals, one of lower energy and another of higher energy than the original pair of overlapping atomic orbitals, and the concept of a particle in a one-dimensional box are implemented in a simplified, nonmathematical method that explains the relative stabilities and reactivities of alkenes with conjugated versus isolated double bonds. In this method, Huckel-type MO's of higher polyenes are constructed by energy rules of linear combination of atomic orbitals. One additional rule is obeyed: bonding molecular orbitals overlap only with bonding molecular orbitals, and antibonding molecular orbitals overlap only with antibonding molecular orbitals.

Self-accommodation of B19' martensite in Ti-Ni shape memory alloys - Part I. Morphological and crystallographic studies of the variant selection rule

NASA Astrophysics Data System (ADS)

Nishida, M.; Nishiura, T.; Kawano, H.; Inamura, T.

2012-06-01

The self-accommodation morphologies of B19‧ martensite in Ti-Ni alloys have been investigated by optical microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Twelve pairs of minimum units consisting of two habit plane variants (HPVs) with V-shaped morphology connected to a ? B19‧ type I variant accommodation twin were observed. Three types of self-accommodation morphologies, based on the V-shaped minimum unit, developed around one of the {111}B2 traces, which were triangular, rhombic and hexangular and consisted of three, four and six HPVs, respectively. In addition, the variant selection rule and the number of possible HPV combinations in each of these self-accommodation morphologies are discussed.

Collisional Lifetimes of Elementary Excitations in Two-Dimensional Systems in the Field of a Strong Electromagnetic Wave

NASA Astrophysics Data System (ADS)

Kovalev, V. M.

2018-04-01

A two-dimensional system with two nonequivalent valleys in the field of a strong circularly polarized electromagnetic wave is considered. It is assumed that the optical selection rules for a given polarization of light allow band-to-band transitions only in valleys of one, optically active, type (two-dimensional layer based on transition metal dichalcogenides, gapped graphene, etc.). This leads to the formation of photon-coupled electron-hole pairs, or an "optical insulator" state. It is assumed that the valleys of the second type (optically inactive) are populated with an equilibrium electron gas. The relaxation of elementary excitations in this hybrid system consisting of an electron gas and a gas of electron-hole pairs caused by the Coulomb interaction between the particles is investigated.

75 FR 310 - Endangered and Threatened Wildlife and Plants; Withdrawal of Proposed Rule to List Cook's Petrel

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

... following predator eradications (Rayner 2008, in litt.; BLI 2009, unpaginated). The minimum world population...). The population of the Cook's petrel on Little Barrier Island was thought to be about 50,000 pairs (BLI...-242) and Rayner (2008, in litt.) determined that the population is approximately 286,000 pairs. The...

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

Sobottka, Marcelo, E-mail: sobottka@mtm.ufsc.br; Hart, Andrew G., E-mail: ahart@dim.uchile.cl

Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that themore » frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.« less

Caudal Regulates the Spatiotemporal Dynamics of Pair-Rule Waves in Tribolium

PubMed Central

El-Sherif, Ezzat; Zhu, Xin; Fu, Jinping; Brown, Susan J.

2014-01-01

In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation. PMID:25329152

Utility of Decision Rules for Transcutaneous Bilirubin Measurements

PubMed Central

Burgos, Anthony E.; Flaherman, Valerie; Chung, Esther K.; Simpson, Elizabeth A.; Goyal, Neera K.; Von Kohorn, Isabelle; Dhepyasuwan, Niramol

2016-01-01

BACKGROUND: Transcutaneous bilirubin (TcB) meters are widely used for screening newborns for jaundice, with a total serum bilirubin (TSB) measurement indicated when the TcB value is classified as “positive” by using a decision rule. The goal of our study was to assess the clinical utility of 3 recommended TcB screening decision rules. METHODS: Paired TcB/TSB measurements were collected at 34 newborn nursery sites. At 27 sites (sample 1), newborns were routinely screened with a TcB measurement. For sample 2, sites that typically screen with TSB levels also obtained a TcB measurement for the study. Three decision rules to define a positive TcB measurement were evaluated: ≥75th percentile on the Bhutani nomogram, 70% of the phototherapy level, and within 3 mg/dL of the phototherapy threshold. The primary outcome was a TSB level at/above the phototherapy threshold. The rate of false-negative TcB screens and percentage of blood draws avoided were calculated for each decision rule. RESULTS: For sample 1, data were analyzed on 911 paired TcB-TSB measurements from a total of 8316 TcB measurements. False-negative rates were <10% with all decision rules; none identified all 31 newborns with a TSB level at/above the phototherapy threshold. The percentage of blood draws avoided ranged from 79.4% to 90.7%. In sample 2, each rule correctly identified all 8 newborns with TSB levels at/above the phototherapy threshold. CONCLUSIONS: Although all of the decision rules can be used effectively to screen newborns for jaundice, each will “miss” some infants with a TSB level at/above the phototherapy threshold. PMID:27244792

Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.

PubMed

Szymanski, Eric S; Kimsey, Isaac J; Al-Hashimi, Hashim M

2017-03-29

The replicative and translational machinery utilizes the unique geometry of canonical G·C and A·T/U Watson-Crick base pairs to discriminate against DNA and RNA mismatches in order to ensure high fidelity replication, transcription, and translation. There is growing evidence that spontaneous errors occur when mismatches adopt a Watson-Crick-like geometry through tautomerization and/or ionization of the bases. Studies employing NMR relaxation dispersion recently showed that wobble dG·dT and rG·rU mismatches in DNA and RNA duplexes transiently form tautomeric and anionic species with probabilities (≈0.01-0.40%) that are in concordance with replicative and translational errors. Although computational studies indicate that these exceptionally short-lived and low-abundance species form Watson-Crick-like base pairs, their conformation could not be directly deduced from the experimental data, and alternative pairing geometries could not be ruled out. Here, we report direct NMR evidence that the transient tautomeric and anionic species form hydrogen-bonded Watson-Crick-like base pairs. A guanine-to-inosine substitution, which selectively knocks out a Watson-Crick-type (G)N2H 2 ···O2(T) hydrogen bond, significantly destabilized the transient tautomeric and anionic species, as assessed by lack of any detectable chemical exchange by imino nitrogen rotating frame spin relaxation (R 1ρ ) experiments. An 15 N R 1ρ NMR experiment targeting the amino nitrogen of guanine (dG-N2) provides direct evidence for Watson-Crick (G)N2H 2 ···O2(T) hydrogen bonding in the transient tautomeric state. The strategy presented in this work can be generally applied to examine hydrogen-bonding patterns in nucleic acid transient states including in other tautomeric and anionic species that are postulated to play roles in replication and translational errors.

Segmental expression of Pax3/7 and engrailed homologs in tardigrade development.

PubMed

Gabriel, Willow N; Goldstein, Bob

2007-06-01

How morphological diversity arises through evolution of gene sequence is a major question in biology. In Drosophila, the genetic basis for body patterning and morphological segmentation has been studied intensively. It is clear that some of the genes in the Drosophila segmentation program are functioning similarly in certain other taxa, although many questions remain about when these gene functions arose and which taxa use these genes similarly to establish diverse body plans. Tardigrades are an outgroup to arthropods in the Ecdysozoa and, as such, can provide insight into how gene functions have evolved among the arthropods and their close relatives. We developed immunostaining methods for tardigrade embryos, and we used cross-reactive antibodies to investigate the expression of homologs of the pair-rule gene paired (Pax3/7) and the segment polarity gene engrailed in the tardigrade Hypsibius dujardini. We find that in H. dujardini embryos, Pax3/7 protein localizes not in a pair-rule pattern but in a segmentally iterated pattern, after the segments are established, in regions of the embryo where neurons later arise. Engrailed protein localizes in the posterior ectoderm of each segment before ectodermal segmentation is apparent. Together with previous results from others, our data support the conclusions that the pair-rule function of Pax3/7 is specific to the arthropods, that some of the ancient functions of Pax3/7 and Engrailed in ancestral bilaterians may have been in neurogenesis, and that Engrailed may have a function in establishing morphological boundaries between segments that is conserved at least among the Panarthropoda.

Food Web Assembly Rules for Generalized Lotka-Volterra Equations.

PubMed

Haerter, Jan O; Mitarai, Namiko; Sneppen, Kim

2016-02-01

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.

Food Web Assembly Rules for Generalized Lotka-Volterra Equations

PubMed Central

Haerter, Jan O.; Mitarai, Namiko; Sneppen, Kim

2016-01-01

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species. PMID:26828363

75 FR 81793 - Endangered and Threatened Wildlife and Plants; Listing Seven Brazilian Bird Species as Endangered...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-28

... and invited them to comment on the proposed listings. We received four comments on the proposed rule... in pairs or small family groups and consumes various insects, spiders, and small frogs (Collar et al... birds, in closely associated pairs, or in small family groups. The bird often relies on army ant (Eciton...

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

PubMed Central

Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-01

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

[Compatibility law of Baizhi formulae and molecular mechanism of core herbal pair "Baizhi-Chuanxiong"].

PubMed

Su, Jin; Tang, Shi-Huan; Guo, Fei-Fei; Li, De-Feng; Zhang, Yi; Xu, Hai-Yu; Yang, Hong-Jun

2018-04-01

By using the traditional Chinese medicine inheritance support system (TCMISS) in this study, the prescription rules of Baizhi formulae were analyzed and the core herbal pair "Baizhi-Chuanxiong" was obtained. Through the systemic analysis of prescription rules of "Baizhi-Chuanxiong" and combined with the pharmacology thinking of "Baizhi-Chuanxiong" in treating headache, the paper was aimed to find out the combination rules containing Baizhi andits molecular mechanisms for treating headaches, and provide the theory basis for further research and reference of Baizhi and its formula. Totally 3 887 prescriptions were included in this study, involving 2 534 Chinese herbs. With a support degree of 20% in analysis, 16 most commonly used drug combinations were screened, which were mainly used to treat 15 types of diseases. Baizhi was often used to treat headache, and the core combination "Baizhi-Chuanxiong" was also often used to treat, consistent with ancient record. A chemical database was established; then the headache and migraine disease targets were retrieved and added in the database to build up the "compounds-targets-pathways "core network of "Baizhi-Chuanxiong" by the internet-based computation platform for IP of TCM (TCM-IP). TCM-IP was then applied to study the molecular mechanism of "Baizhi-Chuanxiong" treatment of headache. The results suggested that37 chemical compounds in the core combination "Baizhi-Chuanxiong" were closely related with headache treatment by adjusting serotonin levels or applying to inflammation-related targets and energy metabolism pathways such as purine metabolism, pyruvate metabolism, fatty acid degradation, carbon metabolism and gluconeogenesis. Copyright© by the Chinese Pharmaceutical Association.

Development and Evaluation of a Diagnostic Documentation Support System using Knowledge Processing

NASA Astrophysics Data System (ADS)

Makino, Kyoko; Hayakawa, Rumi; Terai, Koichi; Fukatsu, Hiroshi

In this paper, we will introduce a system which supports creating diagnostic reports. Diagnostic reports are documents by doctors of radiology describing the existence and nonexistence of abnormalities from the inspection images, such as CT and MRI, and summarize a patient's state and disease. Our system indicates insufficiencies in these reports created by younger doctors, by using knowledge processing based on a medical knowledge dictionary. These indications are not only clerical errors, but the system also analyzes the purpose of the inspection and determines whether a comparison with a former inspection is required, or whether there is any shortage in description. We verified our system by using actual data of 2,233 report pairs, a pair comprised of a report written by a younger doctor and a check result of the report by an experienced doctor. The results of the verification showed that the rules of string analysis for detecting clerical errors and sentence wordiness obtained a recall of over 90% and a precision of over 75%. Moreover, the rules based on a medical knowledge dictionary for detecting the lack of required comparison with a former inspection and the shortage in description for the inspection purpose obtained a recall of over 70%. From these results, we confirmed that our system contributes to the quality improvement of diagnostic reports. We expect that our system can comprehensively support diagnostic documentations by cooperating with the interface which refers to inspection images or past reports.

Interplay of defect doping and Bernal-Fowler rules: A simulation study of the dynamics on ice lattices

NASA Astrophysics Data System (ADS)

Köster, K. W.; Klocke, T.; Wieland, F.; Böhmer, R.

2017-10-01

Protonic defects on ice lattices induced by doping with acids such as HCl and HF or bases such as KOH can facilitate order-disorder transitions. In laboratory experiments KOH doping is efficient in promoting the ordering transition from hexagonal ice I to ice XI, but it is ineffective for other known ice phases, for which HCl can trigger hydrogen ordering. Aiming at understanding these differences, random-walk simulations of the defect diffusion are performed on two- and three-dimensional ice lattices under the constraints imposed by the Bernal-Fowler ice rules. Effective defect diffusion coefficients are calculated for a range of dopants, concentrations, and ice phases. The interaction of different defects, incorporated by different dopants, is investigated to clarify the particular motion-enhancing role played by complementary defect pairs.

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.

PubMed Central

Zhang, X; Gottlieb, P A

1995-01-01

Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCl, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 25 degrees C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCl to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Kobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution on the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system. Images PMID:7784203

A Character Level Based and Word Level Based Approach for Chinese-Vietnamese Machine Translation.

PubMed

Tran, Phuoc; Dinh, Dien; Nguyen, Hien T

2016-01-01

Chinese and Vietnamese have the same isolated language; that is, the words are not delimited by spaces. In machine translation, word segmentation is often done first when translating from Chinese or Vietnamese into different languages (typically English) and vice versa. However, it is a matter for consideration that words may or may not be segmented when translating between two languages in which spaces are not used between words, such as Chinese and Vietnamese. Since Chinese-Vietnamese is a low-resource language pair, the sparse data problem is evident in the translation system of this language pair. Therefore, while translating, whether it should be segmented or not becomes more important. In this paper, we propose a new method for translating Chinese to Vietnamese based on a combination of the advantages of character level and word level translation. In addition, a hybrid approach that combines statistics and rules is used to translate on the word level. And at the character level, a statistical translation is used. The experimental results showed that our method improved the performance of machine translation over that of character or word level translation.

Evolutionary games combining two or three pair coordinations on a square lattice

NASA Astrophysics Data System (ADS)

Király, Balázs; Szabó, György

2017-10-01

We study multiagent logit-rule-driven evolutionary games on a square lattice whose pair interactions are composed of a maximal number of nonoverlapping elementary coordination games describing Ising-type interactions between just two of the available strategies. Using Monte Carlo simulations we investigate the macroscopic noise-level-dependent behavior of the two- and three-pair games and the critical properties of the continuous phase transtitions these systems exhibit. The four-strategy game is shown to be equivalent to a system that consists of two independent and identical Ising models.

Evolutionary games combining two or three pair coordinations on a square lattice.

PubMed

Király, Balázs; Szabó, György

2017-10-01

We study multiagent logit-rule-driven evolutionary games on a square lattice whose pair interactions are composed of a maximal number of nonoverlapping elementary coordination games describing Ising-type interactions between just two of the available strategies. Using Monte Carlo simulations we investigate the macroscopic noise-level-dependent behavior of the two- and three-pair games and the critical properties of the continuous phase transtitions these systems exhibit. The four-strategy game is shown to be equivalent to a system that consists of two independent and identical Ising models.

An Artificial Intelligence Approach for Modeling and Prediction of Water Diffusion Inside a Carbon Nanotube

PubMed Central

2009-01-01

Modeling of water flow in carbon nanotubes is still a challenge for the classic models of fluid dynamics. In this investigation, an adaptive-network-based fuzzy inference system (ANFIS) is presented to solve this problem. The proposed ANFIS approach can construct an input–output mapping based on both human knowledge in the form of fuzzy if-then rules and stipulated input–output data pairs. Good performance of the designed ANFIS ensures its capability as a promising tool for modeling and prediction of fluid flow at nanoscale where the continuum models of fluid dynamics tend to break down. PMID:20596382

An Artificial Intelligence Approach for Modeling and Prediction of Water Diffusion Inside a Carbon Nanotube.

PubMed

Ahadian, Samad; Kawazoe, Yoshiyuki

2009-06-04

Modeling of water flow in carbon nanotubes is still a challenge for the classic models of fluid dynamics. In this investigation, an adaptive-network-based fuzzy inference system (ANFIS) is presented to solve this problem. The proposed ANFIS approach can construct an input-output mapping based on both human knowledge in the form of fuzzy if-then rules and stipulated input-output data pairs. Good performance of the designed ANFIS ensures its capability as a promising tool for modeling and prediction of fluid flow at nanoscale where the continuum models of fluid dynamics tend to break down.

A water market simulator considering pair-wise trades between agents

NASA Astrophysics Data System (ADS)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

USGS Publications Warehouse

Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

2015-01-01

Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

Hard Photodisintegration of a Proton Pair

DOE PAGES

Pomerantz, Ishay; Bubis, Nathaniel; Allada, Kalyan; ...

2010-01-08

We present the first study of high energy photodisintegration of proton-pairs through the gamma + 3He -> p+p+n channel. Photon energies from 0.8 to 4.7 GeV were used in kinematics corresponding to a proton pair with high relative momentum and a neutron nearly at rest. An s^{-11} scaling of the cross section was observed, as predicted by the constituent counting rule. The onset of the scaling is at a higher energy and the cross section is significantly lower then for pn pair photodisintegration. For photon energies below the scaling region, the scaled cross section was found to present a strongmore » energy-dependent structure not observed in deuteron photodisintegration.« less

Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies.

PubMed

Kutchukian, Peter S; Wassermann, Anne Mai; Lindvall, Mika K; Wright, S Kirk; Ottl, Johannes; Jacob, Jaison; Scheufler, Clemens; Marzinzik, Andreas; Brooijmans, Natasja; Glick, Meir

2015-06-01

A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits. © 2014 Society for Laboratory Automation and Screening.

Nucleic acid-based nanoengineering: novel structures for biomedical applications

PubMed Central

Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

2011-01-01

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

Transfer Learning of Classification Rules for Biomarker Discovery and Verification from Molecular Profiling Studies

PubMed Central

Ganchev, Philip; Malehorn, David; Bigbee, William L.; Gopalakrishnan, Vanathi

2013-01-01

We present a novel framework for integrative biomarker discovery from related but separate data sets created in biomarker profiling studies. The framework takes prior knowledge in the form of interpretable, modular rules, and uses them during the learning of rules on a new data set. The framework consists of two methods of transfer of knowledge from source to target data: transfer of whole rules and transfer of rule structures. We evaluated the methods on three pairs of data sets: one genomic and two proteomic. We used standard measures of classification performance and three novel measures of amount of transfer. Preliminary evaluation shows that whole-rule transfer improves classification performance over using the target data alone, especially when there is more source data than target data. It also improves performance over using the union of the data sets. PMID:21571094

Mapping sea ice leads with a coupled numeric/symbolic system

NASA Technical Reports Server (NTRS)

Key, J.; Schweiger, A. J.; Maslanik, J. A.

1990-01-01

A method is presented which facilitates the detection and delineation of leads with single-channel Landsat data by coupling numeric and symbolic procedures. The procedure consists of three steps: (1) using the dynamic threshold method, an image is mapped to a lead/no lead binary image; (2) the likelihood of fragments to be real leads is examined with a set of numeric rules; and (3) pairs of objects are examined geometrically and merged where possible. The processing ends when all fragments are merged and statistical characteristics are determined, and a map of valid lead objects are left which summarizes useful physical in the lead complexes. Direct implementation of domain knowledge and rapid prototyping are two benefits of the rule-based system. The approach is found to be more successfully applied to mid- and high-level processing, and the system can retrieve statistics about sea-ice leads as well as detect the leads.

Learning of Rule Ensembles for Multiple Attribute Ranking Problems

NASA Astrophysics Data System (ADS)

Dembczyński, Krzysztof; Kotłowski, Wojciech; Słowiński, Roman; Szeląg, Marcin

In this paper, we consider the multiple attribute ranking problem from a Machine Learning perspective. We propose two approaches to statistical learning of an ensemble of decision rules from decision examples provided by the Decision Maker in terms of pairwise comparisons of some objects. The first approach consists in learning a preference function defining a binary preference relation for a pair of objects. The result of application of this function on all pairs of objects to be ranked is then exploited using the Net Flow Score procedure, giving a linear ranking of objects. The second approach consists in learning a utility function for single objects. The utility function also gives a linear ranking of objects. In both approaches, the learning is based on the boosting technique. The presented approaches to Preference Learning share good properties of the decision rule preference model and have good performance in the massive-data learning problems. As Preference Learning and Multiple Attribute Decision Aiding share many concepts and methodological issues, in the introduction, we review some aspects bridging these two fields. To illustrate the two approaches proposed in this paper, we solve with them a toy example concerning the ranking of a set of cars evaluated by multiple attributes. Then, we perform a large data experiment on real data sets. The first data set concerns credit rating. Since recent research in the field of Preference Learning is motivated by the increasing role of modeling preferences in recommender systems and information retrieval, we chose two other massive data sets from this area - one comes from movie recommender system MovieLens, and the other concerns ranking of text documents from 20 Newsgroups data set.

The ambivalent effect of lattice structure on a spatial game

NASA Astrophysics Data System (ADS)

Zhang, Hui; Gao, Meng; Li, Zizhen; Maa, Zhihui; Wang, Hailong

2011-06-01

The evolution of cooperation is studied in lattice-structured populations, in which each individual who adopts one of the following strategies ‘always defect' (ALLD), ‘tit-for-tat' (TFT), and ‘always cooperate' (ALLC) plays the repeated Prisoner's Dilemma game with its neighbors according to an asynchronous update rule. Computer simulations are applied to analyse the dynamics depending on major parameters. Mathematical analyses based on invasion probability analysis, mean-field approximation, as well as pair approximation are also used. We find that the lattice structure promotes the evolution of cooperation compared with a non-spatial population, this is also confirmed by invasion probability analysis in one dimension. Meanwhile, it also inhibits the evolution of cooperation due to the advantage of being spiteful, which indicates the key role of specific life-history assumptions. Mean-field approximation fails to predict the outcome of computer simulations. Pair approximation is accurate in two dimensions but fails in one dimension.

76 FR 22741 - Self-Regulatory Organizations; NASDAQ OMX PHLX LLC; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-22

... Exchange Act of 1934 (``Act''),\\1\\ and Rule 19b-4 thereunder,\\2\\ notice is hereby given that on April 14... on the proposed rule change from interested persons. \\1\\ 15 U.S.C. 78s(b)(1). \\2\\ 17 CFR 240.19b-4. I... only on the following Alpha Pairs: AAPL/SPY, AMZN/SPY, CSCO/SPY, F/SPY, GE/SPY, GOOG/SPY, HPQ/SPY, IBM...

Design of Composite Structures Using Knowledge-Based and Case Based Reasoning

NASA Technical Reports Server (NTRS)

Lambright, Jonathan Paul

1996-01-01

A method of using knowledge based and case based reasoning to assist designers during conceptual design tasks of composite structures was proposed. The cooperative use of heuristics, procedural knowledge, and previous similar design cases suggests a potential reduction in design cycle time and ultimately product lead time. The hypothesis of this work is that the design process of composite structures can be improved by using Case-Based Reasoning (CBR) and Knowledge-Based (KB) reasoning in the early design stages. The technique of using knowledge-based and case-based reasoning facilitates the gathering of disparate information into one location that is easily and readily available. The method suggests that the inclusion of downstream life-cycle issues into the conceptual design phase reduces potential of defective, and sub-optimal composite structures. Three industry experts were interviewed extensively. The experts provided design rules, previous design cases, and test problems. A Knowledge Based Reasoning system was developed using the CLIPS (C Language Interpretive Procedural System) environment and a Case Based Reasoning System was developed using the Design Memory Utility For Sharing Experiences (MUSE) xviii environment. A Design Characteristic State (DCS) was used to document the design specifications, constraints, and problem areas using attribute-value pair relationships. The DCS provided consistent design information between the knowledge base and case base. Results indicated that the use of knowledge based and case based reasoning provided a robust design environment for composite structures. The knowledge base provided design guidance from well defined rules and procedural knowledge. The case base provided suggestions on design and manufacturing techniques based on previous similar designs and warnings of potential problems and pitfalls. The case base complemented the knowledge base and extended the problem solving capability beyond the existence of limited well defined rules. The findings indicated that the technique is most effective when used as a design aid and not as a tool to totally automate the composites design process. Other areas of application and implications for future research are discussed.

Disent to Pairing Mechanism

NASA Astrophysics Data System (ADS)

Cheng, Kaijia; Cheng, Shuyu

Up to now, the pairing mechanism is regarded as the rule of thumb criterion of an acceptable theory of superconductivity. It is generally held as a taboo for any theory which is not founded on this basis. However this is not true and it misleads the direction for the theoretical research for both the high and low temperature regions and eventually delays the progress in practice. It is now the time to clear up the situation.

Verification of the H2O Linelists with Theoretically Developed Tools

NASA Technical Reports Server (NTRS)

Ma, Qiancheng; Tipping, R.; Lavrentieva, N. N.; Dudaryonok, A. S.

2013-01-01

Two basic rules (i.e., the pair identity and the smooth variation rules) resulting from the properties of the energy levels and wave functions of H2O states govern how the spectroscopic parameters vary with the H2O lines within the individually defined groups of lines. With these rules, for those lines involving high j states in the same groups, variations of all their spectroscopic parameters (i.e., the transition frequency, intensity, pressure broadened half-width, pressure-induced shift, and temperature exponent) can be well monitored. Thus, the rules can serve as simple and effective tools to screen the H2O spectroscopic data listed in the HITRAN database and verify the latter's accuracies. By checking violations of the rules occurring among the data within the individual groups, possible errors can be picked up and also possible missing lines in the linelist whose intensities are above the threshold can be identified. We have used these rules to check the accuracies of the spectroscopic parameters and the completeness of the linelists for several important H2O vibrational bands. Based on our results, the accuracy of the line frequencies in HITRAN 2008 is consistent. For the line intensity, we have found that there are a substantial number of lines whose intensity values are questionable. With respect to other parameters, many mistakes have been found. The above claims are consistent with a well known fact that values of these parameters in HITRAN contain larger uncertainties. Furthermore, supplements of the missing line list consisting of line assignments and positions can be developed from the screening results.

Understanding the rural population migration pattern of Uttarakhand using Geophysical, Geological and Socio-Economical BigData

NASA Astrophysics Data System (ADS)

Chattopadhyay, Kausik; Chattopadhyay, Pallavi

2017-04-01

Uttarakhand, a Himalayan state of India is facing a worst scenario of rural population migration for the past few decades from hill regions to the planes. While urbanization is believed to be one of the major factors for migration, how geo scientific parameters can impact the population to redraw the demographies of the hills is studied in this research. An attempt is made using density based clustering and Apriori association rule mining on 45 derived variables with a time series of 30 years to understand the rural population migration pattern. Both zone identification and origin-destination pair extraction are formulated as spatial-temporal point clustering problem and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) is applied to solve them. Specifically the population migration is formulated as a 4D point clustering problem and the relative distance between two origin - destination pair with a preference factor is used to fine tune the cluster length. In Apriori, threshold values for confidence and J-measure are kept same as for rule extraction. Rules with maximum confidence level and J-measure are obtained for an antecedent window of 18 months, consequent window of 4 months and time lag of 2 months. From the rules extracted, it can be demonstrated that almost all the geoscience indices are occurring as antecedents for migration episodes. The result demonstrates that the three districts that have registered the highest migration rates are also the districts that have witnessed maximum depletion in water sources. Even though some districts have higher number of landslide incidents, their out migration is less compared to other hill districts. However districts experiencing higher number of earthquakes are experiencing higher out migration. Upper hill region with higher precipitation experience higher migration compared to their lower hill counterpart. However this is not true when compared to the counter parts in the plane regions. Even though temperature fluctuation results in seasonal out migration, it does not have any long term impact. Resource and logistical constraints limit the frequency and extent of observations, necessitating the development of a systematic computational framework that objectively represents environmental variability at the desired spatial scale and such comprehensive big data model can be instrumental in arresting the rural migration which has been posing major threat to the livelihood of this Himalayan state.

Drosophila segmentation: supercomputer simulation of prepattern hierarchy.

PubMed

Hunding, A; Kauffman, S A; Goodwin, B C

1990-08-09

Spontaneous prepattern formation in a two level hierarchy of reaction-diffusion systems is simulated in three space co-ordinates and time, mimicking gap gene and primary pair-rule gene expression. The model rests on the idea of Turing systems of the second kind, in which one prepattern generates position dependent rate constants for a subsequent reaction-diffusion system. Maternal genes are assumed responsible for setting up gradients from the anterior and posterior ends, one of which is needed to stabilize a double period prepattern suggested to underly the read out of the gap genes. The resulting double period pattern in turn stabilizes the next prepattern in the hierarchy, which has a short wavelength with many characteristics of the stripes seen in actual primary pair-rule gene expression. Without such hierarchical stabilization, reaction-diffusion mechanisms yield highly patchy short wave length patterns, and thus unreliable stripes. The model yields seven stable stripes located in the middle of the embryo, with the potential for additional expression near the poles, as observed experimentally. The model does not rely on specific chemical reaction kinetics, rather the effect is general to many such kinetic schemes. This makes it robust to parameter changes, and it has good potential for adapting to size and shape changes as well. The study thus suggests that the crucial organizing principle in early Drosophila embryogenesis is based on global field mechanisms, not on particular local interactions.

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.

PubMed

Wala, Jeremiah; Zhang, Cheng-Zhong; Meyerson, Matthew; Beroukhim, Rameen

2016-07-01

We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis. VariantBam and full documentation are available at github.com/jwalabroad/VariantBam rameen@broadinstitute.org 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.

PPInterFinder--a mining tool for extracting causal relations on human proteins from literature.

PubMed

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein-protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder--a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. DATABASE URL: http://www.biomining-bu.in/ppinterfinder/

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

PubMed Central

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein–protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder—a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. Database URL: http://www.biomining-bu.in/ppinterfinder/ PMID:23325628

Scrutinizing the double superconducting gaps and strong coupling pairing in (Li1−xFex)OHFeSe

PubMed Central

Du, Zengyi; Yang, Xiong; Lin, Hai; Fang, Delong; Du, Guan; Xing, Jie; Yang, Huan; Zhu, Xiyu; Wen, Hai-Hu

2016-01-01

In the field of iron-based superconductors, one of the frontier studies is about the pairing mechanism. The recently discovered (Li1−xFex)OHFeSe superconductor with the transition temperature of about 40 K provides a good platform to check the origin of double superconducting gaps and high transition temperature in the monolayer FeSe thin film. Here we report a scanning tunnelling spectroscopy study on the (Li1−xFex)OHFeSe single crystals. The tunnelling spectrum mimics that of the monolayer FeSe thin film and shows double gaps at about 14.3 and 8.6 meV. Further analysis based on the quasiparticle interference allows us to rule out the d-wave gap, and for the first time assign the larger (smaller) gap to the outer (inner) Fermi pockets (after folding) associating with the dxy (dxz/dyz) orbitals, respectively. The gap ratio amounts to 8.7, which demonstrates the strong coupling mechanism in the present superconducting system. PMID:26822281

Spatial Congruity Effects Reveal Metaphorical Thinking, not Polarity Correspondence.

PubMed

Dolscheid, Sarah; Casasanto, Daniel

2015-01-01

Spatial congruity effects have often been interpreted as evidence for metaphorical thinking, but an alternative account based on polarity correspondence (a.k.a. markedness) has challenged this view. Here we compared metaphor- and polarity-correspondence-based explanations for spatial congruity effects, using musical pitch as a testbed. In one experiment, English speakers classified high- and low-frequency pitches as "high" and "low," or as "front" and "back," to determine whether space-pitch congruity effects could be elicited by any marked spatial continuum. Although both pairs of terms describe bipolar spatial continuums, we found congruity effects only for high/low judgments, indicating that markedness is not sufficient to produce space-pitch congruity effects. A second experiment confirmed that there were no space-pitch congruity effects for another pair of terms that have clear markedness (big/small), but which do not denote spatial height. By contrast, this experiment showed congruity effects for words that cued an appropriate vertical spatial schema (tall/short), even though these words are not used conventionally in English to describe pitches, ruling out explanations for the observed pattern of results based on verbal polysemy. Together, results suggest that space-pitch congruity effects reveal metaphorical uses of spatial schemas, not polarity correspondence effects.

A Character Level Based and Word Level Based Approach for Chinese-Vietnamese Machine Translation

PubMed Central

2016-01-01

Chinese and Vietnamese have the same isolated language; that is, the words are not delimited by spaces. In machine translation, word segmentation is often done first when translating from Chinese or Vietnamese into different languages (typically English) and vice versa. However, it is a matter for consideration that words may or may not be segmented when translating between two languages in which spaces are not used between words, such as Chinese and Vietnamese. Since Chinese-Vietnamese is a low-resource language pair, the sparse data problem is evident in the translation system of this language pair. Therefore, while translating, whether it should be segmented or not becomes more important. In this paper, we propose a new method for translating Chinese to Vietnamese based on a combination of the advantages of character level and word level translation. In addition, a hybrid approach that combines statistics and rules is used to translate on the word level. And at the character level, a statistical translation is used. The experimental results showed that our method improved the performance of machine translation over that of character or word level translation. PMID:27446207

Flight Deck-Based Delegated Separation: Evaluation of an On-Board Interval Management System with Synthetic and Enhanced Vision Technology

NASA Technical Reports Server (NTRS)

Prinzel, Lawrence J., III; Shelton, Kevin J.; Kramer, Lynda J.; Arthur, Jarvis J.; Bailey, Randall E.; Norman, Rober M.; Ellis, Kyle K. E.; Barmore, Bryan E.

2011-01-01

An emerging Next Generation Air Transportation System concept - Equivalent Visual Operations (EVO) - can be achieved using an electronic means to provide sufficient visibility of the external world and other required flight references on flight deck displays that enable the safety, operational tempos, and visual flight rules (VFR)-like procedures for all weather conditions. Synthetic and enhanced flight vision system technologies are critical enabling technologies to EVO. Current research evaluated concepts for flight deck-based interval management (FIM) operations, integrated with Synthetic Vision and Enhanced Vision flight-deck displays and technologies. One concept involves delegated flight deck-based separation, in which the flight crews were paired with another aircraft and responsible for spacing and maintaining separation from the paired aircraft, termed, "equivalent visual separation." The operation required the flight crews to acquire and maintain an "equivalent visual contact" as well as to conduct manual landings in low-visibility conditions. The paper describes results that evaluated the concept of EVO delegated separation, including an off-nominal scenario in which the lead aircraft was not able to conform to the assigned spacing resulting in a loss of separation.

Skyrme RPA description of γ-vibrational states in rare-earth nuclei

NASA Astrophysics Data System (ADS)

Nesterenko, V. O.; Kartavenko, V. G.; Kleinig, W.; Kvasil, J.; Repko, A.; Jolos, R. V.; Reinhard, P.-G.

2016-01-01

The lowest γ-vibrational states with Kπ = 2+γ in well-deformed Dy, Er and Yb isotopes are investigated within the self-consistent separable quasiparticle random-phase-approximation (QRPA) approach based on the Skyrme functional. The energies Eγ and reduced transition probabilities B(E2)γ of the states are calculated with the Skyrme force SV-mas10. We demonstrate the strong effect of the pairing blocking on the energies of γ-vibrational states. It is also shown that collectivity of γ-vibrational states is strictly determined by keeping the Nilsson selection rules in the corresponding lowest 2qp configurations.

Matching next-to-leading order predictions to parton showers in supersymmetric QCD

DOE PAGES

Degrande, Céline; Fuks, Benjamin; Hirschi, Valentin; ...

2016-02-03

We present a fully automated framework based on the FeynRules and MadGraph5_aMC@NLO programs that allows for accurate simulations of supersymmetric QCD processes at the LHC. Starting directly from a model Lagrangian that features squark and gluino interactions, event generation is achieved at the next-to-leading order in QCD, matching short-distance events to parton showers and including the subsequent decay of the produced supersymmetric particles. As an application, we study the impact of higher-order corrections in gluino pair-production in a simplified benchmark scenario inspired by current gluino LHC searches.

Matching next-to-leading order predictions to parton showers in supersymmetric QCD

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

Degrande, Céline; Fuks, Benjamin; Hirschi, Valentin

We present a fully automated framework based on the FeynRules and MadGraph5_aMC@NLO programs that allows for accurate simulations of supersymmetric QCD processes at the LHC. Starting directly from a model Lagrangian that features squark and gluino interactions, event generation is achieved at the next-to-leading order in QCD, matching short-distance events to parton showers and including the subsequent decay of the produced supersymmetric particles. As an application, we study the impact of higher-order corrections in gluino pair-production in a simplified benchmark scenario inspired by current gluino LHC searches.

Description of SHARC-2, the Strategic High-Altitude Atmospheric Radiance Code.

DTIC Science & Technology

1991-03-22

the Rules for Reaction Cards .. ......... 33 7 Summary of the Rules for Auxiliary Information Cards . 35 8 SHARC CO Molecular States Input File...those used in AARC. The ion pair production rate is then obtained from the energy deposition rate by assuming that 35 eV are required to produce an ion...contain three numbers to identify the particular vibrational state (using the standard AFGL - 35 - Table 8. SHARC CO Molecular States Input File. CO

Optimizing the Replication of Multi-Quality Web Applications Using ACO and WoLF

DTIC Science & Technology

2006-09-14

bipartite graph in both directions as they construct solutions, pheromone is used for traversing from one side of the bipartite graph to the other and back...27 3.1.3 Transitioning From 〈d, q〉 pairs to Servers. . . . . 29 3.1.4 Pheromone Update Rule . . . . . . . . . . . . . . 30 vi Page 3.2 WoLFAntDA: A...35 3.2.6 Pheromone Update Rule . . . . . . . . . . . . . . 36 3.2.7 Policy Updates . . . . . . . . . . . . . . . . . . . 36 3.3 The Server-Filling

X exceptionalism in Caenorhabditis speciation.

PubMed

Cutter, Asher D

2017-11-13

Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis. Studies to date implicate improper chromatin regulation of the X-chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self-fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y-chromosome, sex chromosome-dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation. © 2017 John Wiley & Sons Ltd.

Trajectory selection for the Mariner Jupiter/Saturn 1977 Project

NASA Technical Reports Server (NTRS)

Dyer, J. S.; Miles, R. F., Jr.

1974-01-01

This paper describes the use of decision analysis to facilitate a group decision-making problem in the selection of trajectories for the two spacecraft of the Mariner Jupiter/Saturn 1977 Project. This NASA project includes the participation of some eighty scientists divided by specialization among eleven science teams. A set of thirty-two candidate trajectory pairs was developed by the Project in collaboration with the science teams. Each science team then ordinally ranked and assigned cardinal utility function values to the trajectory pairs. These data and statistics derived from collective choice rules were used by the scientists in selecting the preferred trajectory pair.

Generalized rules for the optimization of elastic network models

NASA Astrophysics Data System (ADS)

Lezon, Timothy; Eyal, Eran; Bahar, Ivet

2009-03-01

Elastic network models (ENMs) are widely employed for approximating the coarse-grained equilibrium dynamics of proteins using only a few parameters. An area of current focus is improving the predictive accuracy of ENMs by fine-tuning their force constants to fit specific systems. Here we introduce a set of general rules for assigning ENM force constants to residue pairs. Using a novel method, we construct ENMs that optimally reproduce experimental residue covariances from NMR models of 68 proteins. We analyze the optimal interactions in terms of amino acid types, pair distances and local protein structures to identify key factors in determining the effective spring constants. When applied to several unrelated globular proteins, our method shows an improved correlation with experiment over a standard ENM. We discuss the physical interpretation of our findings as well as its implications in the fields of protein folding and dynamics.

REVERSALS OF GNEVYSHEV-OHL RULE

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

Tlatov, Andrey G., E-mail: tlatov@mail.ru

2013-08-01

We perform an analysis of the number of sunspot groups in activity cycles from 1610 through the present. Here we use the G{sub n} index, which is defined as the average daily number of sunspot groups in cycle n. There is a high positive correlation between the parameter G{sub n} in the current cycle and an analogous parameter in the following cycle G{sub n{sub +1}} both for pairs of even-odd cycles and odd-even activity cycles. In cycle Nos. 10-21 for pairs of even-odd cycles, the ratio of parameter G{sub n} corresponds to the GO rule G{sub n{sub +1}{sup odd}}/G{sub n}{supmore » even}>1. However, during the period {approx}1745-1850, odd cycles were less than the preceding even cycles G{sub n{sub +1}{sup odd}}/G{sub n}{sup even}<1. The ratio of the parameter G{sub n{sub +1}{sup odd}}/G{sub n}{sup even} has a long-term variation within the range 0.5-1.5 with a period of about 21 activity cycles, and it proves the reversal of the GO rule.« less

A Flexible Mechanism of Rule Selection Enables Rapid Feature-Based Reinforcement Learning

PubMed Central

Balcarras, Matthew; Womelsdorf, Thilo

2016-01-01

Learning in a new environment is influenced by prior learning and experience. Correctly applying a rule that maps a context to stimuli, actions, and outcomes enables faster learning and better outcomes compared to relying on strategies for learning that are ignorant of task structure. However, it is often difficult to know when and how to apply learned rules in new contexts. In our study we explored how subjects employ different strategies for learning the relationship between stimulus features and positive outcomes in a probabilistic task context. We test the hypothesis that task naive subjects will show enhanced learning of feature specific reward associations by switching to the use of an abstract rule that associates stimuli by feature type and restricts selections to that dimension. To test this hypothesis we designed a decision making task where subjects receive probabilistic feedback following choices between pairs of stimuli. In the task, trials are grouped in two contexts by blocks, where in one type of block there is no unique relationship between a specific feature dimension (stimulus shape or color) and positive outcomes, and following an un-cued transition, alternating blocks have outcomes that are linked to either stimulus shape or color. Two-thirds of subjects (n = 22/32) exhibited behavior that was best fit by a hierarchical feature-rule model. Supporting the prediction of the model mechanism these subjects showed significantly enhanced performance in feature-reward blocks, and rapidly switched their choice strategy to using abstract feature rules when reward contingencies changed. Choice behavior of other subjects (n = 10/32) was fit by a range of alternative reinforcement learning models representing strategies that do not benefit from applying previously learned rules. In summary, these results show that untrained subjects are capable of flexibly shifting between behavioral rules by leveraging simple model-free reinforcement learning and context-specific selections to drive responses. PMID:27064794

Learning from Physical Analogies: A Study in Analogy and the Explanation Process

DTIC Science & Technology

1988-12-27

support of the various transfer operations, the forward chaining ATRE rule system is paired with an abductive retriever. This is a backward chaining...pO) is believed.3 When a new datum is entered in the database, ATRE exhaustively runs all rules made executable by the datum’s presence in a forward ...ZR) INFLUENESST1 (CTA (AIOUN-O ?V-2)) NERTON V- (ASUM (DISSOLVE-RAT SELF))) ER ) (DSETT (SKSOLUTIO-S -12)COOL (NOTUM (LSSOU-THN-1 A CONTRATO V-P) ER

The Origin of Complex Quantum Amplitudes

NASA Astrophysics Data System (ADS)

Goyal, Philip; Knuth, Kevin H.; Skilling, John

2009-12-01

Physics is real. Measurement produces real numbers. Yet quantum mechanics uses complex arithmetic, in which √-1 is necessary but mysteriously relates to nothing else. By applying the same sort of symmetry arguments that Cox [1, 2] used to justify probability calculus, we are now able to explain this puzzle. The dual device/object nature of observation requires us to describe the world in terms of pairs of real numbers about which we never have full knowledge. These pairs combine according to complex arithmetic, using Feynman's rules.

Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine.

PubMed

Ibáñez, Javier; Vélez, M Dolores; de Andrés, M Teresa; Borrego, Joaquín

2009-11-01

Distinctness, uniformity and stability (DUS) testing of varieties is usually required to apply for Plant Breeders' Rights. This exam is currently carried out using morphological traits, where the establishment of distinctness through a minimum distance is the key issue. In this study, the possibility of using microsatellite markers for establishing the minimum distance in a vegetatively propagated crop (grapevine) has been evaluated. A collection of 991 accessions have been studied with nine microsatellite markers and pair-wise compared, and the highest intra-variety distance and the lowest inter-variety distance determined. The collection included 489 different genotypes, and synonyms and sports. Average values for number of alleles per locus (19), Polymorphic Information Content (0.764) and heterozygosities observed (0.773) and expected (0.785) indicated the high level of polymorphism existing in grapevine. The maximum intra-variety variability found was one allele between two accessions of the same variety, of a total of 3,171 pair-wise comparisons. The minimum inter-variety variability found was two alleles between two pairs of varieties, of a total of 119,316 pair-wise comparisons. In base to these results, the minimum distance required to set distinctness in grapevine with the nine microsatellite markers used could be established in two alleles. General rules for the use of the system as a support for establishing distinctness in vegetatively propagated crops are discussed.

Tc-knirps plays different roles in the specification of antennal and mandibular parasegment boundaries and is regulated by a pair-rule gene in the beetle Tribolium castaneum

PubMed Central

2013-01-01

Background The Drosophila larval head is evolutionarily derived at the genetic and morphological level. In the beetle Tribolium castaneum, development of the larval head more closely resembles the ancestral arthropod condition. Unlike in Drosophila, a knirps homologue (Tc-kni) is required for development of the antennae and mandibles. However, published Tc-kni data are restricted to cuticle phenotypes and Tc-even-skipped and Tc-wingless stainings in knockdown embryos. Hence, it has remained unclear whether the entire antennal and mandibular segments depend on Tc-kni function, and whether the intervening intercalary segment is formed completely. We address these questions with a detailed examination of Tc-kni function. Results By examining the expression of marker genes in RNAi embryos, we show that Tc-kni is required only for the formation of the posterior parts of the antennal and mandibular segments (i.e. the parasegmental boundaries). Moreover, we find that the role of Tc-kni is distinct in these segments: Tc-kni is required for the initiation of the antennal parasegment boundary, but only for the maintenance of the mandibular parasegmental boundary. Surprisingly, Tc-kni controls the timing of expression of the Hox gene Tc-labial in the intercalary segment, although this segment does form in the absence of Tc-kni function. Unexpectedly, we find that the pair-rule gene Tc-even-skipped helps set the posterior boundary of Tc-kni expression in the mandible. Using the mutant antennaless, a likely regulatory Null mutation at the Tc-kni locus, we provide evidence that our RNAi studies represent a Null situation. Conclusions Tc-kni is required for the initiation of the antennal and the maintenance of the mandibular parasegmental boundaries. Tc-kni is not required for specification of the anterior regions of these segments, nor the intervening intercalary segment, confirming that Tc-kni is not a canonical ‘gap-gene’. Our finding that a gap gene orthologue is regulated by a pair rule gene adds to the view that the segmentation gene hierarchies differ between Tribolium and Drosophila upstream of the pair rule gene level. In Tribolium, as in Drosophila, head and trunk segmentation gene networks cooperate to pattern the mandibular segment, albeit involving Tc-kni as novel component. PMID:23777260

[Clinical study on aconite prescriptions with incompatible herbs in different areas based on association rules and analysis on compatibility features].

PubMed

Zuo, Ting; Fan, Xin-sheng; Tian, Shuo; Jiang, Chen-xue; Chen, Fei

2015-03-01

To explore the current application and features of Aconite prescriptions with incompatible herbs in grade A class three hospitals in east China and central China through a clinical study and comparative analysis. Clinical prescriptions containing Aconite with incompatible herbs were collected. Association rules were utilized to analyze the compatible features of these herbs. This analysis found that the frequently used incompatible herba; pairs are Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, with the support rate of 44.45%, occupying nearly half of the surveyed prescriptions; Pinelliae Rhizoma is the most frequently used herb in the two areas, with support rate up to 76.24%. Among the top 10 herbal pairs in the support rate, except for Aconiti Lateralis Radix Praeparata and Pinelliae Rhizoma, the top 10 herbs in Central China were mostly for warming the middle jiao and tonifying qi, such as Zingiberis Rhizoma, Atractylodis Macrocephalae Rhizoma and Codonopsis Radix; Whereas those in east China were mostly for activating and nourishing blood, such as Angelicae Sinensis Radix, Chuanxiong Rhizoma, and Salviae Miltiorrhizae Radix et Rhizoma. Among the top 10 herbal pairs in the support rate, except for Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, the core herbal pairs applied in central China were mainly for resolving phlegm and warming the middle jiao, such as Pinelliae Rhizoma-Glycyrrhizae Radix et Rhizoma, Pinelliae Rhizoma-Zingiberis Rhizoma; Whereas those in east China were principally for activating blood and tonifying qi, like Atractylodis Macrocephalae Rhizoma and Pinelliae Rhizoma, Angelicae Sinensis Radix and Pinelliae Rhizoma. Among the core herbal groups in the two areas, the most frequently used herbal groups in the two areas are Aconiti Lateralis Radix Praeparata, Glycyrrhizae Radix et Rhizoma and Pinelliae Rhizoma with the support rate of 59.73%, accounting for the highest proportion among all of herbal groups. There are the combined clinical application of Aconite with incompatible herbs, mostly with Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, but with differences in the combined application in east China and central China.

Dependence of two-proton radioactivity on nuclear pairing models

NASA Astrophysics Data System (ADS)

Oishi, Tomohiro; Kortelainen, Markus; Pastore, Alessandro

2017-10-01

Sensitivity of two-proton emitting decay to nuclear pairing correlation is discussed within a time-dependent three-body model. We focus on the 6Be nucleus assuming α +p +p configuration, and its decay process is described as a time evolution of the three-body resonance state. For a proton-proton subsystem, a schematic density-dependent contact (SDDC) pairing model is employed. From the time-dependent calculation, we observed the exponential decay rule of a two-proton emission. It is shown that the density dependence does not play a major role in determining the decay width, which can be controlled only by the asymptotic strength of the pairing interaction. This asymptotic pairing sensitivity can be understood in terms of the dynamics of the wave function driven by the three-body Hamiltonian, by monitoring the time-dependent density distribution. With this simple SDDC pairing model, there remains an impossible trinity problem: it cannot simultaneously reproduce the empirical Q value, decay width, and the nucleon-nucleon scattering length. This problem suggests that a further sophistication of the theoretical pairing model is necessary, utilizing the two-proton radioactivity data as the reference quantities.

Structural DNA Nanotechnology: State of the Art and Future Perspective

PubMed Central

2015-01-01

Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson–Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming. PMID:25029570

An Application of the Phosphorus Consistent Rule for Environmentally Acceptable Cost-Efficient Management of Broiler Litter in Crop Production

NASA Technical Reports Server (NTRS)

Paudel, Krishna P.; Limaye, Ashutosh; Adhikari, Murali; Martin, Neil R., Jr.

2004-01-01

We calculated the profitability of using broiler litter as a source of plant nutrients using the phosphorus consistent litter application rule. The cost saving by using litter is 37% over the use of chemical fertilizer-only option to meet the nutrient needs of major crops grown in Alabama. In the optimal solution, only a few routes of all the possible routes developed were used for inter- and intra- county litter hauling. If litter is not adopted as the sole source of crop nutrients, the best environmental policy may be to pair the phosphorus consistent rule with taxes, marketable permits, and subsidies.flaws

Visual perceptual learning by operant conditioning training follows rules of contingency.

PubMed

Kim, Dongho; Seitz, Aaron R; Watanabe, Takeo

2015-01-01

Visual perceptual learning (VPL) can occur as a result of a repetitive stimulus-reward pairing in the absence of any task. This suggests that rules that guide Conditioning, such as stimulus-reward contingency (e.g. that stimulus predicts the likelihood of reward), may also guide the formation of VPL. To address this question, we trained subjects with an operant conditioning task in which there were contingencies between the response to one of three orientations and the presence of reward. Results showed that VPL only occurred for positive contingencies, but not for neutral or negative contingencies. These results suggest that the formation of VPL is influenced by similar rules that guide the process of Conditioning.

Visual perceptual learning by operant conditioning training follows rules of contingency

PubMed Central

Kim, Dongho; Seitz, Aaron R; Watanabe, Takeo

2015-01-01

Visual perceptual learning (VPL) can occur as a result of a repetitive stimulus-reward pairing in the absence of any task. This suggests that rules that guide Conditioning, such as stimulus-reward contingency (e.g. that stimulus predicts the likelihood of reward), may also guide the formation of VPL. To address this question, we trained subjects with an operant conditioning task in which there were contingencies between the response to one of three orientations and the presence of reward. Results showed that VPL only occurred for positive contingencies, but not for neutral or negative contingencies. These results suggest that the formation of VPL is influenced by similar rules that guide the process of Conditioning. PMID:26028984

From bare to renormalized order parameter in gauge space: Structure and reactions

NASA Astrophysics Data System (ADS)

Potel, G.; Idini, A.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

2017-09-01

It is not physically obvious why one can calculate with similar accuracy, as compared to the experimental data, the absolute cross section associated with two-nucleon transfer processes between members of pairing rotational bands, making use of simple BCS (constant matrix elements) or of many-body [Nambu-Gorkov (NG), nuclear field theory (NFT)] spectroscopic amplitudes. Restoration of spontaneous symmetry breaking and associated emergent generalized rigidity in gauge space provides the answer and points to a new emergence: A physical sum rule resulting from the intertwining of structure and reaction processes, closely connected with the central role induced pairing interaction plays in structure, together with the fact that successive transfer dominates Cooper pair tunneling.

Charged particle layers in the Debye limit.

PubMed

Golden, Kenneth I; Kalman, Gabor J; Kyrkos, Stamatios

2002-09-01

We develop an equivalent of the Debye-Hückel weakly coupled equilibrium theory for layered classical charged particle systems composed of one single charged species. We consider the two most important configurations, the charged particle bilayer and the infinite superlattice. The approach is based on the link provided by the classical fluctuation-dissipation theorem between the random-phase approximation response functions and the Debye equilibrium pair correlation function. Layer-layer pair correlation functions, screened and polarization potentials, static structure functions, and static response functions are calculated. The importance of the perfect screening and compressibility sum rules in determining the overall behavior of the system, especially in the r--> infinity limit, is emphasized. The similarities and differences between the quasi-two-dimensional bilayer and the quasi-three-dimensional superlattice are highlighted. An unexpected behavior that emerges from the analysis is that the screened potential, the correlations, and the screening charges carried by the individual layers exhibit a marked nonmonotonic dependence on the layer separation.

Modified Hartree-Fock-Bogoliubov theory at finite temperature

NASA Astrophysics Data System (ADS)

Dinh Dang, Nguyen; Arima, Akito

2003-07-01

The modified Hartree-Fock-Bogoliubov (MHFB) theory at finite temperature is derived, which conserves the unitarity relation of the particle-density matrix. This is achieved by constructing a modified-quasiparticle-density matrix, where the fluctuation of the quasiparticle number is microscopically built in. This matrix can be directly obtained from the usual quasiparticle-density matrix by applying the secondary Bogoliubov transformation, which includes the quasiparticle-occupation number. It is shown that, in the limit of constant pairing parameter, the MHFB theory yields the previously obtained modified BCS (MBCS) equations. It is also proved that the modified quasiparticle-random-phase approximation, which is based on the MBCS quasiparticle excitations, conserves the Ikeda sum rule. The numerical calculations of the pairing gap, heat capacity, level density, and level-density parameter within the MBCS theory are carried out for 120Sn. The results show that the superfluid-normal phase transition is completely washed out. The applicability of the MBCS up to a temperature as high as T˜5 MeV is analyzed in detail.

Superfluid Density of Neutrons in the Inner Crust of Neutron Stars: New Life for Pulsar Glitch Models

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Pethick, C. J.

2017-08-01

Calculations of the effects of band structure on the neutron superfluid density in the crust of neutron stars made under the assumption that the effects of pairing are small [N. Chamel, Phys. Rev. C 85, 035801 (2012)] lead to moments of inertia of superfluid neutrons so small that the crust alone is insufficient to account for the magnitude of neutron star glitches. Inspired by earlier work on ultracold atomic gases in an optical lattice, we investigate fermions with attractive interactions in a periodic lattice in the mean-field approximation. The effects of band structure are suppressed when the pairing gap is of order or greater than the strength of the lattice potential. By applying the results to the inner crust of neutron stars, we conclude that the reduction of the neutron superfluid density is considerably less than previously estimated and, consequently, it is premature to rule out models of glitches based on neutron superfluidity in the crust.

Superfluid Density of Neutrons in the Inner Crust of Neutron Stars: New Life for Pulsar Glitch Models.

PubMed

Watanabe, Gentaro; Pethick, C J

2017-08-11

Calculations of the effects of band structure on the neutron superfluid density in the crust of neutron stars made under the assumption that the effects of pairing are small [N. Chamel, Phys. Rev. C 85, 035801 (2012)PRVCAN0556-2813] lead to moments of inertia of superfluid neutrons so small that the crust alone is insufficient to account for the magnitude of neutron star glitches. Inspired by earlier work on ultracold atomic gases in an optical lattice, we investigate fermions with attractive interactions in a periodic lattice in the mean-field approximation. The effects of band structure are suppressed when the pairing gap is of order or greater than the strength of the lattice potential. By applying the results to the inner crust of neutron stars, we conclude that the reduction of the neutron superfluid density is considerably less than previously estimated and, consequently, it is premature to rule out models of glitches based on neutron superfluidity in the crust.

Phase synchronization of delta and theta oscillations increase during the detection of relevant lexical information.

PubMed

Brunetti, Enzo; Maldonado, Pedro E; Aboitiz, Francisco

2013-01-01

During monitoring of the discourse, the detection of the relevance of incoming lexical information could be critical for its incorporation to update mental representations in memory. Because, in these situations, the relevance for lexical information is defined by abstract rules that are maintained in memory, a central aspect to elucidate is how an abstract level of knowledge maintained in mind mediates the detection of the lower-level semantic information. In the present study, we propose that neuronal oscillations participate in the detection of relevant lexical information, based on "kept in mind" rules deriving from more abstract semantic information. We tested our hypothesis using an experimental paradigm that restricted the detection of relevance to inferences based on explicit information, thus controlling for ambiguities derived from implicit aspects. We used a categorization task, in which the semantic relevance was previously defined based on the congruency between a kept in mind category (abstract knowledge), and the lexical semantic information presented. Our results show that during the detection of the relevant lexical information, phase synchronization of neuronal oscillations selectively increases in delta and theta frequency bands during the interval of semantic analysis. These increments occurred irrespective of the semantic category maintained in memory, had a temporal profile specific for each subject, and were mainly induced, as they had no effect on the evoked mean global field power. Also, recruitment of an increased number of pairs of electrodes was a robust observation during the detection of semantic contingent words. These results are consistent with the notion that the detection of relevant lexical information based on a particular semantic rule, could be mediated by increasing the global phase synchronization of neuronal oscillations, which may contribute to the recruitment of an extended number of cortical regions.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

Analysis and Simulation of the Simplified Aircraft-Based Paired Approach Concept With the ALAS Alerting Algorithm in Conjunction With Echelon and Offset Strategies

NASA Technical Reports Server (NTRS)

Torres-Pomales, Wilfredo; Madden, Michael M.; Butler, Rickey W.; Perry, Raleigh B.

2014-01-01

This report presents analytical and simulation results of an investigation into proposed operational concepts for closely spaced parallel runways, including the Simplified Aircraft-based Paired Approach (SAPA) with alerting and an escape maneuver, MITRE?s echelon spacing and no escape maneuver, and a hybrid concept aimed at lowering the visibility minima. We found that the SAPA procedure can be used at 950 ft separations or higher with next-generation avionics and that 1150 ft separations or higher is feasible with current-rule compliant ADS-B OUT. An additional 50 ft reduction in runway separation for the SAPA procedure is possible if different glideslopes are used. For the echelon concept we determined that current generation aircraft cannot conduct paired approaches on parallel paths using echelon spacing on runways less than 1400 ft apart and next-generation aircraft will not be able to conduct paired approach on runways less than 1050 ft apart. The hybrid concept added alerting and an escape maneuver starting 1 NM from the threshold when flying the echelon concept. This combination was found to be effective, but the probability of a collision can be seriously impacted if the turn component of the escape maneuver has to be disengaged near the ground (e.g. 300 ft or below) due to airport buildings and surrounding terrain. We also found that stabilizing the approach path in the straight-in segment was only possible if the merge point was at least 1.5 to 2 NM from the threshold unless the total system error can be sufficiently constrained on the offset path and final turn.

Conditional maximum-entropy method for selecting prior distributions in Bayesian statistics

NASA Astrophysics Data System (ADS)

Abe, Sumiyoshi

2014-11-01

The conditional maximum-entropy method (abbreviated here as C-MaxEnt) is formulated for selecting prior probability distributions in Bayesian statistics for parameter estimation. This method is inspired by a statistical-mechanical approach to systems governed by dynamics with largely separated time scales and is based on three key concepts: conjugate pairs of variables, dimensionless integration measures with coarse-graining factors and partial maximization of the joint entropy. The method enables one to calculate a prior purely from a likelihood in a simple way. It is shown, in particular, how it not only yields Jeffreys's rules but also reveals new structures hidden behind them.

Dielectric dispersion for short double-strand DNA.

PubMed

Omori, Shinji; Katsumoto, Yoichi; Yasuda, Akio; Asami, Koji

2006-05-01

A complex dielectric constant for double-strand DNA molecules with a length of not greater than 120 base pairs in an aqueous solution containing 30 mM NaCl was systematically measured as a function of chain length in such a way that experimental uncertainties associated with the molecular-weight distribution of specimens were virtually excluded. In contrast to the past experimental and theoretical studies for much longer DNA molecules, both the molar specific dielectric increment and the relaxation time are proportional to the chain length. These scaling rules cannot be accounted for by any theory so far proposed that gives analytical expressions for those two quantities in the long-chain limit.

The Three Forms of Molecular Oxygen.

ERIC Educational Resources Information Center

Laing, Michael

1989-01-01

Finds that a logical application of the simple rules of the molecular orbital bonding theory for diatomic molecules predicted the existence of three spin isomers of the oxygen molecule: one triplet form with two unpaired electrons and two singlet forms with all electrons paired. (MVL)

Computer language for identifying chemicals with comprehensive two-dimensional gas chromatography and mass spectrometry.

PubMed

Reichenbach, Stephen E; Kottapalli, Visweswara; Ni, Mingtian; Visvanathan, Arvind

2005-04-15

This paper describes a language for expressing criteria for chemical identification with comprehensive two-dimensional gas chromatography paired with mass spectrometry (GC x GC-MS) and presents computer-based tools implementing the language. The Computer Language for Indentifying Chemicals (CLIC) allows expressions that describe rules (or constraints) for selecting chemical peaks or data points based on multi-dimensional chromatographic properties and mass spectral characteristics. CLIC offers chromatographic functions of retention times, functions of mass spectra, numbers for quantitative and relational evaluation, and logical and arithmetic operators. The language is demonstrated with the compound-class selection rules described by Welthagen et al. [W. Welthagen, J. Schnelle-Kreis, R. Zimmermann, J. Chromatogr. A 1019 (2003) 233-249]. A software implementation of CLIC provides a calculator-like graphical user-interface (GUI) for building and applying selection expressions. From the selection calculator, expressions can be used to select chromatographic peaks that meet the criteria or create selection chromatograms that mask data points inconsistent with the criteria. Selection expressions can be combined with graphical, geometric constraints in the retention-time plane as a powerful component for chemical identification with template matching or used to speed and improve mass spectrum library searches.

A Chaotic Home Environment Accounts for the Association between Respect for Rules Disposition and Reading Comprehension: A Twin Study

PubMed Central

Taylor, Jeanette; Hart, Sara A.

2014-01-01

This study examined the association between socioemotional dispositions from the developmental propensity model and reading comprehension and whether those associations could be accounted for by level of chaos in the home. Data from 342 monozygotic and 333 same-sex dizygotic twin pairs age 7-13 years were used. A parent rated the twins on sympathy, respect for rules, negative emotionality, and daring and level of chaos in the twins’ home. Reading comprehension was measured using a state-wide school assessment. Only respect for rules significantly and uniquely predicted reading comprehension. Biometric models indicated that respect for rules was positively associated with reading comprehension via the shared environment and home chaos accounted for a significant amount of that shared environmental variance even after controlling for family income. Children with higher respect for rules have better reading comprehension scores in school and this relationship owes partly to the level of chaos in the family home. PMID:25328362

Violation of the isolated square rule for group 13-15 oligomers: theoretical prediction of a new class of inorganic polymers.

PubMed

Timoshkin, Alexey Y; Schaefer, Henry F

2005-02-21

It is widely thought that the oligomer compounds [RMYR]n (M-group 13, Y-group 15 element) should obey the isolated square rule found for the boron-nitrogen cages. In contrast to these expectations, the needle-shaped oligomers, which violate this rule, are more stable compared to the cage (fullerene-like) oligomers for all MY pairs (M = B, Al, Ga, In; Y = N, P, As). The stability of the needle-shaped clusters improves with increasing oligomerization degree. Thus, the isolated square rule, which is analogous to the isolated pentagon rule widely applied for fullerenes, should not serve as the basis for searches for the most stable structures of the inorganic oligomers. Generation of the needle-shaped oligomers from the group 13 and 15 hydrides is thermodynamically favorable. A synthesis of novel inorganic polymers, formed by fusion of trimeric M3Y3 rings, is expected to be viable.

Scaling features of noncoding DNA

NASA Technical Reports Server (NTRS)

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

1999-01-01

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

PubMed Central

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo

2017-01-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. PMID:28213527

Two-Particle Four-Mode Interferometer for Atoms

NASA Astrophysics Data System (ADS)

Dussarrat, Pierre; Perrier, Maxime; Imanaliev, Almazbek; Lopes, Raphael; Aspect, Alain; Cheneau, Marc; Boiron, Denis; Westbrook, Christoph I.

2017-10-01

We present a free-space interferometer to observe two-particle interference of a pair of atoms with entangled momenta. The source of atom pairs is a Bose-Einstein condensate subject to a dynamical instability, and the interferometer is realized using Bragg diffraction on optical lattices, in the spirit of our recent Hong-Ou-Mandel experiment. We report on an observation ruling out the possibility of a purely mixed state at the input of the interferometer. We explain how our current setup can be extended to enable a test of a Bell inequality on momentum observables.

Detecting causality from online psychiatric texts using inter-sentential language patterns

PubMed Central

2012-01-01

Background Online psychiatric texts are natural language texts expressing depressive problems, published by Internet users via community-based web services such as web forums, message boards and blogs. Understanding the cause-effect relations embedded in these psychiatric texts can provide insight into the authors’ problems, thus increasing the effectiveness of online psychiatric services. Methods Previous studies have proposed the use of word pairs extracted from a set of sentence pairs to identify cause-effect relations between sentences. A word pair is made up of two words, with one coming from the cause text span and the other from the effect text span. Analysis of the relationship between these words can be used to capture individual word associations between cause and effect sentences. For instance, (broke up, life) and (boyfriend, meaningless) are two word pairs extracted from the sentence pair: “I broke up with my boyfriend. Life is now meaningless to me”. The major limitation of word pairs is that individual words in sentences usually cannot reflect the exact meaning of the cause and effect events, and thus may produce semantically incomplete word pairs, as the previous examples show. Therefore, this study proposes the use of inter-sentential language patterns such as ≪broke up, boyfriend>,

Hidden patterns of reciprocity.

PubMed

Syi

2014-03-21

Reciprocity can help the evolution of cooperation. To model both types of reciprocity, we need the concept of strategy. In the case of direct reciprocity there are four second-order action rules (Simple Tit-for-tat, Contrite Tit-for-tat, Pavlov, and Grim Trigger), which are able to promote cooperation. In the case of indirect reciprocity the key component of cooperation is the assessment rule. There are, again, four elementary second-order assessment rules (Image Scoring, Simple Standing, Stern Judging, and Shunning). The eight concepts can be formalized in an ontologically thin way we need only an action predicate and a value function, two agent concepts, and the constant of goodness. The formalism helps us to discover that the action and assessment rules can be paired, and that they show the same patterns. The logic of these patterns can be interpreted with the concept of punishment that has an inherent paradoxical nature. Copyright © 2013 Elsevier Ltd. All rights reserved.

47 CFR 22.719 - Additional channel policy for rural radiotelephone stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... radiotelephone stations. 22.719 Section 22.719 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED... policy for rural radiotelephone stations. The rules in this section govern the processing of applications for central office stations that request a rural radiotelephone channel pair when the applicant has...

A simple rule for quadrupedal gait generation determined by leg loading feedback: a modeling study

PubMed Central

Fukuoka, Yasuhiro; Habu, Yasushi; Fukui, Takahiro

2015-01-01

We discovered a specific rule for generating typical quadrupedal gaits (the order of the movement of four legs) through a simulated quadrupedal locomotion, in which unprogrammed gaits (diagonal/lateral sequence walks, left/right-lead canters, and left/right-lead transverse gallops) spontaneously emerged because of leg loading feedbacks to the CPGs hard-wired to produce a default trot. Additionally, all gaits transitioned according to speed, as seen in animals. We have therefore hypothesized that various gaits derive from a trot because of posture control through leg loading feedback. The body tilt on the two support legs of each diagonal pair during trotting was classified into three types (level, tilted up, or tilted down) according to speed. The load difference between the two legs led to the phase difference between their CPGs via the loading feedbacks, resulting in nine gaits (32: three tilts to the power of two diagonal pairs) including the aforementioned. PMID:25639661

Cortical Power-Density Changes of Different Frequency Bands in Visually Guided Associative Learning: A Human EEG-Study

PubMed Central

Puszta, András; Katona, Xénia; Bodosi, Balázs; Pertich, Ákos; Nyujtó, Diána; Braunitzer, Gábor; Nagy, Attila

2018-01-01

The computer-based Rutgers Acquired Equivalence test (RAET) is a widely used paradigm to test the function of subcortical structures in visual associative learning. The test consists of an acquisition (pair learning) and a test (rule transfer) phase, associated with the function of the basal ganglia and the hippocampi, respectively. Obviously, such a complex task also requires cortical involvement. To investigate the activity of different cortical areas during this test, 64-channel EEG recordings were recorded in 24 healthy volunteers. Fast-Fourier and Morlet wavelet convolution analyses were performed on the recordings. The most robust power changes were observed in the theta (4–7 Hz) and gamma (>30 Hz) frequency bands, in which significant power elevation was observed in the vast majority of the subjects, over the parieto-occipital and temporo-parietal areas during the acquisition phase. The involvement of the frontal areas in the acquisition phase was remarkably weaker. No remarkable cortical power elevations were found in the test phase. In fact, the power of the alpha and beta bands was significantly decreased over the parietooccipital areas. We conclude that the initial acquisition of the image pairs requires strong cortical involvement, but once the pairs have been learned, neither retrieval nor generalization requires strong cortical contribution. PMID:29867412

Cortical Power-Density Changes of Different Frequency Bands in Visually Guided Associative Learning: A Human EEG-Study.

PubMed

Puszta, András; Katona, Xénia; Bodosi, Balázs; Pertich, Ákos; Nyujtó, Diána; Braunitzer, Gábor; Nagy, Attila

2018-01-01

The computer-based Rutgers Acquired Equivalence test (RAET) is a widely used paradigm to test the function of subcortical structures in visual associative learning. The test consists of an acquisition (pair learning) and a test (rule transfer) phase, associated with the function of the basal ganglia and the hippocampi, respectively. Obviously, such a complex task also requires cortical involvement. To investigate the activity of different cortical areas during this test, 64-channel EEG recordings were recorded in 24 healthy volunteers. Fast-Fourier and Morlet wavelet convolution analyses were performed on the recordings. The most robust power changes were observed in the theta (4-7 Hz) and gamma (>30 Hz) frequency bands, in which significant power elevation was observed in the vast majority of the subjects, over the parieto-occipital and temporo-parietal areas during the acquisition phase. The involvement of the frontal areas in the acquisition phase was remarkably weaker. No remarkable cortical power elevations were found in the test phase. In fact, the power of the alpha and beta bands was significantly decreased over the parietooccipital areas. We conclude that the initial acquisition of the image pairs requires strong cortical involvement, but once the pairs have been learned, neither retrieval nor generalization requires strong cortical contribution.

Parental and Home Environmental Facilitators of Sugar-Sweetened Beverage Consumption among Overweight and Obese Latino Youth

PubMed Central

Bogart, Laura M.; Cowgill, Burt O.; Sharma, Andrea J.; Uyeda, Kimberly; Sticklor, Laurel A.; Alijewicz, Katie E.; Schuster, Mark A.

2013-01-01

Objective To explore parental and home environmental facilitators of sugar-sweetened beverage (SSB) and water consumption among obese/overweight Latino youth. Methods Semi-structured interviews were conducted with 55 overweight/obese Latino youth aged 10-18 and 55 parents, recruited from school-based clinics and a school in one West-coast district. All youth consumed SSBs regularly and lived in a home where SSBs were available. We used qualitative methods to examine key themes around beliefs about SSBs and water, facilitators of SSB and water consumption, and barriers to reducing SSB consumption. Results A few parents and youth believed that sports drinks are healthy. Although nearly all felt that water is healthy, most parents and about half of youth thought that tap water is unsafe. About half of parent-child dyads had discordant beliefs regarding their perceptions of tap water. About half of parents believed that home-made culturally relevant drinks (e.g., aguas frescas), which typically contain sugar, fruit, and water, were healthy due to their “natural” ingredients. Participants cited home availability as a key factor in SSB consumption. About half of parents set no rules about SSB consumption at home. Among those with rules, most parent-child pairs differed on their beliefs about the content of the rules, and youth reported few consequences for breaking rules. Conclusions Obesity programs for Latino youth should address misconceptions around water, and discuss culturally relevant drinks and sports drinks as potential sources of weight gain. Healthcare providers can help parents set appropriate rules by educating about the risks of keeping SSBs at home. PMID:23680295

Automated knowledge-base refinement

NASA Technical Reports Server (NTRS)

Mooney, Raymond J.

1994-01-01

Over the last several years, we have developed several systems for automatically refining incomplete and incorrect knowledge bases. These systems are given an imperfect rule base and a set of training examples and minimally modify the knowledge base to make it consistent with the examples. One of our most recent systems, FORTE, revises first-order Horn-clause knowledge bases. This system can be viewed as automatically debugging Prolog programs based on examples of correct and incorrect I/O pairs. In fact, we have already used the system to debug simple Prolog programs written by students in a programming language course. FORTE has also been used to automatically induce and revise qualitative models of several continuous dynamic devices from qualitative behavior traces. For example, it has been used to induce and revise a qualitative model of a portion of the Reaction Control System (RCS) of the NASA Space Shuttle. By fitting a correct model of this portion of the RCS to simulated qualitative data from a faulty system, FORTE was also able to correctly diagnose simple faults in this system.

Moral empiricism and the bias for act-based rules.

PubMed

Ayars, Alisabeth; Nichols, Shaun

2017-10-01

Previous studies on rule learning show a bias in favor of act-based rules, which prohibit intentionally producing an outcome but not merely allowing the outcome. Nichols, Kumar, Lopez, Ayars, and Chan (2016) found that exposure to a single sample violation in which an agent intentionally causes the outcome was sufficient for participants to infer that the rule was act-based. One explanation is that people have an innate bias to think rules are act-based. We suggest an alternative empiricist account: since most rules that people learn are act-based, people form an overhypothesis (Goodman, 1955) that rules are typically act-based. We report three studies that indicate that people can use information about violations to form overhypotheses about rules. In study 1, participants learned either three "consequence-based" rules that prohibited allowing an outcome or three "act-based" rules that prohibiting producing the outcome; in a subsequent learning task, we found that participants who had learned three consequence-based rules were more likely to think that the new rule prohibited allowing an outcome. In study 2, we presented participants with either 1 consequence-based rule or 3 consequence-based rules, and we found that those exposed to 3 such rules were more likely to think that a new rule was also consequence based. Thus, in both studies, it seems that learning 3 consequence-based rules generates an overhypothesis to expect new rules to be consequence-based. In a final study, we used a more subtle manipulation. We exposed participants to examples act-based or accident-based (strict liability) laws and then had them learn a novel rule. We found that participants who were exposed to the accident-based laws were more likely to think a new rule was accident-based. The fact that participants' bias for act-based rules can be shaped by evidence from other rules supports the idea that the bias for act-based rules might be acquired as an overhypothesis from the preponderance of act-based rules. Copyright © 2017 Elsevier B.V. All rights reserved.

Video-based data acquisition system for use in eye blink classical conditioning procedures in sheep.

PubMed

Nation, Kelsey; Birge, Adam; Lunde, Emily; Cudd, Timothy; Goodlett, Charles; Washburn, Shannon

2017-10-01

Pavlovian eye blink conditioning (EBC) has been extensively studied in humans and laboratory animals, providing one of the best-understood models of learning in neuroscience. EBC has been especially useful in translational studies of cerebellar and hippocampal function. We recently reported a novel extension of EBC procedures for use in sheep, and now describe new advances in a digital video-based system. The system delivers paired presentations of conditioned stimuli (CSs; a tone) and unconditioned stimuli (USs; an air puff to the eye), or CS-alone "unpaired" trials. This system tracks the linear distance between the eyelids to identify blinks occurring as either unconditioned (URs) or conditioned (CRs) responses, to a resolution of 5 ms. A separate software application (Eye Blink Reviewer) is used to review and autoscore the trial CRs and URs, on the basis of a set of predetermined rules, permitting an operator to confirm (or rescore, if needed) the autoscore results, thereby providing quality control for accuracy of scoring. Learning curves may then be quantified in terms of the frequencies of CRs over sessions, both on trials with paired CS-US presentations and on CS-alone trials. The latency to CR onset, latency to CR peak, and occurrence of URs are also obtained. As we demonstrated in two example cases, this video-based system provides efficient automated means to conduct EBC in sheep and can facilitate fully powered studies with multigroup designs that involve paired and unpaired training. This can help extend new studies in sheep, a species well suited for translational studies of neurodevelopmental disorders resulting from gestational exposure to drugs, toxins, or intrauterine distress.

Ice-based altitude distribution of natural radiation annual exposure rate in the Antarctica zone over the latitude range 69 degrees S-77 degrees S using a pair-filter thermoluminescence method.

PubMed

Nakajima, T; Kamiyama, T; Fujii, Y; Motoyama, H; Esumi, S

1995-12-01

Both ice-based altitude distributions of natural ionizing radiation exposure and the quasi-effective energy of natural radiation over Antartica over the latitude range 69 degrees S - 77 degrees S during approx. 500 days were measured using thermoluminescent dosimeters. The results shows that dependence on altitude above sea level of the exposure rate increases by almost three-fold with each increase of 2000 m of altitude, thus deviating from the general rule stating that the exposure rate should double with each 2000 m. Although the exposure rate shows a dependence on altitude, altitude dependence of the quasi-effective energy of natural radiation over Antartica is not observed. In the present study it is observed that natural radiation occurring over the ice base of Antartica consists mainly of cosmic rays.

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

Xia, Shuangluo; Vashishtha, Ashwani; Bulkley, David

During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold dependingmore » on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.« less

Appetite and growth: a longitudinal sibling analysis.

PubMed

van Jaarsveld, Cornelia H M; Boniface, David; Llewellyn, Clare H; Wardle, Jane

2014-04-01

Identifying early markers of future obesity risk can help target preventive interventions. Several studies have shown that a heartier appetite in infancy is a risk factor for more rapid weight gain, but to date no investigations have been able to rule out familial confounding. To use a sibling design (data from same-sex, dizygotic twin pairs) to test the hypothesis that sibling differences in infant appetite predicted differential weight gain during childhood. Gemini is a population-based twin cohort among the general United Kingdom population born between March 1, 2007, and December 15, 2007. Growth trajectories were analyzed from birth to age 15 months. Appetite-discordant pairs were selected from 800 nonidentical, same-sex twin pairs. Appetite during the first 3 months of life was assessed with the food responsiveness (FR) and satiety responsiveness (SR) subscales from the Baby Eating Behaviour Questionnaire. Discordance was defined as a within-pair difference of at least 1 SD. A mean of 11.5 weight measurements per child were available between birth and age 15 months. Multilevel models, adjusted for sex and birth weight, compared growth curves for the higher-appetite vs lower-appetite twins. In total, 172 pairs were discordant for SR and 121 pairs for FR. Within-pair analyses showed that those with higher FR and those with lower SR grew faster than their sibling. At age 6 months, those with higher FR were 654 (95% CI, 395-913) g heavier and at age 15 months were 991 (95% CI, 484-1498) g heavier. For sibling pairs discordant for SR, the weight differences between siblings were 637 (95% CI, 438-836) g at age 6 months and 918 (95% CI, 569-1267) g at age 15 months. A heartier appetite (indexed with higher FR or lower SR) in early infancy is prospectively associated with more rapid growth up to age 15 months in a design controlling for potential familial confounding, supporting a causal role for appetite in childhood weight gain. Appetite could be an early marker for risk of weight gain in the current obesogenic environment and might be a potential target for preventive interventions.

Teaching Chess to Young Children.

ERIC Educational Resources Information Center

Bankauskas, Deborah

2000-01-01

Presents suggestions for teaching chess to young children as part of the problem-solving component of a kindergarten mathematics curriculum. Discusses the introduction of pairs of chess characters, playing challenge games with teachers to enhance skill development, and writing down the rules of the game. Notes that children's problem-solving and…

Discussion Strategies for the Inclusion of ALL Students

ERIC Educational Resources Information Center

Weih, Timothy G.

2015-01-01

Student-centered discussion strategies are described in this article in pursuance of insuring that ALL student voices have a chance to be heard in the classroom. Discussion strategies that are presented include the following: The 10 Second Rule, Think-Pair-Share, Quick Writes, Recorder-Reporter, and K-W-L.

Classical Control System Design: A non-Graphical Method for Finding the Exact System Parameters

NASA Astrophysics Data System (ADS)

Hussein, Mohammed Tawfik

2008-06-01

The Root Locus method of control system design was developed in the 1940's. It is a set of rules that helps in sketching the path traced by the roots of the closed loop characteristic equation of the system, as a parameter such as a controller gain, k, is varied. The procedure provides approximate sketching guidelines. Designs on control systems using the method are therefore not exact. This paper aims at a non-graphical method for finding the exact system parameters to place a pair of complex conjugate poles on a specified damping ratio line. The overall procedure is based on the exact solution of complex equations on the PC using numerical methods.

Professional Ethics in the College and University Science Curriculum

NASA Astrophysics Data System (ADS)

Kovac, Jeffrey

Scientific ethics is a subset of professional ethics, the special rules of conduct adopted by those engaged in one of the pursuits regarded as professions, such as law, medicine, engineering and science. Professional ethics derive from a moral ideal based on service. This ideal leads to a pair of bargains: an internal bargain that defines the internal code of practice within the profession, and an external bargain that defines the relationship between the profession and society. This article develops the internal and external bargains that are the basis of scientific ethics from both an historical and a philosophical perspective and makes suggestions as to how the teaching of scientific ethics can be integrated into the undergraduate curriculum.

Equivalence principle and quantum mechanics: quantum simulation with entangled photons.

PubMed

Longhi, S

2018-01-15

Einstein's equivalence principle (EP) states the complete physical equivalence of a gravitational field and corresponding inertial field in an accelerated reference frame. However, to what extent the EP remains valid in non-relativistic quantum mechanics is a controversial issue. To avoid violation of the EP, Bargmann's superselection rule forbids a coherent superposition of states with different masses. Here we suggest a quantum simulation of non-relativistic Schrödinger particle dynamics in non-inertial reference frames, which is based on the propagation of polarization-entangled photon pairs in curved and birefringent optical waveguides and Hong-Ou-Mandel quantum interference measurement. The photonic simulator can emulate superposition of mass states, which would lead to violation of the EP.

Weighing the Evidence in Peters' Rule: Does Neuronal Morphology Predict Connectivity?

PubMed

Rees, Christopher L; Moradi, Keivan; Ascoli, Giorgio A

2017-02-01

Although the importance of network connectivity is increasingly recognized, identifying synapses remains challenging relative to the routine characterization of neuronal morphology. Thus, researchers frequently employ axon-dendrite colocations as proxies of potential connections. This putative equivalence, commonly referred to as Peters' rule, has been recently studied at multiple levels and scales, fueling passionate debates regarding its validity. Our critical literature review identifies three conceptually distinct but often confused applications: inferring neuron type circuitry, predicting synaptic contacts among individual cells, and estimating synapse numbers within neuron pairs. Paradoxically, at the originally proposed cell-type level, Peters' rule remains largely untested. Leveraging Hippocampome.org, we validate and refine the relationship between axonal-dendritic colocations and synaptic circuits, clarifying the interpretation of existing and forthcoming data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Conducting a thermal conductivity survey

NASA Technical Reports Server (NTRS)

Allen, P. B.

1985-01-01

A physically transparent approximate theory of phonon decay rates is presented starting from a pair potential model of the interatomic forces in an insulator or semiconductor. The theory applies in the classical regime and relates the 3-phonon decay rate to the third derivative of the pair potential. Phonon dispersion relations do not need to be calculated, as sum rules relate all the needed quantities directly to the pair potential. The Brillouin zone averaged phonon lifetime turns out to involve a dimensionless measure of the anharmonicity multiplied by an effective density of states for 3-phonon decay. Results are given for rare gas and alkali halide crystals. For rare gases, the results are in good agreement with more elaborate perturbation calculations. Comparison to experimental data on phonon linewidths and thermal conductivity are made.

Leadership, personality and social feedback

PubMed Central

Ang, Tzo Zen; Sweetman, Gemma; Johnstone, Rufus A; Manica, Andrea

2009-01-01

In a recent paper, we showed that leadership arises from individual behavioral differences in pairs of foraging stickleback (Gasterosteus aculeatus). Foraging data from randomly combined pairs of fish were analyzed using Markov Chain models to infer the individual movement rules underlying joint behavior. While both fish responded to partner movement, bolder individuals were the least responsive and showed greater individual initiative. Shy partners were more faithful followers and were also found to bring about greater leadership tendencies in their bold partners. The ability of such followers to inspire bolder fish suggests that leadership may be dependent on individual temperament differences, reinforced by social feedback. PMID:19721883

A prospective cluster-randomized trial to implement the Canadian CT Head Rule in emergency departments

PubMed Central

Stiell, Ian G.; Clement, Catherine M.; Grimshaw, Jeremy M.; Brison, Robert J.; Rowe, Brian H.; Lee, Jacques S.; Shah, Amit; Brehaut, Jamie; Holroyd, Brian R.; Schull, Michael J.; McKnight, R. Douglas; Eisenhauer, Mary A.; Dreyer, Jonathan; Letovsky, Eric; Rutledge, Tim; MacPhail, Iain; Ross, Scott; Perry, Jeffrey J.; Ip, Urbain; Lesiuk, Howard; Bennett, Carol; Wells, George A.

2010-01-01

Background The Canadian CT Head Rule was developed to allow physicians to be more selective when ordering computed tomography (CT) imaging for patients with minor head injury. We sought to evaluate the effectiveness of implementing this validated decision rule at multiple emergency departments. Methods We conducted a matched-pair cluster-randomized trial that compared the outcomes of 4531 patients with minor head injury during two 12-month periods (before and after) at hospital emergency departments in Canada, six of which were randomly allocated as intervention sites and six as control sites. At the intervention sites, active strategies, including education, changes to policy and real-time reminders on radiologic requisitions were used to implement the Canadian CT Head Rule. The main outcome measure was referral for CT scan of the head. Results Baseline characteristics of patients were similar when comparing control to intervention sites. At the intervention sites, the proportion of patients referred for CT imaging increased from the “before” period (62.8%) to the “after” period (76.2%) (difference +13.3%, 95% CI 9.7%–17.0%). At the control sites, the proportion of CT imaging usage also increased, from 67.5% to 74.1% (difference +6.7%, 95% CI 2.6%–10.8%). The change in mean imaging rates from the “before” period to the “after” period for intervention versus control hospitals was not significant (p = 0.16). There were no missed brain injuries or adverse outcomes. Interpretation Our knowledge–translation-based trial of the Canadian CT Head Rule did not reduce rates of CT imaging in Canadian emergency departments. Future studies should identify strategies to deal with barriers to implementation of this decision rule and explore more effective approaches to knowledge translation. (ClinicalTrials.gov trial register no. NCT00993252) PMID:20732978

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

PubMed Central

2015-01-01

Background Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression relationship is not the only regulatory relationship between miRNAs and their targets, and some miRNAs can positively regulate a mRNA by binding at the 5' UTR of the mRNA. Results This work focuses on the detection of both inverse and positive regulatory relationships from a paired miRNA and mRNA expression data set of HCV patients through a 'change-to-change' method which can derive connected discriminatory rules. Our study uncovered many novel miRNA-mRNA regulatory modules. In particular, it was revealed that GFRA2 is positively regulated by miR-557, miR-765 and miR-17-3p that probably bind at different locations of the 5' UTR of this mRNA. The expression relationship between GFRA2 and any of these three miRNAs has not been studied before, although separate research for this gene and these miRNAs have all drawn conclusions linked to hepatocellular carcinoma. This suggests that the binding of mRNA GFRA2 with miR-557, miR-765, or miR-17-3p, or their combinations, is worthy of further investigation by experimentation. We also report another mRNA QKI which has a strong inverse expression relationship with miR-129 and miR-493-3p which may bind at the 3' UTR of QKI with a perfect sequence match. Furthermore, the interaction between hsa-miR-129-5p (previous ID: hsa-miR-129) and QKI is supported with CLIP-Seq data from starBase. Our method can be easily extended for the expression data analysis of other diseases. Conclusion Our rule discovery method is useful for integrating binding information and expression profile for identifying HCV miRNA-mRNA regulatory modules and can be applied to the study of the expression profiles of other complex human diseases. PMID:25707620

Machine learning with naturally labeled data for identifying abbreviation definitions.

PubMed

Yeganova, Lana; Comeau, Donald C; Wilbur, W John

2011-06-09

The rapid growth of biomedical literature requires accurate text analysis and text processing tools. Detecting abbreviations and identifying their definitions is an important component of such tools. Most existing approaches for the abbreviation definition identification task employ rule-based methods. While achieving high precision, rule-based methods are limited to the rules defined and fail to capture many uncommon definition patterns. Supervised learning techniques, which offer more flexibility in detecting abbreviation definitions, have also been applied to the problem. However, they require manually labeled training data. In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data. Positive training examples are naturally occurring potential abbreviation-definition pairs in text. Negative training examples are generated by randomly mixing potential abbreviations with unrelated potential definitions. The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form. This approach does not require manually labeled training data. We evaluate the performance of our algorithm on the Ab3P, BIOADI and Medstract corpora. Our system demonstrated results that compare favourably to the existing Ab3P and BIOADI systems. We achieve an F-measure of 91.36% on Ab3P corpus, and an F-measure of 87.13% on BIOADI corpus which are superior to the results reported by Ab3P and BIOADI systems. Moreover, we outperform these systems in terms of recall, which is one of our goals.

Traffic accident in Cuiabá-MT: an analysis through the data mining technology.

PubMed

Galvão, Noemi Dreyer; de Fátima Marin, Heimar

2010-01-01

The traffic road accidents (ATT) are non-intentional events with an important magnitude worldwide, mainly in the urban centers. This article aims to analyzes data related to the victims of ATT recorded by the Justice Secretariat and Public Security (SEJUSP) in hospital morbidity and mortality incidence at the city of Cuiabá-MT during 2006, using data mining technology. An observational, retrospective and exploratory study of the secondary data bases was carried out. The three database selected were related using the probabilistic method, through the free software RecLink. One hundred and thirty-nine (139) real pairs of victims of ATT were obtained. In this related database the data mining technology was applied with the software WEKA using the Apriori algorithm. The result generated 10 best rules, six of them were considered according to the parameters established that indicated a useful and comprehensible knowledge to characterize the victims of accidents in Cuiabá. Finally, the findings of the associative rules showed peculiarities of the road traffic accident victims in Cuiabá and highlight the need of prevention measures in the collision accidents for males.

Odd-frequency superconductivity induced in topological insulators with and without hexagonal warping.

PubMed

Vasenko, A S; Golubov, A A; Silkin, V M; Chulkov, E V

2017-07-26

We study the effect of the Fermi surface anisotropy on the odd-frequency spin-triplet pairing component of the induced pair potential. We consider a superconductor/ ferromagnetic insulator (S/FI) hybrid structure formed on the 3D topological insulator (TI) surface. In this case three ingredients ensure the possibility of the odd-frequency pairing: (1) the topological surface states, (2) the induced pair potential, and (3) the magnetic moment of a nearby ferromagnetic insulator. We take into account the strong anisotropy of the Dirac point in topological insulators when the chemical potential lies well above the Dirac cone and its constant energy contour has a snowflake shape. Within this model, we propose that the S/FI boundary should be properly aligned with respect to the snowflake constant energy contour to have an odd-frequency symmetry of the corresponding pairing component and to insure the Majorana bound state at the S/FI boundary. For arbitrary orientation of the boundary, the Majorana bound state is absent. This provides a selection rule to the realization of Majorana modes in S/FI hybrid structures, formed on the topological insulator surface.

Probing a chemical compass: novel variants of low-frequency reaction yield detected magnetic resonance.

PubMed

Maeda, Kiminori; Storey, Jonathan G; Liddell, Paul A; Gust, Devens; Hore, P J; Wedge, C J; Timmel, Christiane R

2015-02-07

We present a study of a carotenoid-porphyrin-fullerene triad previously shown to function as a chemical compass: the photogenerated carotenoid-fullerene radical pair recombines at a rate sensitive to the orientation of an applied magnetic field. To characterize the system we develop a time-resolved Low-Frequency Reaction Yield Detected Magnetic Resonance (tr-LF-RYDMR) technique; the effect of varying the relative orientation of applied static and 36 MHz oscillating magnetic fields is shown to be strongly dependent on the strength of the oscillating magnetic field. RYDMR is a diagnostic test for involvement of the radical pair mechanism in the magnetic field sensitivity of reaction rates or yields, and has previously been applied in animal behavioural experiments to verify the involvement of radical-pair-based intermediates in the magnetic compass sense of migratory birds. The spectroscopic selection rules governing RYDMR are well understood at microwave frequencies for which the so-called 'high-field approximation' is valid, but at lower frequencies different models are required. For example, the breakdown of the rotating frame approximation has recently been investigated, but less attention has so far been given to orientation effects. Here we gain physical insights into the interplay of the different magnetic interactions affecting low-frequency RYDMR experiments performed in the challenging regime in which static and oscillating applied magnetic fields as well as internal electron-nuclear hyperfine interactions are of comparable magnitude. Our observations aid the interpretation of existing RYDMR-based animal behavioural studies and will inform future applications of the technique to verify and characterize further the biological receptors involved in avian magnetoreception.

Flexible Ionic-Electronic Hybrid Oxide Synaptic TFTs with Programmable Dynamic Plasticity for Brain-Inspired Neuromorphic Computing.

PubMed

John, Rohit Abraham; Ko, Jieun; Kulkarni, Mohit R; Tiwari, Naveen; Chien, Nguyen Anh; Ing, Ng Geok; Leong, Wei Lin; Mathews, Nripan

2017-08-01

Emulation of biological synapses is necessary for future brain-inspired neuromorphic computational systems that could look beyond the standard von Neuman architecture. Here, artificial synapses based on ionic-electronic hybrid oxide-based transistors on rigid and flexible substrates are demonstrated. The flexible transistors reported here depict a high field-effect mobility of ≈9 cm 2 V -1 s -1 with good mechanical performance. Comprehensive learning abilities/synaptic rules like paired-pulse facilitation, excitatory and inhibitory postsynaptic currents, spike-time-dependent plasticity, consolidation, superlinear amplification, and dynamic logic are successfully established depicting concurrent processing and memory functionalities with spatiotemporal correlation. The results present a fully solution processable approach to fabricate artificial synapses for next-generation transparent neural circuits. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

PubMed

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

2017-05-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The Common Prescription Patterns Based on the Hierarchical Clustering of Herb-Pairs Efficacies

PubMed Central

2016-01-01

Prescription patterns are rules or regularities used to generate, recognize, or judge a prescription. Most of existing studies focused on the specific prescription patterns for diverse diseases or syndromes, while little attention was paid to the common patterns, which reflect the global view of the regularities of prescriptions. In this paper, we designed a method CPPM to find the common prescription patterns. The CPPM is based on the hierarchical clustering of herb-pair efficacies (HPEs). Firstly, HPEs were hierarchically clustered; secondly, the individual herbs are labeled by the HPEC (the clusters of HPEs); and then the prescription patterns were extracted from the combinations of HPEC; finally the common patterns are recognized statistically. The results showed that HPEs have hierarchical clustering structure. When the clustering level is 2 and the HPEs were classified into two clusters, the common prescription patterns are obvious. Among 332 candidate prescriptions, 319 prescriptions follow the common patterns. The description of the patterns is that if a prescription contains the herbs of the cluster (C 1), it is very likely to have other herbs of another cluster (C 2); while a prescription has the herbs of C 2, it may have no herbs of C 1. Finally, we discussed that the common patterns are mathematically coincident with the Blood-Qi theory. PMID:27190534

Discovering H-bonding rules in crystals with inductive logic programming.

PubMed

Ando, Howard Y; Dehaspe, Luc; Luyten, Walter; Van Craenenbroeck, Elke; Vandecasteele, Henk; Van Meervelt, Luc

2006-01-01

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Relationship between ion pair geometries and electrostatic strengths in proteins.

PubMed Central

Kumar, Sandeep; Nussinov, Ruth

2002-01-01

The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins. PMID:12202384

[Data mining analysis of regularity of formulas containing Salviae Miltiorrhizae Radix et Rhizoma-Carthami Flos medicin pair in Dictionary of Chinese Medicine Prescription].

PubMed

Cui, Yi-Ran; Liu, Xin; Shen, Dan; Yang, Hong-Jun; Tang, Shi-Huan

2016-02-01

In this study, formulas containing Salviae Miltiorrhizae Radix et Rhizoma-Carthami Flos in the database of Dictionary of Chinese Medicine Prescription (DCMP) were extracted by using traditional Chinese medicine inheritance support system (TCMISS). The drugs pairs and formula composition rules were analyzed with data mining methods, such as association rules, improved mutual information method and complex system entropy clustering. Totally 39 formulas were included in this study and involved 280 Chinese medicines. The top 5 Chinese medicines most frequently used were Danggui (Angelica sinensis), Chuanxiong (Ligusticum chuanxiong), Xiangfu (Cyperi Rhizoma), Baishao(Radix Paeoniae Alba), Taoren(Prunus persica) and Shengdihuang (Radix Rehmanniae Recens). Six core medicinal pairs were obtained through clustering analysis, namely Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Xiangfu (Cyperi Rhizoma)-Honghua (Carthami Flos), Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Baishao (Radix Paeoniae Alba)-Honghua (Carthami Flos), Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Danggui (A. sinensis)-Xiagnfu (Cyperi Rhizoma)-Honghua (Carthami Flos), Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Danggui (A. sinensis)-Baishao (Radix Paeoniae Alba)-Honghua (Carthami Flos), Honghua (Carthami Flos)-Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Baishao (Radix Paeoniae Alba)-Danggui (A. sinensis), Danshen (Salviae Miltiorrhizae Radix et Rhizoma)-Baishao (Radix Paeoniae Alba)-Honghua (Carthami Flos)-Danggui (A. sinensis). The support degree was set at 11 (38.46%), with a confidence coefficient of 80%, and then 38 associated pairs were screened. These results suggested that Salviae Miltiorrhizae Radix et Rhizoma, Carthami Flos is often combined with herbs for activating blood and promoting circulation of qi to treat gynecopathy, stasis blood pain syndrome, stroke and other syndromes. Copyright© by the Chinese Pharmaceutical Association.

76 FR 67512 - Self-Regulatory Organizations; Chicago Mercantile Exchange, Inc.; Notice of Filing and Order...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-01

... changes amend current CME rules to expand its cleared-only, foreign currency (``FX'') swaps offering to support the introduction of (1) Twenty-six new foreign FX currency derivatives for over-the counter (``OTC'') cash settlement; and (2) eleven new FX non- deliverable forward transaction currency pairs for...

Effect of Personnel Quality on the Performance of Patriot Air Defense System Operators,

DTIC Science & Technology

1992-01-01

comparable officer-enlisted pair operates a similar facil- ity that controls the activities of three to six batteries. At battery level, the enlisted...them in relation to prescribed rules of engagement. 2Automatic in this context means that the computer identifies an aircraft as friendly, hostile, or

Salary Equity Studies: The State of the Art. ASHE Annual Meeting 1982 Paper.

ERIC Educational Resources Information Center

Hengstler, Dennis D.; And Others

The strengths and weaknesses of various methodologies in conducting salary equity studies are examined. Particular attention is paid to the problems of identifying appropriate matches in the paired-comparison approach and to the sample, predictor and decision-rule problems associated with the regression analysis approach. In addition, highlights…

Technetium: The First Radioelement on the Periodic Table

ERIC Educational Resources Information Center

Johnstone, Erik V.; Yates, Mary Anne; Poineau, Frederic; Sattelberger, Alfred P.; Czerwinski, Kenneth R.

2017-01-01

The radioactive nature of technetium is discussed using a combination of introductory nuclear physics concepts and empirical trends observed in the chart of the nuclides and the periodic table of the elements. Trends such as the enhanced stability of nucleon pairs, magic numbers, and Mattauch's rule are described. The concepts of nuclear binding…

Self-assembling DNA nanotubes to connect molecular landmarks

NASA Astrophysics Data System (ADS)

Mohammed, Abdul M.; Šulc, Petr; Zenk, John; Schulman, Rebecca

2017-05-01

Within cells, nanostructures are often organized using local assembly rules that produce long-range order. Because these rules can take into account the cell's current structure and state, they can enable complexes, organelles or cytoskeletal structures to assemble around existing cellular components to form architectures. Although many methods for self-assembling biomolecular nanostructures have been developed, few can be programmed to assemble structures whose form depends on the identity and organization of structures already present in the environment. Here, we demonstrate that DNA nanotubes can grow to connect pairs of molecular landmarks with different separation distances and relative orientations. DNA tile nanotubes nucleate at these landmarks and grow while their free ends diffuse. The nanotubes can then join end to end to form stable connections, with unconnected nanotubes selectively melted away. Connections form between landmark pairs separated by 1-10 µm in more than 75% of cases and can span a surface or three dimensions. This point-to-point assembly process illustrates how self-assembly kinetics can be designed to produce structures with a desired physical property rather than a specific shape.

Conditional imitation might promote cooperation under high temptations to defect

NASA Astrophysics Data System (ADS)

Dai, Qionglin; Li, Haihong; Cheng, Hongyan; Qian, Xiaolan; Zhang, Mei; Yang, Junzhong

2012-07-01

In this paper we introduce a conditional imitation rule into an evolutionary game, in which the imitation probabilities of individuals are determined by a function of payoff difference and two crucial parameters μ and σ. The parameter μ characterizes the most adequate goal for individuals and the parameter σ characterizes the tolerance of individuals. By using the pair approximation method and numerical simulations, we find an anomalous cooperation enhancement in which the cooperation level shows a nonmonotonic variation with the increase of temptation. The parameter μ affects the regime of the payoff parameter which supports the anomalous cooperation enhancement, whereas the parameter σ plays a decisive role on the appearance of the nonmonotonic variation of the cooperation level. Furthermore, to give explicit implications for the parameters μ and σ we present an alterative form of the conditional imitation rule based on the benefit and the cost incurred to individuals during strategy updates. In this way, we also provide a phenomenological interpretation for the nonmonotonic behavior of cooperation with the increase of temptation. The results give a clue that a higher cooperation level could be obtained under adverse environments for cooperation by applying the conditional imitation rule, which is possible to be manipulated in real life. More generally, the results in this work might point out an efficient way to maintain cooperation in the risky environments to cooperators.

The effect of multiple primary rules on cancer incidence rates and trends

PubMed Central

Weir, Hannah K.; Johnson, Christopher J.; Ward, Kevin C.; Coleman, Michel P.

2018-01-01

Purpose An examination of multiple primary cancers can provide insight into the etiologic role of genes, the environment, and prior cancer treatment on a cancer patient’s risk of developing a subsequent cancer. Different rules for registering multiple primary cancers (MP) are used by cancer registries throughout the world making data comparisons difficult. Methods We evaluated the effect of SEER and IARC/IACR rules on cancer incidence rates and trends using data from the SEER Program. We estimated age-standardized incidence rate (ASIR) and trends (1975–2011) for the top 26 cancer categories using joinpoint regression analysis. Results ASIRs were higher using SEER compared to IARC/IACR rules for all cancers combined (3 %) and, in rank order, melanoma (9 %), female breast (7 %), urinary bladder (6 %), colon (4 %), kidney and renal pelvis (4 %), oral cavity and pharynx (3 %), lung and bronchus (2 %), and non-Hodgkin lymphoma (2 %). ASIR differences were largest for patients aged 65+ years. Trends were similar using both MP rules with the exception of cancers of the urinary bladder, and kidney and renal pelvis. Conclusions The choice of multiple primary coding rules effects incidence rates and trends. Compared to SEER MP coding rules, IARC/IACR rules are less complex, have not changed over time, and report fewer multiple primary cancers, particularly cancers that occur in paired organs, at the same anatomic site and with the same or related histologic type. Cancer registries collecting incidence data using SEER rules may want to consider including incidence rates and trends using IARC/IACR rules to facilitate international data comparisons. PMID:26809509

Interaction between colloidal particles on an oil-water interface in dilute and dense phases.

PubMed

Parolini, Lucia; Law, Adam D; Maestro, Armando; Buzza, D Martin A; Cicuta, Pietro

2015-05-20

The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system.

Asynchronous inputs alter excitability, spike timing, and topography in primary auditory cortex

PubMed Central

Pandya, Pritesh K.; Moucha, Raluca; Engineer, Navzer D.; Rathbun, Daniel L.; Vazquez, Jessica; Kilgard, Michael P.

2010-01-01

Correlation-based synaptic plasticity provides a potential cellular mechanism for learning and memory. Studies in the visual and somatosensory systems have shown that behavioral and surgical manipulation of sensory inputs leads to changes in cortical organization that are consistent with the operation of these learning rules. In this study, we examine how the organization of primary auditory cortex (A1) is altered by tones designed to decrease the average input correlation across the frequency map. After one month of separately pairing nucleus basalis stimulation with 2 and 14 kHz tones, a greater proportion of A1 neurons responded to frequencies below 2 kHz and above 14 kHz. Despite the expanded representation of these tones, cortical excitability was specifically reduced in the high and low frequency regions of A1, as evidenced by increased neural thresholds and decreased response strength. In contrast, in the frequency region between the two paired tones, driven rates were unaffected and spontaneous firing rate was increased. Neural response latencies were increased across the frequency map when nucleus basalis stimulation was associated with asynchronous activation of the high and low frequency regions of A1. This set of changes did not occur when pulsed noise bursts were paired with nucleus basalis stimulation. These results are consistent with earlier observations that sensory input statistics can shape cortical map organization and spike timing. PMID:15855025

The analysis of photon pair source at telecom wavelength based on the BBO crystal (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gajewski, Andrzej; Kolenderski, Piotr L.

2016-10-01

There are several problems that must be solved in order to increase the distance of quantum communication protocols based on photons as an information carriers. One of them is the dispersion, whose effects can be minimized by engineering spectral properties of transmitted photons. In particular, it is expected that positively correlated photon pairs can be very useful. We present the full characterization of a source of single photon pairs at a telecom wavelength based on type II spontaneous parametric down conversion (SPDC) process in a beta-barium borate (BBO) crystal. In the type II process, a pump photon, which is polarized extraordinarily, splits in a nonlinear medium into signal and idler photons, which are polarized perpendicularly to each other. In order for the process to be efficient a phase matching condition must be fulfilled. These conditions originate from momentum and energy conservation rules and put severe restrictions on source parameters. Seemingly, these conditions force the photon pair to be negatively correlated in their spectral domain. However, it is possible to achieve positive correlation for pulsed pumping. The experimentally available degrees of freedom of a source are the width of the pumping beam, the collected modes' widths, the length of the nonlinear crystal and the duration of the pumping pulse. In our numerical model we use the following figures of merit: the pair production rate, the efficiency of photon coupling into a single mode fiber, the spectral correlation of the coupled photon pair. The last one is defined as the Pearson correlation parameter for a joint spectral distribution. The aim here is to find the largest positive spectral correlation and the highest coupling efficiency. By resorting to the numerical model Ref. [1] we showed in Ref. [2], that by careful adjustment of the pump's and the collected modes' characteristics, one can optimize any of the source's parameters. Our numerical outcomes conform to the experimental results presented in Refs [3,4]. Here we investigate typical, experimentally available source parameters: the widths of the pump beam and collected modes ranging from 20μm to 500m, the crystal length ranging from 1mm to 7.5mm while the pulse duration is set to 50fs, 100fs or 150fs. We achieve the correlation coefficient value as high as approximately 0.8, or - for different values of parameters - coupling efficiency equal to 0.76.

Cognitive control level of action for analyzing verbal reports in educative clinical simulation situations.

PubMed

Morineau, Thierry; Meineri, Sebastien; Chapelain, Pascal

2017-03-01

Several methods and theoretical frameworks have been proposed for efficient debriefing after clinical simulation sessions. In these studies, however, the cognitive processes underlying the debriefing stage are not directly addressed. Cognitive control constitutes a conceptual link between behavior and reflection on behavior to apprehend debriefing cognitively. Our goal was to analyze cognitive control from verbal reports using the Skill-Rule-Knowledge model. This model considers different cognitive control levels from skill-based to rule-based and knowledge-based control. An experiment was conducted with teams of nursing students who were confronted with emergency scenarios during high-fidelity simulation sessions. Participants' descriptions of their actions were asked in the course of the simulation scenarios or during the debriefing stage. 52 nursing students working in 26 pairs participated in this study. Participants were divided into two groups: an "in situ" group in which they had to describe their actions at different moments of a deteriorating patient scenario, and a "debriefing" group, in which, at the same moments, they had to describe their actions displayed on a video recording. In addition to a cognitive analysis, the teams' clinical performance was measured. The cognitive control level in the debriefing group was generally higher than in the in situ group. Good team performance was associated with a high level of cognitive control after a patient's significant state deterioration. These findings are in conformity with the "Skill-Rule-Knowledge" model. The debriefing stage allows a deeper reflection on action compared with the in situ condition. If an abnormal event occurs as an adverse event, then participants' mental processes tend to migrate towards knowledge-based control. This migration particularly concerns students with the best clinical performance. Thus, this cognitive framework can help to strengthen the analysis of verbal reports. Copyright © 2016 Elsevier Ltd. All rights reserved.

77 FR 52977 - Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule; Market Risk Capital Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... Corporation 12 CFR Parts 324, 325 Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule... 325 RIN 3064-AD97 Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule; Market Risk... the agencies' current capital rules. In this NPR (Advanced Approaches and Market Risk NPR) the...

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules

NASA Astrophysics Data System (ADS)

Hassanpour, Saeed; O'Connor, Martin J.; Das, Amar K.

Rule bases are increasingly being used as repositories of knowledge content on the Semantic Web. As the size and complexity of these rule bases increases, developers and end users need methods of rule abstraction to facilitate rule management. In this paper, we describe a rule abstraction method for Semantic Web Rule Language (SWRL) rules that is based on lexical analysis and a set of heuristics. Our method results in a tree data structure that we exploit in creating techniques to visualize, paraphrase, and categorize SWRL rules. We evaluate our approach by applying it to several biomedical ontologies that contain SWRL rules, and show how the results reveal rule patterns within the rule base. We have implemented our method as a plug-in tool for Protégé-OWL, the most widely used ontology modeling software for the Semantic Web. Our tool can allow users to rapidly explore content and patterns in SWRL rule bases, enabling their acquisition and management.

Instrumentation of Java Bytecode for Runtime Analysis

NASA Technical Reports Server (NTRS)

Goldberg, Allen; Haveland, Klaus

2003-01-01

This paper describes JSpy, a system for high-level instrumentation of Java bytecode and its use with JPaX, OUT system for runtime analysis of Java programs. JPaX monitors the execution of temporal logic formulas and performs predicative analysis of deadlocks and data races. JSpy s input is an instrumentation specification, which consists of a collection of rules, where a rule is a predicate/action pair The predicate is a conjunction of syntactic constraints on a Java statement, and the action is a description of logging information to be inserted in the bytecode corresponding to the statement. JSpy is built using JTrek an instrumentation package at a lower level of abstraction.

The Emerging Field of RNA Nanotechnology

PubMed Central

Guo, Peixuan

2011-01-01

RNA can be designed and manipulated just like DNA while having different rules for base-pairing and displaying functions similar to proteins. The large variety of loops and motifs in RNA allow them to fold into numerous complicated structures. This diversity provides a platform for identifying viable building blocks for particle assemblies, substrate binding and manufacture engineering. RNA thermal stability allows production of multivalent nanostructures with defined stoichiometry. Here we review the unique qualities of RNA nanotechnology and their distinct properties inside the body. We describe techniques for constructing RNA nanoparticles from different building blocks and their applications in nanomedicine. Finally, we discuss challenges in predicting and synthesizing RNA and offer some perspectives on the yield and cost of RNA production. PMID:21102465

Mining Gene Regulatory Networks by Neural Modeling of Expression Time-Series.

PubMed

Rubiolo, Mariano; Milone, Diego H; Stegmayer, Georgina

2015-01-01

Discovering gene regulatory networks from data is one of the most studied topics in recent years. Neural networks can be successfully used to infer an underlying gene network by modeling expression profiles as times series. This work proposes a novel method based on a pool of neural networks for obtaining a gene regulatory network from a gene expression dataset. They are used for modeling each possible interaction between pairs of genes in the dataset, and a set of mining rules is applied to accurately detect the subjacent relations among genes. The results obtained on artificial and real datasets confirm the method effectiveness for discovering regulatory networks from a proper modeling of the temporal dynamics of gene expression profiles.

Towards XNA nanotechnology: new materials from synthetic genetic polymers

PubMed Central

Pinheiro, Vitor B.; Holliger, Philipp

2014-01-01

Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry. PMID:24745974

Theoretical Insights into Monometallofullerene Th@C76: Strong Covalent Interaction between Thorium and the Carbon Cage.

PubMed

Zhao, Pei; Zhao, Xiang; Ehara, Masahiro

2018-03-19

Th@C 76 has been studied by density functional theory combined with statistical mechanics calculations. The results reveal that Th@ T d (19151)-C 76 satisfying the isolated pentagon rule possesses the lowest energy. Nevertheless, considering the enthalpy-entropy interplay, Th@ C 1 (17418)-C 76 with one pair of adjacent pentagons is thermodynamically favorable at elevated temperatures, which is reported for the first time. The bonding critical points in both isomers were analyzed to disclose covalent interactions between the inner Th and cages. In addition, the Wiberg bond orders of M-C bonding in different endohedral metallofullerenes (EMFs) were investigated to prove stronger covalent interactions of Th-C in Th-based EMFs.

QRPA plus phonon coupling model and the photoabsorption cross section for 18,20,22O

NASA Astrophysics Data System (ADS)

Colò, G.; Bortignon, P. F.

2001-12-01

We have calculated the electric dipole strength distributions in the unstable neutron-rich oxygen isotopes 18,20,22O, in a model which include up to four quasiparticle-type configurations. The model is the extension, to include the effect of the pairing correlations, of a previous model very successful around closed shell nuclei, and it is based on the quasiparticle-phonon coupling. Low-lying dipole strength is found, which exhausts between 5 and 10% of the Thomas-Reiche-Kuhn (TRK) energy-weighted sum rule (EWSR) below 15 MeV excitation energy, in rather good agreement with recent experimental data. The role of the phonon coupling is shown to be crucial in order to obtain this result.

A naturally-occurring new lead-based halocuprate(I)

NASA Astrophysics Data System (ADS)

Welch, Mark D.; Rumsey, Michael S.; Kleppe, Annette K.

2016-06-01

Pb2Cu(OH)2I3 is a new type of halocuprate(I) that is a framework of alternating [Pb4(OH)4]4+ and [Cu2I6]4- units. The structure has been determined in orthorhombic space group Fddd to R1=0.037, wR2=0.057, GoF=1.016. Unit cell parameters are a=16.7082(9) Å, b=20.8465(15) Å, c=21.0159(14) Å, V=7320.0(8) Å3 (Z=32). There is no synthetic counterpart. The structure is based upon a cubane-like Pb4(OH)4 nucleus that is coordinated to sixteen iodide ions. Cu+ ions are inserted into pairs of adjacent edge-sharing tetrahedral sites in the iodide motif to form [Cu2I6]4- groups. The Raman spectrum of Pb2Cu(OH)2I3 has two O-H stretching modes and as such is consistent with space group Fddd, with two non-equivalent OH groups, rather than the related space group I41/acd which has only one non-equivalent OH group. Consideration of the 18-electron rule implies that there is a Cu=Cu double bond, which may be consistent with the short Cu…Cu distance of 2.78 Å, although the dearth of published data on the interpretation of Cu…Cu distances in halocuprate(I) compounds does not allow a clear-cut interpretation of this interatomic distance. The orthorhombic structure is compared with that of the synthetic halocuprate(I) compound Pb2Cu(OH)2BrI2 with space group I41/acd and having chains of corner-linked CuI4 tetrahedra rather than isolated Cu2I6 pairs. The paired motif found in Pb2Cu(OH)2I3 cannot be achieved in space group I41/acd and, conversely, the chain motif cannot be achieved in space group Fddd. As such, the space group defines either a chain or an isolated-pair motif. The existence of Pb2Cu(OH)2I3 suggests a new class of inorganic halocuprate(I)s based upon the Pb4(OH)4 group.

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2012-06-27

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... clearing organizations. In the internal cross-margining program, there is no need for two separate accounts... Organizations; The Options Clearing Corporation; Notice of Filing of Proposed Rule Change to Allow for an Expansion of OCC's Internal Cross-Margining Program to Include the Ability of a Pair of Affiliated Clearing...

Parent-Child Communication about Adolescent Tobacco and Alcohol Use: What Do Parents Say and Does It Affect Youth Behavior?

ERIC Educational Resources Information Center

Ennett, Susan T.; Bauman, Karl E.; Foshee, Vangie A.; Pemberton, Michael; Hicks, Katherine A.

2001-01-01

Adolescent-parent pairs (N=537) were interviewed concerning their communication about tobacco and alcohol use. Parent communication reports identified three domains: rules and discipline; consequences and circumstances; and media influences. Results show that parent-child communication was not related to initiation of smoking or drinking. However,…

Before You Search that Locker.

ERIC Educational Resources Information Center

Dowling-Sendor, Benjamin

1998-01-01

In DesRoches v Caprio, federal district court ruled in favor of Jim DesRoches who had decided not to consent to a search of his backpack for a pair of allegedly stolen sneakers. Judge Robert G. Doumar decided the need to find the stolen sneakers did not outweigh the students' privacy interest and offered guidelines about school searches for stolen…

Bimodal emotion congruency is critical to preverbal infants' abstract rule learning.

PubMed

Tsui, Angeline Sin Mei; Ma, Yuen Ki; Ho, Anna; Chow, Hiu Mei; Tseng, Chia-huei

2016-05-01

Extracting general rules from specific examples is important, as we must face the same challenge displayed in various formats. Previous studies have found that bimodal presentation of grammar-like rules (e.g. ABA) enhanced 5-month-olds' capacity to acquire a rule that infants failed to learn when the rule was presented with visual presentation of the shapes alone (circle-triangle-circle) or auditory presentation of the syllables (la-ba-la) alone. However, the mechanisms and constraints for this bimodal learning facilitation are still unknown. In this study, we used audio-visual relation congruency between bimodal stimulation to disentangle possible facilitation sources. We exposed 8- to 10-month-old infants to an AAB sequence consisting of visual faces with affective expressions and/or auditory voices conveying emotions. Our results showed that infants were able to distinguish the learned AAB rule from other novel rules under bimodal stimulation when the affects in audio and visual stimuli were congruently paired (Experiments 1A and 2A). Infants failed to acquire the same rule when audio-visual stimuli were incongruently matched (Experiment 2B) and when only the visual (Experiment 1B) or the audio (Experiment 1C) stimuli were presented. Our results highlight that bimodal facilitation in infant rule learning is not only dependent on better statistical probability and redundant sensory information, but also the relational congruency of audio-visual information. A video abstract of this article can be viewed at https://m.youtube.com/watch?v=KYTyjH1k9RQ. © 2015 John Wiley & Sons Ltd.

Report on Pairing-based Cryptography.

PubMed

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

Report on Pairing-based Cryptography

PubMed Central

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

Allometric scaling: analysis of LD50 data.

PubMed

Burzala-Kowalczyk, Lidia; Jongbloed, Geurt

2011-04-01

The need to identify toxicologically equivalent doses across different species is a major issue in toxicology and risk assessment. In this article, we investigate interspecies scaling based on the allometric equation applied to the single, oral LD (50) data previously analyzed by Rhomberg and Wolff. We focus on the statistical approach, namely, regression analysis of the mentioned data. In contrast to Rhomberg and Wolff's analysis of species pairs, we perform an overall analysis based on the whole data set. From our study it follows that if one assumes one single scaling rule for all species and substances in the data set, then β = 1 is the most natural choice among a set of candidates known in the literature. In fact, we obtain quite narrow confidence intervals for this parameter. However, the estimate of the variance in the model is relatively high, resulting in rather wide prediction intervals. © 2010 Society for Risk Analysis.

Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

PubMed Central

Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

2015-01-01

Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

On Decision-Making Among Multiple Rule-Bases in Fuzzy Control Systems

NASA Technical Reports Server (NTRS)

Tunstel, Edward; Jamshidi, Mo

1997-01-01

Intelligent control of complex multi-variable systems can be a challenge for single fuzzy rule-based controllers. This class of problems cam often be managed with less difficulty by distributing intelligent decision-making amongst a collection of rule-bases. Such an approach requires that a mechanism be chosen to ensure goal-oriented interaction between the multiple rule-bases. In this paper, a hierarchical rule-based approach is described. Decision-making mechanisms based on generalized concepts from single-rule-based fuzzy control are described. Finally, the effects of different aggregation operators on multi-rule-base decision-making are examined in a navigation control problem for mobile robots.

Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era.

PubMed

Teng, Jade L L; Tang, Ying; Huang, Yi; Guo, Feng-Biao; Wei, Wen; Chen, Jonathan H K; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

2016-01-01

Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA-DNA hybridization (DDH) and "digital DDH" after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA-DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. "Digital DDH" based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3-92.9 and 98.1-99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by "digital DDH" than traditional DDH.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

PubMed Central

Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-01-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

PubMed

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-02-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model

DOE PAGES

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2015-11-04

Liquids are condensed matter in which atoms are strongly correlated in position and momentum. The atomic pair density function (PDF) is used often in describing such correlation. However, elucidation of many properties requires higher degrees of correlation than the pair correlation. For instance, viscosity depends upon the stress correlations in space and time. We examine the cross correlation between the stress correlation at the atomic level and the PDF for two-dimensional liquids. We introduce the concept of the stress-resolved pair distribution function (SRPDF) that uses the sign of atomic-level stress as a selection rule to include particles from density correlations.more » The connection between SRPDFs and stress correlation function is explained through an approximation in which the shear stress is replaced by a pseudospin. Lastly, we further assess the possibility of interpreting the long-range stress correlation as a consequence of short-range Ising-like pseudospin interactions.« less

Link!: Potential Field Guidance Algorithm for In-Flight Linking of Multi-Rotor Aircraft

NASA Technical Reports Server (NTRS)

Cooper, John R.; Rothhaar, Paul M.

2017-01-01

Link! is a multi-center NASA e ort to study the feasibility of multi-aircraft aerial docking systems. In these systems, a group of vehicles physically link to each other during flight to form a larger ensemble vehicle with increased aerodynamic performance and mission utility. This paper presents a potential field guidance algorithm for a group of multi-rotor vehicles to link to each other during flight. The linking is done in pairs. Each vehicle first selects a mate. Then the potential field is constructed with three rules: move towards the mate, avoid collisions with non-mates, and stay close to the rest of the group. Once a pair links, they are then considered to be a single vehicle. After each pair is linked, the process repeats until there is only one vehicle left. The paper contains simulation results for a system of 16 vehicles.

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RuleMonkey: software for stochastic simulation of rule-based models

PubMed Central

2010-01-01

Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models. PMID:20673321

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair

NASA Astrophysics Data System (ADS)

Wang, Yujie; Wang, Zhen; Wang, Yanli; Liu, Taigang; Zhang, Wenbing

2018-01-01

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

Degeneration of the Y chromosome in evolutionary aging models

NASA Astrophysics Data System (ADS)

Lobo, M. P.; Onody, R. N.

2005-06-01

The Y chromosomes are genetically degenerated and do not recombine with their matching partners X. Recombination of XX pairs is pointed out as the key factor for the Y chromosome degeneration. However, there is an additional evolutionary force driving sex-chromosomes evolution. Here we show this mechanism by means of two different evolutionary models, in which sex chromosomes with non-recombining XX and XY pairs of chromosomes is considered. Our results show three curious effects. First, we observed that even when both XX and XY pairs of chromosomes do not recombine, the Y chromosomes still degenerate. Second, the accumulation of mutations on Y chromosomes followed a completely different pattern then those accumulated on X chromosomes. And third, the models may differ with respect to sexual proportion. These findings suggest that a more primeval mechanism rules the evolution of Y chromosomes due exclusively to the sex-chromosomes asymmetry itself, i.e., the fact that Y chromosomes never experience female bodies. Over aeons, natural selection favored X chromosomes spontaneously, even if at the very beginning of evolution, both XX and XY pairs of chromosomes did not recombine.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

41G crew activities

NASA Image and Video Library

2009-06-25

41G-102-003 (5-13 Oct 1984) ---- Astronaut Kathryn D. Sullivan, 41-G mission specialist, floats into a middeck scene to join a more stationary pair of crewmembers---Astronauts Robert L. Crippen, crew commander; and Jon A. McBride, pilot. The protruding article near the stowage lockers is a Krimsky rule, part of the near vision acuity experiment in which recent NASA space travelers have participated.

We're Not in Kansas Anymore: The TOTO Strategy for Decoding Vowel Pairs

ERIC Educational Resources Information Center

Meese, Ruth Lyn

2016-01-01

Vowel teams such as vowel digraphs present a challenge to struggling readers. Some researchers assert that phonics generalizations such as the "two vowels go walking and the first one does the talking" rule do not hold often enough to be reliable for children. Others suggest that some vowel teams are highly regular and that children can…

75 FR 1109 - Self-Regulatory Organizations; BATS Exchange, Inc.; Notice of Filing of Proposed Rule Change To...

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2010-01-08

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Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

The beetle Tribolium castaneum has a fushi tarazu homolog expressed in stripes during segmentation

NASA Technical Reports Server (NTRS)

Brown, S. J.; Hilgenfeld, R. B.; Denell, R. E.; Spooner, B. S. (Principal Investigator)

1994-01-01

The genetic control of embryonic organization is far better understood for the fruit fly Drosophila melanogaster than for any other metazoan. A gene hierarchy acts during oogenesis and embryogenesis to regulate the establishment of segmentation along the anterior-posterior axis, and homeotic selector genes define developmental commitments within each parasegmental unit delineated. One of the most intensively studied Drosophila segmentation genes is fushi tarazu (ftz), a pair-rule gene expressed in stripes that is important for the establishment of the parasegmental boundaries. Although ftz is flanked by homeotic selector genes conserved throughout the metazoa, there is no evidence that it was part of the ancestral homeotic complex, and it has been unclear when the gene arose and acquired a role in segmentation. We show here that the beetle Tribolium castaneum has a ftz homolog located in its Homeotic complex and expressed in a pair-rule fashion, albeit in a register differing from that of the fly gene. These and other observations demonstrate that a ftz gene preexisted the radiation of holometabolous insects and suggest that it has a role in beetle embryogenesis which differs somewhat from that described in flies.

Precision matters for position decoding in the early fly embryo

NASA Astrophysics Data System (ADS)

Petkova, Mariela D.; Tkacik, Gasper; Wieschaus, Eric F.; Bialek, William; Gregor, Thomas

Genetic networks can determine cell fates in multicellular organisms with precision that often reaches the physical limits of the system. However, it is unclear how the organism uses this precision and whether it has biological content. Here we address this question in the developing fly embryo, in which a genetic network of patterning genes reaches 1% precision in positioning cells along the embryo axis. The network consists of three interconnected layers: an input layer of maternal gradients, a processing layer of gap genes, and an output layer of pair-rule genes with seven-striped patterns. From measurements of gap gene protein expression in hundreds of wild-type embryos we construct a ``decoder'', which is a look-up table that determines cellular positions from the concentration means, variances and co-variances. When we apply the decoder to measurements in mutant embryos lacking various combinations of the maternal inputs, we predict quantitative changes in the output layer such as missing, altered or displaced stripes. We confirm these predictions by measuring pair-rule expression in the mutant embryos. Our results thereby show that the precision of the patterning network is biologically meaningful and a necessary feature for decoding cell positions in the early fly embryo.

Temperature-induced Lifshitz transition in WTe 2

DOE PAGES

Wu, Yun; Jo, Na Hyun; Ochi, Masayuki; ...

2015-10-12

In this study, we use ultrahigh resolution, tunable, vacuum ultraviolet laser-based, angle-resolved photoemission spectroscopy (ARPES), temperature- and field-dependent resistivity, and thermoelectric power (TEP) measurements to study the electronic properties of WTe 2, a compound that manifests exceptionally large, temperature-dependent magnetoresistance. The Fermi surface consists of two pairs of electron and two pairs of hole pockets along the X–Γ–X direction. Using detailed ARPES temperature scans, we find a rare example of a temperature-induced Lifshitz transition at T≃160 K, associated with the complete disappearance of the hole pockets. Our electronic structure calculations show a clear and substantial shift of the chemical potentialmore » μ(T) due to the semimetal nature of this material driven by modest changes in temperature. This change of Fermi surface topology is also corroborated by the temperature dependence of the TEP that shows a change of slope at T≈175 K and a breakdown of Kohler’s rule in the 70–140 K range. Our results and the mechanisms driving the Lifshitz transition and transport anomalies are relevant to other systems, such as pnictides, 3D Dirac semimetals, and Weyl semimetals.« less

Carbon Nanotube Based Molecular Electronics

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1998-01-01

Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

PubMed

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

Liquid-assisted grinding and ion pairing regulates percentage conversion and diastereoselectivity of the Wittig reaction under mechanochemical conditions.

PubMed

Denlinger, Kendra Leahy; Ortiz-Trankina, Lianna; Carr, Preston; Benson, Kingsley; Waddell, Daniel C; Mack, James

2018-01-01

Mechanochemistry is maturing as a discipline and continuing to grow, so it is important to continue understanding the rules governing the system. In a mechanochemical reaction, the reactants are added into a vessel along with one or more grinding balls and the vessel is shaken at high speeds to facilitate a chemical reaction. The dielectric constant of the solvent used in liquid-assisted grinding (LAG) and properly chosen counter-ion pairing increases the percentage conversion of stilbenes in a mechanochemical Wittig reaction. Utilizing stepwise addition/evaporation of ethanol in liquid-assisted grinding also allows for the tuning of the diastereoselectivity in the Wittig reaction.

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques

PubMed Central

Mande, Sharmila S.

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm. PMID:27124399

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.

PubMed

Tandon, Disha; Haque, Mohammed Monzoorul; Mande, Sharmila S

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.

Maintenance rehearsal: the key to the role attention plays in storage and forgetting.

PubMed

McFarlane, Kimberley A; Humphreys, Michael S

2012-07-01

Research with the maintenance-rehearsal paradigm, in which word pairs are rehearsed as distractor material during a series of digit recall trials, has previously indicated that low frequency and new word pairs capture attention to a greater degree than high frequency and old word pairs. This impacts delayed recognition of the pairs and interferes with immediate digit recall. The effect on immediate digit recall may provide the missing converging evidence for the role of attention in memory. In the current study, 3 experiments were conducted to further investigate the role of attention capture and novelty in storage and forgetting. In addition to the previously established effects, the novelty of switching rehearsal between 2 pairs was found to impair both digit recall and memory for the first pair. The attentional effects we obtained were dependent upon participant expectation, and forgetting appears to be due to interference with consolidation rather than decay or traditional associative interference. Finally, the attentional effects we observed in associative recognition were primarily reflected in a lowering of the false alarm rate with increases in the strength of the parent pairs. Although dual-process models can accommodate this finding on the assumption that recollection is invoked at test alongside familiarity, we showed that the level of recall in this paradigm is so small that recollection can be ruled out. Accordingly, our results are challenging for the existing models of associative recognition to accommodate. 2012 APA, all rights reserved

A rule-based software test data generator

NASA Technical Reports Server (NTRS)

Deason, William H.; Brown, David B.; Chang, Kai-Hsiung; Cross, James H., II

1991-01-01

Rule-based software test data generation is proposed as an alternative to either path/predicate analysis or random data generation. A prototype rule-based test data generator for Ada programs is constructed and compared to a random test data generator. Four Ada procedures are used in the comparison. Approximately 2000 rule-based test cases and 100,000 randomly generated test cases are automatically generated and executed. The success of the two methods is compared using standard coverage metrics. Simple statistical tests showing that even the primitive rule-based test data generation prototype is significantly better than random data generation are performed. This result demonstrates that rule-based test data generation is feasible and shows great promise in assisting test engineers, especially when the rule base is developed further.

Rule groupings: An approach towards verification of expert systems

NASA Technical Reports Server (NTRS)

Mehrotra, Mala

1991-01-01

Knowledge-based expert systems are playing an increasingly important role in NASA space and aircraft systems. However, many of NASA's software applications are life- or mission-critical and knowledge-based systems do not lend themselves to the traditional verification and validation techniques for highly reliable software. Rule-based systems lack the control abstractions found in procedural languages. Hence, it is difficult to verify or maintain such systems. Our goal is to automatically structure a rule-based system into a set of rule-groups having a well-defined interface to other rule-groups. Once a rule base is decomposed into such 'firewalled' units, studying the interactions between rules would become more tractable. Verification-aid tools can then be developed to test the behavior of each such rule-group. Furthermore, the interactions between rule-groups can be studied in a manner similar to integration testing. Such efforts will go a long way towards increasing our confidence in the expert-system software. Our research efforts address the feasibility of automating the identification of rule groups, in order to decompose the rule base into a number of meaningful units.

Neighborhood perceptions and parent outcomes in family based prevention programs for Thai adolescents: the role of program engagement.

PubMed

Byrnes, Hilary F; Miller, Brenda A; Chamratrithirong, Aphichat; Rhucharoenpornpanich, Orratai; Cupp, Pamela K; Atwood, Katharine A; Fongkaew, Warunee; Rosati, Michael J; Chookhare, Warunee

2011-01-01

Due to concerns over Thai adolescent risky behaviors, effective prevention strategies are needed. Determining the role neighborhood context plays in program engagement and outcomes may inform these strategies. This study includes 170 mother-adolescent pairs (M = 13.44, SD = .52) in Bangkok, Thailand in a prevention program for adolescent substance use and sexual risk. Neighborhoods were related to engagement, which was critical to outcomes. Neighborhood disorganization was related to confidence in program effects and program completion. Completion was related to increased ATOD communication. Neighborhood cohesion was related to less program enjoyment, while neighborhood social control was related to more enjoyment. Enjoyment was related to increased ATOD communication and formation and monitoring of alcohol rules. Prevention strategies should focus on neighborhood contexts and enhancing engagement.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Uthe, Peter B; Howard, Cameron M; Pacheco, Kimberly A O; Cox, Kari K; Henry, James A; Bailey, Suzanna L; Horick, Sarah M; Nguyen, Binh; Wilson, W David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.

Functional analysis of coordinated cleavage in V(D)J recombination.

PubMed

Kim, D R; Oettinger, M A

1998-08-01

V(D)J recombination in vivo requires a pair of signals with distinct spacer elements of 12 and 23 bp that separate conserved heptamer and nonamer motifs. Cleavage in vitro by the RAG1 and RAG2 proteins can occur at individual signals when the reaction buffer contains Mn2+, but cleavage is restricted to substrates containing two signals when Mg2+ is the divalent cation. By using a novel V(D)J cleavage substrate, we show that while the RAG proteins alone establish a moderate preference for a 12/23 pair versus a 12/12 pair, a much stricter dependence of cleavage on the 12/23 signal pair is produced by the inclusion of HMG1 and competitor double-stranded DNA. The competitor DNA serves to inhibit the cleavage of substrates carrying a 12/12 or 23/23 pair, as well as the cutting at individual signals in 12/23 substrates. We show that a 23/33 pair is more efficiently recombined than a 12/33 pair, suggesting that the 12/23 rule can be generalized to a requirement for spacers that differ from each other by a single helical turn. Furthermore, we suggest that a fixed spatial orientation of signals is required for cleavage. In general, the same signal variants that can be cleaved singly can function under conditions in which a signal pair is required. However, a chemically modified substrate with one noncleavable signal enables us to show that formation of a functional cleavage complex is mechanistically separable from the cleavage reaction itself and that although cleavage requires a pair of signals, cutting does not have to occur simultaneously at both. The implications of these results are discussed with respect to the mechanism of V(D)J recombination and the generation of chromosomal translocations.

Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs.

PubMed

Kimoto, Michiko; Hirao, Ichiro

2017-10-20

Genetic alphabet expansion technology, the introduction of unnatural bases or base pairs into replicable DNA, has rapidly advanced as a new synthetic biology area. A hydrophobic unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibited high fidelity as a third base pair in PCR. SELEX methods using the Ds-Px pair enabled high-affinity DNA aptamer generation, and introducing a few Ds bases into DNA aptamers extremely augmented their affinities and selectivities to target proteins. Here, to further scrutinize the functions of this highly hydrophobic Ds base, the thermal stabilities of double-stranded DNAs (dsDNA) containing a noncognate Ds-Ds or G-Ds pair were examined. The thermal stability of the Ds-Ds self-pair was as high as that of the natural G-C pair, and apart from the generally higher stability of the G-C pair than that of the A-T pair, most of the 5'-pyrimidine-Ds-purine-3' sequences, such as CDsA and TDsA, exhibited higher stability than the 5'-purine-Ds-pyrimidine-3' sequences, such as GDsC and ADsC, in dsDNAs. This trait enabled the GC-content-independent control of the thermal stability of the designed dsDNA fragments. The melting temperatures of dsDNA fragments containing the Ds-Ds pair can be predicted from the nearest-neighbor parameters including the Ds base. In addition, the noncognate G-Ds pair can efficiently distinguish its neighboring cognate natural base pairs from noncognate pairs. We demonstrated that real-time PCR using primers containing Ds accurately detected a single-nucleotide mismatch in target DNAs. These unique properties of the Ds base that affect the stabilities of the neighboring base pairs could impart new functions to DNA molecules and technologies.

Selection rules for Cooper pairing in two-dimensional interfaces and sheets

NASA Astrophysics Data System (ADS)

Scheurer, Mathias S.; Agterberg, Daniel F.; Schmalian, Jörg

2017-12-01

Thin sheets deposited on a substrate and interfaces of correlated materials offer a plethora of routes towards the realization of exotic phases of matter. In these systems, inversion symmetry is broken which strongly affects the properties of possible instabilities—in particular in the superconducting channel. By combining symmetry and energetic arguments, we derive general and experimentally accessible selection rules for Cooper instabilities in noncentrosymmetric systems, which yield necessary and sufficient conditions for spontaneous time-reversal-symmetry breaking at the superconducting transition and constrain the orientation of the triplet vector. We discuss in detail the implications for various different materials. For instance, we conclude that the pairing state in thin layers of Sr2RuO4 must, as opposed to its bulk superconducting state, preserve time-reversal symmetry with its triplet vector being parallel to the plane of the system. All triplet states of this system allowed by the selection rules are predicted to display topological Majorana modes at dislocations or at the edge of the system. Applying our results to the LaAlO3/SrTiO3 heterostructures, we find that while the condensates of the (001) and (110) oriented interfaces must be time-reversal symmetric, spontaneous time-reversal-symmetry breaking can only occur for the less studied (111) interface. We also discuss the consequences for thin layers of URu2Si2 and UPt3 as well as for single-layer FeSe. On a more general level, our considerations might serve as a design principle in the search for time-reversal-symmetry-breaking superconductivity in the absence of external magnetic fields.

Neural networks supporting switching, hypothesis testing, and rule application

PubMed Central

Liu, Zhiya; Braunlich, Kurt; Wehe, Hillary S.; Seger, Carol A.

2015-01-01

We identified dynamic changes in recruitment of neural connectivity networks across three phases of a flexible rule learning and set-shifting task similar to the Wisconsin Card Sort Task: switching, rule learning via hypothesis testing, and rule application. During fMRI scanning, subjects viewed pairs of stimuli that differed across four dimensions (letter, color, size, screen location), chose one stimulus, and received feedback. Subjects were informed that the correct choice was determined by a simple unidimensional rule, for example “choose the blue letter.” Once each rule had been learned and correctly applied for 4-7 trials, subjects were cued via either negative feedback or visual cues to switch to learning a new rule. Task performance was divided into three phases: Switching (first trial after receiving the switch cue), hypothesis testing (subsequent trials through the last error trial), and rule application (correct responding after the rule was learned). We used both univariate analysis to characterize activity occurring within specific regions of the brain, and a multivariate method, constrained principal component analysis for fMRI (fMRI-CPCA), to investigate how distributed regions coordinate to subserve different processes. As hypothesized, switching was subserved by a limbic network including the ventral striatum, thalamus, and parahippocampal gyrus, in conjunction with cortical salience network regions including the anterior cingulate and frontoinsular cortex. Activity in the ventral striatum was associated with switching regardless of how switching was cued; visually cued shifts were associated with additional visual cortical activity. After switching, as subjects moved into the hypothesis testing phase, a broad fronto-parietal-striatal network (associated with the cognitive control, dorsal attention, and salience networks) increased in activity. This network was sensitive to rule learning speed, with greater extended activity for the slowest learning speed late in the time course of learning. As subjects shifted from hypothesis testing to rule application, activity in this network decreased and activity in the somatomotor and default mode networks increased. PMID:26197092

Neural networks supporting switching, hypothesis testing, and rule application.

PubMed

Liu, Zhiya; Braunlich, Kurt; Wehe, Hillary S; Seger, Carol A

2015-10-01

We identified dynamic changes in recruitment of neural connectivity networks across three phases of a flexible rule learning and set-shifting task similar to the Wisconsin Card Sort Task: switching, rule learning via hypothesis testing, and rule application. During fMRI scanning, subjects viewed pairs of stimuli that differed across four dimensions (letter, color, size, screen location), chose one stimulus, and received feedback. Subjects were informed that the correct choice was determined by a simple unidimensional rule, for example "choose the blue letter". Once each rule had been learned and correctly applied for 4-7 trials, subjects were cued via either negative feedback or visual cues to switch to learning a new rule. Task performance was divided into three phases: Switching (first trial after receiving the switch cue), hypothesis testing (subsequent trials through the last error trial), and rule application (correct responding after the rule was learned). We used both univariate analysis to characterize activity occurring within specific regions of the brain, and a multivariate method, constrained principal component analysis for fMRI (fMRI-CPCA), to investigate how distributed regions coordinate to subserve different processes. As hypothesized, switching was subserved by a limbic network including the ventral striatum, thalamus, and parahippocampal gyrus, in conjunction with cortical salience network regions including the anterior cingulate and frontoinsular cortex. Activity in the ventral striatum was associated with switching regardless of how switching was cued; visually cued shifts were associated with additional visual cortical activity. After switching, as subjects moved into the hypothesis testing phase, a broad fronto-parietal-striatal network (associated with the cognitive control, dorsal attention, and salience networks) increased in activity. This network was sensitive to rule learning speed, with greater extended activity for the slowest learning speed late in the time course of learning. As subjects shifted from hypothesis testing to rule application, activity in this network decreased and activity in the somatomotor and default mode networks increased. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

PubMed Central

Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

Theoretical determination of one-electron redox potentials for DNA bases, base pairs, and stacks.

PubMed

Paukku, Y; Hill, G

2011-05-12

Electron affinities, ionization potentials, and redox potentials for DNA bases, base pairs, and N-methylated derivatives are computed at the DFT/M06-2X/6-31++G(d,p) level of theory. Redox properties of a guanine-guanine stack model are explored as well. Reduction and oxidation potentials are in good agreement with the experimental ones. Electron affinities of base pairs were found to be negative. Methylation of canonical bases affects the ionization potentials the most. Base pair formation and base stacking lower ionization potentials by 0.3 eV. Pairing of guanine with the 5-methylcytosine does not seem to influence the redox properties of this base pair much.

When Actions Speak Too Much Louder than Words: Hand Gestures Disrupt Word Learning when Phonetic Demands Are High

ERIC Educational Resources Information Center

Kelly, Spencer D.; Lee, Angela L.

2012-01-01

It is now widely accepted that hand gestures help people understand and learn language. Here, we provide an exception to this general rule--when phonetic demands are high, gesture actually hurts. Native English-speaking adults were instructed on the meaning of novel Japanese word pairs that were for non-native speakers phonetically hard (/ite/ vs.…

Insights into the crystal chemistry of Earth materials rendered by electron density distributions: Pauling's rules revisited

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

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-05-20

Pauling's first two rules are examined in terms of the accumulation of the electron density between bonded pairs of atoms for a relatively large number of oxide and silicate crystals and siloxane molecules. The distribution of the electron density shows that the radius of the oxygen atom is not fixed, but that it actually decreases systematically from ~1.40 Å to ~ 0.65 Å as the polarizing power and the electronegativity of the bonded metal atoms increase and the distribution of the O atom is progressively polarized and contracted along the bond vectors by the impact of the bonded interactions. Themore » contractions result in an aspherical oxygen atom that displays as many different bonded “radii” as it has bonded interactions. The bonded radii for the metal atoms match the Shannon and Prewitt ionic radii for the more electropositive atoms like potassium and sodium, but they are systematically larger for the more electronegative atoms like aluminum, silicon and phosphorous. Pauling's first rule is based on the assumption that the radius of the oxide anion is fixed and that the radii of the cations are such that radius sum of the spherical oxide anion and a cation necessarily equals the separation between the cation-anion bonded pair with the coordination number of the cation being determined by the ratio of the radii of the cation and anion. In the case of the bonded radii, the sum of the bonded radii for the metal atoms and the oxide anion necessarily equals the bond lengths by virtue of the way that the bonded radii were determined in the partitioning of the electron density along the bond path into metal and O atom parts. But, the radius ratio for the O and M atoms is an unsatisfactory rule for determining the coordination number of the metal atom inasmuch as a bonded O atom is not, in general, spherical, and its size varies substantially along its bonded directions. But by counting the number of bond paths that radiate from a bonded atom, the coordination number of the atom is determined uniquely independent of the asphericity and sizes of the atom. A power law connection established between the bond lengths and bond strengths for crystals and molecules is mirrored by a comparable power law connection between bond length and the accumulation of the electron density between bonded pairs of atoms, a connection that is consistent with Pauling's electroneutrality postulate that the charges of the atoms in an oxide are negligibly small. The connection indicates that a one-to-one correspondence exists between the accumulation between a pair of bonded atoms and the Pauling bond strength for M-O bonded interaction for all atoms of the periodic table. The connection provides a common basis for understanding the success of the manifold applications that have been made with the bond valence theory model together with the modeling of crystal structures, chemical zoning, leaching and cation transport in batteries and the like. We believe that the wide spread applications of the model in mineralogy and material science owes much of its success to the direct connection between bond strength and the quantum mechanical observable, the electron density distribution. Comparable power law expressions established for the bonded interactions for both crystals and molecules support Pauling's assertion that his second rule has significance for molecules as well as for crystals. A simple expression is found that provides a one to one connection between the accumulation of the electron density between bonded M and O atoms and the Pauling bond strength for all M atoms of the periodic table with ~ 95 % of the variation of the bond strength being explained in terms of a linear dependence on the accumulated electron density. Compelling evidence is presented that supports the argument that the Si-O bonded interactions for tiny siloxane molecules and silicate crystals are chemically equivalent.« less

HERB: A production system for programming with hierarchical expert rule bases: User's manual, HERB Version 1. 0

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

Hummel, K.E.

1987-12-01

Expert systems are artificial intelligence programs that solve problems requiring large amounts of heuristic knowledge, based on years of experience and tradition. Production systems are domain-independent tools that support the development of rule-based expert systems. This document describes a general purpose production system known as HERB. This system was developed to support the programming of expert systems using hierarchically structured rule bases. HERB encourages the partitioning of rules into multiple rule bases and supports the use of multiple conflict resolution strategies. Multiple rule bases can also be placed on a system stack and simultaneously searched during each interpreter cycle. Bothmore » backward and forward chaining rules are supported by HERB. The condition portion of each rule can contain both patterns, which are matched with facts in a data base, and LISP expressions, which are explicitly evaluated in the LISP environment. Properties of objects can also be stored in the HERB data base and referenced within the scope of each rule. This document serves both as an introduction to the principles of LISP-based production systems and as a user's manual for the HERB system. 6 refs., 17 figs.« less

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex†

PubMed Central

Crenshaw, Charisse M.; Wade, Jacqueline E.; Arthanari, Haribabu; Frueh, Dominique; Lane, Benjamin F.; Núñez, Megan E.

2011-01-01

The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G→T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using CD spectroscopy and UV melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)2chrysi3+ cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. NMR spectra are also consistent with a well-conserved B-form duplex structure. In the 2D NOESY spectra, base-sugar and imino-imino crosspeaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2–3 base pairs immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10−6. This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair. PMID:21902242

An investigation of care-based vs. rule-based morality in frontotemporal dementia, Alzheimer's disease, and healthy controls.

PubMed

Carr, Andrew R; Paholpak, Pongsatorn; Daianu, Madelaine; Fong, Sylvia S; Mather, Michelle; Jimenez, Elvira E; Thompson, Paul; Mendez, Mario F

2015-11-01

Behavioral changes in dementia, especially behavioral variant frontotemporal dementia (bvFTD), may result in alterations in moral reasoning. Investigators have not clarified whether these alterations reflect differential impairment of care-based vs. rule-based moral behavior. This study investigated 18 bvFTD patients, 22 early onset Alzheimer's disease (eAD) patients, and 20 healthy age-matched controls on care-based and rule-based items from the Moral Behavioral Inventory and the Social Norms Questionnaire, neuropsychological measures, and magnetic resonance imaging (MRI) regions of interest. There were significant group differences with the bvFTD patients rating care-based morality transgressions less severely than the eAD group and rule-based moral behavioral transgressions more severely than controls. Across groups, higher care-based morality ratings correlated with phonemic fluency on neuropsychological tests, whereas higher rule-based morality ratings correlated with increased difficulty set-shifting and learning new rules to tasks. On neuroimaging, severe care-based reasoning correlated with cortical volume in right anterior temporal lobe, and rule-based reasoning correlated with decreased cortical volume in the right orbitofrontal cortex. Together, these findings suggest that frontotemporal disease decreases care-based morality and facilitates rule-based morality possibly from disturbed contextual abstraction and set-shifting. Future research can examine whether frontal lobe disorders and bvFTD result in a shift from empathic morality to the strong adherence to conventional rules. Published by Elsevier Ltd.

An Investigation of Care-Based vs. Rule-Based Morality in Frontotemporal Dementia, Alzheimer’s Disease, and Healthy Controls

PubMed Central

Carr, Andrew R.; Paholpak, Pongsatorn; Daianu, Madelaine; Fong, Sylvia S.; Mather, Michelle; Jimenez, Elvira E.; Thompson, Paul; Mendez, Mario F.

2015-01-01

Behavioral changes in dementia, especially behavioral variant frontotemporal dementia (bvFTD), may result in alterations in moral reasoning. Investigators have not clarified whether these alterations reflect differential impairment of care-based vs. rule-based moral behavior. This study investigated 18 bvFTD patients, 22 early onset Alzheimer’s disease (eAD) patients, and 20 healthy age-matched controls on care-based and rule-based items from the Moral Behavioral Inventory and the Social Norms Questionnaire, neuropsychological measures, and magnetic resonance imaging (MRI) regions of interest. There were significant group differences with the bvFTD patients rating care-based morality transgressions less severely than the eAD group and rule-based moral behavioral transgressions more severely than controls. Across groups, higher care-based morality ratings correlated with phonemic fluency on neuropsychological tests, whereas higher rule-based morality ratings correlated with increased difficulty set-shifting and learning new rules to tasks. On neuroimaging, severe care-based reasoning correlated with cortical volume in right anterior temporal lobe, and rule-based reasoning correlated with decreased cortical volume in the right orbitofrontal cortex. Together, these findings suggest that frontotemporal disease decreases care-based morality and facilitates rule-based morality possibly from disturbed contextual abstraction and set-shifting. Future research can examine whether frontal lobe disorders and bvFTD result in a shift from empathic morality to the strong adherence to conventional rules. PMID:26432341

A Swarm Optimization approach for clinical knowledge mining.

PubMed

Christopher, J Jabez; Nehemiah, H Khanna; Kannan, A

2015-10-01

Rule-based classification is a typical data mining task that is being used in several medical diagnosis and decision support systems. The rules stored in the rule base have an impact on classification efficiency. Rule sets that are extracted with data mining tools and techniques are optimized using heuristic or meta-heuristic approaches in order to improve the quality of the rule base. In this work, a meta-heuristic approach called Wind-driven Swarm Optimization (WSO) is used. The uniqueness of this work lies in the biological inspiration that underlies the algorithm. WSO uses Jval, a new metric, to evaluate the efficiency of a rule-based classifier. Rules are extracted from decision trees. WSO is used to obtain different permutations and combinations of rules whereby the optimal ruleset that satisfies the requirement of the developer is used for predicting the test data. The performance of various extensions of decision trees, namely, RIPPER, PART, FURIA and Decision Tables are analyzed. The efficiency of WSO is also compared with the traditional Particle Swarm Optimization. Experiments were carried out with six benchmark medical datasets. The traditional C4.5 algorithm yields 62.89% accuracy with 43 rules for liver disorders dataset where as WSO yields 64.60% with 19 rules. For Heart disease dataset, C4.5 is 68.64% accurate with 98 rules where as WSO is 77.8% accurate with 34 rules. The normalized standard deviation for accuracy of PSO and WSO are 0.5921 and 0.5846 respectively. WSO provides accurate and concise rulesets. PSO yields results similar to that of WSO but the novelty of WSO lies in its biological motivation and it is customization for rule base optimization. The trade-off between the prediction accuracy and the size of the rule base is optimized during the design and development of rule-based clinical decision support system. The efficiency of a decision support system relies on the content of the rule base and classification accuracy. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Automated visualization of rule-based models

PubMed Central

Tapia, Jose-Juan; Faeder, James R.

2017-01-01

Frameworks such as BioNetGen, Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size. Also, inferring design motifs that emerge from biochemical interactions is an open problem, so current approaches to visualize model architecture rely on manual interpretation of the model. Here, we present three new visualization tools that constitute an automated visualization framework for rule-based models: (i) a compact rule visualization that efficiently displays each rule, (ii) the atom-rule graph that conveys regulatory interactions in the model as a bipartite network, and (iii) a tunable compression pipeline that incorporates expert knowledge and produces compact diagrams of model architecture when applied to the atom-rule graph. The compressed graphs convey network motifs and architectural features useful for understanding both small and large rule-based models, as we show by application to specific examples. Our tools also produce more readable diagrams than current approaches, as we show by comparing visualizations of 27 published models using standard graph metrics. We provide an implementation in the open source and freely available BioNetGen framework, but the underlying methods are general and can be applied to rule-based models from the Kappa and Simmune frameworks also. We expect that these tools will promote communication and analysis of rule-based models and their eventual integration into comprehensive whole-cell models. PMID:29131816

Compartmental and Spatial Rule-Based Modeling with Virtual Cell.

PubMed

Blinov, Michael L; Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Bloom, Judy E; Loew, Leslie M

2017-10-03

In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations deterministic solvers or the Smoldyn stochastic simulator. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Revised Interim Final Consolidated Enforcement Response and Penalty Policy for the Pre-Renovation Education Rule; Renovation, Repair and Painting Rule; and Lead-Based Paint Activities Rule

EPA Pesticide Factsheets

This is the revised version of the Interim Final Consolidated Enforcement Response and Penalty Policy for the Pre-Renovation Education Rule; Renovation, Repair and Painting Rule; and Lead-Based Paint Activities Rule.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

The relationship of Asperger's syndrome to autism: a preliminary EEG coherence study.

PubMed

Duffy, Frank H; Shankardass, Aditi; McAnulty, Gloria B; Als, Heidelise

2013-07-31

It has long been debated whether Asperger's Syndrome (ASP) should be considered part of the Autism Spectrum Disorders (ASD) or whether it constitutes a unique entity. The Diagnostic and Statistical Manual, fourth edition (DSM-IV) differentiated ASP from high functioning autism. However, the new DSM-5 umbrellas ASP within ASD, thus eliminating the ASP diagnosis. To date, no clear biomarkers have reliably distinguished ASP and ASD populations. This study uses EEG coherence, a measure of brain connectivity, to explore possible neurophysiological differences between ASP and ASD. Voluminous coherence data derived from all possible electrode pairs and frequencies were previously reduced by principal components analysis (PCA) to produce a smaller number of unbiased, data-driven coherence factors. In a previous study, these factors significantly and reliably differentiated neurotypical controls from ASD subjects by discriminant function analysis (DFA). These previous DFA rules are now applied to an ASP population to determine if ASP subjects classify as control or ASD subjects. Additionally, a new set of coherence based DFA rules are used to determine whether ASP and ASD subjects can be differentiated from each other. Using prior EEG coherence based DFA rules that successfully classified subjects as either controls or ASD, 96.2% of ASP subjects are classified as ASD. However, when ASP subjects are directly compared to ASD subjects using new DFA rules, 92.3% ASP subjects are identified as separate from the ASD population. By contrast, five randomly selected subsamples of ASD subjects fail to reach significance when compared to the remaining ASD populations. When represented by the discriminant variable, both the ASD and ASD populations are normally distributed. Within a control-ASD dichotomy, an ASP population falls closer to ASD than controls. However, when compared directly with ASD, an ASP population is distinctly separate. The ASP population appears to constitute a neurophysiologically identifiable, normally distributed entity within the higher functioning tail of the ASD population distribution. These results must be replicated with a larger sample given their potentially immense clinical, emotional and financial implications for affected individuals, their families and their caregivers.

The relationship of Asperger’s syndrome to autism: a preliminary EEG coherence study

PubMed Central

2013-01-01

Background It has long been debated whether Asperger’s Syndrome (ASP) should be considered part of the Autism Spectrum Disorders (ASD) or whether it constitutes a unique entity. The Diagnostic and Statistical Manual, fourth edition (DSM-IV) differentiated ASP from high functioning autism. However, the new DSM-5 umbrellas ASP within ASD, thus eliminating the ASP diagnosis. To date, no clear biomarkers have reliably distinguished ASP and ASD populations. This study uses EEG coherence, a measure of brain connectivity, to explore possible neurophysiological differences between ASP and ASD. Methods Voluminous coherence data derived from all possible electrode pairs and frequencies were previously reduced by principal components analysis (PCA) to produce a smaller number of unbiased, data-driven coherence factors. In a previous study, these factors significantly and reliably differentiated neurotypical controls from ASD subjects by discriminant function analysis (DFA). These previous DFA rules are now applied to an ASP population to determine if ASP subjects classify as control or ASD subjects. Additionally, a new set of coherence based DFA rules are used to determine whether ASP and ASD subjects can be differentiated from each other. Results Using prior EEG coherence based DFA rules that successfully classified subjects as either controls or ASD, 96.2% of ASP subjects are classified as ASD. However, when ASP subjects are directly compared to ASD subjects using new DFA rules, 92.3% ASP subjects are identified as separate from the ASD population. By contrast, five randomly selected subsamples of ASD subjects fail to reach significance when compared to the remaining ASD populations. When represented by the discriminant variable, both the ASD and ASD populations are normally distributed. Conclusions Within a control-ASD dichotomy, an ASP population falls closer to ASD than controls. However, when compared directly with ASD, an ASP population is distinctly separate. The ASP population appears to constitute a neurophysiologically identifiable, normally distributed entity within the higher functioning tail of the ASD population distribution. These results must be replicated with a larger sample given their potentially immense clinical, emotional and financial implications for affected individuals, their families and their caregivers. PMID:23902729

Stability of non-Watson-Crick G-A/A-G base pair in synthetic DNA and RNA oligonucleotides.

PubMed

Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

2004-03-01

A non-Watson-Crick G-A/A-G base pair is found in SECIS (selenocysteine-insertion sequence) element in the 3'-untranslated region of Se-protein mRNAs and in the functional site of the hammerhead ribozyme. We studied the stability of G-A/A-G base pair (bold) in 17mer GT(U)GACGGAAACCGGAAC synthetic DNA and RNA oligonucleotides by thermal melting experiments and gel electrophoresis. The measured Tm value of DNA oligonucleotide having G-A/A-G pair showed an intermediate value (58 degrees C) between that of Watson-Crick G-C/C-G base pair (75 degrees C) and that of G-G/A-A of non-base-pair (40 degrees C). Similar thermal melting patterns were obtained with RNA oligonucleotides. This result indicates that the secondary structure of oligonucleotide having G-A/A-G base pair is looser than that of the G-C type Watson-Crick base pair. In the comparison between RNA and DNA having G-A/A-G base pair, the Tm value of the RNA oligonucleotide was 11 degrees C lower than that of DNA, indicating that DNA has a more rigid structure than RNA. The stained pattern of oligonucleotide on polyacrylamide gel clarified that the mobility of the DNA oligonucleotide G-A/A-G base pair changed according to the urea concentration from the rigid state (near the mobility of G-C/C-G oligonucleotide) in the absence of urea to the random state (near the mobility of G-G/A-A oligonucleotide) in 7 M urea. However, the RNA oligonucleotide with G-A/A-G pair moved at an intermediate mobility between that of oligonucleotide with G-C/C-G and of the oligonucleotide with G-G/A-A, and the mobility pattern did not depend on urea concentration. Thus, DNA and RNA oligonucleotides with the G-A/A-G base pair showed a pattern indicating an intermediate structure between the rigid Watson-Crick base pair and the random structure of non-base pair. RNA with G-A/A-G base pair has the intermediate structure not influenced by urea concentration. Finally, this study indicated that the intermediate rigidity imparted by Non-Watson-Crick base pair in SECIS element plays an important role in the selenocysteine expression by UGA codon.

Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

Asymptotic 3-loop heavy flavor corrections to the charged current structure functions FLW+-W-(x ,Q2) and F2W+-W-(x ,Q2)

NASA Astrophysics Data System (ADS)

Behring, A.; Blümlein, J.; Falcioni, G.; De Freitas, A.; von Manteuffel, A.; Schneider, C.

2016-12-01

We derive the massive Wilson coefficients for the heavy flavor contributions to the nonsinglet charged current deep-inelastic scattering structure functions FLW+(x ,Q2)-FLW-(x ,Q2) and F2W+(x ,Q2)-F2W-(x ,Q2) in the asymptotic region Q2≫m2 to 3-loop order in quantum chromodynamics at general values of the Mellin variable N and the momentum fraction x . Besides the heavy quark pair production, also the single heavy flavor excitation s →c contributes. Numerical results are presented for the charm quark contributions, and consequences on the unpolarized Bjorken sum rule and Adler sum rule are discussed.

Rules based process window OPC

NASA Astrophysics Data System (ADS)

O'Brien, Sean; Soper, Robert; Best, Shane; Mason, Mark

2008-03-01

As a preliminary step towards Model-Based Process Window OPC we have analyzed the impact of correcting post-OPC layouts using rules based methods. Image processing on the Brion Tachyon was used to identify sites where the OPC model/recipe failed to generate an acceptable solution. A set of rules for 65nm active and poly were generated by classifying these failure sites. The rules were based upon segment runlengths, figure spaces, and adjacent figure widths. 2.1 million sites for active were corrected in a small chip (comparing the pre and post rules based operations), and 59 million were found at poly. Tachyon analysis of the final reticle layout found weak margin sites distinct from those sites repaired by rules-based corrections. For the active layer more than 75% of the sites corrected by rules would have printed without a defect indicating that most rulesbased cleanups degrade the lithographic pattern. Some sites were missed by the rules based cleanups due to either bugs in the DRC software or gaps in the rules table. In the end dramatic changes to the reticle prevented catastrophic lithography errors, but this method is far too blunt. A more subtle model-based procedure is needed changing only those sites which have unsatisfactory lithographic margin.

Sex ratios provide evidence for monozygotic twinning in the ring-tailed lemur, Lemur catta.

PubMed

St Clair, John; Campbell-Palmer, Roisin; Lathe, Richard

2014-02-01

Monozygotic (MZ) twinning is generally considered to be rare in species other than human. We inspected sex ratios in European zoo-bred ring-tailed lemurs (Lemur catta), revealing a significant excess of same-sex twins. Of 94 pairs, 60 (64%) were either both males or both females (p = .004). Application of the Weinberg differential rule argues that 27% of all twins in this species are MZ pairs. In this protected species, where twinning is commonplace (~50% of newborns are twins), the probable existence of frequent MZ twinning has ramifications for breeding programs aimed to maximize genetic diversity, and suggests that twin studies in a species other than human could have potential as a medical research tool.

Learning to predict chemical reactions.

PubMed

Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

2011-09-26

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert does not handle. A web interface to the machine learning based mechanistic reaction predictor is accessible through our chemoinformatics portal ( http://cdb.ics.uci.edu) under the Toolkits section.

Learning to Predict Chemical Reactions

PubMed Central

Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

2011-01-01

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert does not handle. A web interface to the machine learning based mechanistic reaction predictor is accessible through our chemoinformatics portal (http://cdb.ics.uci.edu) under the Toolkits section. PMID:21819139

Search asymmetries: parallel processing of uncertain sensory information.

PubMed

Vincent, Benjamin T

2011-08-01

What is the mechanism underlying search phenomena such as search asymmetry? Two-stage models such as Feature Integration Theory and Guided Search propose parallel pre-attentive processing followed by serial post-attentive processing. They claim search asymmetry effects are indicative of finding pairs of features, one processed in parallel, the other in serial. An alternative proposal is that a 1-stage parallel process is responsible, and search asymmetries occur when one stimulus has greater internal uncertainty associated with it than another. While the latter account is simpler, only a few studies have set out to empirically test its quantitative predictions, and many researchers still subscribe to the 2-stage account. This paper examines three separate parallel models (Bayesian optimal observer, max rule, and a heuristic decision rule). All three parallel models can account for search asymmetry effects and I conclude that either people can optimally utilise the uncertain sensory data available to them, or are able to select heuristic decision rules which approximate optimal performance. Copyright © 2011 Elsevier Ltd. All rights reserved.

The organization of societal conflicts by pavement ants Tetramorium caespitum: an agent-based model of amine-mediated decision making

PubMed Central

Hoover, Kevin M.; Bubak, Andrew N.; Law, Isaac J.; Yaeger, Jazmine D. W.; Renner, Kenneth J.; Swallow, John G.; Greene, Michael J.

2016-01-01

Abstract Ant colonies self-organize to solve complex problems despite the simplicity of an individual ant’s brain. Pavement ant Tetramorium caespitum colonies must solve the problem of defending the territory that they patrol in search of energetically rich forage. When members of 2 colonies randomly interact at the territory boundary a decision to fight occurs when: 1) there is a mismatch in nestmate recognition cues and 2) each ant has a recent history of high interaction rates with nestmate ants. Instead of fighting, some ants will decide to recruit more workers from the nest to the fighting location, and in this way a positive feedback mediates the development of colony wide wars. In ants, the monoamines serotonin (5-HT) and octopamine (OA) modulate many behaviors associated with colony organization and in particular behaviors associated with nestmate recognition and aggression. In this article, we develop and explore an agent-based model that conceptualizes how individual changes in brain concentrations of 5-HT and OA, paired with a simple threshold-based decision rule, can lead to the development of colony wide warfare. Model simulations do lead to the development of warfare with 91% of ants fighting at the end of 1 h. When conducting a sensitivity analysis, we determined that uncertainty in monoamine concentration signal decay influences the behavior of the model more than uncertainty in the decision-making rule or density. We conclude that pavement ant behavior is consistent with the detection of interaction rate through a single timed interval rather than integration of multiple interactions. PMID:29491915

The organization of societal conflicts by pavement ants Tetramorium caespitum: an agent-based model of amine-mediated decision making.

PubMed

Hoover, Kevin M; Bubak, Andrew N; Law, Isaac J; Yaeger, Jazmine D W; Renner, Kenneth J; Swallow, John G; Greene, Michael J

2016-06-01

Ant colonies self-organize to solve complex problems despite the simplicity of an individual ant's brain. Pavement ant Tetramorium caespitum colonies must solve the problem of defending the territory that they patrol in search of energetically rich forage. When members of 2 colonies randomly interact at the territory boundary a decision to fight occurs when: 1) there is a mismatch in nestmate recognition cues and 2) each ant has a recent history of high interaction rates with nestmate ants. Instead of fighting, some ants will decide to recruit more workers from the nest to the fighting location, and in this way a positive feedback mediates the development of colony wide wars. In ants, the monoamines serotonin (5-HT) and octopamine (OA) modulate many behaviors associated with colony organization and in particular behaviors associated with nestmate recognition and aggression. In this article, we develop and explore an agent-based model that conceptualizes how individual changes in brain concentrations of 5-HT and OA, paired with a simple threshold-based decision rule, can lead to the development of colony wide warfare. Model simulations do lead to the development of warfare with 91% of ants fighting at the end of 1 h. When conducting a sensitivity analysis, we determined that uncertainty in monoamine concentration signal decay influences the behavior of the model more than uncertainty in the decision-making rule or density. We conclude that pavement ant behavior is consistent with the detection of interaction rate through a single timed interval rather than integration of multiple interactions.

Classification Based on Pruning and Double Covered Rule Sets for the Internet of Things Applications

PubMed Central

Zhou, Zhongmei; Wang, Weiping

2014-01-01

The Internet of things (IOT) is a hot issue in recent years. It accumulates large amounts of data by IOT users, which is a great challenge to mining useful knowledge from IOT. Classification is an effective strategy which can predict the need of users in IOT. However, many traditional rule-based classifiers cannot guarantee that all instances can be covered by at least two classification rules. Thus, these algorithms cannot achieve high accuracy in some datasets. In this paper, we propose a new rule-based classification, CDCR-P (Classification based on the Pruning and Double Covered Rule sets). CDCR-P can induce two different rule sets A and B. Every instance in training set can be covered by at least one rule not only in rule set A, but also in rule set B. In order to improve the quality of rule set B, we take measure to prune the length of rules in rule set B. Our experimental results indicate that, CDCR-P not only is feasible, but also it can achieve high accuracy. PMID:24511304

Classification based on pruning and double covered rule sets for the internet of things applications.

PubMed

Li, Shasha; Zhou, Zhongmei; Wang, Weiping

2014-01-01

The Internet of things (IOT) is a hot issue in recent years. It accumulates large amounts of data by IOT users, which is a great challenge to mining useful knowledge from IOT. Classification is an effective strategy which can predict the need of users in IOT. However, many traditional rule-based classifiers cannot guarantee that all instances can be covered by at least two classification rules. Thus, these algorithms cannot achieve high accuracy in some datasets. In this paper, we propose a new rule-based classification, CDCR-P (Classification based on the Pruning and Double Covered Rule sets). CDCR-P can induce two different rule sets A and B. Every instance in training set can be covered by at least one rule not only in rule set A, but also in rule set B. In order to improve the quality of rule set B, we take measure to prune the length of rules in rule set B. Our experimental results indicate that, CDCR-P not only is feasible, but also it can achieve high accuracy.

pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

Allograph priming is based on abstract letter identities: Evidence from Japanese kana.

PubMed

Kinoshita, Sachiko; Schubert, Teresa; Verdonschot, Rinus G

2018-04-23

It is well-established that allographs like the uppercase and lowercase forms of the Roman alphabet (e.g., a and A) map onto the same "abstract letter identity," orthographic representations that are independent of the visual form. Consistent with this, in the allograph match task ("Are 'a' and 'A' the same letter?"), priming by a masked letter prime is equally robust for visually dissimilar prime-target pairs (e.g., d and D) and similar pairs (e.g., c and C). However, in principle this pattern of priming is also consistent with the possibility that allograph priming is purely phonological, based on the letter name. Because different allographic forms of the same letter, by definition, share a letter name, it is impossible to rule out this possibility a priori. In the present study, we investigated the influence of shared letter names by taking advantage of the fact that Japanese is written in two distinct writing systems, syllabic kana-that has two parallel forms, hiragana and katakana-and logographic kanji. Using the allograph match task, we tested whether a kanji prime with the same pronunciation as the target kana (e.g., - い, both pronounced /i/) produces the same amount of priming as a kana prime in the opposite kana form (e.g., イ- い). We found that the kana primes produced substantially greater priming than the phonologically identical kanji prime, which we take as evidence that allograph priming is based on abstract kana identity, not purely phonology. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Self-assembled bionanostructures: proteins following the lead of DNA nanostructures

PubMed Central

2014-01-01

Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction. PMID:24491139

Fulde-Ferrell-Larkin-Ovchinnikov correlation and free fluids in the one-dimensional attractive Hubbard model

NASA Astrophysics Data System (ADS)

Cheng, Song; Yu, Yi-Cong; Batchelor, M. T.; Guan, Xi-Wen

2018-03-01

In this Rapid Communication, we show that low-energy macroscopic properties of the one-dimensional (1D) attractive Hubbard model exhibit two fluids of bound pairs and of unpaired fermions. Using the thermodynamic Bethe ansatz equations of the model, we first determine the low-temperature phase diagram and analytically calculate the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) pairing correlation function for the partially polarized phase. We then show that for such an FFLO-like state in the low-density regime the effective chemical potentials of bound pairs and unpaired fermions behave like two free fluids. Consequently, the susceptibility, compressibility, and specific heat obey simple additivity rules, indicating the "free" particle nature of interacting fermions on a 1D lattice. In contrast to the continuum Fermi gases, the correlation critical exponents and thermodynamics of the attractive Hubbard model essentially depend on two lattice interacting parameters. Finally, we study scaling functions, the Wilson ratio and susceptibility, which provide universal macroscopic properties and dimensionless constants of interacting fermions at low energy.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

Rule groupings: A software engineering approach towards verification of expert systems

NASA Technical Reports Server (NTRS)

Mehrotra, Mala

1991-01-01

Currently, most expert system shells do not address software engineering issues for developing or maintaining expert systems. As a result, large expert systems tend to be incomprehensible, difficult to debug or modify and almost impossible to verify or validate. Partitioning rule based systems into rule groups which reflect the underlying subdomains of the problem should enhance the comprehensibility, maintainability, and reliability of expert system software. Attempts were made to semiautomatically structure a CLIPS rule base into groups of related rules that carry the same type of information. Different distance metrics that capture relevant information from the rules for grouping are discussed. Two clustering algorithms that partition the rule base into groups of related rules are given. Two independent evaluation criteria are developed to measure the effectiveness of the grouping strategies. Results of the experiment with three sample rule bases are presented.

Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers

PubMed Central

Rahman, Khondaker M.; James, Colin H.; Thurston, David E.

2011-01-01

Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two electrophilic imine moieties (or their equivalent) capable of forming covalent aminal linkages with guanine C2-NH2 functionalities. The PBD dimer SJG-136, which has a C8–O–(CH2)3–O–C8′′ central linker joining the two PBD moieties, is currently undergoing phase II clinical trials and current research is focused on developing analogues of SJG-136 with different linker lengths and substitution patterns. Using a reversed-phase ion pair HPLC/MS method to evaluate interaction with oligonucleotides of varying length and sequence, we recently reported (JACS, 2009, 131, 13 756) that SJG-136 can form three different types of adducts: inter- and intrastrand cross-linked adducts, and mono-alkylated adducts. These studies have now been extended to include PBD dimers with a longer central linker (C8–O–(CH2)5–O–C8′), demonstrating that the type and distribution of adducts appear to depend on (i) the length of the C8/C8′-linker connecting the two PBD units, (ii) the positioning of the two reactive guanine bases on the same or opposite strands, and (iii) their separation (i.e. the number of base pairs, usually ATs, between them). Based on these data, a set of rules are emerging that can be used to predict the DNA–interaction behaviour of a PBD dimer of particular C8–C8′ linker length towards a given DNA sequence. These observations suggest that it may be possible to design PBD dimers to target specific DNA sequences. PMID:21427082

Cognitive changes in conjunctive rule-based category learning: An ERP approach.

PubMed

Rabi, Rahel; Joanisse, Marc F; Zhu, Tianshu; Minda, John Paul

2018-06-25

When learning rule-based categories, sufficient cognitive resources are needed to test hypotheses, maintain the currently active rule in working memory, update rules after feedback, and to select a new rule if necessary. Prior research has demonstrated that conjunctive rules are more complex than unidimensional rules and place greater demands on executive functions like working memory. In our study, event-related potentials (ERPs) were recorded while participants performed a conjunctive rule-based category learning task with trial-by-trial feedback. In line with prior research, correct categorization responses resulted in a larger stimulus-locked late positive complex compared to incorrect responses, possibly indexing the updating of rule information in memory. Incorrect trials elicited a pronounced feedback-locked P300 elicited which suggested a disconnect between perception, and the rule-based strategy. We also examined the differential processing of stimuli that were able to be correctly classified by the suboptimal single-dimensional rule ("easy" stimuli) versus those that could only be correctly classified by the optimal, conjunctive rule ("difficult" stimuli). Among strong learners, a larger, late positive slow wave emerged for difficult compared with easy stimuli, suggesting differential processing of category items even though strong learners performed well on the conjunctive category set. Overall, the findings suggest that ERP combined with computational modelling can be used to better understand the cognitive processes involved in rule-based category learning.

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

An evaluation and implementation of rule-based Home Energy Management System using the Rete algorithm.

PubMed

Kawakami, Tomoya; Fujita, Naotaka; Yoshihisa, Tomoki; Tsukamoto, Masahiko

2014-01-01

In recent years, sensors become popular and Home Energy Management System (HEMS) takes an important role in saving energy without decrease in QoL (Quality of Life). Currently, many rule-based HEMSs have been proposed and almost all of them assume "IF-THEN" rules. The Rete algorithm is a typical pattern matching algorithm for IF-THEN rules. Currently, we have proposed a rule-based Home Energy Management System (HEMS) using the Rete algorithm. In the proposed system, rules for managing energy are processed by smart taps in network, and the loads for processing rules and collecting data are distributed to smart taps. In addition, the number of processes and collecting data are reduced by processing rules based on the Rete algorithm. In this paper, we evaluated the proposed system by simulation. In the simulation environment, rules are processed by a smart tap that relates to the action part of each rule. In addition, we implemented the proposed system as HEMS using smart taps.

N Reasons Why Production-Rules are Insufficient Models for Expert System Knowledge Representation Schemes

DTIC Science & Technology

1991-02-01

3 2.2 Hybrid Rule/Fact Schemas .............................................................. 3 3 THE LIMITATIONS OF RULE BASED KNOWLEDGE...or hybrid rule/fact schemas. 2 UNCLASSIFIED .WA UNCLASSIFIED ERL-0520-RR 2.1 Propositional Logic The simplest form of production-rules are based upon...requirements which may lead to poor system performance. 2.2 Hybrid Rule/Fact Schemas Hybrid rule/fact relationships (also known as Predicate Calculus ) have

BRST Formalism for Systems with Higher Order Derivatives of Gauge Parameters

NASA Astrophysics Data System (ADS)

Nirov, Kh. S.

For a wide class of mechanical systems, invariant under gauge transformations with arbitrary higher order time derivatives of gauge parameters, the equivalence of Lagrangian and Hamiltonian BRST formalisms is proved. It is shown that the Ostrogradsky formalism establishes the natural rules to relate the BFV ghost canonical pairs with the ghosts and antighosts introduced by the Lagrangian approach. Explicit relation between corresponding gauge-fixing terms is obtained.

Watershed-scale evaluation of Humboldt Redwood Company’s Habitat Conservation Plan timber harvest best management practices, Railroad Gulch, Elk River, California

Treesearch

Andrew Stubblefield; Shane Beach; Nicolas M. Harrison; Michelle Haskins

2017-01-01

The objective of this study is to test the effectiveness of California Forest Practice Rules and additional best management practices implemented as part of Humboldt Redwood Company’s Habitat Conservation Plan and Watershed Analysis prescriptions, in limiting the delivery of management-derived sediment. A paired watershed study format is being utilized to...

Multi-Excitonic Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Scheibner, M.; Stinaff, E. A.; Doty, M. F.; Ware, M. E.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

With the ability to create coupled pairs of quantum dots, the next step towards the realization of semiconductor based quantum information processing devices can be taken. However, so far little knowledge has been gained on these artificial molecules. Our photoluminescence experiments on single InAs/GaAs quantum dot molecules provide the systematics of coupled quantum dots by delineating the spectroscopic features of several key charge configurations in such quantum systems, including X, X^+,X^2+, XX, XX^+ (with X being the neutral exciton). We extract general rules which determine the formation of molecular states of coupled quantum dots. These include the fact that quantum dot molecules provide the possibility to realize various spin configurations and to switch the electron hole exchange interaction on and off by shifting charges inside the molecule. This knowledge will be valuable in developing implementations for quantum information processing.

Analysis of Traffic Conflicts in a Mixed-Airspace Evaluation of Airborne Separation Assurance

NASA Technical Reports Server (NTRS)

Lewis, Timothy A.

2013-01-01

A pair of human-in-the-loop simulation evaluations of a distributed air/ground separation assurance system have been conducted to investigate the function allocation between humans and automation systems as well as ground-based and airborne agents in the Next Generation Air Transportation System and beyond. This paper focuses on an analysis of certain critical conflicts observed between self-separating aircraft and ground-managed traffic in the same airspace. The principal cause of each conflict is identified and potential mitigations are discussed, such as: the sharing of trajectory intent information between the ground and the air; more cautious trajectory planning by the self-separating aircraft; and more equitable rules-of-the-road between the self-separating aircraft and ground-managed aircraft. This analysis will inform the ongoing design of an airborne separation assurance automation tool.

Sequence-based design of bioactive small molecules that target precursor microRNAs.

PubMed

Velagapudi, Sai Pradeep; Gallo, Steven M; Disney, Matthew D

2014-04-01

Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.

Sequence-based design of bioactive small molecules that target precursor microRNAs

PubMed Central

Velagapudi, Sai Pradeep; Gallo, Steven M.; Disney, Matthew D.

2014-01-01

Oligonucleotides are designed to target RNA using base pairing rules, however, they are hampered by poor cellular delivery and non-specific stimulation of the immune system. Small molecules are preferred as lead drugs or probes, but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate). Amongst 29 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Importantly, microRNA profiling shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide. PMID:24509821

The infection algorithm: an artificial epidemic approach for dense stereo correspondence.

PubMed

Olague, Gustavo; Fernández, Francisco; Pérez, Cynthia B; Lutton, Evelyne

2006-01-01

We present a new bio-inspired approach applied to a problem of stereo image matching. This approach is based on an artificial epidemic process, which we call the infection algorithm. The problem at hand is a basic one in computer vision for 3D scene reconstruction. It has many complex aspects and is known as an extremely difficult one. The aim is to match the contents of two images in order to obtain 3D information that allows the generation of simulated projections from a viewpoint that is different from the ones of the initial photographs. This process is known as view synthesis. The algorithm we propose exploits the image contents in order to produce only the necessary 3D depth information, while saving computational time. It is based on a set of distributed rules, which propagate like an artificial epidemic over the images. Experiments on a pair of real images are presented, and realistic reprojected images have been generated.

Probabilistic grammatical model for helix‐helix contact site classification

PubMed Central

2013-01-01

Background Hidden Markov Models power many state‐of‐the‐art tools in the field of protein bioinformatics. While excelling in their tasks, these methods of protein analysis do not convey directly information on medium‐ and long‐range residue‐residue interactions. This requires an expressive power of at least context‐free grammars. However, application of more powerful grammar formalisms to protein analysis has been surprisingly limited. Results In this work, we present a probabilistic grammatical framework for problem‐specific protein languages and apply it to classification of transmembrane helix‐helix pairs configurations. The core of the model consists of a probabilistic context‐free grammar, automatically inferred by a genetic algorithm from only a generic set of expert‐based rules and positive training samples. The model was applied to produce sequence based descriptors of four classes of transmembrane helix‐helix contact site configurations. The highest performance of the classifiers reached AUCROC of 0.70. The analysis of grammar parse trees revealed the ability of representing structural features of helix‐helix contact sites. Conclusions We demonstrated that our probabilistic context‐free framework for analysis of protein sequences outperforms the state of the art in the task of helix‐helix contact site classification. However, this is achieved without necessarily requiring modeling long range dependencies between interacting residues. A significant feature of our approach is that grammar rules and parse trees are human‐readable. Thus they could provide biologically meaningful information for molecular biologists. PMID:24350601

Challenges for Rule Systems on the Web

NASA Astrophysics Data System (ADS)

Hu, Yuh-Jong; Yeh, Ching-Long; Laun, Wolfgang

The RuleML Challenge started in 2007 with the objective of inspiring the issues of implementation for management, integration, interoperation and interchange of rules in an open distributed environment, such as the Web. Rules are usually classified as three types: deductive rules, normative rules, and reactive rules. The reactive rules are further classified as ECA rules and production rules. The study of combination rule and ontology is traced back to an earlier active rule system for relational and object-oriented (OO) databases. Recently, this issue has become one of the most important research problems in the Semantic Web. Once we consider a computer executable policy as a declarative set of rules and ontologies that guides the behavior of entities within a system, we have a flexible way to implement real world policies without rewriting the computer code, as we did before. Fortunately, we have de facto rule markup languages, such as RuleML or RIF to achieve the portability and interchange of rules for different rule systems. Otherwise, executing real-life rule-based applications on the Web is almost impossible. Several commercial or open source rule engines are available for the rule-based applications. However, we still need a standard rule language and benchmark for not only to compare the rule systems but also to measure the progress in the field. Finally, a number of real-life rule-based use cases will be investigated to demonstrate the applicability of current rule systems on the Web.

Interactions between children with juvenile rheumatoid arthritis and their mothers.

PubMed

Power, Thomas G; Dahlquist, Lynnda M; Thompson, Suzanne M; Warren, Robert

2003-01-01

To determine the degree to which mothers of children with juvenile rheumatoid arthritis (JRA) show an overprotective or highly controlling interaction style. We videotaped 84 mother-child pairs (42 JRA and 42 healthy, ages 6 to 13) while working on a collaborative problem-solving task. Based on physical therapy evaluations, children in the JRA group were assigned to "more severe" (n = 19) and "milder" (n = 22) arthritis subgroups. Results showed numerous differences between mothers of children with more severe arthritis and the other mothers (no differences between the milder arthritis and healthy comparison groups were found). Compared to mothers in the other two groups, mothers of children with more severe arthritis were more directive of their children's behavior during the task, showing higher rates of structure and rule setting, general clues, and prompting the child for an answer. Sequential analyses showed that mothers in the more severe group appeared to treat the task in a more evaluative manner, being more likely than other mothers to respond to correct answers with positive feedback and to incorrect answers with structure and rule setting. Mothers in the other groups were more likely to respond to both correct and incorrect answers with specific clues. We discuss how these differences in interactional style might impact the social development of children with JRA.

Multiple effect of social influence on cooperation in interdependent network games.

PubMed

Jiang, Luo-Luo; Li, Wen-Jing; Wang, Zhen

2015-10-01

The social influence exists widely in the human society, where individual decision-making process (from congressional election to electronic commerce) may be affected by the attitude and behavior of others belonging to different social networks. Here, we couple the snowdrift (SD) game and the prisoner's dilemma (PD) game on two interdependent networks, where strategies in both games are associated by social influence to mimick the majority rule. More accurately, individuals' strategies updating refers to social learning (based on payoff difference) and above-mentioned social influence (related with environment of interdependent group), which is controlled by social influence strength s. Setting s = 0 decouples the networks and returns the traditional network game; while its increase involves the interactions between networks. By means of numerous Monte Carlo simulations, we find that such a mechanism brings multiple influence to the evolution of cooperation. Small s leads to unequal cooperation level in both games, because social learning is still the main updating rule for most players. Though intermediate and large s guarantees the synchronized evolution of strategy pairs, cooperation finally dies out and reaches a completely dominance in both cases. Interestingly, these observations are attributed to the expansion of cooperation clusters. Our work may provide a new understanding to the emergence of cooperation in intercorrelated social systems.

Multiple effect of social influence on cooperation in interdependent network games

NASA Astrophysics Data System (ADS)

Jiang, Luo-Luo; Li, Wen-Jing; Wang, Zhen

2015-10-01

The social influence exists widely in the human society, where individual decision-making process (from congressional election to electronic commerce) may be affected by the attitude and behavior of others belonging to different social networks. Here, we couple the snowdrift (SD) game and the prisoner’s dilemma (PD) game on two interdependent networks, where strategies in both games are associated by social influence to mimick the majority rule. More accurately, individuals’ strategies updating refers to social learning (based on payoff difference) and above-mentioned social influence (related with environment of interdependent group), which is controlled by social influence strength s. Setting s = 0 decouples the networks and returns the traditional network game; while its increase involves the interactions between networks. By means of numerous Monte Carlo simulations, we find that such a mechanism brings multiple influence to the evolution of cooperation. Small s leads to unequal cooperation level in both games, because social learning is still the main updating rule for most players. Though intermediate and large s guarantees the synchronized evolution of strategy pairs, cooperation finally dies out and reaches a completely dominance in both cases. Interestingly, these observations are attributed to the expansion of cooperation clusters. Our work may provide a new understanding to the emergence of cooperation in intercorrelated social systems.

Dynamics and Removal Pathway of Edge Dislocations in Imperfectly Attached PbTe Nanocrystal Pairs: Toward Design Rules for Oriented Attachment.

PubMed

Ondry, Justin C; Hauwiller, Matthew R; Alivisatos, A Paul

2018-04-24

Using in situ high-resolution TEM, we study the structure and dynamics of well-defined edge dislocations in imperfectly attached PbTe nanocrystals. We identify that attachment of PbTe nanocrystals on both {100} and {110} facets gives rise to b = a/2⟨110⟩ edge dislocations. Based on the Burgers vector of individual dislocations, we can identify the glide plane of the dislocations. We observe that defects in particles attached on {100} facets have glide planes that quickly intersect the surface, and HRTEM movies show that the defects follow the glide plane to the surface. For {110} attached particles, the glide plane is collinear with the attachment direction, which does not provide an easy path for the dislocation to reach the surface. Indeed, HRTEM movies of dislocations for {110} attached particles show that defect removal is much slower. Further, we observe conversion from pure edge dislocations in imperfectly attached particles to dislocations with mixed edge and screw character, which has important implications for crystal growth. Finally, we observe that dislocations initially closer to the surface have a higher speed of removal, consistent with the strong dislocation free surface attractive force. Our results provide important design rules for defect-free attachment of preformed nanocrystals into epitaxial assemblies.

Handling Data Skew in MapReduce Cluster by Using Partition Tuning

PubMed

Gao, Yufei; Zhou, Yanjie; Zhou, Bing; Shi, Lei; Zhang, Jiacai

2017-01-01

The healthcare industry has generated large amounts of data, and analyzing these has emerged as an important problem in recent years. The MapReduce programming model has been successfully used for big data analytics. However, data skew invariably occurs in big data analytics and seriously affects efficiency. To overcome the data skew problem in MapReduce, we have in the past proposed a data processing algorithm called Partition Tuning-based Skew Handling (PTSH). In comparison with the one-stage partitioning strategy used in the traditional MapReduce model, PTSH uses a two-stage strategy and the partition tuning method to disperse key-value pairs in virtual partitions and recombines each partition in case of data skew. The robustness and efficiency of the proposed algorithm were tested on a wide variety of simulated datasets and real healthcare datasets. The results showed that PTSH algorithm can handle data skew in MapReduce efficiently and improve the performance of MapReduce jobs in comparison with the native Hadoop, Closer, and locality-aware and fairness-aware key partitioning (LEEN). We also found that the time needed for rule extraction can be reduced significantly by adopting the PTSH algorithm, since it is more suitable for association rule mining (ARM) on healthcare data. © 2017 Yufei Gao et al.

Handling Data Skew in MapReduce Cluster by Using Partition Tuning.

PubMed

Gao, Yufei; Zhou, Yanjie; Zhou, Bing; Shi, Lei; Zhang, Jiacai

2017-01-01

The healthcare industry has generated large amounts of data, and analyzing these has emerged as an important problem in recent years. The MapReduce programming model has been successfully used for big data analytics. However, data skew invariably occurs in big data analytics and seriously affects efficiency. To overcome the data skew problem in MapReduce, we have in the past proposed a data processing algorithm called Partition Tuning-based Skew Handling (PTSH). In comparison with the one-stage partitioning strategy used in the traditional MapReduce model, PTSH uses a two-stage strategy and the partition tuning method to disperse key-value pairs in virtual partitions and recombines each partition in case of data skew. The robustness and efficiency of the proposed algorithm were tested on a wide variety of simulated datasets and real healthcare datasets. The results showed that PTSH algorithm can handle data skew in MapReduce efficiently and improve the performance of MapReduce jobs in comparison with the native Hadoop, Closer, and locality-aware and fairness-aware key partitioning (LEEN). We also found that the time needed for rule extraction can be reduced significantly by adopting the PTSH algorithm, since it is more suitable for association rule mining (ARM) on healthcare data.

Handling Data Skew in MapReduce Cluster by Using Partition Tuning

PubMed Central

Zhou, Yanjie; Zhou, Bing; Shi, Lei

2017-01-01

The healthcare industry has generated large amounts of data, and analyzing these has emerged as an important problem in recent years. The MapReduce programming model has been successfully used for big data analytics. However, data skew invariably occurs in big data analytics and seriously affects efficiency. To overcome the data skew problem in MapReduce, we have in the past proposed a data processing algorithm called Partition Tuning-based Skew Handling (PTSH). In comparison with the one-stage partitioning strategy used in the traditional MapReduce model, PTSH uses a two-stage strategy and the partition tuning method to disperse key-value pairs in virtual partitions and recombines each partition in case of data skew. The robustness and efficiency of the proposed algorithm were tested on a wide variety of simulated datasets and real healthcare datasets. The results showed that PTSH algorithm can handle data skew in MapReduce efficiently and improve the performance of MapReduce jobs in comparison with the native Hadoop, Closer, and locality-aware and fairness-aware key partitioning (LEEN). We also found that the time needed for rule extraction can be reduced significantly by adopting the PTSH algorithm, since it is more suitable for association rule mining (ARM) on healthcare data. PMID:29065568

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase η

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

Patra, Amritaj; Zhang, Qianqian; Lei, Li

2015-02-09

The most prevalent lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the “A rule”). In some cases frameshifts are also common. X-ray structures with abasic sites in oligonucleotides have been reported for several microbial and human DNA polymerases (pols), e.g. Dpo4, RB69, KlenTaq, yeast pol ι, human (h) pol ι, and human pol β. We reported previously that hpol η is a major pol involved in abasic site bypass (Choi, J.-Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F.more » P. (2010 J. Mol. Biol. 404, 34–44). hpol η inserted all four dNTPs in steady-state and pre-steady-state assays, preferentially inserting A and G. In LC-MS analysis of primer-template pairs, A and G were inserted but little C or T was inserted. Frameshifts were observed when an appropriate pyrimidine was positioned 5' to the abasic site in the template. In x-ray structures of hpol η with a non-hydrolyzable analog of dATP or dGTP opposite an abasic site, H-bonding was observed between the phosphate 5' to the abasic site and water H-bonded to N1 and N6 of A and N1 and O6 of G nucleoside triphosphate analogs, offering an explanation for what appears to be a “purine rule.” A structure was also obtained for an A inserted and bonded in the primer opposite the abasic site, but it did not pair with a 5' T in the template. Finally, we conclude that hpol η, a major copying enzyme with abasic sites, follows a purine rule, which can also lead to frameshifts. The phenomenon can be explained with H-bonds.« less

Structural analysis of online handwritten mathematical symbols based on support vector machines

NASA Astrophysics Data System (ADS)

Simistira, Foteini; Papavassiliou, Vassilis; Katsouros, Vassilis; Carayannis, George

2013-01-01

Mathematical expression recognition is still a very challenging task for the research community mainly because of the two-dimensional (2d) structure of mathematical expressions (MEs). In this paper, we present a novel approach for the structural analysis between two on-line handwritten mathematical symbols of a ME, based on spatial features of the symbols. We introduce six features to represent the spatial affinity of the symbols and compare two multi-class classification methods that employ support vector machines (SVMs): one based on the "one-against-one" technique and one based on the "one-against-all", in identifying the relation between a pair of symbols (i.e. subscript, numerator, etc). A dataset containing 1906 spatial relations derived from the Competition on Recognition of Online Handwritten Mathematical Expressions (CROHME) 2012 training dataset is constructed to evaluate the classifiers and compare them with the rule-based classifier of the ILSP-1 system participated in the contest. The experimental results give an overall mean error rate of 2.61% for the "one-against-one" SVM approach, 6.57% for the "one-against-all" SVM technique and 12.31% error rate for the ILSP-1 classifier.

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

PubMed Central

2018-01-01

Abstract DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone. PMID:29228337

Interactional leader–follower sensorimotor communication strategies during repetitive joint actions

PubMed Central

Candidi, Matteo; Curioni, Arianna; Donnarumma, Francesco; Sacheli, Lucia Maria; Pezzulo, Giovanni

2015-01-01

Non-verbal communication is the basis of animal interactions. In dyadic leader–follower interactions, leaders master the ability to carve their motor behaviour in order to ‘signal’ their future actions and internal plans while these signals influence the behaviour of follower partners, who automatically tend to imitate the leader even in complementary interactions. Despite their usefulness, signalling and imitation have a biomechanical cost, and it is unclear how this cost–benefits trade-off is managed during repetitive dyadic interactions that present learnable regularities. We studied signalling and imitation dynamics (indexed by movement kinematics) in pairs of leaders and followers during a repetitive, rule-based, joint action. Trial-by-trial Bayesian model comparison was used to evaluate the relation between signalling, imitation and pair performance. The different models incorporate different hypotheses concerning the factors (past interactions versus online movements) influencing the leader's signalling (or follower's imitation) kinematics. This approach showed that (i) leaders' signalling strategy improves future couple performance, (ii) leaders used the history of past interactions to shape their signalling, (iii) followers' imitative behaviour is more strongly affected by the online movement of the leader. This study elucidates the ways online sensorimotor communication help individuals align their task representations and ultimately improves joint action performance. PMID:26333815

The Effect of Illumination on Stereo DTM Quality: Simulations in Support of Europa Exploration

NASA Astrophysics Data System (ADS)

Kirk, R. L.; Howington-Kraus, E.; Hare, T. M.; Jorda, L.

2016-06-01

We have investigated how the quality of stereoscopically measured topography degrades with varying illumination, in particular the ranges of incidence angles and illumination differences over which useful digital topographic models (DTMs) can be recovered. Our approach is to make high-fidelity simulated image pairs of known topography and compare DTMs from stereoanalysis of these images with the input data. Well-known rules of thumb for horizontal resolution (>3-5 pixels) and matching precision (~0.2-0.3 pixels) are generally confirmed, but the best achievable resolution at high incidence angles is ~15 pixels, probably as a result of smoothing internal to the matching algorithm. Single-pass stereo imaging of Europa is likely to yield DTMs of consistent (optimal) quality for all incidence angles ≤85°, and certainly for incidence angles between 40° and 85°. Simulations with pairs of images in which the illumination is not consistent support the utility of shadow tip distance (STD) as a measure of illumination difference, but also suggest new and simpler criteria for evaluating the suitability of stereopairs based on illumination geometry. Our study was motivated by the needs of a mission to Europa, but the approach and (to first order) the results described here are relevant to a wide range of planetary investigations.

Interactional leader-follower sensorimotor communication strategies during repetitive joint actions.

PubMed

Candidi, Matteo; Curioni, Arianna; Donnarumma, Francesco; Sacheli, Lucia Maria; Pezzulo, Giovanni

2015-09-06

Non-verbal communication is the basis of animal interactions. In dyadic leader-follower interactions, leaders master the ability to carve their motor behaviour in order to 'signal' their future actions and internal plans while these signals influence the behaviour of follower partners, who automatically tend to imitate the leader even in complementary interactions. Despite their usefulness, signalling and imitation have a biomechanical cost, and it is unclear how this cost-benefits trade-off is managed during repetitive dyadic interactions that present learnable regularities. We studied signalling and imitation dynamics (indexed by movement kinematics) in pairs of leaders and followers during a repetitive, rule-based, joint action. Trial-by-trial Bayesian model comparison was used to evaluate the relation between signalling, imitation and pair performance. The different models incorporate different hypotheses concerning the factors (past interactions versus online movements) influencing the leader's signalling (or follower's imitation) kinematics. This approach showed that (i) leaders' signalling strategy improves future couple performance, (ii) leaders used the history of past interactions to shape their signalling, (iii) followers' imitative behaviour is more strongly affected by the online movement of the leader. This study elucidates the ways online sensorimotor communication help individuals align their task representations and ultimately improves joint action performance. © 2015 The Author(s).

Rotational-translational fourier imaging system

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2004-01-01

This invention has the ability to create Fourier-based images with only two grid pairs. The two grid pairs are manipulated in a manner that allows (1) a first grid pair to provide multiple real components of the Fourier-based image and (2) a second grid pair to provide multiple imaginary components of the Fourier-based image. The novelty of this invention resides in the use of only two grid pairs to provide the same imaging information that has been traditionally collected with multiple grid pairs.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.

PubMed

de Sousa, Miguel M; Munteanu, Cristian R; Pazos, Alejandro; Fonseca, Nuno A; Camacho, Rui; Magalhães, A L

2011-02-21

A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools. Copyright © 2010 Elsevier Ltd. All rights reserved.

Pilot Interactions in an Over-Constrained Conflict Scenario as Studied in a Piloted Simulation of Autonomous Aircraft Operations

NASA Technical Reports Server (NTRS)

Wing, David J.; Barhydt, Richard; Barmore, Bryan; Krishnamurthy, Karthik

2003-01-01

Feasibility and safety of autonomous aircraft operations were studied in a multi-piloted simulation of overconstrained traffic conflicts to determine the need for, and utility of, priority flight rules to maintain safety in this extraordinary and potentially hazardous situation. An overconstrained traffic conflict is one in which the separation assurance objective is incompatible with other objectives. In addition, a proposed scheme for implementing priority flight rules by staggering the alerting time between the two aircraft in conflict was tested for effectiveness. The feasibility study was conducted through a simulation in the Air Traffic Operations Laboratory at the NASA Langley Research Center. This research activity is a continuation of the Distributed Air-Ground Traffic Management feasibility analysis reported in the 4th USA/Europe Air Traffic Management R&D Seminar in December 2001 (paper #48). The over-constrained conflict scenario studied here consisted of two piloted aircraft that were assigned an identical en-route waypoint arrival time and altitude crossing restriction. The simulation results indicated that the pilots safely resolved the conflict without the need for a priority flight rule system. Occurrences of unnecessary maneuvering near the common waypoint were traced to false conflict alerts, generated as the result of including waypoint constraint information in the broadcast data link message issued from each aircraft. This result suggests that, in the conservative interests of safety, broadcast intent information should be based on the commanded trajectory and not on the Flight Management System flight plan, to which the aircraft may not actually adhere. The use of priority flight rules had no effect on the percentage of the aircraft population meeting completely predictable which aircraft in a given pair would meet the constraints and which aircraft would make the first maneuver to yield right-of-way. Therefore, the proposed scheme for implementing priority flight rules through staggering the alerting time between the two aircraft was completely effective. The data and observations from this experiment, together with results from the previously reported study, support the feasibility of autonomous aircraft operations.

Efficient Implementation of the Pairing on Mobilephones Using BREW

NASA Astrophysics Data System (ADS)

Yoshitomi, Motoi; Takagi, Tsuyoshi; Kiyomoto, Shinsaku; Tanaka, Toshiaki

Pairing based cryptosystems can accomplish novel security applications such as ID-based cryptosystems, which have not been constructed efficiently without the pairing. The processing speed of the pairing based cryptosystems is relatively slow compared with the other conventional public key cryptosystems. However, several efficient algorithms for computing the pairing have been proposed, namely Duursma-Lee algorithm and its variant ηT pairing. In this paper, we present an efficient implementation of the pairing over some mobilephones. Moreover, we compare the processing speed of the pairing with that of the other standard public key cryptosystems, i. e. RSA cryptosystem and elliptic curve cryptosystem. Indeed the processing speed of our implementation in ARM9 processors on BREW achieves under 100 milliseconds using the supersingular curve over F397. In addition, the pairing is more efficient than the other public key cryptosystems, and the pairing can be achieved enough also on BREW mobilephones. It has become efficient enough to implement security applications, such as short signature, ID-based cryptosystems or broadcast encryption, using the pairing on BREW mobilephones.

Implementing a Commercial Rule Base as a Medication Order Safety Net

PubMed Central

Reichley, Richard M.; Seaton, Terry L.; Resetar, Ervina; Micek, Scott T.; Scott, Karen L.; Fraser, Victoria J.; Dunagan, W. Claiborne; Bailey, Thomas C.

2005-01-01

A commercial rule base (Cerner Multum) was used to identify medication orders exceeding recommended dosage limits at five hospitals within BJC HealthCare, an integrated health care system. During initial testing, clinical pharmacists determined that there was an excessive number of nuisance and clinically insignificant alerts, with an overall alert rate of 9.2%. A method for customizing the commercial rule base was implemented to increase rule specificity for problematic rules. The system was subsequently deployed at two facilities and achieved alert rates of less than 1%. Pharmacists screened these alerts and contacted ordering physicians in 21% of cases. Physicians made therapeutic changes in response to 38% of alerts presented to them. By applying simple techniques to customize rules, commercial rule bases can be used to rapidly deploy a safety net to screen drug orders for excessive dosages, while preserving the rule architecture for later implementations of more finely tuned clinical decision support. PMID:15802481

Rule groupings in expert systems using nearest neighbour decision rules, and convex hulls

NASA Technical Reports Server (NTRS)

Anastasiadis, Stergios

1991-01-01

Expert System shells are lacking in many areas of software engineering. Large rule based systems are not semantically comprehensible, difficult to debug, and impossible to modify or validate. Partitioning a set of rules found in CLIPS (C Language Integrated Production System) into groups of rules which reflect the underlying semantic subdomains of the problem, will address adequately the concerns stated above. Techniques are introduced to structure a CLIPS rule base into groups of rules that inherently have common semantic information. The concepts involved are imported from the field of A.I., Pattern Recognition, and Statistical Inference. Techniques focus on the areas of feature selection, classification, and a criteria of how 'good' the classification technique is, based on Bayesian Decision Theory. A variety of distance metrics are discussed for measuring the 'closeness' of CLIPS rules and various Nearest Neighbor classification algorithms are described based on the above metric.

Automated revision of CLIPS rule-bases

NASA Technical Reports Server (NTRS)

Murphy, Patrick M.; Pazzani, Michael J.

1994-01-01

This paper describes CLIPS-R, a theory revision system for the revision of CLIPS rule-bases. CLIPS-R may be used for a variety of knowledge-base revision tasks, such as refining a prototype system, adapting an existing system to slightly different operating conditions, or improving an operational system that makes occasional errors. We present a description of how CLIPS-R revises rule-bases, and an evaluation of the system on three rule-bases.

Validity and reliability of clinical prediction rules used to screen for cervical spine injury in alert low-risk patients with blunt trauma to the neck: part 2. A systematic review from the Cervical Assessment and Diagnosis Research Evaluation (CADRE) Collaboration.

PubMed

Moser, N; Lemeunier, N; Southerst, D; Shearer, H; Murnaghan, K; Sutton, D; Côté, P

2018-06-01

To update findings of the 2000-2010 Bone and Joint Decade Task Force on Neck Pain and its Associated Disorders (Neck Pain Task Force) on the validity and reliability of clinical prediction rules used to screen for cervical spine injury in alert low-risk adult patients with blunt trauma to the neck. We searched four databases from 2005 to 2015. Pairs of independent reviewers critically appraised eligible studies using the modified QUADAS-2 and QAREL criteria. We synthesized low risk of bias studies following best evidence synthesis principles. We screened 679 citations; five had a low risk of bias and were included in our synthesis. The sensitivity of the Canadian C-spine rule ranged from 0.90 to 1.00 with negative predictive values ranging from 99 to 100%. Inter-rater reliability of the Canadian C-spine rule varied from k = 0.60 between nurses and physicians to k = 0.93 among paramedics. The inter-rater reliability of the Nexus Low-Risk Criteria was k = 0.53 between resident physicians and faculty physicians. Our review adds new evidence to the Neck Pain Task Force and supports the use of clinical prediction rules in emergency care settings to screen for cervical spine injury in alert low-risk adult patients with blunt trauma to the neck. The Canadian C-spine rule consistently demonstrated excellent sensitivity and negative predictive values. Our review, however, suggests that the reproducibility of the clinical predictions rules varies depending on the examiners level of training and experience.

Concurrence of rule- and similarity-based mechanisms in artificial grammar learning.

PubMed

Opitz, Bertram; Hofmann, Juliane

2015-03-01

A current theoretical debate regards whether rule-based or similarity-based learning prevails during artificial grammar learning (AGL). Although the majority of findings are consistent with a similarity-based account of AGL it has been argued that these results were obtained only after limited exposure to study exemplars, and performance on subsequent grammaticality judgment tests has often been barely above chance level. In three experiments the conditions were investigated under which rule- and similarity-based learning could be applied. Participants were exposed to exemplars of an artificial grammar under different (implicit and explicit) learning instructions. The analysis of receiver operating characteristics (ROC) during a final grammaticality judgment test revealed that explicit but not implicit learning led to rule knowledge. It also demonstrated that this knowledge base is built up gradually while similarity knowledge governed the initial state of learning. Together these results indicate that rule- and similarity-based mechanisms concur during AGL. Moreover, it could be speculated that two different rule processes might operate in parallel; bottom-up learning via gradual rule extraction and top-down learning via rule testing. Crucially, the latter is facilitated by performance feedback that encourages explicit hypothesis testing. Copyright © 2015 Elsevier Inc. All rights reserved.

An ensemble of SVM classifiers based on gene pairs.

PubMed

Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

2013-07-01

In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cooperation of a Dissatisfied Adaptive Prisoner's Dilemma in Spatial Structures

NASA Astrophysics Data System (ADS)

Zhang, Wen; Li, Yao-Sheng; Du, Peng; Xu, Chen

2013-10-01

We study the cooperative behavior of a dissatisfied adaptive prisoner's dilemma via a pair updating rule. We compare two kinds of relationship among the competing agents, one is the well-mixed population and the other is the two-dimensional square lattice. It is found that the cooperation emerges in both the cases and the frequency of cooperation is enhanced in the square lattice. Though it is impossible for the cooperators to have a higher average payoff than that of the defectors in the well-mixed case, the cooperators in the spatial square lattice could have higher average payoffs in certain regions of the game parameters. We theoretically analyze the well-mixed case exactly and the square lattice by pair approximation. The theoretic results are in agreement with the simulation data.

Envisaging quantum transport phenomenon in a muddled base pair of DNA

NASA Astrophysics Data System (ADS)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Detection of pseudosinusoidal epileptic seizure segments in the neonatal EEG by cascading a rule-based algorithm with a neural network.

PubMed

Karayiannis, Nicolaos B; Mukherjee, Amit; Glover, John R; Ktonas, Periklis Y; Frost, James D; Hrachovy, Richard A; Mizrahi, Eli M

2006-04-01

This paper presents an approach to detect epileptic seizure segments in the neonatal electroencephalogram (EEG) by characterizing the spectral features of the EEG waveform using a rule-based algorithm cascaded with a neural network. A rule-based algorithm screens out short segments of pseudosinusoidal EEG patterns as epileptic based on features in the power spectrum. The output of the rule-based algorithm is used to train and compare the performance of conventional feedforward neural networks and quantum neural networks. The results indicate that the trained neural networks, cascaded with the rule-based algorithm, improved the performance of the rule-based algorithm acting by itself. The evaluation of the proposed cascaded scheme for the detection of pseudosinusoidal seizure segments reveals its potential as a building block of the automated seizure detection system under development.

Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

PubMed

Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

2015-10-12

A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular switching behavior in isosteric DNA base pairs.

PubMed

Jissy, A K; Konar, Sukanya; Datta, Ayan

2013-04-15

The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phase transitions in Nowak Sznajd opinion dynamics

NASA Astrophysics Data System (ADS)

Wołoszyn, Maciej; Stauffer, Dietrich; Kułakowski, Krzysztof

2007-05-01

The Nowak modification of the Sznajd opinion dynamics model on the square lattice assumes that with probability β the opinions flip due to mass-media advertising from down to up, and vice versa. Besides, with probability α the Sznajd rule applies that a neighbour pair agreeing in its two opinions convinces all its six neighbours of that opinion. Our Monte Carlo simulations and mean-field theory find sharp phase transitions in the parameter space.

Code-switched English Pronunciation Modeling for Swahili Spoken Term Detection (Pub Version, Open Access)

DTIC Science & Technology

2016-05-03

using additional English resources. 2. Background The Babel program1 is an international collaborative effort sponsored by the US Intelligence Advanced...phenomenon is not as well studied for English / African language pairs, but some results are available8,9. 3. Experimental Setup The Swahili analysis...word pronunciations. From the analysis it was concluded that in most cases English words were pronounced using standard English letter-to-sound rules

Isospectral drums and simple groups

NASA Astrophysics Data System (ADS)

Thas, Koen

Nearly every known pair of isospectral but nonisometric manifolds — with as most famous members isospectral bounded ℝ-planar domains which makes one “not hear the shape of a drum” [M. Kac, Can one hear the shape of a drum? Amer. Math. Monthly 73(4 part 2) (1966) 1-23] — arise from the (group theoretical) Gassmann-Sunada method. Moreover, all the known ℝ-planar examples (so counter examples to Kac’s question) are constructed through a famous specialization of this method, called transplantation. We first describe a number of very general classes of length equivalent manifolds, with as particular cases isospectral manifolds, in each of the constructions starting from a given example that arises itself from the Gassmann-Sunada method. The constructions include the examples arising from the transplantation technique (and thus in particular the known planar examples). To that end, we introduce four properties — called FF, MAX, PAIR and INV — inspired by natural physical properties (which rule out trivial constructions), that are satisfied for each of the known planar examples. Vice versa, we show that length equivalent manifolds with FF, MAX, PAIR and INV which arise from the Gassmann-Sunada method, must fall under one of our prior constructions, thus describing a precise classification of these objects. Due to the nature of our constructions and properties, a deep connection with finite simple groups occurs which seems, perhaps, rather surprising in the context of this paper. On the other hand, our properties define in some sense physically irreducible pairs of length equivalent manifolds — “atoms” of general pairs of length equivalent manifolds, in that such a general pair of manifolds is patched up out of irreducible pairs — and that is precisely what simple groups are for general groups.

77 FR 73498 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-10

... Effectiveness of a Proposed Rule Change To Amend Its Rule Related to Multi-Class Broad- Based Index Option... Rule Change The Exchange proposes to amend its rule related to multi-class broad-based index option... is to (i) clarify that the term ``Multi-Class Broad-Based Index Option Spread Order (Multi-Class...

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

Using Rule-Based Computer Programming to Unify Communication Rules Research.

ERIC Educational Resources Information Center

Sanford, David L.; Roach, J. W.

This paper proposes the use of a rule-based computer programming language as a standard for the expression of rules, arguing that the adoption of a standard would enable researchers to communicate about rules in a consistent and significant way. Focusing on the formal equivalence of artificial intelligence (AI) programming to different types of…

Efficiency in Rule- vs. Plan-Based Movements Is Modulated by Action-Mode.

PubMed

Scheib, Jean P P; Stoll, Sarah; Thürmer, J Lukas; Randerath, Jennifer

2018-01-01

The rule/plan motor cognition (RPMC) paradigm elicits visually indistinguishable motor outputs, resulting from either plan- or rule-based action-selection, using a combination of essentially interchangeable stimuli. Previous implementations of the RPMC paradigm have used pantomimed movements to compare plan- vs. rule-based action-selection. In the present work we attempt to determine the generalizability of previous RPMC findings to real object interaction by use of a grasp-to-rotate task. In the plan task, participants had to use prospective planning to achieve a comfortable post-handle rotation hand posture. The rule task used implementation intentions (if-then rules) leading to the same comfortable end-state. In Experiment A, we compare RPMC performance of 16 healthy participants in pantomime and real object conditions of the experiment, within-subjects. Higher processing efficiency of rule- vs. plan-based action-selection was supported by diffusion model analysis. Results show a significant response-time increase in the pantomime condition compared to the real object condition and a greater response-time advantage of rule-based vs. plan-based actions in the pantomime compared to the real object condition. In Experiment B, 24 healthy participants performed the real object RPMC task in a task switching vs. a blocked condition. Results indicate that plan-based action-selection leads to longer response-times and less efficient information processing than rule-based action-selection in line with previous RPMC findings derived from the pantomime action-mode. Particularly in the task switching mode, responses were faster in the rule compared to the plan task suggesting a modulating influence of cognitive load. Overall, results suggest an advantage of rule-based action-selection over plan-based action-selection; whereby differential mechanisms appear to be involved depending on the action-mode. We propose that cognitive load is a factor that modulates the advantageous effect of implementation intentions in motor cognition on different levels as illustrated by the varying speed advantages and the variation in diffusion parameters per action-mode or condition, respectively.

Reducing the Conflict Factors Strategies in Question Answering System

NASA Astrophysics Data System (ADS)

Suwarningsih, W.; Purwarianti, A.; Supriana, I.

2017-03-01

A rule-based system is prone to conflict as new knowledge every time will emerge and indirectly must sign in to the knowledge base that is used by the system. A conflict occurred between the rules in the knowledge base can lead to the errors of reasoning or reasoning circulation. Therefore, when added, the new rules will lead to conflict with other rules, and the only rules that really can be added to the knowledge base. From these conditions, this paper aims to propose a conflict resolution strategy for a medical debriefing system by analyzing scenarios based upon the runtime to improve the efficiency and reliability of systems.

The SLE-key test serological signature: new insights into the course of lupus.

PubMed

Putterman, Chaim; Pisetsky, David S; Petri, Michelle; Caricchio, Roberto; Wu, Alan H B; Sanz, Ignacio; Oates, Jim C; Wallace, Steve; Sorek, Rachel; Gerwien, Robert; Safer, Pennina; Jakobi-Brook, Keren; Cohen, Irun R

2018-06-04

We previously described the multiplex autoantibody SLE-key Rule-Out test, which detects a signature of autoantibody reactivity that distinguishes healthy subjects from SLE patients with 94% sensitivity, 75% specificity and 93% negative predictive value; thus, an individual manifesting a positive Rule-Out test score is unlikely to have SLE (e.g. lupus is excluded). The objective of this current study was to evaluate the stability of the lupus-associated signature over time. We used banked serum samples from healthy subjects (n = 51) and lupus patients (n = 50 individual samples and n = 181 paired samples, for a total of n = 412 serum samples). The samples were drawn at different times after diagnosis to analyse the impact on the SLE-key Rule-Out test of time elapsed since diagnosis and any changes in disease activity (as reflected by the SLEDAI score). The SLE signature remains stable for the first 10 years after diagnosis; in this time frame, <10% of patients manifested a positive Rule-Out score and the SLE-key Rule-Out score was independent of the underlying disease activity as reflected by the SLEDAI score. After ⩾10 years, ∼30% of lupus subjects scored as SLE Ruled-Out; the proportion of patients manifesting this status was even greater in the subset of individuals with a SLEDAI score of 0. These findings raise the possibility that a significant number of SLE patients manifest a change in their serological signature over time, and that such a signature change may signify an evolution in the immunological features of their disease relevant to patient management.

Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2009-01-01

The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the…

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

PubMed

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SIRE: A Simple Interactive Rule Editor for NICBES

NASA Technical Reports Server (NTRS)

Bykat, Alex

1988-01-01

To support evolution of domain expertise, and its representation in an expert system knowledge base, a user-friendly rule base editor is mandatory. The Nickel Cadmium Battery Expert System (NICBES), a prototype of an expert system for the Hubble Space Telescope power storage management system, does not provide such an editor. In the following, a description of a Simple Interactive Rule Base Editor (SIRE) for NICBES is described. The SIRE provides a consistent internal representation of the NICBES knowledge base. It supports knowledge presentation and provides a user-friendly and code language independent medium for rule addition and modification. The SIRE is integrated with NICBES via an interface module. This module provides translation of the internal representation to Prolog-type rules (Horn clauses), latter rule assertion, and a simple mechanism for rule selection for its Prolog inference engine.

Homography-based multiple-camera person-tracking

NASA Astrophysics Data System (ADS)

Turk, Matthew R.

2009-01-01

Multiple video cameras are cheaply installed overlooking an area of interest. While computerized single-camera tracking is well-developed, multiple-camera tracking is a relatively new problem. The main multi-camera problem is to give the same tracking label to all projections of a real-world target. This is called the consistent labelling problem. Khan and Shah (2003) introduced a method to use field of view lines to perform multiple-camera tracking. The method creates inter-camera meta-target associations when objects enter at the scene edges. They also said that a plane-induced homography could be used for tracking, but this method was not well described. Their homography-based system would not work if targets use only one side of a camera to enter the scene. This paper overcomes this limitation and fully describes a practical homography-based tracker. A new method to find the feet feature is introduced. The method works especially well if the camera is tilted, when using the bottom centre of the target's bounding-box would produce inaccurate results. The new method is more accurate than the bounding-box method even when the camera is not tilted. Next, a method is presented that uses a series of corresponding point pairs "dropped" by oblivious, live human targets to find a plane-induced homography. The point pairs are created by tracking the feet locations of moving targets that were associated using the field of view line method. Finally, a homography-based multiple-camera tracking algorithm is introduced. Rules governing when to create the homography are specified. The algorithm ensures that homography-based tracking only starts after a non-degenerate homography is found. The method works when not all four field of view lines are discoverable; only one line needs to be found to use the algorithm. To initialize the system, the operator must specify pairs of overlapping cameras. Aside from that, the algorithm is fully automatic and uses the natural movement of live targets for training. No calibration is required. Testing shows that the algorithm performs very well in real-world sequences. The consistent labelling problem is solved, even for targets that appear via in-scene entrances. Full occlusions are handled. Although implemented in Matlab, the multiple-camera tracking system runs at eight frames per second. A faster implementation would be suitable for real-world use at typical video frame rates.

Significance testing of rules in rule-based models of human problem solving

NASA Technical Reports Server (NTRS)

Lewis, C. M.; Hammer, J. M.

1986-01-01

Rule-based models of human problem solving have typically not been tested for statistical significance. Three methods of testing rules - analysis of variance, randomization, and contingency tables - are presented. Advantages and disadvantages of the methods are also described.

The Interactive Effects of the Availability of Objectives and/or Rules on Computer-Based Learning: A Replication.

ERIC Educational Resources Information Center

Merrill, Paul F.; And Others

To replicate and extend the results of a previous study, this project investigated the effects of behavioral objectives and/or rules on computer-based learning task performance. The 133 subjects were randomly assigned to an example-only, objective-example, rule example, or objective-rule example group. The availability of rules and/or objectives…

WellnessRules: A Web 3.0 Case Study in RuleML-Based Prolog-N3 Profile Interoperation

NASA Astrophysics Data System (ADS)

Boley, Harold; Osmun, Taylor Michael; Craig, Benjamin Larry

An interoperation study, WellnessRules, is described, where rules about wellness opportunities are created by participants in rule languages such as Prolog and N3, and translated within a wellness community using RuleML/XML. The wellness rules are centered around participants, as profiles, encoding knowledge about their activities conditional on the season, the time-of-day, the weather, etc. This distributed knowledge base extends FOAF profiles with a vocabulary and rules about wellness group networking. The communication between participants is organized through Rule Responder, permitting wellness-profile translation and distributed querying across engines. WellnessRules interoperates between rules and queries in the relational (Datalog) paradigm of the pure-Prolog subset of POSL and in the frame (F-logic) paradigm of N3. An evaluation of Rule Responder instantiated for WellnessRules revealed acceptable Web response times.

Text generation from Taiwanese Sign Language using a PST-based language model for augmentative communication.

PubMed

Wu, Chung-Hsien; Chiu, Yu-Hsien; Guo, Chi-Shiang

2004-12-01

This paper proposes a novel approach to the generation of Chinese sentences from ill-formed Taiwanese Sign Language (TSL) for people with hearing impairments. First, a sign icon-based virtual keyboard is constructed to provide a visualized interface to retrieve sign icons from a sign database. A proposed language model (LM), based on a predictive sentence template (PST) tree, integrates a statistical variable n-gram LM and linguistic constraints to deal with the translation problem from ill-formed sign sequences to grammatical written sentences. The PST tree trained by a corpus collected from the deaf schools was used to model the correspondence between signed and written Chinese. In addition, a set of phrase formation rules, based on trigger pair category, was derived for sentence pattern expansion. These approaches improved the efficiency of text generation and the accuracy of word prediction and, therefore, improved the input rate. For the assessment of practical communication aids, a reading-comprehension training program with ten profoundly deaf students was undertaken in a deaf school in Tainan, Taiwan. Evaluation results show that the literacy aptitude test and subjective satisfactory level are significantly improved.

Comparison of clinical knowledge bases for summarization of electronic health records.

PubMed

McCoy, Allison B; Sittig, Dean F; Wright, Adam

2013-01-01

Automated summarization tools that create condition-specific displays may improve clinician efficiency. These tools require new kinds of knowledge that is difficult to obtain. We compared five problem-medication pair knowledge bases generated using four previously described knowledge base development approaches. The number of pairs in the resulting mapped knowledge bases varied widely due to differing mapping techniques from the source terminologies, ranging from 2,873 to 63,977,738 pairs. The number of overlapping pairs across knowledge bases was low, with one knowledge base having half of the pairs overlapping with another knowledge base, and most having less than a third overlapping. Further research is necessary to better evaluate the knowledge bases independently in additional settings, and to identify methods to integrate the knowledge bases.

78 FR 62417 - Regulatory Capital Rules: Regulatory Capital, Implementation of Basel III, Capital Adequacy...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-22

..., Standardized Approach for Risk-Weighted Assets, Market Discipline and Disclosure Requirements, Advanced Approaches Risk-Based Capital Rule, and Market Risk Capital Rule AGENCY: Federal Deposit Insurance... Assets, Market Discipline and Disclosure Requirements, Advanced Approaches Risk-Based Capital Rule, and...

Architecture For The Optimization Of A Machining Process In Real Time Through Rule-Based Expert System

NASA Astrophysics Data System (ADS)

Serrano, Rafael; González, Luis Carlos; Martín, Francisco Jesús

2009-11-01

Under the project SENSOR-IA which has had financial funding from the Order of Incentives to the Regional Technology Centers of the Counsil of Innovation, Science and Enterprise of Andalusia, an architecture for the optimization of a machining process in real time through rule-based expert system has been developed. The architecture consists of an acquisition system and sensor data processing engine (SATD) from an expert system (SE) rule-based which communicates with the SATD. The SE has been designed as an inference engine with an algorithm for effective action, using a modus ponens rule model of goal-oriented rules.The pilot test demonstrated that it is possible to govern in real time the machining process based on rules contained in a SE. The tests have been done with approximated rules. Future work includes an exhaustive collection of data with different tool materials and geometries in a database to extract more precise rules.

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

PubMed Central

Lee, Joon-Hwa; Bae, Sung-Hun; Choi, Byong-Seok

2000-01-01

In contrast to the highly mutagenic pyrimidine(6–4)pyrimidone photoproduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685–9689]. To determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW/GA duplex) contains a mismatched base pair between the 3′ T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3′ T (T6) of the Dewar lesion formed stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW/GA duplex were much larger than those of a second duplex that contains the Dewar lesion and opposing A15 and A16 residues (DW/AA duplex). The DW/GA duplex showed poorer stacking interactions at the two bases of the Dewar product and at the adjacent A7⋅T14 base pair than did the DW/AA duplex. These structural features imply that no thermal stability or conformational benefit is obtained by incorporating a G instead of an A opposite the 3′ T of the Dewar lesion. These properties may thus facilitate the preferential incorporation of an A in accordance with the A rule during translesion replication and lead to the low frequency of 3′ T→C mutations observed at this site. PMID:10758155

Fully Convolutional Network-Based Multifocus Image Fusion.

PubMed

Guo, Xiaopeng; Nie, Rencan; Cao, Jinde; Zhou, Dongming; Qian, Wenhua

2018-07-01

As the optical lenses for cameras always have limited depth of field, the captured images with the same scene are not all in focus. Multifocus image fusion is an efficient technology that can synthesize an all-in-focus image using several partially focused images. Previous methods have accomplished the fusion task in spatial or transform domains. However, fusion rules are always a problem in most methods. In this letter, from the aspect of focus region detection, we propose a novel multifocus image fusion method based on a fully convolutional network (FCN) learned from synthesized multifocus images. The primary novelty of this method is that the pixel-wise focus regions are detected through a learning FCN, and the entire image, not just the image patches, are exploited to train the FCN. First, we synthesize 4500 pairs of multifocus images by repeatedly using a gaussian filter for each image from PASCAL VOC 2012, to train the FCN. After that, a pair of source images is fed into the trained FCN, and two score maps indicating the focus property are generated. Next, an inversed score map is averaged with another score map to produce an aggregative score map, which take full advantage of focus probabilities in two score maps. We implement the fully connected conditional random field (CRF) on the aggregative score map to accomplish and refine a binary decision map for the fusion task. Finally, we exploit the weighted strategy based on the refined decision map to produce the fused image. To demonstrate the performance of the proposed method, we compare its fused results with several start-of-the-art methods not only on a gray data set but also on a color data set. Experimental results show that the proposed method can achieve superior fusion performance in both human visual quality and objective assessment.

Branchpoint selection in the splicing of U12-dependent introns in vitro.

PubMed

McConnell, Timothy S; Cho, Soo-Jin; Frilander, Mikko J; Steitz, Joan A

2002-05-01

In metazoans, splicing of introns from pre-mRNAs can occur by two pathways: the major U2-dependent or the minor U12-dependent pathways. Whereas the U2-dependent pathway has been well characterized, much about the U12-dependent pathway remains to be discovered. Most of the information regarding U12-type introns has come from in vitro studies of a very few known introns of this class. To expand our understanding of U12-type splicing, especially to test the hypothesis that the simple base-pairing mechanism between the intron and U12 snRNA defines the branchpoint of U12-dependent introns, additional in vitro splicing substrates were created from three putative U12-type introns: the third intron of the Xenopus RPL1 a gene (XRP), the sixth intron of the Xenopus TFIIS.oA gene (XTF), and the first intron of the human Sm E gene (SME). In vitro splicing in HeLa nuclear extract confirmed U12-dependent splicing of each of these introns. Surprisingly, branchpoint mapping of the XRP splicing intermediate shows use of the upstream rather than the downstream of two consecutive adenosines within the branchpoint sequence (BPS), contrary to the prediction based on alignment with the sixth intron of human P120, a U12-dependent intron whose branch site was previously determined. Also, in the SME intron, the position of the branchpoint A residue within the region base paired with U12 differs from that in P120 and XTF. Analysis of these three additional introns therefore rules out simple models for branchpoint selection by the U12-type spliceosome.

Branchpoint selection in the splicing of U12-dependent introns in vitro.

PubMed Central

McConnell, Timothy S; Cho, Soo-Jin; Frilander, Mikko J; Steitz, Joan A

2002-01-01

In metazoans, splicing of introns from pre-mRNAs can occur by two pathways: the major U2-dependent or the minor U12-dependent pathways. Whereas the U2-dependent pathway has been well characterized, much about the U12-dependent pathway remains to be discovered. Most of the information regarding U12-type introns has come from in vitro studies of a very few known introns of this class. To expand our understanding of U12-type splicing, especially to test the hypothesis that the simple base-pairing mechanism between the intron and U12 snRNA defines the branchpoint of U12-dependent introns, additional in vitro splicing substrates were created from three putative U12-type introns: the third intron of the Xenopus RPL1 a gene (XRP), the sixth intron of the Xenopus TFIIS.oA gene (XTF), and the first intron of the human Sm E gene (SME). In vitro splicing in HeLa nuclear extract confirmed U12-dependent splicing of each of these introns. Surprisingly, branchpoint mapping of the XRP splicing intermediate shows use of the upstream rather than the downstream of two consecutive adenosines within the branchpoint sequence (BPS), contrary to the prediction based on alignment with the sixth intron of human P120, a U12-dependent intron whose branch site was previously determined. Also, in the SME intron, the position of the branchpoint A residue within the region base paired with U12 differs from that in P120 and XTF. Analysis of these three additional introns therefore rules out simple models for branchpoint selection by the U12-type spliceosome. PMID:12022225

Application of the weighted-density approximation to the accurate description of electron-positron correlation effects in materials

NASA Astrophysics Data System (ADS)

Callewaert, Vincent; Saniz, Rolando; Barbiellini, Bernardo; Bansil, Arun; Partoens, Bart

2017-08-01

We discuss positron-annihilation lifetimes for a set of illustrative bulk materials within the framework of the weighted-density approximation (WDA). The WDA can correctly describe electron-positron correlations in strongly inhomogeneous systems, such as surfaces, where the applicability of (semi-)local approximations is limited. We analyze the WDA in detail and show that the electrons which cannot screen external charges efficiently, such as the core electrons, cannot be treated accurately via the pair correlation of the homogeneous electron gas. We discuss how this problem can be addressed by reducing the screening in the homogeneous electron gas by adding terms depending on the gradient of the electron density. Further improvements are obtained when core electrons are treated within the LDA and the valence electron using the WDA. Finally, we discuss a semiempirical WDA-based approach in which a sum rule is imposed to reproduce the experimental lifetimes.

Fuzzy logic particle tracking velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.

1993-01-01

Fuzzy logic has proven to be a simple and robust method for process control. Instead of requiring a complex model of the system, a user defined rule base is used to control the process. In this paper the principles of fuzzy logic control are applied to Particle Tracking Velocimetry (PTV). Two frames of digitally recorded, single exposure particle imagery are used as input. The fuzzy processor uses the local particle displacement information to determine the correct particle tracks. Fuzzy PTV is an improvement over traditional PTV techniques which typically require a sequence (greater than 2) of image frames for accurately tracking particles. The fuzzy processor executes in software on a PC without the use of specialized array or fuzzy logic processors. A pair of sample input images with roughly 300 particle images each, results in more than 200 velocity vectors in under 8 seconds of processing time.

Accelerated exploration of multi-principal element alloys with solid solution phases

PubMed Central

Senkov, O.N.; Miller, J.D.; Miracle, D.B.; Woodward, C.

2015-01-01

Recent multi-principal element, high entropy alloy (HEA) development strategies vastly expand the number of candidate alloy systems, but also pose a new challenge—how to rapidly screen thousands of candidate alloy systems for targeted properties. Here we develop a new approach to rapidly assess structural metals by combining calculated phase diagrams with simple rules based on the phases present, their transformation temperatures and useful microstructures. We evaluate over 130,000 alloy systems, identifying promising compositions for more time-intensive experimental studies. We find the surprising result that solid solution alloys become less likely as the number of alloy elements increases. This contradicts the major premise of HEAs—that increased configurational entropy increases the stability of disordered solid solution phases. As the number of elements increases, the configurational entropy rises slowly while the probability of at least one pair of elements favouring formation of intermetallic compounds increases more rapidly, explaining this apparent contradiction. PMID:25739749

A Variational Statistical-Field Theory for Polar Liquid Mixtures

NASA Astrophysics Data System (ADS)

Zhuang, Bilin; Wang, Zhen-Gang

Using a variational field-theoretic approach, we derive a molecularly-based theory for polar liquid mixtures. The resulting theory consists of simple algebraic expressions for the free energy of mixing and the dielectric constant as functions of mixture composition. Using only the dielectric constants and the molar volumes of the pure liquid constituents, the theory evaluates the mixture dielectric constants in good agreement with the experimental values for a wide range of liquid mixtures, without using adjustable parameters. In addition, the theory predicts that liquids with similar dielectric constants and molar volumes dissolve well in each other, while sufficient disparity in these parameters result in phase separation. The calculated miscibility map on the dielectric constant-molar volume axes agrees well with known experimental observations for a large number of liquid pairs. Thus the theory provides a quantification for the well-known empirical ``like-dissolves-like'' rule. Bz acknowledges the A-STAR fellowship for the financial support.

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

Okutsu, N.; Shimamura, K.; Shimizu, E.

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-Cmore » base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.« less

RANWAR: rank-based weighted association rule mining from gene expression and methylation data.

PubMed

Mallik, Saurav; Mukhopadhyay, Anirban; Maulik, Ujjwal

2015-01-01

Ranking of association rules is currently an interesting topic in data mining and bioinformatics. The huge number of evolved rules of items (or, genes) by association rule mining (ARM) algorithms makes confusion to the decision maker. In this article, we propose a weighted rule-mining technique (say, RANWAR or rank-based weighted association rule-mining) to rank the rules using two novel rule-interestingness measures, viz., rank-based weighted condensed support (wcs) and weighted condensed confidence (wcc) measures to bypass the problem. These measures are basically depended on the rank of items (genes). Using the rank, we assign weight to each item. RANWAR generates much less number of frequent itemsets than the state-of-the-art association rule mining algorithms. Thus, it saves time of execution of the algorithm. We run RANWAR on gene expression and methylation datasets. The genes of the top rules are biologically validated by Gene Ontologies (GOs) and KEGG pathway analyses. Many top ranked rules extracted from RANWAR that hold poor ranks in traditional Apriori, are highly biologically significant to the related diseases. Finally, the top rules evolved from RANWAR, that are not in Apriori, are reported.

Observation of χ c1 Decays into Vector Meson Pairs ΦΦ, ωω and, ωΦ

DOE PAGES

Ablikim, M.; Achasov, M. N.; An, L.; ...

2011-08-22

Using (106±4)×10⁶ ψ(3686) events accumulated with the BESIII detector at the BEPCII e⁺e⁻ collider, we present the first measurement of decays of χ c1 to vector meson pairs ΦΦ, ωω, and ωΦ. The branching fractions are measured to be (4.4±0.3±0.5)×10⁻⁴, (6.0±0.3±0.7)×10⁻⁴, and (2.2±0.6±0.2)×10⁻⁵, for χ c1 →ΦΦ, ωω, and ωΦ, respectively, which indicates that the hadron helicity selection rule is significantly violated in χ cJ decays. In addition, the measurement of χ cJ→ωΦ provides the first indication of the rate of doubly OZI-suppressed χ cJ decay. Finally, we present improved measurements for the branching fractions of χ c0 and χmore » c2 to vector meson pairs.« less

Observation of {chi}{sub c1} Decays into Vector Meson Pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}

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

Ablikim, M.; An, Z. H.; Bai, J. Z.

Using (106{+-}4)x10{sup 6} {psi}(3686) events accumulated with the BESIII detector at the BEPCII e{sup +}e{sup -} collider, we present the first measurement of decays of {chi}{sub c1} to vector meson pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}. The branching fractions are measured to be (4.4{+-}0.3{+-}0.5)x10{sup -4}, (6.0{+-}0.3{+-}0.7)x10{sup -4}, and (2.2{+-}0.6{+-}0.2)x10{sup -5}, for {chi}{sub c1}{yields}{phi}{phi}, {omega}{omega}, and {omega}{phi}, respectively, which indicates that the hadron helicity selection rule is significantly violated in {chi}{sub cJ} decays. In addition, the measurement of {chi}{sub cJ}{yields}{omega}{phi} provides the first indication of the rate of doubly OZI-suppressed {chi}{sub cJ} decay. Finally, we present improved measurements for the branching fractionsmore » of {chi}{sub c0} and {chi}{sub c2} to vector meson pairs.« less

Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors

PubMed Central

2018-01-01

ABSTRACT Long-germ insects, such as the fruit fly Drosophila melanogaster, pattern their segments simultaneously, whereas short-germ insects, such as the beetle Tribolium castaneum, pattern their segments sequentially, from anterior to posterior. Although the two modes of segmentation at first appear quite distinct, much of this difference might simply reflect developmental heterochrony. We now show here that, in both Drosophila and Tribolium, segment patterning occurs within a common framework of sequential Caudal, Dichaete and Odd-paired expression. In Drosophila, these transcription factors are expressed like simple timers within the blastoderm, whereas in Tribolium they form wavefronts that sweep from anterior to posterior across the germband. In Drosophila, all three are known to regulate pair-rule gene expression and influence the temporal progression of segmentation. We propose that these regulatory roles are conserved in short-germ embryos, and that therefore the changing expression profiles of these genes across insects provide a mechanistic explanation for observed differences in the timing of segmentation. In support of this hypothesis, we demonstrate that Odd-paired is essential for segmentation in Tribolium, contrary to previous reports. PMID:29724758

Electron—phonon Coupling and the Superconducting Phase Diagram of the LaAlO3—SrTiO3 Interface

PubMed Central

Boschker, Hans; Richter, Christoph; Fillis-Tsirakis, Evangelos; Schneider, Christof W.; Mannhart, Jochen

2015-01-01

The superconductor at the LaAlO3—SrTiO3 interface provides a model system for the study of two-dimensional superconductivity in the dilute carrier density limit. Here we experimentally address the pairing mechanism in this superconductor. We extract the electron—phonon spectral function from tunneling spectra and conclude, without ruling out contributions of further pairing channels, that electron—phonon mediated pairing is strong enough to account for the superconducting critical temperatures. Furthermore, we discuss the electron—phonon coupling in relation to the superconducting phase diagram. The electron—phonon spectral function is independent of the carrier density, except for a small part of the phase diagram in the underdoped region. The tunneling measurements reveal that the increase of the chemical potential with increasing carrier density levels off and is zero in the overdoped region of the phase diagram. This indicates that the additionally induced carriers do not populate the band that hosts the superconducting state and that the superconducting order parameter therefore is weakened by the presence of charge carriers in another band. PMID:26169351

Helping enhances productivity in campo flicker ( Colaptes campestris) cooperative groups

NASA Astrophysics Data System (ADS)

Dias, Raphael Igor; Webster, Michael S.; Macedo, Regina H.

2015-06-01

Reproductive adults in many bird species are assisted by non-breeding auxiliary helpers at the nest, yet the impact of auxiliaries on reproduction is variable and not always obvious. In this study, we tested Hamilton's rule and evaluated the effect of auxiliaries on productivity in the facultative cooperative breeder campo flicker ( Colaptes campestris campestris). Campo flickers have a variable mating system, with some groups having auxiliaries and others lacking them (i.e., unassisted pairs). Most auxiliaries are closely related to the breeding pair (primary auxiliaries), but some auxiliaries (secondary auxiliaries) are unrelated females that joined established groups. We found no effect of breeder quality (body condition) or territory quality (food availability) on group productivity, but the presence of auxiliaries increased the number of fledglings produced relative to unassisted pairs. Nonetheless, the indirect benefit of helping was small and did not outweigh the costs of delayed breeding and so seemed insufficient to explain the evolution of cooperative breeding in campo flickers. We concluded that some ecological constraints must limit dispersal or independent breeding, making staying in the group a "best-of-a-bad-job" situation for auxiliaries.

Helping enhances productivity in campo flicker (Colaptes campestris) cooperative groups.

PubMed

Dias, Raphael Igor; Webster, Michael S; Macedo, Regina H

2015-06-01

Reproductive adults in many bird species are assisted by non-breeding auxiliary helpers at the nest, yet the impact of auxiliaries on reproduction is variable and not always obvious. In this study, we tested Hamilton's rule and evaluated the effect of auxiliaries on productivity in the facultative cooperative breeder campo flicker (Colaptes campestris campestris). Campo flickers have a variable mating system, with some groups having auxiliaries and others lacking them (i.e., unassisted pairs). Most auxiliaries are closely related to the breeding pair (primary auxiliaries), but some auxiliaries (secondary auxiliaries) are unrelated females that joined established groups. We found no effect of breeder quality (body condition) or territory quality (food availability) on group productivity, but the presence of auxiliaries increased the number of fledglings produced relative to unassisted pairs. Nonetheless, the indirect benefit of helping was small and did not outweigh the costs of delayed breeding and so seemed insufficient to explain the evolution of cooperative breeding in campo flickers. We concluded that some ecological constraints must limit dispersal or independent breeding, making staying in the group a "best-of-a-bad-job" situation for auxiliaries.

Development of a tunable diode laser sensor for measurements of gas turbine exhaust temperature

NASA Astrophysics Data System (ADS)

Liu, X.; Jeffries, J. B.; Hanson, R. K.; Hinckley, K. M.; Woodmansee, M. A.

2006-03-01

A tunable diode laser (TDL) temperature sensor is designed, constructed, tested, and demonstrated in the exhaust of an industrial gas turbine. Temperature is determined from the ratio of the measured absorbance of two water vapor overtone transitions in the near infrared where telecommunication diode lasers are available. Design rules are developed to select the optimal pair of transitions for direct absorption measurements using spectral simulations by systematically examining the absorption strength, spectral isolation, and temperature sensitivity to maximize temperature accuracy in the core flow and minimize sensitivity to water vapor in the cold boundary layer. The contribution to temperature uncertainty from the spectroscopic database is evaluated and precise line-strength data are measured for the selected transitions. Gas-temperature measurements in a heated cell are used to verify the sensor accuracy (over the temperature range of 350 to 1000 K, ΔT˜2 K for the optimal line pair and ΔT˜5 K for an alternative line pair). Field measurements of exhaust-gas temperature in an industrial gas turbine demonstrate the practical utility of TDL sensing in harsh industrial environments.

Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism

PubMed Central

Yusupov, Marat; Yusupova, Gulnara

2014-01-01

The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes. PMID:24765524

A geometric constraint, the head-to-tail exclusion rule, may be the basis for the isolated-pentagon rule in fullerenes with more than 60 vertices

PubMed Central

Schein, Stan; Friedrich, Tara

2008-01-01

Carbon atoms self-assemble into the famous soccer-ball shaped Buckminsterfullerene (C60), the smallest fullerene cage that obeys the isolated-pentagon rule (IPR). Carbon atoms self-assemble into larger (n > 60 vertices) empty cages as well—but only the few that obey the IPR—and at least 1 small fullerene (n ≤ 60) with adjacent pentagons. Clathrin protein also self-assembles into small fullerene cages with adjacent pentagons, but just a few of those. We asked why carbon atoms and clathrin proteins self-assembled into just those IPR and small cage isomers. In answer, we described a geometric constraint—the head-to-tail exclusion rule—that permits self-assembly of just the following fullerene cages: among the 5,769 possible small cages (n ≤ 60 vertices) with adjacent pentagons, only 15; the soccer ball (n = 60); and among the 216,739 large cages with 60 < n ≤ 84 vertices, only the 50 IPR ones. The last finding was a complete surprise. Here, by showing that the largest permitted fullerene with adjacent pentagons is one with 60 vertices and a ring of interleaved hexagons and pentagon pairs, we prove that for all n > 60, the head-to-tail exclusion rule permits only (and all) fullerene cages and nanotubes that obey the IPR. We therefore suggest that self-assembly that obeys the IPR may be explained by the head-to-tail exclusion rule, a geometric constraint. PMID:19050075

Rule acquisition in formal decision contexts based on formal, object-oriented and property-oriented concept lattices.

PubMed

Ren, Yue; Li, Jinhai; Aswani Kumar, Cherukuri; Liu, Wenqi

2014-01-01

Rule acquisition is one of the main purposes in the analysis of formal decision contexts. Up to now, there have been several types of rules in formal decision contexts such as decision rules, decision implications, and granular rules, which can be viewed as ∧-rules since all of them have the following form: "if conditions 1,2,…, and m hold, then decisions hold." In order to enrich the existing rule acquisition theory in formal decision contexts, this study puts forward two new types of rules which are called ∨-rules and ∨-∧ mixed rules based on formal, object-oriented, and property-oriented concept lattices. Moreover, a comparison of ∨-rules, ∨-∧ mixed rules, and ∧-rules is made from the perspectives of inclusion and inference relationships. Finally, some real examples and numerical experiments are conducted to compare the proposed rule acquisition algorithms with the existing one in terms of the running efficiency.

Rule Acquisition in Formal Decision Contexts Based on Formal, Object-Oriented and Property-Oriented Concept Lattices

PubMed Central

Ren, Yue; Aswani Kumar, Cherukuri; Liu, Wenqi

2014-01-01

Rule acquisition is one of the main purposes in the analysis of formal decision contexts. Up to now, there have been several types of rules in formal decision contexts such as decision rules, decision implications, and granular rules, which can be viewed as ∧-rules since all of them have the following form: “if conditions 1,2,…, and m hold, then decisions hold.” In order to enrich the existing rule acquisition theory in formal decision contexts, this study puts forward two new types of rules which are called ∨-rules and ∨-∧ mixed rules based on formal, object-oriented, and property-oriented concept lattices. Moreover, a comparison of ∨-rules, ∨-∧ mixed rules, and ∧-rules is made from the perspectives of inclusion and inference relationships. Finally, some real examples and numerical experiments are conducted to compare the proposed rule acquisition algorithms with the existing one in terms of the running efficiency. PMID:25165744

Technetium: The First Radioelement on the Periodic Table

DOE PAGES

Johnstone, Erik V.; Yates, Mary Anne; Poineau, Frederic; ...

2017-02-21

The radioactive nature of technetium is discussed using a combination of introductory nuclear physics concepts and empirical trends observed in the chart of the nuclides and the periodic table of the elements. Trends such as the enhanced stability of nucleon pairs, magic numbers, and Mattauch's rule are described. Here, the concepts of nuclear binding energies and the nuclear shell model are introduced and used to explain the relative stability of radionuclides and, in particular, the isotopes of technetium.

Group Centric Information Sharing Using Hierarchical Models

DTIC Science & Technology

2011-01-01

enable people to create data using RDF, build vocabularies using web ontology language (OWL), write rules and query data stores using SPARQL [8...a strict joined and the document was added with a strict add. In order to represent the fact that an action is allowed (or not), we have created a...greatly improve the system’s readiness to handle any number of access decision queries . a. The pair is tested against the gSIS Join and Add semantics

Comparison of the Structure and Expression of Odd-Skipped and Two Related Genes That Encode a New Family of Zinc Finger Proteins in Drosophila

PubMed Central

Hart, M. C.; Wang, L.; Coulter, D. E.

1996-01-01

The odd-skipped (odd) gene, which was identified on the basis of a pair-rule segmentation phenotype in mutant embryos, is initially expressed in the Drosophila embryo in seven pair-rule stripes, but later exhibits a segment polarity-like pattern for which no phenotypic correlate is apparent. We have molecularly characterized two embryonically expressed odd-cognate genes, sob and bowel (bowl), that encode proteins with highly conserved C(2)H(2) zinc fingers. While the Sob and Bowl proteins each contain five tandem fingers, the Odd protein lacks a fifth (C-terminal) finger and is also less conserved among the four common fingers. Reminiscent of many segmentation gene paralogues, the closely linked odd and sob genes are expressed during embryogenesis in similar striped patterns; in contrast, the less-tightly linked bowl gene is expressed in a distinctly different pattern at the termini of the early embryo. Although our results indicate that odd and sob are more likely than bowl to share overlapping developmental roles, some functional divergence between the Odd and Sob proteins is suggested by the absence of homology outside the zinc fingers, and also by amino acid substitutions in the Odd zinc fingers at positions that appear to be constrained in Sob and Bowl. PMID:8878683

Optimizing Noble Gas-Water Interactions via Monte Carlo Simulations.

PubMed

Warr, Oliver; Ballentine, Chris J; Mu, Junju; Masters, Andrew

2015-11-12

In this work we present optimized noble gas-water Lennard-Jones 6-12 pair potentials for each noble gas. Given the significantly different atomic nature of water and the noble gases, the standard Lorentz-Berthelot mixing rules produce inaccurate unlike molecular interactions between these two species. Consequently, we find simulated Henry's coefficients deviate significantly from their experimental counterparts for the investigated thermodynamic range (293-353 K at 1 and 10 atm), due to a poor unlike potential well term (εij). Where εij is too high or low, so too is the strength of the resultant noble gas-water interaction. This observed inadequacy in using the Lorentz-Berthelot mixing rules is countered in this work by scaling εij for helium, neon, argon, and krypton by factors of 0.91, 0.8, 1.1, and 1.05, respectively, to reach a much improved agreement with experimental Henry's coefficients. Due to the highly sensitive nature of the xenon εij term, coupled with the reasonable agreement of the initial values, no scaling factor is applied for this noble gas. These resulting optimized pair potentials also accurately predict partitioning within a CO2-H2O binary phase system as well as diffusion coefficients in ambient water. This further supports the quality of these interaction potentials. Consequently, they can now form a well-grounded basis for the future molecular modeling of multiphase geological systems.

Simulating water markets with transaction costs

NASA Astrophysics Data System (ADS)

Erfani, Tohid; Binions, Olga; Harou, Julien J.

2014-06-01

This paper presents an optimization model to simulate short-term pair-wise spot-market trading of surface water abstraction licenses (water rights). The approach uses a node-arc multicommodity formulation that tracks individual supplier-receiver transactions in a water resource network. This enables accounting for transaction costs between individual buyer-seller pairs and abstractor-specific rules and behaviors using constraints. Trades are driven by economic demand curves that represent each abstractor's time-varying water demand. The purpose of the proposed model is to assess potential hydrologic and economic outcomes of water markets and aid policy makers in designing water market regulations. The model is applied to the Great Ouse River basin in Eastern England. The model assesses the potential weekly water trades and abstractions that could occur in a normal and a dry year. Four sectors (public water supply, energy, agriculture, and industrial) are included in the 94 active licensed water diversions. Each license's unique environmental restrictions are represented and weekly economic water demand curves are estimated. Rules encoded as constraints represent current water management realities and plausible stakeholder-informed water market behaviors. Results show buyers favor sellers who can supply large volumes to minimize transactions. The energy plant cooling and agricultural licenses, often restricted from obtaining water at times when it generates benefits, benefit most from trades. Assumptions and model limitations are discussed. This article was corrected on 13 JUN 2014. See the end of the full text for details.

When More Is Less: Feedback Effects in Perceptual Category Learning

ERIC Educational Resources Information Center

Maddox, W. Todd; Love, Bradley C.; Glass, Brian D.; Filoteo, J. Vincent

2008-01-01

Rule-based and information-integration category learning were compared under minimal and full feedback conditions. Rule-based category structures are those for which the optimal rule is verbalizable. Information-integration category structures are those for which the optimal rule is not verbalizable. With minimal feedback subjects are told whether…

Movement rules for individual-based models of stream fish

Treesearch

Steven F. Railsback; Roland H. Lamberson; Bret C. Harvey; Walter E. Duffy

1999-01-01

Abstract - Spatially explicit individual-based models (IBMs) use movement rules to determine when an animal departs its current location and to determine its movement destination; these rules are therefore critical to accurate simulations. Movement rules typically define some measure of how an individual's expected fitness varies among locations, under the...

Extending rule-based methods to model molecular geometry and 3D model resolution.

PubMed

Hoard, Brittany; Jacobson, Bruna; Manavi, Kasra; Tapia, Lydia

2016-08-01

Computational modeling is an important tool for the study of complex biochemical processes associated with cell signaling networks. However, it is challenging to simulate processes that involve hundreds of large molecules due to the high computational cost of such simulations. Rule-based modeling is a method that can be used to simulate these processes with reasonably low computational cost, but traditional rule-based modeling approaches do not include details of molecular geometry. The incorporation of geometry into biochemical models can more accurately capture details of these processes, and may lead to insights into how geometry affects the products that form. Furthermore, geometric rule-based modeling can be used to complement other computational methods that explicitly represent molecular geometry in order to quantify binding site accessibility and steric effects. We propose a novel implementation of rule-based modeling that encodes details of molecular geometry into the rules and binding rates. We demonstrate how rules are constructed according to the molecular curvature. We then perform a study of antigen-antibody aggregation using our proposed method. We simulate the binding of antibody complexes to binding regions of the shrimp allergen Pen a 1 using a previously developed 3D rigid-body Monte Carlo simulation, and we analyze the aggregate sizes. Then, using our novel approach, we optimize a rule-based model according to the geometry of the Pen a 1 molecule and the data from the Monte Carlo simulation. We use the distances between the binding regions of Pen a 1 to optimize the rules and binding rates. We perform this procedure for multiple conformations of Pen a 1 and analyze the impact of conformation and resolution on the optimal rule-based model. We find that the optimized rule-based models provide information about the average steric hindrance between binding regions and the probability that antibodies will bind to these regions. These optimized models quantify the variation in aggregate size that results from differences in molecular geometry and from model resolution.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

PubMed

Misirli, Goksel; Cavaliere, Matteo; Waites, William; Pocock, Matthew; Madsen, Curtis; Gilfellon, Owen; Honorato-Zimmer, Ricardo; Zuliani, Paolo; Danos, Vincent; Wipat, Anil

2016-03-15

Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf anil.wipat@newcastle.ac.uk or vdanos@inf.ed.ac.uk. © The Author 2015. Published by Oxford University Press.

Optical tuning of electronic valleys (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sie, Edbert J.; Gedik, Nuh

2017-02-01

Monolayer transition-metal dichalcogenides such as MoS2 and WS2 are prime examples of atomically thin semiconducting crystals that exhibit remarkable electronic and optical properties. They have a pair of valleys that can serve as a new electronic degree of freedom, and these valleys obey optical selection rules with circularly polarized light. Here, we discuss how ultrafast laser pulses can be used to tune their energy levels in a controllable valley-selective manner. The energy tunability is extremely large, comparable to what would be obtained using a hundred Tesla of magnetic field. We will also show that such valley tunability can be performed while we effectively manipulate the valley selection rules. Finally, we will explore the prospect of using this technique through photoemission spectroscopy to create a new phase of matter called a valley Floquet topological insulator.

Obtaining tight bounds on higher-order interferences with a 5-path interferometer

NASA Astrophysics Data System (ADS)

Kauten, Thomas; Keil, Robert; Kaufmann, Thomas; Pressl, Benedikt; Brukner, Časlav; Weihs, Gregor

2017-03-01

Within the established theoretical framework of quantum mechanics, interference always occurs between pairs of paths through an interferometer. Higher order interferences with multiple constituents are excluded by Born’s rule and can only exist in generalized probabilistic theories. Thus, high-precision experiments searching for such higher order interferences are a powerful method to distinguish between quantum mechanics and more general theories. Here, we perform such a test in an optical multi-path interferometer, which avoids crucial systematic errors, has access to the entire phase space and is more stable than previous experiments. Our results are in accordance with quantum mechanics and rule out the existence of higher order interference terms in optical interferometry to an extent that is more than four orders of magnitude smaller than the expected pairwise interference, refining previous bounds by two orders of magnitude.

Model of wealth and goods dynamics in a closed market

NASA Astrophysics Data System (ADS)

Ausloos, Marcel; Peķalski, Andrzej

2007-01-01

A simple computer simulation model of a closed market on a fixed network with free flow of goods and money is introduced. The model contains only two variables: the amount of goods and money beside the size of the system. An initially flat distribution of both variables is presupposed. We show that under completely random rules, i.e. through the choice of interacting agent pairs on the network and of the exchange rules that the market stabilizes in time and shows diversification of money and goods. We also indicate that the difference between poor and rich agents increases for small markets, as well as for systems in which money is steadily deduced from the market through taxation. It is also found that the price of goods decreases when taxes are introduced, likely due to the less availability of money.

Higher Rates of DZ Twinning in a Twenty-First Century Birth Cohort.

PubMed

Rhea, Sally Ann; Corley, Robin P; Heath, Andrew C; Iacono, William G; Neale, Michael C; Hewitt, John K

2017-09-01

The Colorado Twin Registry is a population based registry initiated in 1984 with the involvement of the Colorado Department of Health, Division of Vital Statistics. Recruitment includes birth cohorts several years prior to 1984 and all subsequent years. As part of a recent evaluation of Colorado birth records for the years 2006 through 2008 we became aware of a shifting trend in the proportion of MZ and DZ twins in the Colorado population. Historically (Bulmer 1970 The biology of twinning in man, Clarendon, Oxford) we have expected a 1/3, 1/3, 1/3 ratio of MZ, same-sex DZ and opposite sex DZ twins in Caucasian populations. An excess of MZ pairs in most studies was assumed to be due to selection bias. Somewhat more recently, Hur et al.(1995 Behav Genet 25, 337-340) provided evidence that the DZ twinning rate was falling and that therefore selection bias was not the reason for higher MZ enrollment in most twin studies. They suggested that twin researchers might consider strategies to over-enroll DZ pairs to maximize statistical power. In contrast, we now find that of the 3217 twin births in Colorado from 2006 to 2008 with identified sex information the MZ rate is estimated at only 22%, and we have corroborating reports from other states of similar estimates. These were calculated applying Weinberg's rule which assumes an equal birth rate for same sex and opposite sex DZ pairs so that the proportion of MZ in a sample is the proportion of same sex (MM + FF) minus the proportion of opposite-sex (MF, FM). We explore factors, such as an increase in the proportion of non-Caucasian parents and an increase in average maternal age, which may contribute to this shift.

Generalized interpretation scheme for arbitrary HR InSAR image pairs

NASA Astrophysics Data System (ADS)

Boldt, Markus; Thiele, Antje; Schulz, Karsten

2013-10-01

Land cover classification of remote sensing imagery is an important topic of research. For example, different applications require precise and fast information about the land cover of the imaged scenery (e.g., disaster management and change detection). Focusing on high resolution (HR) spaceborne remote sensing imagery, the user has the choice between passive and active sensor systems. Passive systems, such as multispectral sensors, have the disadvantage of being dependent from weather influences (fog, dust, clouds, etc.) and time of day, since they work in the visible part of the electromagnetic spectrum. Here, active systems like Synthetic Aperture Radar (SAR) provide improved capabilities. As an interactive method analyzing HR InSAR image pairs, the CovAmCohTM method was introduced in former studies. CovAmCoh represents the joint analysis of locality (coefficient of variation - Cov), backscatter (amplitude - Am) and temporal stability (coherence - Coh). It delivers information on physical backscatter characteristics of imaged scene objects or structures and provides the opportunity to detect different classes of land cover (e.g., urban, rural, infrastructure and activity areas). As example, railway tracks are easily distinguishable from other infrastructure due to their characteristic bluish coloring caused by the gravel between the sleepers. In consequence, imaged objects or structures have a characteristic appearance in CovAmCoh images which allows the development of classification rules. In this paper, a generalized interpretation scheme for arbitrary InSAR image pairs using the CovAmCoh method is proposed. This scheme bases on analyzing the information content of typical CovAmCoh imagery using the semisupervised k-means clustering. It is shown that eight classes model the main local information content of CovAmCoh images sufficiently and can be used as basis for a classification scheme.

Common-Sense Rule Inference

NASA Astrophysics Data System (ADS)

Lombardi, Ilaria; Console, Luca

In the paper we show how rule-based inference can be made more flexible by exploiting semantic information associated with the concepts involved in the rules. We introduce flexible forms of common sense reasoning in which whenever no rule applies to a given situation, the inference engine can fire rules that apply to more general or to similar situations. This can be obtained by defining new forms of match between rules and the facts in the working memory and new forms of conflict resolution. We claim that in this way we can overcome some of the brittleness problems that are common in rule-based systems.

Rule-Based Event Processing and Reaction Rules

NASA Astrophysics Data System (ADS)

Paschke, Adrian; Kozlenkov, Alexander

Reaction rules and event processing technologies play a key role in making business and IT / Internet infrastructures more agile and active. While event processing is concerned with detecting events from large event clouds or streams in almost real-time, reaction rules are concerned with the invocation of actions in response to events and actionable situations. They state the conditions under which actions must be taken. In the last decades various reaction rule and event processing approaches have been developed, which for the most part have been advanced separately. In this paper we survey reaction rule approaches and rule-based event processing systems and languages.

Efficiency in Rule- vs. Plan-Based Movements Is Modulated by Action-Mode

PubMed Central

Scheib, Jean P. P.; Stoll, Sarah; Thürmer, J. Lukas; Randerath, Jennifer

2018-01-01

The rule/plan motor cognition (RPMC) paradigm elicits visually indistinguishable motor outputs, resulting from either plan- or rule-based action-selection, using a combination of essentially interchangeable stimuli. Previous implementations of the RPMC paradigm have used pantomimed movements to compare plan- vs. rule-based action-selection. In the present work we attempt to determine the generalizability of previous RPMC findings to real object interaction by use of a grasp-to-rotate task. In the plan task, participants had to use prospective planning to achieve a comfortable post-handle rotation hand posture. The rule task used implementation intentions (if-then rules) leading to the same comfortable end-state. In Experiment A, we compare RPMC performance of 16 healthy participants in pantomime and real object conditions of the experiment, within-subjects. Higher processing efficiency of rule- vs. plan-based action-selection was supported by diffusion model analysis. Results show a significant response-time increase in the pantomime condition compared to the real object condition and a greater response-time advantage of rule-based vs. plan-based actions in the pantomime compared to the real object condition. In Experiment B, 24 healthy participants performed the real object RPMC task in a task switching vs. a blocked condition. Results indicate that plan-based action-selection leads to longer response-times and less efficient information processing than rule-based action-selection in line with previous RPMC findings derived from the pantomime action-mode. Particularly in the task switching mode, responses were faster in the rule compared to the plan task suggesting a modulating influence of cognitive load. Overall, results suggest an advantage of rule-based action-selection over plan-based action-selection; whereby differential mechanisms appear to be involved depending on the action-mode. We propose that cognitive load is a factor that modulates the advantageous effect of implementation intentions in motor cognition on different levels as illustrated by the varying speed advantages and the variation in diffusion parameters per action-mode or condition, respectively. PMID:29593612

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Traditional versus rule-based programming techniques - Application to the control of optional flight information

NASA Technical Reports Server (NTRS)

Ricks, Wendell R.; Abbott, Kathy H.

1987-01-01

A traditional programming technique for controlling the display of optional flight information in a civil transport cockpit is compared to a rule-based technique for the same function. This application required complex decision logic and a frequently modified rule base. The techniques are evaluated for execution efficiency and implementation ease; the criterion used to calculate the execution efficiency is the total number of steps required to isolate hypotheses that were true and the criteria used to evaluate the implementability are ease of modification and verification and explanation capability. It is observed that the traditional program is more efficient than the rule-based program; however, the rule-based programming technique is more applicable for improving programmer productivity.

On the fusion of tuning parameters of fuzzy rules and neural network

NASA Astrophysics Data System (ADS)

Mamuda, Mamman; Sathasivam, Saratha

2017-08-01

Learning fuzzy rule-based system with neural network can lead to a precise valuable empathy of several problems. Fuzzy logic offers a simple way to reach at a definite conclusion based upon its vague, ambiguous, imprecise, noisy or missing input information. Conventional learning algorithm for tuning parameters of fuzzy rules using training input-output data usually end in a weak firing state, this certainly powers the fuzzy rule and makes it insecure for a multiple-input fuzzy system. In this paper, we introduce a new learning algorithm for tuning the parameters of the fuzzy rules alongside with radial basis function neural network (RBFNN) in training input-output data based on the gradient descent method. By the new learning algorithm, the problem of weak firing using the conventional method was addressed. We illustrated the efficiency of our new learning algorithm by means of numerical examples. MATLAB R2014(a) software was used in simulating our result The result shows that the new learning method has the best advantage of training the fuzzy rules without tempering with the fuzzy rule table which allowed a membership function of the rule to be used more than one time in the fuzzy rule base.

Sequence dependency of canonical base pair opening in the DNA double helix

PubMed Central

Villa, Alessandra

2017-01-01

The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. PMID:28369121

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases.

PubMed

Song, Qi-Xia; Ding, Zhen-Dong; Liu, Jian-Hua; Li, Yan; Wang, Hai-Jun

2013-03-01

N6-methyladenine (m(6)A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH(3). Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m(6)A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH(3) changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m(6)A:G and trans-m(6)A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m(6)A to cis-m(6)A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m(6)A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

Bootstrapping language acquisition.

PubMed

Abend, Omri; Kwiatkowski, Tom; Smith, Nathaniel J; Goldwater, Sharon; Steedman, Mark

2017-07-01

The semantic bootstrapping hypothesis proposes that children acquire their native language through exposure to sentences of the language paired with structured representations of their meaning, whose component substructures can be associated with words and syntactic structures used to express these concepts. The child's task is then to learn a language-specific grammar and lexicon based on (probably contextually ambiguous, possibly somewhat noisy) pairs of sentences and their meaning representations (logical forms). Starting from these assumptions, we develop a Bayesian probabilistic account of semantically bootstrapped first-language acquisition in the child, based on techniques from computational parsing and interpretation of unrestricted text. Our learner jointly models (a) word learning: the mapping between components of the given sentential meaning and lexical words (or phrases) of the language, and (b) syntax learning: the projection of lexical elements onto sentences by universal construction-free syntactic rules. Using an incremental learning algorithm, we apply the model to a dataset of real syntactically complex child-directed utterances and (pseudo) logical forms, the latter including contextually plausible but irrelevant distractors. Taking the Eve section of the CHILDES corpus as input, the model simulates several well-documented phenomena from the developmental literature. In particular, the model exhibits syntactic bootstrapping effects (in which previously learned constructions facilitate the learning of novel words), sudden jumps in learning without explicit parameter setting, acceleration of word-learning (the "vocabulary spurt"), an initial bias favoring the learning of nouns over verbs, and one-shot learning of words and their meanings. The learner thus demonstrates how statistical learning over structured representations can provide a unified account for these seemingly disparate phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Optical signature of Mg-doped GaN: Transfer processes

NASA Astrophysics Data System (ADS)

Callsen, G.; Wagner, M. R.; Kure, T.; Reparaz, J. S.; Bügler, M.; Brunnmeier, J.; Nenstiel, C.; Hoffmann, A.; Hoffmann, M.; Tweedie, J.; Bryan, Z.; Aygun, S.; Kirste, R.; Collazo, R.; Sitar, Z.

2012-08-01

Mg doping of high quality, metal organic chemical vapor deposition grown GaN films results in distinct traces in their photoluminescence and photoluminescence excitation spectra. We analyze GaN:Mg grown on sapphire substrates and identify two Mg related acceptor states, one additional acceptor state and three donor states that are involved in the donor-acceptor pair band transitions situated at 3.26-3.29 eV in GaN:Mg. The presented determination of the donor-acceptor pair band excitation channels by photoluminescence excitation spectroscopy in conjunction with temperature-dependent photoluminescence measurements results in a direct determination of the donor and acceptor binding, localization, and activation energies, which is put into a broader context based on Haynes's rule. Furthermore, we analyze the biexponential decay dynamics of the photoluminescence signal of the acceptor and donor bound excitons. As all observed lifetimes scale with the localization energy of the donor and acceptor related bound excitons, defect and complex bound excitons can be excluded as their origin. Detailed analysis of the exciton transfer processes in the close energetic vicinity of the GaN band edge reveals excitation via free and bound excitonic channels but also via an excited state as resolved for the deepest localized Mg related acceptor bound exciton. For the two Mg acceptor states, we determine binding energies of 164 ± 5 and 195 ± 5 meV, which is in good agreement with recent density functional theory results. This observation confirms and quantifies the general dual nature of acceptor states in GaN based on the presented analysis of the photoluminescence and photoluminescence excitation spectra.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs.

PubMed

McCoy, A B; Wright, A; Krousel-Wood, M; Thomas, E J; McCoy, J A; Sittig, D F

2015-01-01

Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

PubMed Central

Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

2015-01-01

Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

GraDit: graph-based data repair algorithm for multiple data edits rule violations

NASA Astrophysics Data System (ADS)

Ode Zuhayeni Madjida, Wa; Gusti Bagus Baskara Nugraha, I.

2018-03-01

Constraint-based data cleaning captures data violation to a set of rule called data quality rules. The rules consist of integrity constraint and data edits. Structurally, they are similar, where the rule contain left hand side and right hand side. Previous research proposed a data repair algorithm for integrity constraint violation. The algorithm uses undirected hypergraph as rule violation representation. Nevertheless, this algorithm can not be applied for data edits because of different rule characteristics. This study proposed GraDit, a repair algorithm for data edits rule. First, we use bipartite-directed hypergraph as model representation of overall defined rules. These representation is used for getting interaction between violation rules and clean rules. On the other hand, we proposed undirected graph as violation representation. Our experimental study showed that algorithm with undirected graph as violation representation model gave better data quality than algorithm with undirected hypergraph as representation model.

Target-Based Maintenance of Privacy Preserving Association Rules

ERIC Educational Resources Information Center

Ahluwalia, Madhu V.

2011-01-01

In the context of association rule mining, the state-of-the-art in privacy preserving data mining provides solutions for categorical and Boolean association rules but not for quantitative association rules. This research fills this gap by describing a method based on discrete wavelet transform (DWT) to protect input data privacy while preserving…

Combination Rules for Morse-Based van der Waals Force Fields.

PubMed

Yang, Li; Sun, Lei; Deng, Wei-Qiao

2018-02-15

In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

An expert system for natural language processing

NASA Technical Reports Server (NTRS)

Hennessy, John F.

1988-01-01

A solution to the natural language processing problem that uses a rule based system, written in OPS5, to replace the traditional parsing method is proposed. The advantage to using a rule based system are explored. Specifically, the extensibility of a rule based solution is discussed as well as the value of maintaining rules that function independently. Finally, the power of using semantics to supplement the syntactic analysis of a sentence is considered.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation

PubMed Central

2014-01-01

Introduction Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory or degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Methods Three multi-center genome-wide transcriptomic data sets (Affymetrix HG-U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule-based classifiers to discriminate the disease groups. The rules were ranked with respect to Kiendl’s statistical relevance index, and the resulting rule set was optimized by pruning. The rule sets were inferred separately from data of one of three centers and applied to the two remaining centers for validation. All rules from the optimized rule sets of all centers were used to analyze their biological relevance applying the software Pathway Studio. Results The optimized rule sets for the three centers contained a total of 29, 20, and 8 rules (including 10, 8, and 4 rules for ‘RA’), respectively. The mean sensitivity for the prediction of RA based on six center-to-center tests was 96% (range 90% to 100%), that for OA 86% (range 40% to 100%). The mean specificity for RA prediction was 94% (range 80% to 100%), that for OA 96% (range 83.3% to 100%). The average overall accuracy of the three different rule-based classifiers was 91% (range 80% to 100%). Unbiased analyses by Pathway Studio of the gene sets obtained by discrimination of RA from OA and CG with rule-based classifiers resulted in the identification of the pathogenetically and/or therapeutically relevant interferon-gamma and GM-CSF pathways. Conclusion First-time application of rule-based classifiers for the discrimination of RA resulted in high performance, with means for all assessment parameters close to or higher than 90%. In addition, this unbiased, new approach resulted in the identification not only of pathways known to be critical to RA, but also of novel molecules such as serine/threonine kinase 10. PMID:24690414

[Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

PubMed

Brovarets', O O

2013-01-01

At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

Association Rule-based Predictive Model for Machine Failure in Industrial Internet of Things

NASA Astrophysics Data System (ADS)

Kwon, Jung-Hyok; Lee, Sol-Bee; Park, Jaehoon; Kim, Eui-Jik

2017-09-01

This paper proposes an association rule-based predictive model for machine failure in industrial Internet of things (IIoT), which can accurately predict the machine failure in real manufacturing environment by investigating the relationship between the cause and type of machine failure. To develop the predictive model, we consider three major steps: 1) binarization, 2) rule creation, 3) visualization. The binarization step translates item values in a dataset into one or zero, then the rule creation step creates association rules as IF-THEN structures using the Lattice model and Apriori algorithm. Finally, the created rules are visualized in various ways for users’ understanding. An experimental implementation was conducted using R Studio version 3.3.2. The results show that the proposed predictive model realistically predicts machine failure based on association rules.

A logical model of cooperating rule-based systems

NASA Technical Reports Server (NTRS)

Bailin, Sidney C.; Moore, John M.; Hilberg, Robert H.; Murphy, Elizabeth D.; Bahder, Shari A.

1989-01-01

A model is developed to assist in the planning, specification, development, and verification of space information systems involving distributed rule-based systems. The model is based on an analysis of possible uses of rule-based systems in control centers. This analysis is summarized as a data-flow model for a hypothetical intelligent control center. From this data-flow model, the logical model of cooperating rule-based systems is extracted. This model consists of four layers of increasing capability: (1) communicating agents, (2) belief-sharing knowledge sources, (3) goal-sharing interest areas, and (4) task-sharing job roles.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

The neural basis for novel semantic categorization.

PubMed

Koenig, Phyllis; Smith, Edward E; Glosser, Guila; DeVita, Chris; Moore, Peachie; McMillan, Corey; Gee, Jim; Grossman, Murray

2005-01-15

We monitored regional cerebral activity with BOLD fMRI during acquisition of a novel semantic category and subsequent categorization of test stimuli by a rule-based strategy or a similarity-based strategy. We observed different patterns of activation in direct comparisons of rule- and similarity-based categorization. During rule-based category acquisition, subjects recruited anterior cingulate, thalamic, and parietal regions to support selective attention to perceptual features, and left inferior frontal cortex to helps maintain rules in working memory. Subsequent rule-based categorization revealed anterior cingulate and parietal activation while judging stimuli whose conformity with the rules was readily apparent, and left inferior frontal recruitment during judgments of stimuli whose conformity was less apparent. By comparison, similarity-based category acquisition showed recruitment of anterior prefrontal and posterior cingulate regions, presumably to support successful retrieval of previously encountered exemplars from long-term memory, and bilateral temporal-parietal activation for perceptual feature integration. Subsequent similarity-based categorization revealed temporal-parietal, posterior cingulate, and anterior prefrontal activation. These findings suggest that large-scale networks support relatively distinct categorization processes during the acquisition and judgment of semantic category knowledge.

Rule-based simulation models

NASA Technical Reports Server (NTRS)

Nieten, Joseph L.; Seraphine, Kathleen M.

1991-01-01

Procedural modeling systems, rule based modeling systems, and a method for converting a procedural model to a rule based model are described. Simulation models are used to represent real time engineering systems. A real time system can be represented by a set of equations or functions connected so that they perform in the same manner as the actual system. Most modeling system languages are based on FORTRAN or some other procedural language. Therefore, they must be enhanced with a reaction capability. Rule based systems are reactive by definition. Once the engineering system has been decomposed into a set of calculations using only basic algebraic unary operations, a knowledge network of calculations and functions can be constructed. The knowledge network required by a rule based system can be generated by a knowledge acquisition tool or a source level compiler. The compiler would take an existing model source file, a syntax template, and a symbol table and generate the knowledge network. Thus, existing procedural models can be translated and executed by a rule based system. Neural models can be provide the high capacity data manipulation required by the most complex real time models.

Thermal transport in topological-insulator-based superconducting hybrid structures with mixed singlet and triplet pairing states.

PubMed

Li, Hai; Zhao, Yuan Yuan

2017-11-22

In the framework of the Bogoliubov-de Gennes equation, we investigate the thermal transport properties in topological-insulator-based superconducting hybrid structures with mixed spin-singlet and spin-triplet pairing states, and emphasize the different manifestations of the spin-singlet and spin-triplet pairing states in the thermal transport signatures. It is revealed that the temperature-dependent differential thermal conductance strongly depends on the components of the pairing state, and the negative differential thermal conductance only occurs in the spin-singlet pairing state dominated regime. It is also found that the thermal conductance is profoundly sensitive to the components of the pairing state. In the spin-singlet pairing state controlled regime, the thermal conductance obviously oscillates with the phase difference and junction length. With increasing the proportion of the spin-triplet pairing state, the oscillating characteristic of the thermal conductance fades out distinctly. These results suggest an alternative route for distinguishing the components of pairing states in topological-insulator-based superconducting hybrid structures.

Giant Faraday effect due to Pauli exclusion principle in 3D topological insulators.

PubMed

Paudel, Hari P; Leuenberger, Michael N

2014-02-26

Experiments using ARPES, which is based on the photoelectric effect, show that the surface states in 3D topological insulators (TI) are helical. Here we consider Weyl interface fermions due to band inversion in narrow-bandgap semiconductors, such as Pb1-xSnxTe. The positive and negative energy solutions can be identified by means of opposite helicity in terms of the spin helicity operator in 3D TI as ĥ(TI) = (1/ |p|_ |) β (σ|_ x p|_ ) · z^, where β is a Dirac matrix and z^ points perpendicular to the interface. Using the 3D Dirac equation and bandstructure calculations we show that the transitions between positive and negative energy solutions, giving rise to electron-hole pairs, obey strict optical selection rules. In order to demonstrate the consequences of these selection rules, we consider the Faraday effect due to the Pauli exclusion principle in a pump-probe setup using a 3D TI double interface of a PbTe/Pb₀.₃₁Sn₀.₆₉Te/PbTe heterostructure. For that we calculate the optical conductivity tensor of this heterostructure, which we use to solve Maxwell's equations. The Faraday rotation angle exhibits oscillations as a function of probe wavelength and thickness of the heterostructure. The maxima in the Faraday rotation angle are of the order of mrds.

78 FR 76973 - Regulatory Capital Rules: Regulatory Capital, Implementation of Basel III, Capital Adequacy...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-20

... Discipline and Disclosure Requirements, Advanced Approaches Risk-Based Capital Rule, and Market Risk Capital..., 2013, a document adopting a final rule that revises its risk-based and leverage capital requirements... risk-based and leverage capital requirements for banking organizations. An allowance for additional...

Dynamic Approaches to Language Processing

ERIC Educational Resources Information Center

Srinivasan, Narayanan

2007-01-01

Symbolic rule-based approaches have been a preferred way to study language and cognition. Dissatisfaction with rule-based approaches in the 1980s lead to alternative approaches to study language, the most notable being the dynamic approaches to language processing. Dynamic approaches provide a significant alternative by not being rule-based and…

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Investigation of model-based physical design restrictions (Invited Paper)

NASA Astrophysics Data System (ADS)

Lucas, Kevin; Baron, Stanislas; Belledent, Jerome; Boone, Robert; Borjon, Amandine; Couderc, Christophe; Patterson, Kyle; Riviere-Cazaux, Lionel; Rody, Yves; Sundermann, Frank; Toublan, Olivier; Trouiller, Yorick; Urbani, Jean-Christophe; Wimmer, Karl

2005-05-01

As lithography and other patterning processes become more complex and more non-linear with each generation, the task of physical design rules necessarily increases in complexity also. The goal of the physical design rules is to define the boundary between the physical layout structures which will yield well from those which will not. This is essentially a rule-based pre-silicon guarantee of layout correctness. However the rapid increase in design rule requirement complexity has created logistical problems for both the design and process functions. Therefore, similar to the semiconductor industry's transition from rule-based to model-based optical proximity correction (OPC) due to increased patterning complexity, opportunities for improving physical design restrictions by implementing model-based physical design methods are evident. In this paper we analyze the possible need and applications for model-based physical design restrictions (MBPDR). We first analyze the traditional design rule evolution, development and usage methodologies for semiconductor manufacturers. Next we discuss examples of specific design rule challenges requiring new solution methods in the patterning regime of low K1 lithography and highly complex RET. We then evaluate possible working strategies for MBPDR in the process development and product design flows, including examples of recent model-based pre-silicon verification techniques. Finally we summarize with a proposed flow and key considerations for MBPDR implementation.

Gestalt grouping via closure degrades suprathreshold depth percepts.

PubMed

Deas, Lesley M; Wilcox, Laurie M

2014-08-19

It is well known that the perception of depth is susceptible to changes in configuration. For example, stereoscopic precision for a pair of vertical lines can be dramatically reduced when these lines are connected to form a closed object. Here, we extend this paradigm to suprathreshold estimates of perceived depth. Using a touch-sensor, observers made quantitative estimates of depth between a vertical line pair presented in isolation or as edges of a closed rectangular object with different figural interpretations. First, we show that the amount of depth estimated within a closed rectangular object is consistently reduced relative to the vertical edges presented in isolation or when they form the edges of two segmented objects. We then demonstrate that the reduction in perceived depth for closed objects is modulated by manipulations that influence perceived closure of the central figure. Depth percepts were most disrupted when the horizontal connectors and vertical lines matched in color. Perceived depth increased slightly when the connectors had opposite contrast polarity, but increased dramatically when flankers were added. Thus, as grouping cues were added to counter the interpretation of a closed object, the depth degradation effect was systematically eliminated. The configurations tested here rule out explanations based on early, local interactions such as inhibition or cue conflict; instead, our results provide strong evidence of the impact of Gestalt grouping, via closure, on depth magnitude percepts from stereopsis. © 2014 ARVO.

The research of selection model based on LOD in multi-scale display of electronic map

NASA Astrophysics Data System (ADS)

Zhang, Jinming; You, Xiong; Liu, Yingzhen

2008-10-01

This paper proposes a selection model based on LOD to aid the display of electronic map. The ratio of display scale to map scale is regarded as a LOD operator. The categorization rule, classification rule, elementary rule and spatial geometry character rule of LOD operator setting are also concluded.

Research on key technology of the verification system of steel rule based on vision measurement

NASA Astrophysics Data System (ADS)

Jia, Siyuan; Wang, Zhong; Liu, Changjie; Fu, Luhua; Li, Yiming; Lu, Ruijun

2018-01-01

The steel rule plays an important role in quantity transmission. However, the traditional verification method of steel rule based on manual operation and reading brings about low precision and low efficiency. A machine vison based verification system of steel rule is designed referring to JJG1-1999-Verificaiton Regulation of Steel Rule [1]. What differentiates this system is that it uses a new calibration method of pixel equivalent and decontaminates the surface of steel rule. Experiments show that these two methods fully meet the requirements of the verification system. Measuring results strongly prove that these methods not only meet the precision of verification regulation, but also improve the reliability and efficiency of the verification system.

Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

PubMed

Méndez-Arriaga, José M; Maldonado, Carmen R; Dobado, José A; Galindo, Miguel A

2018-03-26

DNA sequences comprising noncanonical 7-deazaguanine ( 7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-Ag I -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of Ag I ions, 7C G-C and 7C A-T Watson-Crick base pairs ( 7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-Ag I -C and 7C A-Ag I -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

PubMed

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-08

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

PubMed Central

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-01

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Comparative study of the dissociation energies of Ni2 and Ni2(+)

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

1992-01-01

Computations at the internally contracted averaged coupled-pair-functional level of theory yield a dissociation energy (Do) for Ni2(+) that is 0.17 eV larger than that of Ni2. This finding is consistent with the collision-induced dissociation experiments of Lian, Su, and Armentrout, but rules out the results from the resonant two-photon dissociation experiments of Lessen and Brucat, which predict that the Do value of Ni2(+) is about 1 eV larger than that of Ni2.

Connecting clinical and actuarial prediction with rule-based methods.

PubMed

Fokkema, Marjolein; Smits, Niels; Kelderman, Henk; Penninx, Brenda W J H

2015-06-01

Meta-analyses comparing the accuracy of clinical versus actuarial prediction have shown actuarial methods to outperform clinical methods, on average. However, actuarial methods are still not widely used in clinical practice, and there has been a call for the development of actuarial prediction methods for clinical practice. We argue that rule-based methods may be more useful than the linear main effect models usually employed in prediction studies, from a data and decision analytic as well as a practical perspective. In addition, decision rules derived with rule-based methods can be represented as fast and frugal trees, which, unlike main effects models, can be used in a sequential fashion, reducing the number of cues that have to be evaluated before making a prediction. We illustrate the usability of rule-based methods by applying RuleFit, an algorithm for deriving decision rules for classification and regression problems, to a dataset on prediction of the course of depressive and anxiety disorders from Penninx et al. (2011). The RuleFit algorithm provided a model consisting of 2 simple decision rules, requiring evaluation of only 2 to 4 cues. Predictive accuracy of the 2-rule model was very similar to that of a logistic regression model incorporating 20 predictor variables, originally applied to the dataset. In addition, the 2-rule model required, on average, evaluation of only 3 cues. Therefore, the RuleFit algorithm appears to be a promising method for creating decision tools that are less time consuming and easier to apply in psychological practice, and with accuracy comparable to traditional actuarial methods. (c) 2015 APA, all rights reserved).

Classical Wave Model of Quantum-Like Processing in Brain

NASA Astrophysics Data System (ADS)

Khrennikov, A.

2011-01-01

We discuss the conjecture on quantum-like (QL) processing of information in the brain. It is not based on the physical quantum brain (e.g., Penrose) - quantum physical carriers of information. In our approach the brain created the QL representation (QLR) of information in Hilbert space. It uses quantum information rules in decision making. The existence of such QLR was (at least preliminary) confirmed by experimental data from cognitive psychology. The violation of the law of total probability in these experiments is an important sign of nonclassicality of data. In so called "constructive wave function approach" such data can be represented by complex amplitudes. We presented 1,2 the QL model of decision making. In this paper we speculate on a possible physical realization of QLR in the brain: a classical wave model producing QLR . It is based on variety of time scales in the brain. Each pair of scales (fine - the background fluctuations of electromagnetic field and rough - the cognitive image scale) induces the QL representation. The background field plays the crucial role in creation of "superstrong QL correlations" in the brain.

Is the Great Barracuda (Sphyraena barracuda) a reef fish or a pelagic fish? The phylogeographic perspective

PubMed Central

Randall, John E.; Bowen, Brian W.

2013-01-01

Current taxonomy indicates a single global species of the Great Barracuda (Sphyraena barracuda) despite differences in color and behavior between Atlantic and Pacific forms. To investigate these differences and qualify the dispersal characteristics of this unique coastal– pelagic teleost (bony fish), we conducted a global phylogeographic survey of 246 specimens from thirteen sampling locations using a 629-base pair fragment of mtDNA cytochrome b. Data indicate high overall gene flow in the Indo-Pacific over large distances (>16,500 km) bridging several biogeographic barriers. The West Atlantic population contains an mtDNA lineage that is divergent from the Indo-Pacific (d = 1.9%), while the East Atlantic (N = 23) has two mutations (d = 0.6%) apart from the Indo-Pacific. While we cannot rule out distinct evolutionary partitions among ocean basins based on behavior, coloration, and near-monophyly between Atlantic and Indo-Pacific subpopulations, more investigation is required before taxonomic status is revised. Overall, the pattern of high global dispersal and connectivity in S. barracuda more closely resembles those reported for large oceanic predators than reef-associated teleosts. PMID:25594680

Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS).

PubMed

Sharma, Nidhi; Hoshika, Shuichi; Hutter, Daniel; Bradley, Kevin M; Benner, Steven A

2014-10-13

Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of a rule base for decision making in general practice.

PubMed Central

Essex, B; Healy, M

1994-01-01

BACKGROUND. Decision making in general practice relies heavily on judgmental expertise. It should be possible to codify this expertise into rules and principles. AIM. A study was undertaken to evaluate the effectiveness, of rules from a rule base designed to improve students' and trainees' management decisions relating to patients seen in general practice. METHOD. The rule base was developed after studying decisions about and management of thousands of patients seen in one general practice over an eight year period. Vignettes were presented to 93 fourth year medical students and 179 general practitioner trainees. They recorded their perception and management of each case before and after being presented with a selection of relevant rules. Participants also commented on their level of agreement with each of the rules provided with the vignettes. A panel of five independent assessors then rated as good, acceptable or poor, the participants' perception and management of each case before and after seeing the rules. RESULTS. Exposure to a few selected rules of thumb improved the problem perception and management decisions of both undergraduates and trainees. The degree of improvement was not related to previous experience or to the stated level of agreement with the proposed rules. The assessors identified difficulties students and trainees experienced in changing their perceptions and management decisions when the rules suggested options they had not considered. CONCLUSION. The rules developed to improve decision making skills in general practice are effective when used with vignettes. The next phase is to transform the rule base into an expert system to train students and doctors to acquire decision making skills. It could also be used to provide decision support when confronted with difficult management decisions in general practice. PMID:8204334

Analysis, Simulation, and Verification of Knowledge-Based, Rule-Based, and Expert Systems

NASA Technical Reports Server (NTRS)

Hinchey, Mike; Rash, James; Erickson, John; Gracanin, Denis; Rouff, Chris

2010-01-01

Mathematically sound techniques are used to view a knowledge-based system (KBS) as a set of processes executing in parallel and being enabled in response to specific rules being fired. The set of processes can be manipulated, examined, analyzed, and used in a simulation. The tool that embodies this technology may warn developers of errors in their rules, but may also highlight rules (or sets of rules) in the system that are underspecified (or overspecified) and need to be corrected for the KBS to operate as intended. The rules embodied in a KBS specify the allowed situations, events, and/or results of the system they describe. In that sense, they provide a very abstract specification of a system. The system is implemented through the combination of the system specification together with an appropriate inference engine, independent of the algorithm used in that inference engine. Viewing the rule base as a major component of the specification, and choosing an appropriate specification notation to represent it, reveals how additional power can be derived from an approach to the knowledge-base system that involves analysis, simulation, and verification. This innovative approach requires no special knowledge of the rules, and allows a general approach where standardized analysis, verification, simulation, and model checking techniques can be applied to the KBS.

A fuzzy classifier system for process control

NASA Technical Reports Server (NTRS)

Karr, C. L.; Phillips, J. C.

1994-01-01

A fuzzy classifier system that discovers rules for controlling a mathematical model of a pH titration system was developed by researchers at the U.S. Bureau of Mines (USBM). Fuzzy classifier systems successfully combine the strengths of learning classifier systems and fuzzy logic controllers. Learning classifier systems resemble familiar production rule-based systems, but they represent their IF-THEN rules by strings of characters rather than in the traditional linguistic terms. Fuzzy logic is a tool that allows for the incorporation of abstract concepts into rule based-systems, thereby allowing the rules to resemble the familiar 'rules-of-thumb' commonly used by humans when solving difficult process control and reasoning problems. Like learning classifier systems, fuzzy classifier systems employ a genetic algorithm to explore and sample new rules for manipulating the problem environment. Like fuzzy logic controllers, fuzzy classifier systems encapsulate knowledge in the form of production rules. The results presented in this paper demonstrate the ability of fuzzy classifier systems to generate a fuzzy logic-based process control system.

Pair cascades in the magnetospheres of strongly magnetized neutron stars

NASA Astrophysics Data System (ADS)

Medin, Zach; Lai, Dong

2010-08-01

We present numerical simulations of electron-positron pair cascades in the magnetospheres of magnetic neutron stars for a wide range of surface fields (Bp = 1012-1015 G), rotation periods (0.1-10 s) and field geometries. This has been motivated by the discovery in recent years of a number of radio pulsars with inferred magnetic fields comparable to those of magnetars. Evolving the cascade generated by a primary electron or positron after it has been accelerated in the inner gap of the magnetosphere, we follow the spatial development of the cascade until the secondary photons and electron-positron pairs leave the magnetosphere, and we obtain the pair multiplicity and the energy spectra of the cascade pairs and photons under various conditions. Going beyond previous works, which were restricted to weaker fields (B <~ afew × 1012 G), we have incorporated in our simulations detailed treatments of physical processes that are potentially important (especially in the high-field regime) but were either neglected or crudely treated before, including photon splitting with the correct selection rules for photon polarization modes, one-photon pair production into low Landau levels for the e+/-, and resonant inverse Compton scattering from polar cap hotspots. We find that even for B >> BQ = 4 × 1013 G, photon splitting has a small effect on the multiplicity of the cascade since a majority of the photons in the cascade cannot split. One-photon decay into e+ e- pairs at low Landau levels, however, becomes the dominant pair production channel when B >~ 3 × 1012 G; this tends to suppress synchrotron radiation so that the cascade can develop only at a larger distance from the stellar surface. Nevertheless, we find that the total number of pairs and their energy spectrum produced in the cascade depend mainly on the polar cap voltage BpP-2, and are weakly dependent on Bp (and P) alone. We discuss the implications of our results for the radio pulsar death line and for the hard X-ray emission from magnetized neutron stars.

A neural network architecture for implementation of expert systems for real time monitoring

NASA Technical Reports Server (NTRS)

Ramamoorthy, P. A.

1991-01-01

Since neural networks have the advantages of massive parallelism and simple architecture, they are good tools for implementing real time expert systems. In a rule based expert system, the antecedents of rules are in the conjunctive or disjunctive form. We constructed a multilayer feedforward type network in which neurons represent AND or OR operations of rules. Further, we developed a translator which can automatically map a given rule base into the network. Also, we proposed a new and powerful yet flexible architecture that combines the advantages of both fuzzy expert systems and neural networks. This architecture uses the fuzzy logic concepts to separate input data domains into several smaller and overlapped regions. Rule-based expert systems for time critical applications using neural networks, the automated implementation of rule-based expert systems with neural nets, and fuzzy expert systems vs. neural nets are covered.

When more is less: Feedback effects in perceptual category learning ☆

PubMed Central

Maddox, W. Todd; Love, Bradley C.; Glass, Brian D.; Filoteo, J. Vincent

2008-01-01

Rule-based and information-integration category learning were compared under minimal and full feedback conditions. Rule-based category structures are those for which the optimal rule is verbalizable. Information-integration category structures are those for which the optimal rule is not verbalizable. With minimal feedback subjects are told whether their response was correct or incorrect, but are not informed of the correct category assignment. With full feedback subjects are informed of the correctness of their response and are also informed of the correct category assignment. An examination of the distinct neural circuits that subserve rule-based and information-integration category learning leads to the counterintuitive prediction that full feedback should facilitate rule-based learning but should also hinder information-integration learning. This prediction was supported in the experiment reported below. The implications of these results for theories of learning are discussed. PMID:18455155

Organizational Knowledge Transfer Using Ontologies and a Rule-Based System

NASA Astrophysics Data System (ADS)

Okabe, Masao; Yoshioka, Akiko; Kobayashi, Keido; Yamaguchi, Takahira

In recent automated and integrated manufacturing, so-called intelligence skill is becoming more and more important and its efficient transfer to next-generation engineers is one of the urgent issues. In this paper, we propose a new approach without costly OJT (on-the-job training), that is, combinational usage of a domain ontology, a rule ontology and a rule-based system. Intelligence skill can be decomposed into pieces of simple engineering rules. A rule ontology consists of these engineering rules as primitives and the semantic relations among them. A domain ontology consists of technical terms in the engineering rules and the semantic relations among them. A rule ontology helps novices get the total picture of the intelligence skill and a domain ontology helps them understand the exact meanings of the engineering rules. A rule-based system helps domain experts externalize their tacit intelligence skill to ontologies and also helps novices internalize them. As a case study, we applied our proposal to some actual job at a remote control and maintenance office of hydroelectric power stations in Tokyo Electric Power Co., Inc. We also did an evaluation experiment for this case study and the result supports our proposal.

A Market-Basket Approach to Predict the Acute Aquatic Toxicity of Munitions and Energetic Materials.

PubMed

Burgoon, Lyle D

2016-06-01

An ongoing challenge in chemical production, including the production of insensitive munitions and energetics, is the ability to make predictions about potential environmental hazards early in the process. To address this challenge, a quantitative structure activity relationship model was developed to predict acute fathead minnow toxicity of insensitive munitions and energetic materials. Computational predictive toxicology models like this one may be used to identify and prioritize environmentally safer materials early in their development. The developed model is based on the Apriori market-basket/frequent itemset mining approach to identify probabilistic prediction rules using chemical atom-pairs and the lethality data for 57 compounds from a fathead minnow acute toxicity assay. Lethality data were discretized into four categories based on the Globally Harmonized System of Classification and Labelling of Chemicals. Apriori identified toxicophores for categories two and three. The model classified 32 of the 57 compounds correctly, with a fivefold cross-validation classification rate of 74 %. A structure-based surrogate approach classified the remaining 25 chemicals correctly at 48 %. This result is unsurprising as these 25 chemicals were fairly unique within the larger set.

Improving the Interpretability of Classification Rules Discovered by an Ant Colony Algorithm: Extended Results.

PubMed

Otero, Fernando E B; Freitas, Alex A

2016-01-01

Most ant colony optimization (ACO) algorithms for inducing classification rules use a ACO-based procedure to create a rule in a one-at-a-time fashion. An improved search strategy has been proposed in the cAnt-Miner[Formula: see text] algorithm, where an ACO-based procedure is used to create a complete list of rules (ordered rules), i.e., the ACO search is guided by the quality of a list of rules instead of an individual rule. In this paper we propose an extension of the cAnt-Miner[Formula: see text] algorithm to discover a set of rules (unordered rules). The main motivations for this work are to improve the interpretation of individual rules by discovering a set of rules and to evaluate the impact on the predictive accuracy of the algorithm. We also propose a new measure to evaluate the interpretability of the discovered rules to mitigate the fact that the commonly used model size measure ignores how the rules are used to make a class prediction. Comparisons with state-of-the-art rule induction algorithms, support vector machines, and the cAnt-Miner[Formula: see text] producing ordered rules are also presented.

An XML-Based Manipulation and Query Language for Rule-Based Information

NASA Astrophysics Data System (ADS)

Mansour, Essam; Höpfner, Hagen

Rules are utilized to assist in the monitoring process that is required in activities, such as disease management and customer relationship management. These rules are specified according to the application best practices. Most of research efforts emphasize on the specification and execution of these rules. Few research efforts focus on managing these rules as one object that has a management life-cycle. This paper presents our manipulation and query language that is developed to facilitate the maintenance of this object during its life-cycle and to query the information contained in this object. This language is based on an XML-based model. Furthermore, we evaluate the model and language using a prototype system applied to a clinical case study.

Base Flipping in V(D)J Recombination: Insights into the Mechanism of Hairpin Formation, the 12/23 Rule, and the Coordination of Double-Strand Breaks▿ †

PubMed Central

Bischerour, Julien; Lu, Catherine; Roth, David B.; Chalmers, Ronald

2009-01-01

Tn5 transposase cleaves the transposon end using a hairpin intermediate on the transposon end. This involves a flipped base that is stacked against a tryptophan residue in the protein. However, many other members of the cut-and-paste transposase family, including the RAG1 protein, produce a hairpin on the flanking DNA. We have investigated the reversed polarity of the reaction for RAG recombination. Although the RAG proteins appear to employ a base-flipping mechanism using aromatic residues, the putatively flipped base is not at the expected location and does not appear to stack against any of the said aromatic residues. We propose an alternative model in which a flipped base is accommodated in a nonspecific pocket or cleft within the recombinase. This is consistent with the location of the flipped base at position −1 in the coding flank, which can be occupied by purine or pyrimidine bases that would be difficult to stabilize using a single, highly specific, interaction. Finally, during this work we noticed that the putative base-flipping events on either side of the 12/23 recombination signal sequence paired complex are coupled to the nicking steps and serve to coordinate the double-strand breaks on either side of the complex. PMID:19720743

Integrated layout based Monte-Carlo simulation for design arc optimization

NASA Astrophysics Data System (ADS)

Shao, Dongbing; Clevenger, Larry; Zhuang, Lei; Liebmann, Lars; Wong, Robert; Culp, James

2016-03-01

Design rules are created considering a wafer fail mechanism with the relevant design levels under various design cases, and the values are set to cover the worst scenario. Because of the simplification and generalization, design rule hinders, rather than helps, dense device scaling. As an example, SRAM designs always need extensive ground rule waivers. Furthermore, dense design also often involves "design arc", a collection of design rules, the sum of which equals critical pitch defined by technology. In design arc, a single rule change can lead to chain reaction of other rule violations. In this talk we present a methodology using Layout Based Monte-Carlo Simulation (LBMCS) with integrated multiple ground rule checks. We apply this methodology on SRAM word line contact, and the result is a layout that has balanced wafer fail risks based on Process Assumptions (PAs). This work was performed at the IBM Microelectronics Div, Semiconductor Research and Development Center, Hopewell Junction, NY 12533

Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

PubMed Central

Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

2014-01-01

The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

Implementation of artificial intelligence rules in a data base management system

NASA Technical Reports Server (NTRS)

Feyock, S.

1986-01-01

The intelligent front end prototype was transformed into a RIM-integrated system. A RIM-based expert system was written which demonstrated the developed capability. The use of rules to produce extensibility of the intelligent front end, including the concept of demons and rule manipulation rules were investigated. Innovative approaches such as syntax programming were to be considered.

Rule-Based and Information-Integration Category Learning in Normal Aging

ERIC Educational Resources Information Center

Maddox, W. Todd; Pacheco, Jennifer; Reeves, Maia; Zhu, Bo; Schnyer, David M.

2010-01-01

The basal ganglia and prefrontal cortex play critical roles in category learning. Both regions evidence age-related structural and functional declines. The current study examined rule-based and information-integration category learning in a group of older and younger adults. Rule-based learning is thought to involve explicit, frontally mediated…

Assessment of Matrix Multiplication Learning with a Rule-Based Analytical Model--"A Bayesian Network Representation"

ERIC Educational Resources Information Center

Zhang, Zhidong

2016-01-01

This study explored an alternative assessment procedure to examine learning trajectories of matrix multiplication. It took rule-based analytical and cognitive task analysis methods specifically to break down operation rules for a given matrix multiplication. Based on the analysis results, a hierarchical Bayesian network, an assessment model,…

Automated implementation of rule-based expert systems with neural networks for time-critical applications

NASA Technical Reports Server (NTRS)

Ramamoorthy, P. A.; Huang, Song; Govind, Girish

1991-01-01

In fault diagnosis, control and real-time monitoring, both timing and accuracy are critical for operators or machines to reach proper solutions or appropriate actions. Expert systems are becoming more popular in the manufacturing community for dealing with such problems. In recent years, neural networks have revived and their applications have spread to many areas of science and engineering. A method of using neural networks to implement rule-based expert systems for time-critical applications is discussed here. This method can convert a given rule-based system into a neural network with fixed weights and thresholds. The rules governing the translation are presented along with some examples. We also present the results of automated machine implementation of such networks from the given rule-base. This significantly simplifies the translation process to neural network expert systems from conventional rule-based systems. Results comparing the performance of the proposed approach based on neural networks vs. the classical approach are given. The possibility of very large scale integration (VLSI) realization of such neural network expert systems is also discussed.

Verification and Validation of KBS with Neural Network Components

NASA Technical Reports Server (NTRS)

Wen, Wu; Callahan, John

1996-01-01

Artificial Neural Network (ANN) play an important role in developing robust Knowledge Based Systems (KBS). The ANN based components used in these systems learn to give appropriate predictions through training with correct input-output data patterns. Unlike traditional KBS that depends on a rule database and a production engine, the ANN based system mimics the decisions of an expert without specifically formulating the if-than type of rules. In fact, the ANNs demonstrate their superiority when such if-then type of rules are hard to generate by human expert. Verification of traditional knowledge based system is based on the proof of consistency and completeness of the rule knowledge base and correctness of the production engine.These techniques, however, can not be directly applied to ANN based components.In this position paper, we propose a verification and validation procedure for KBS with ANN based components. The essence of the procedure is to obtain an accurate system specification through incremental modification of the specifications using an ANN rule extraction algorithm.

Association rule mining in the US Vaccine Adverse Event Reporting System (VAERS).

PubMed

Wei, Lai; Scott, John

2015-09-01

Spontaneous adverse event reporting systems are critical tools for monitoring the safety of licensed medical products. Commonly used signal detection algorithms identify disproportionate product-adverse event pairs and may not be sensitive to more complex potential signals. We sought to develop a computationally tractable multivariate data-mining approach to identify product-multiple adverse event associations. We describe an application of stepwise association rule mining (Step-ARM) to detect potential vaccine-symptom group associations in the US Vaccine Adverse Event Reporting System. Step-ARM identifies strong associations between one vaccine and one or more adverse events. To reduce the number of redundant association rules found by Step-ARM, we also propose a clustering method for the post-processing of association rules. In sample applications to a trivalent intradermal inactivated influenza virus vaccine and to measles, mumps, rubella, and varicella (MMRV) vaccine and in simulation studies, we find that Step-ARM can detect a variety of medically coherent potential vaccine-symptom group signals efficiently. In the MMRV example, Step-ARM appears to outperform univariate methods in detecting a known safety signal. Our approach is sensitive to potentially complex signals, which may be particularly important when monitoring novel medical countermeasure products such as pandemic influenza vaccines. The post-processing clustering algorithm improves the applicability of the approach as a screening method to identify patterns that may merit further investigation. Copyright © 2015 John Wiley & Sons, Ltd.

Stacking interactions and DNA intercalation

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

Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo

2009-01-01

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observedmore » proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.« less

Rule Extracting based on MCG with its Application in Helicopter Power Train Fault Diagnosis

NASA Astrophysics Data System (ADS)

Wang, M.; Hu, N. Q.; Qin, G. J.

2011-07-01

In order to extract decision rules for fault diagnosis from incomplete historical test records for knowledge-based damage assessment of helicopter power train structure. A method that can directly extract the optimal generalized decision rules from incomplete information based on GrC was proposed. Based on semantic analysis of unknown attribute value, the granule was extended to handle incomplete information. Maximum characteristic granule (MCG) was defined based on characteristic relation, and MCG was used to construct the resolution function matrix. The optimal general decision rule was introduced, with the basic equivalent forms of propositional logic, the rules were extracted and reduction from incomplete information table. Combined with a fault diagnosis example of power train, the application approach of the method was present, and the validity of this method in knowledge acquisition was proved.

Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers

PubMed Central

Field, Amanda; Xiang, Jie; Anderson, W. Ray; Graham, Patricia; Pick, Leslie

2016-01-01

The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos, but mutations result in a pair-rule phenotype. This was explained by the interaction of Ftz-F1 with the homeodomain protein Ftz that is expressed in stripes in the primordia of segments missing in either ftz-f1 or ftz mutants. Ftz-F1 and Ftz were shown to physically interact and coordinately activate the expression of ftz itself and engrailed by synergistic binding to composite Ftz-F1/Ftz binding sites. However, attempts to identify additional target genes on the basis of Ftz-F1/ Ftz binding alone has met with only limited success. To discern rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos. Ftz-F1-responsive genes most highly regulated included engrailed and nine additional genes expressed in patterns dependent on both ftz and ftz-f1. Candidate enhancers for these genes were identified by combining BDTNP Ftz ChIP-chip data with a computational search for Ftz-F1 binding sites. Of eight enhancer reporter genes tested in transgenic embryos, six generated expression patterns similar to the corresponding endogenous gene and expression was lost in ftz mutants. These studies identified a new set of Ftz-F1 targets, all of which are co-regulated by Ftz. Comparative analysis of enhancers containing Ftz/Ftz-F1 binding sites that were or were not bona fide targets in vivo suggested that GAF negatively regulates enhancers that contain Ftz/Ftz-F1 binding sites but are not actually utilized. These targets include other regulatory factors as well as genes involved directly in morphogenesis, providing insight into how pair-rule genes establish the body pattern. PMID:27723822

Automated rule-base creation via CLIPS-Induce

NASA Technical Reports Server (NTRS)

Murphy, Patrick M.

1994-01-01

Many CLIPS rule-bases contain one or more rule groups that perform classification. In this paper we describe CLIPS-Induce, an automated system for the creation of a CLIPS classification rule-base from a set of test cases. CLIPS-Induce consists of two components, a decision tree induction component and a CLIPS production extraction component. ID3, a popular decision tree induction algorithm, is used to induce a decision tree from the test cases. CLIPS production extraction is accomplished through a top-down traversal of the decision tree. Nodes of the tree are used to construct query rules, and branches of the tree are used to construct classification rules. The learned CLIPS productions may easily be incorporated into a large CLIPS system that perform tasks such as accessing a database or displaying information.

Modified Levenberg-Marquardt Method for RÖSSLER Chaotic System Fuzzy Modeling Training

NASA Astrophysics Data System (ADS)

Wang, Yu-Hui; Wu, Qing-Xian; Jiang, Chang-Sheng; Xue, Ya-Li; Fang, Wei

Generally, fuzzy approximation models require some human knowledge and experience. Operator's experience is involved in the mathematics of fuzzy theory as a collection of heuristic rules. The main goal of this paper is to present a new method for identifying unknown nonlinear dynamics such as Rössler system without any human knowledge. Instead of heuristic rules, the presented method uses the input-output data pairs to identify the Rössler chaotic system. The training algorithm is a modified Levenberg-Marquardt (L-M) method, which can adjust the parameters of each linear polynomial and fuzzy membership functions on line, and do not rely on experts' experience excessively. Finally, it is applied to training Rössler chaotic system fuzzy identification. Comparing this method with the standard L-M method, the convergence speed is accelerated. The simulation results demonstrate the effectiveness of the proposed method.

Linear solvation energy relationships (LSER): 'rules of thumb' for Vi/100, π*, Βm, and αm estimation and use in aquatic toxicology

USGS Publications Warehouse

Hickey, James P.

1996-01-01

This chapter provides a listing of the increasing variety of organic moieties and heteroatom group for which Linear Solvation Energy Relationship (LSER) values are available, and the LSER variable estimation rules. The listings include values for typical nitrogen-, sulfur- and phosphorus-containing moieties, and general organosilicon and organotin groups. The contributions by an ion pair situation to the LSER values are also offered in Table 1, allowing estimation of parameters for salts and zwitterions. The guidelines permit quick estimation of values for the four primary LSER variables Vi/100, π*, Βm, and αm by summing the contribtuions from its components. The use of guidelines and Table 1 significantly simplifies computation of values for the LSER variables for most possible organic comppounds in the environment, including the larger compounds of environmental and biological interest.

Structure, stability, and cluster-cage interactions in nitride clusterfullerenes M3N@C2n (M = Sc, Y; 2n = 68-98): a density functional theory study.

PubMed

Popov, Alexey A; Dunsch, Lothar

2007-09-26

Extensive semiempirical calculations of the hexaanions of IPR (isolated pentagon rule) and non-IPR isomers of C(68)-C(88) and IPR isomers of C(90)-C(98) followed by DFT calculations of the lowest energy structures were performed to find the carbon cages that can provide the most stable isomers of M(3)N@C(2n) clusterfullerenes (M = Sc, Y) with Y as a model for rare earth ions. DFT calculations of isomers of M(3)N@C(2n) (M = Sc, Y; 2n = 68-98) based on the most stable C(2n)(6-) cages were also performed. The lowest energy isomers found by this methodology for Sc(3)N@C(68), Sc(3)N@C(78), Sc(3)N@C(80), Y(3)N@C(78), Y(3)N@C(80), Y(3)N@C(84), Y(3)N@C(86), and Y(3)N@C(88) are those that have been shown to exist by single-crystal X-ray studies as Sc(3)N@C(2n) (2n = 68, 78, 80), Dy(3)N@C(80), and Tb(3)N@C(2n) (2n = 80, 84, 86, 88) clusterfullerenes. Reassignment of the carbon cage of Sc(2)@C(76) to the non-IPR Cs: 17490 isomer is also proposed. The stability of nitride clusterfullerenes was found to correlate well with the stability of the empty 6-fold charged cages. However, the dimensions of the cage in terms of its ability to encapsulate M(3)N clusters were also found to be an important factor, especially for the medium size cages and the large Y(3)N cluster. In some cases the most stable structures are based on the different cage isomers for Sc(3)N and Y(3)N clusters. Up to the cage size of C(84), non-IPR isomers of C(2n)(6-) and M(3)N@C(2n) were found to compete with or to be even more stable than IPR isomers. However, the number of adjacent pentagon pairs in the most stable non-IPR isomers decreases as cage size increases: the most stable M(3)N@C(2n) isomers have three such pairs for 2n = 68-72, two pairs for n = 74-80, and only one pair for n = 82, 84. For C(86) and C(88) the lowest energy IPR isomers are much more stable than any non-IPR isomer. The trends in the stability of the fullerene isomers and the cluster-cage binding energies are discussed, and general rules for stability of clusterfullerenes are established. Finally, the high yield of M(3)N@C(80) (Ih) clusterfullerenes for any metal is explained by the exceptional stability of the C(80)(6-) (Ih: 31924) cage, rationalized by the optimum distribution of the pentagons leading to the minimization of the steric strain, and structural similarities of C(80) (Ih: 31924) with the lowest energy non-IPR isomers of C(760(6-), C(78)(6-), C(82)(6-), and C(84)(6-) pointed out.

A two-stage stochastic rule-based model to determine pre-assembly buffer content

NASA Astrophysics Data System (ADS)

Gunay, Elif Elcin; Kula, Ufuk

2018-01-01

This study considers instant decision-making needs of the automobile manufactures for resequencing vehicles before final assembly (FA). We propose a rule-based two-stage stochastic model to determine the number of spare vehicles that should be kept in the pre-assembly buffer to restore the altered sequence due to paint defects and upstream department constraints. First stage of the model decides the spare vehicle quantities, where the second stage model recovers the scrambled sequence respect to pre-defined rules. The problem is solved by sample average approximation (SAA) algorithm. We conduct a numerical study to compare the solutions of heuristic model with optimal ones and provide following insights: (i) as the mismatch between paint entrance and scheduled sequence decreases, the rule-based heuristic model recovers the scrambled sequence as good as the optimal resequencing model, (ii) the rule-based model is more sensitive to the mismatch between the paint entrance and scheduled sequences for recovering the scrambled sequence, (iii) as the defect rate increases, the difference in recovery effectiveness between rule-based heuristic and optimal solutions increases, (iv) as buffer capacity increases, the recovery effectiveness of the optimization model outperforms heuristic model, (v) as expected the rule-based model holds more inventory than the optimization model.

Testing the SI × SC rule: Pollen-pistil interactions in interspecific crosses between members of the tomato clade (Solanum section Lycopersicon, Solanaceae).

PubMed

Baek, You Soon; Covey, Paul A; Petersen, Jennifer J; Chetelat, Roger T; McClure, Bruce; Bedinger, Patricia A

2015-02-01

Interspecific reproductive barriers (IRBs) act to ensure species integrity by preventing hybridization. Previous studies on interspecific crosses in the tomato clade have focused on the success of fruit and seed set. The SI × SC rule (SI species × SC species crosses are incompatible, but the reciprocal crosses are compatible) often applies to interspecific crosses. Because SI systems in the Solanaceae affect pollen tube growth, we focused on this process in a comprehensive study of interspecific crosses in the tomato clade to test whether the SI × SC rule was always followed. Pollen tube growth was assessed in reciprocal crosses between all 13 species of the tomato clade using fluorescence microscopy. In crosses between SC and SI species, pollen tube growth follows the SI × SC rule: interspecific pollen tube rejection occurs when SI species are pollinated by SC species, but in the reciprocal crosses (SC × SI), pollen tubes reach ovaries. However, pollen tube rejection occurred in some crosses between pairs of SC species, demonstrating that a fully functional SI system is not necessary for pollen tube rejection in interspecific crosses. Further, gradations in the strength of both pistil and pollen IRBs were revealed in interspecific crosses using SC populations of generally SI species. The SI × SC rule explains many of the compatibility relations in the tomato clade, but exceptions occur with more recently evolved SC species and accessions, revealing differences in strength of both pistil and pollen IRBs. © 2015 Botanical Society of America, Inc.

Learning rules for spike timing-dependent plasticity depend on dendritic synapse location.

PubMed

Letzkus, Johannes J; Kampa, Björn M; Stuart, Greg J

2006-10-11

Previous studies focusing on the temporal rules governing changes in synaptic strength during spike timing-dependent synaptic plasticity (STDP) have paid little attention to the fact that synaptic inputs are distributed across complex dendritic trees. During STDP, propagation of action potentials (APs) back to the site of synaptic input is thought to trigger plasticity. However, in pyramidal neurons, backpropagation of single APs is decremental, whereas high-frequency bursts lead to generation of distal dendritic calcium spikes. This raises the question whether STDP learning rules depend on synapse location and firing mode. Here, we investigate this issue at synapses between layer 2/3 and layer 5 pyramidal neurons in somatosensory cortex. We find that low-frequency pairing of single APs at positive times leads to a distance-dependent shift to long-term depression (LTD) at distal inputs. At proximal sites, this LTD could be converted to long-term potentiation (LTP) by dendritic depolarizations suprathreshold for BAC-firing or by high-frequency AP bursts. During AP bursts, we observed a progressive, distance-dependent shift in the timing requirements for induction of LTP and LTD, such that distal synapses display novel timing rules: they potentiate when inputs are activated after burst onset (negative timing) but depress when activated before burst onset (positive timing). These findings could be explained by distance-dependent differences in the underlying dendritic voltage waveforms driving NMDA receptor activation during STDP induction. Our results suggest that synapse location within the dendritic tree is a crucial determinant of STDP, and that synapses undergo plasticity according to local rather than global learning rules.

Rule-based navigation control design for autonomous flight

NASA Astrophysics Data System (ADS)

Contreras, Hugo; Bassi, Danilo

2008-04-01

This article depicts a navigation control system design that is based on a set of rules in order to follow a desired trajectory. The full control of the aircraft considered here comprises: a low level stability control loop, based on classic PID controller and the higher level navigation whose main job is to exercise lateral control (course) and altitude control, trying to follow a desired trajectory. The rules and PID gains were adjusted systematically according to the result of flight simulation. In spite of its simplicity, the rule-based navigation control proved to be robust, even with big perturbation, like crossing winds.

Bi-directional ROADM with one pair of NxN cyclic-AWGs for over N wavelength channels configuration

NASA Astrophysics Data System (ADS)

Tsai, Cheng-Mu

2018-01-01

This paper presents a bidirectional optical add-drop multiplexer (BROADM) with permitting white spectral channels input in bidirectional configuration. The filter routing rule of array waveguide grating (AWG) is applied for the wavelength channels (WCs) that need to be added and dropped by using the corresponding tunable fiber Bragg gratings (FBGs). The other WCs pass through output by tuning FBG filter spectra away from the WCs. The bandwidth between two adjacent WCs of each pair of ports in AWG is wider than one channel spacing so that the filter spectra of FBG is tuned to free spectral range (FSR) region to realize the wavelength routing function without interfering other WCs. The WCs can be flexibly handled by installing the corresponding tunable FBG. Therefore, the proposed BROADM is more flexible and has higher transmission capacity in the optical network.

Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

PubMed Central

Wright, Adam; Laxmisan, Archana; Ottosen, Madelene J; McCoy, Jacob A; Butten, David; Sittig, Dean F

2012-01-01

Objective We describe a novel, crowdsourcing method for generating a knowledge base of problem–medication pairs that takes advantage of manually asserted links between medications and problems. Methods Through iterative review, we developed metrics to estimate the appropriateness of manually entered problem–medication links for inclusion in a knowledge base that can be used to infer previously unasserted links between problems and medications. Results Clinicians manually linked 231 223 medications (55.30% of prescribed medications) to problems within the electronic health record, generating 41 203 distinct problem–medication pairs, although not all were accurate. We developed methods to evaluate the accuracy of the pairs, and after limiting the pairs to those meeting an estimated 95% appropriateness threshold, 11 166 pairs remained. The pairs in the knowledge base accounted for 183 127 total links asserted (76.47% of all links). Retrospective application of the knowledge base linked 68 316 medications not previously linked by a clinician to an indicated problem (36.53% of unlinked medications). Expert review of the combined knowledge base, including inferred and manually linked problem–medication pairs, found a sensitivity of 65.8% and a specificity of 97.9%. Conclusion Crowdsourcing is an effective, inexpensive method for generating a knowledge base of problem–medication pairs that is automatically mapped to local terminologies, up-to-date, and reflective of local prescribing practices and trends. PMID:22582202

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks.

PubMed

Jolles, Jolle W; Fleetwood-Wilson, Adeline; Nakayama, Shinnosuke; Stumpe, Martin C; Johnstone, Rufus A; Manica, Andrea

2015-01-01

Social animals must time and coordinate their behaviour to ensure the benefits of grouping, resulting in collective movements and the potential emergence of leaders and followers. However, individuals often differ consistently from one another in how they cope with their environment, a phenomenon known as animal personality, which may affect how individuals use coordination rules and requiring them to compromise. Here we tracked the movements of pairs of three-spined sticklebacks, Gasterosteus aculeatus , separated by a transparent partition that allowed them to observe and interact with one another in a context containing cover. Individuals differed consistently in their tendency to approach their partner's compartment during collective movements. The strength of this social attraction was positively correlated with the behavioural coordination between members of a pair but was negatively correlated with an individual's tendency to lead. Social attraction may form part of a broader behavioural syndrome as it was predicted by the boldness of an individual, measured in isolation prior to the observation of pairs, and by the boldness of the partner. We found that bolder fish, and those paired with bolder partners, tended to approach their partner's compartment less closely. These findings provide important insights into the mechanisms that govern the dynamics and functioning of social groups and the emergence and maintenance of consistent behavioural differences.

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks

PubMed Central

Jolles, Jolle W.; Fleetwood-Wilson, Adeline; Nakayama, Shinnosuke; Stumpe, Martin C.; Johnstone, Rufus A.; Manica, Andrea

2015-01-01

Social animals must time and coordinate their behaviour to ensure the benefits of grouping, resulting in collective movements and the potential emergence of leaders and followers. However, individuals often differ consistently from one another in how they cope with their environment, a phenomenon known as animal personality, which may affect how individuals use coordination rules and requiring them to compromise. Here we tracked the movements of pairs of three-spined sticklebacks, Gasterosteus aculeatus, separated by a transparent partition that allowed them to observe and interact with one another in a context containing cover. Individuals differed consistently in their tendency to approach their partner's compartment during collective movements. The strength of this social attraction was positively correlated with the behavioural coordination between members of a pair but was negatively correlated with an individual's tendency to lead. Social attraction may form part of a broader behavioural syndrome as it was predicted by the boldness of an individual, measured in isolation prior to the observation of pairs, and by the boldness of the partner. We found that bolder fish, and those paired with bolder partners, tended to approach their partner's compartment less closely. These findings provide important insights into the mechanisms that govern the dynamics and functioning of social groups and the emergence and maintenance of consistent behavioural differences. PMID:25598543

76 FR 1145 - Alabama Power Company; Notice of Application for Amendment of License and Soliciting Comments...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

... drought-based temporary variance of the Martin Project rule curve and minimum flow releases at the Yates... requesting a drought- based temporary variance to the Martin Project rule curve. The rule curve variance...

Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

PubMed Central

Bennett, Kristin P.

2014-01-01

We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

Evidence that the association of childhood trauma with psychosis and related psychopathology is not explained by gene-environment correlation: A monozygotic twin differences approach.

PubMed

Lecei, Aleksandra; Decoster, Jeroen; De Hert, Marc; Derom, Catherine; Jacobs, Nele; Menne-Lothmann, Claudia; van Os, Jim; Thiery, Evert; Rutten, Bart P F; Wichers, Marieke; van Winkel, Ruud

2018-05-21

Converging evidence supports childhood trauma as possible causal risk for psychosis and related psychopathology. However, studies have shown that baseline psychotic symptoms may actually increase risk for subsequent victimization, suggesting that exposure to CT is not random but may result from pre-existing vulnerability. Therefore, studies testing whether the association between CT and psychopathology persists when accounting for gene-environment correlation are much needed. A monozygotic (MZ) twin differences approach was used to examine whether differences in CT exposure among MZ twin pairs would be associated with MZ differences in symptoms. As MZ twins are genetically identical, within-pair correlations between CT exposure and psychopathology rule out the possibility that the association is solely attributable to gene-environment correlation. 266 monozygotic twins (133 pairs) from a larger general population study were available for analysis. CT was associated with symptoms of psychosis (B = 0.62; SE = 0.08, p < .001) and overall psychopathology (B = 43.13; SE = 6.27; p < .001). There were measurable differences within pairs in CT exposure and symptoms, allowing for meaningful within-pair differences. Within-pair differences in CT exposure were associated with within-pair differences in symptoms of psychosis (B = 0.35; SE = 0.16; p = .024), as well as with overall psychopathology (B = 29.22; SE = 12.24; p = .018), anxiety (B = 0.65; SE = 0.21; p = .002) and depression (B = 0.37; SE = 0.18; p = .043). While it is not unlikely that pre-existing vulnerability may increase the risk for traumatic exposures, such gene-environment correlation does not explain away the association between CT and psychopathology. The present findings thus suggest that at least part of the association between CT and psychopathology may be causal. Copyright © 2018. Published by Elsevier B.V.

Acuity of a Cryptochrome and Vision-Based Magnetoreception System in Birds

PubMed Central

Solov'yov, Ilia A.; Mouritsen, Henrik; Schulten, Klaus

2010-01-01

Abstract The magnetic compass of birds is embedded in the visual system and it has been hypothesized that the primary sensory mechanism is based on a radical pair reaction. Previous models of magnetoreception have assumed that the radical pair-forming molecules are rigidly fixed in space, and this assumption has been a major objection to the suggested hypothesis. In this article, we investigate theoretically how much disorder is permitted for the radical pair-forming, protein-based magnetic compass in the eye to remain functional. Our study shows that only one rotational degree of freedom of the radical pair-forming protein needs to be partially constrained, while the other two rotational degrees of freedom do not impact the magnetoreceptive properties of the protein. The result implies that any membrane-associated protein is sufficiently restricted in its motion to function as a radical pair-based magnetoreceptor. We relate our theoretical findings to the cryptochromes, currently considered the likeliest candidate to furnish radical pair-based magnetoreception. PMID:20655831

A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs

PubMed Central

Lee, Dong-Hoon; Liu, Yinling; Lee, Hyun-Wook; Xia, Bo; Brice, Allyn R.; Park, Sung-Hyun; Balduf, Hunter; Dominy, Brian N.; Cao, Weiguo

2015-01-01

The uracil DNA glycosylase superfamily consists of several distinct families. Family 2 mismatch-specific uracil DNA glycosylase (MUG) from Escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, T/U, G/U and C/U. Family 1 uracil N-glycosylase (UNG) from E. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the A/U base pair. Here, we report the identification of an important structural determinant that underlies the functional difference between MUG and UNG. Substitution of a Lys residue at position 68 with Asn in MUG not only accelerates the removal of uracil from mismatched base pairs but also enables the enzyme to gain catalytic activity on A/U base pairs. Binding and kinetic analysis demonstrate that the MUG-K68N substitution results in enhanced ground state binding and transition state interactions. Molecular modeling reveals that MUG-K68N, UNG-N123 and family 5 Thermus thermophiles UDGb-A111N can form bidentate hydrogen bonds with the N3 and O4 moieties of the uracil base. Genetic analysis indicates the gain of function for A/U base pairs allows the MUG-K68N mutant to remove uracil incorporated into the genome during DNA replication. The implications of this study in the origin of life are discussed. PMID:25550433

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Automatic rule generation for high-level vision

NASA Technical Reports Server (NTRS)

Rhee, Frank Chung-Hoon; Krishnapuram, Raghu

1992-01-01

A new fuzzy set based technique that was developed for decision making is discussed. It is a method to generate fuzzy decision rules automatically for image analysis. This paper proposes a method to generate rule-based approaches to solve problems such as autonomous navigation and image understanding automatically from training data. The proposed method is also capable of filtering out irrelevant features and criteria from the rules.

Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

PubMed

Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

2009-03-18

It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

On adiabatic pair potentials of highly charged colloid particles

NASA Astrophysics Data System (ADS)

Sogami, Ikuo S.

2018-03-01

Generalizing the Debye-Hückel formalism, we develop a new mean field theory for adiabatic pair potentials of highly charged particles in colloid dispersions. The unoccupied volume and the osmotic pressure are the key concepts to describe the chemical and thermodynamical equilibrium of the gas of small ions in the outside region of all of the colloid particles. To define the proper thermodynamic quantities, it is postulated to take an ensemble averaging with respect to the particle configurations in the integrals for their densities consisting of the electric potential satisfying a set of equations that are derived by linearizing the Poisson-Boltzmann equation. With the Fourier integral representation of the electric potential, we calculate first the internal electric energy of the system from which the Helmholtz free energy is obtained through the Legendre transformation. Then, the Gibbs free energy is calculated using both ways of the Legendre transformation with respect to the unoccupied volume and the summation of chemical potentials. The thermodynamic functions provide three types of pair potentials, all of which are inversely proportional to the fraction of the unoccupied volume. At the limit when the fraction factor reduces to unity, the Helmholtz pair potential turns exactly into the well known Derjaguin-Landau-Verwey-Overbeek repulsive potential. The Gibbs pair potential possessing a medium-range strong repulsive part and a long-range weak attractive tail can explain the Schulze-Hardy rule for coagulation in combination with the van der Waals-London potential and describes a rich variety of phenomena of phase transitions observed in the dilute dispersions of highly charged particles.

A Rule-Based System Implementing a Method for Translating FOL Formulas into NL Sentences

NASA Astrophysics Data System (ADS)

Mpagouli, Aikaterini; Hatzilygeroudis, Ioannis

In this paper, we mainly present the implementation of a system that translates first order logic (FOL) formulas into natural language (NL) sentences. The motivation comes from an intelligent tutoring system teaching logic as a knowledge representation language, where it is used as a means for feedback to the students-users. FOL to NL conversion is achieved by using a rule-based approach, where we exploit the pattern matching capabilities of rules. So, the system consists of rule-based modules corresponding to the phases of our translation methodology. Facts are used in a lexicon providing lexical and grammatical information that helps in producing the NL sentences. The whole system is implemented in Jess, a java-implemented rule-based programming tool. Experimental results confirm the success of our choices.

Explanation-based learning in infancy.

PubMed

Baillargeon, Renée; DeJong, Gerald F

2017-10-01

In explanation-based learning (EBL), domain knowledge is leveraged in order to learn general rules from few examples. An explanation is constructed for initial exemplars and is then generalized into a candidate rule that uses only the relevant features specified in the explanation; if the rule proves accurate for a few additional exemplars, it is adopted. EBL is thus highly efficient because it combines both analytic and empirical evidence. EBL has been proposed as one of the mechanisms that help infants acquire and revise their physical rules. To evaluate this proposal, 11- and 12-month-olds (n = 260) were taught to replace their current support rule (that an object is stable when half or more of its bottom surface is supported) with a more sophisticated rule (that an object is stable when half or more of the entire object is supported). Infants saw teaching events in which asymmetrical objects were placed on a base, followed by static test displays involving a novel asymmetrical object and a novel base. When the teaching events were designed to facilitate EBL, infants learned the new rule with as few as two (12-month-olds) or three (11-month-olds) exemplars. When the teaching events were designed to impede EBL, however, infants failed to learn the rule. Together, these results demonstrate that even infants, with their limited knowledge about the world, benefit from the knowledge-based approach of EBL.

Theory of nodal s ±-wave pairing symmetry in the Pu-based 115 superconductor family

DOE PAGES

Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

2015-02-27

The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-T c superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scatteringmore » channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

On optimal fuzzy best proximity coincidence points of fuzzy order preserving proximal Ψ(σ, α)-lower-bounding asymptotically contractive mappings in non-Archimedean fuzzy metric spaces.

PubMed

De la Sen, Manuel; Abbas, Mujahid; Saleem, Naeem

2016-01-01

This paper discusses some convergence properties in fuzzy ordered proximal approaches defined by [Formula: see text]-sequences of pairs, where [Formula: see text] is a surjective self-mapping and [Formula: see text] where Aand Bare nonempty subsets of and abstract nonempty set X and [Formula: see text] is a partially ordered non-Archimedean fuzzy metric space which is endowed with a fuzzy metric M, a triangular norm * and an ordering [Formula: see text] The fuzzy set M takes values in a sequence or set [Formula: see text] where the elements of the so-called switching rule [Formula: see text] are defined from [Formula: see text] to a subset of [Formula: see text] Such a switching rule selects a particular realization of M at the nth iteration and it is parameterized by a growth evolution sequence [Formula: see text] and a sequence or set [Formula: see text] which belongs to the so-called [Formula: see text]-lower-bounding mappings which are defined from [0, 1] to [0, 1]. Some application examples concerning discrete systems under switching rules and best approximation solvability of algebraic equations are discussed.

Redundancy checking algorithms based on parallel novel extension rule

NASA Astrophysics Data System (ADS)

Liu, Lei; Yang, Yang; Li, Guangli; Wang, Qi; Lü, Shuai

2017-05-01

Redundancy checking (RC) is a key knowledge reduction technology. Extension rule (ER) is a new reasoning method, first presented in 2003 and well received by experts at home and abroad. Novel extension rule (NER) is an improved ER-based reasoning method, presented in 2009. In this paper, we first analyse the characteristics of the extension rule, and then present a simple algorithm for redundancy checking based on extension rule (RCER). In addition, we introduce MIMF, a type of heuristic strategy. Using the aforementioned rule and strategy, we design and implement RCHER algorithm, which relies on MIMF. Next we design and implement an RCNER (redundancy checking based on NER) algorithm based on NER. Parallel computing greatly accelerates the NER algorithm, which has weak dependence among tasks when executed. Considering this, we present PNER (parallel NER) and apply it to redundancy checking and necessity checking. Furthermore, we design and implement the RCPNER (redundancy checking based on PNER) and NCPPNER (necessary clause partition based on PNER) algorithms as well. The experimental results show that MIMF significantly influences the acceleration of algorithm RCER in formulae on a large scale and high redundancy. Comparing PNER with NER and RCPNER with RCNER, the average speedup can reach up to the number of task decompositions when executed. Comparing NCPNER with the RCNER-based algorithm on separating redundant formulae, speedup increases steadily as the scale of the formulae is incrementing. Finally, we describe the challenges that the extension rule will be faced with and suggest possible solutions.

Rule-based topology system for spatial databases to validate complex geographic datasets

NASA Astrophysics Data System (ADS)

Martinez-Llario, J.; Coll, E.; Núñez-Andrés, M.; Femenia-Ribera, C.

2017-06-01

A rule-based topology software system providing a highly flexible and fast procedure to enforce integrity in spatial relationships among datasets is presented. This improved topology rule system is built over the spatial extension Jaspa. Both projects are open source, freely available software developed by the corresponding author of this paper. Currently, there is no spatial DBMS that implements a rule-based topology engine (considering that the topology rules are designed and performed in the spatial backend). If the topology rules are applied in the frontend (as in many GIS desktop programs), ArcGIS is the most advanced solution. The system presented in this paper has several major advantages over the ArcGIS approach: it can be extended with new topology rules, it has a much wider set of rules, and it can mix feature attributes with topology rules as filters. In addition, the topology rule system can work with various DBMSs, including PostgreSQL, H2 or Oracle, and the logic is performed in the spatial backend. The proposed topology system allows users to check the complex spatial relationships among features (from one or several spatial layers) that require some complex cartographic datasets, such as the data specifications proposed by INSPIRE in Europe and the Land Administration Domain Model (LADM) for Cadastral data.

Rule based artificial intelligence expert system for determination of upper extremity impairment rating.

PubMed

Lim, I; Walkup, R K; Vannier, M W

1993-04-01

Quantitative evaluation of upper extremity impairment, a percentage rating most often determined using a rule based procedure, has been implemented on a personal computer using an artificial intelligence, rule-based expert system (AI system). In this study, the rules given in Chapter 3 of the AMA Guides to the Evaluation of Permanent Impairment (Third Edition) were used to develop such an AI system for the Apple Macintosh. The program applies the rules from the Guides in a consistent and systematic fashion. It is faster and less error-prone than the manual method, and the results have a higher degree of precision, since intermediate values are not truncated.

Simulating water markets with transaction costs

PubMed Central

Erfani, Tohid; Binions, Olga; Harou, Julien J

2014-01-01

This paper presents an optimization model to simulate short-term pair-wise spot-market trading of surface water abstraction licenses (water rights). The approach uses a node-arc multicommodity formulation that tracks individual supplier-receiver transactions in a water resource network. This enables accounting for transaction costs between individual buyer-seller pairs and abstractor-specific rules and behaviors using constraints. Trades are driven by economic demand curves that represent each abstractor's time-varying water demand. The purpose of the proposed model is to assess potential hydrologic and economic outcomes of water markets and aid policy makers in designing water market regulations. The model is applied to the Great Ouse River basin in Eastern England. The model assesses the potential weekly water trades and abstractions that could occur in a normal and a dry year. Four sectors (public water supply, energy, agriculture, and industrial) are included in the 94 active licensed water diversions. Each license's unique environmental restrictions are represented and weekly economic water demand curves are estimated. Rules encoded as constraints represent current water management realities and plausible stakeholder-informed water market behaviors. Results show buyers favor sellers who can supply large volumes to minimize transactions. The energy plant cooling and agricultural licenses, often restricted from obtaining water at times when it generates benefits, benefit most from trades. Assumptions and model limitations are discussed. Key Points Transaction tracking hydro-economic optimization models simulate water markets Proposed model formulation incorporates transaction costs and trading behavior Water markets benefit users with the most restricted water access PMID:25598558

Simulating water markets with transaction costs.

PubMed

Erfani, Tohid; Binions, Olga; Harou, Julien J

2014-06-01

This paper presents an optimization model to simulate short-term pair-wise spot-market trading of surface water abstraction licenses (water rights). The approach uses a node-arc multicommodity formulation that tracks individual supplier-receiver transactions in a water resource network. This enables accounting for transaction costs between individual buyer-seller pairs and abstractor-specific rules and behaviors using constraints. Trades are driven by economic demand curves that represent each abstractor's time-varying water demand. The purpose of the proposed model is to assess potential hydrologic and economic outcomes of water markets and aid policy makers in designing water market regulations. The model is applied to the Great Ouse River basin in Eastern England. The model assesses the potential weekly water trades and abstractions that could occur in a normal and a dry year. Four sectors (public water supply, energy, agriculture, and industrial) are included in the 94 active licensed water diversions. Each license's unique environmental restrictions are represented and weekly economic water demand curves are estimated. Rules encoded as constraints represent current water management realities and plausible stakeholder-informed water market behaviors. Results show buyers favor sellers who can supply large volumes to minimize transactions. The energy plant cooling and agricultural licenses, often restricted from obtaining water at times when it generates benefits, benefit most from trades. Assumptions and model limitations are discussed. Transaction tracking hydro-economic optimization models simulate water marketsProposed model formulation incorporates transaction costs and trading behaviorWater markets benefit users with the most restricted water access.

Simulation-Based Rule Generation Considering Readability

PubMed Central

Yahagi, H.; Shimizu, S.; Ogata, T.; Hara, T.; Ota, J.

2015-01-01

Rule generation method is proposed for an aircraft control problem in an airport. Designing appropriate rules for motion coordination of taxiing aircraft in the airport is important, which is conducted by ground control. However, previous studies did not consider readability of rules, which is important because it should be operated and maintained by humans. Therefore, in this study, using the indicator of readability, we propose a method of rule generation based on parallel algorithm discovery and orchestration (PADO). By applying our proposed method to the aircraft control problem, the proposed algorithm can generate more readable and more robust rules and is found to be superior to previous methods. PMID:27347501