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Sample records for resistance-encoding region encodes

  1. Environmental cycle of antibiotic resistance encoded genes: A systematic review

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    R. ghanbari

    2017-12-01

    Full Text Available Antibiotic-resistant bacteria and genes enter the environment in different ways. The release of these factors into the environment has increased concerns related to public health. The aim of the study was to evaluate the antibiotic resistance genes (ARGs in the environmental resources. In this systematic review, the data were extracted from valid sources of information including ScienceDirect, PubMed, Google Scholar and SID. Evaluation and selection of articles were conducted on the basis of the PRISMA checklist. A total of 39 articles were included in the study, which were chosen from a total of 1249 papers. The inclusion criterion was the identification of genes encoding antibiotic resistance against the eight important groups of antibiotics determined by using the PCR technique in the environmental sources including municipal and hospital wastewater treatment plants, animal and agricultural wastes, effluents from treatment plants, natural waters, sediments, and drinking waters. In this study, 113 genes encoding antibiotic resistance to eight groups of antibiotics (beta-lactams, aminoglycosides, tetracyclines, macrolides, sulfonamides, chloramphenicol, glycopeptides and quinolones were identified in various environments. Antibiotic resistance genes were found in all the investigated environments. The investigation of microorganisms carrying these genes shows that most of the bacteria especially gram-negative bacteria are effective in the acquisition and the dissemination of these pollutants in the environment. Discharging the raw wastewaters and effluents from wastewater treatments acts as major routes in the dissemination of ARGs into environment sources and can pose hazards to public health.

  2. Mobile antibiotic resistance encoding elements promote their own diversity.

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    Geneviève Garriss

    2009-12-01

    Full Text Available Integrating conjugative elements (ICEs are a class of bacterial mobile genetic elements that disseminate via conjugation and then integrate into the host cell genome. The SXT/R391 family of ICEs consists of more than 30 different elements that all share the same integration site in the host chromosome but often encode distinct properties. These elements contribute to the spread of antibiotic resistance genes in several gram-negative bacteria including Vibrio cholerae, the agent of cholera. Here, using comparative analyses of the genomes of several SXT/R391 ICEs, we found evidence that the genomes of these elements have been shaped by inter-ICE recombination. We developed a high throughput semi-quantitative method to explore the genetic determinants involved in hybrid ICE formation. Recombinant ICE formation proved to be relatively frequent, and to depend on host (recA and ICE (s065 and s066 loci, which can independently and potentially cooperatively mediate hybrid ICE formation. s065 and s066, which are found in all SXT/R391 ICEs, are orthologues of the bacteriophage lambda Red recombination genes bet and exo, and the s065/s066 recombination system is the first Red-like recombination pathway to be described in a conjugative element. Neither ICE excision nor conjugative transfer proved to be essential for generation of hybrid ICEs. Instead conjugation facilitates the segregation of hybrids and could provide a means to select for functional recombinant ICEs containing novel combinations of genes conferring resistance to antibiotics. Thus, ICEs promote their own diversity and can yield novel mobile elements capable of disseminating new combinations of antibiotic resistance genes.

  3. Plasmid-Mediated Florfenicol Resistance Encoded by the floR Gene in Escherichia coli Isolated from Cattle

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    Cloeckaert, Axel; Baucheron, Sylvie; Flaujac, Geraldine; Schwarz, Stefan; Kehrenberg, Corinna; Martel, Jean-Louis; Chaslus-Dancla, Elisabeth

    2000-01-01

    A florfenicol resistance gene almost identical to floR of Salmonella enterica serovar Typhimurium DT104 was detected on 110- to 125-kb plasmids in Escherichia coli isolates of animal origin. Analysis of the floR gene flanking regions of one of the plasmids showed that they were different from those encountered in S. enterica serovar Typhimurium DT104. PMID:10991873

  4. Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources.

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    Claudia Fernández-Alarcón

    Full Text Available Incompatibility group A/C (IncA/C plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla(CMY-2 gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla(CMY-2 plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.

  5. Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources.

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    Fernández-Alarcón, Claudia; Singer, Randall S; Johnson, Timothy J

    2011-01-01

    Incompatibility group A/C (IncA/C) plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR) phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla(CMY-2) gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla(CMY-2) plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.

  6. Class 1 Integron-Borne, Multiple-Antibiotic Resistance Encoded by a 150-Kilobase Conjugative Plasmid in Epidemic Vibrio cholerae O1 Strains Isolated in Guinea-Bissau

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    Dalsgaard, Anders; Forslund, Anita; Petersen, Andreas; Brown, Derek J.; Dias, Francisco; Monteiro, Serifo; Mølbak, Kåre; Aaby, Peter; Rodrigues, Amabelia; Sandström, Anita

    2000-01-01

    In the 1996–1997 cholera epidemic in Guinea-Bissau, surveillance for antimicrobial resistance showed the emergence of a multidrug-resistant strain of Vibrio cholerae O1 during the course of the epidemic. The strain was resistant to ampicillin, erythromycin, tetracycline, furazolidone, aminoglycosides, trimethoprim, and sulfamethoxazole. Concomitant with the emergence of this strain, we observed a resurgence in the number of registered cholera cases as well as an increase in the case fatality rate from 1.0% before the emergence of the multiple-drug-resistant strain to 5.3% after the emergence of the strain. Our study shows that the strain contained a 150-kb conjugative multiple-antibiotic resistance plasmid with class 1 integron-borne gene cassettes encoding resistance to trimethoprim (dhfrXII) and aminoglycosides [ant(3")-1a]). The finding of transferable resistance to almost all of the antibiotics commonly used to treat cholera is of great public health concern. Studies should be carried out to determine to what extent the strain or its resistance genes have been spread to other areas where cholera is endemic. PMID:11015401

  7. Clonal diversity and detection of carbapenem resistance encoding genes among multidrug-resistant Acinetobacter baumannii isolates recovered from patients and environment in two intensive care units in a Moroccan hospital

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    Uwingabiye, Jean; Lemnouer, Abdelhay; Roca, Ignasi; Alouane, Tarek; Frikh, Mohammed; Belefquih, Bouchra; Bssaibis, Fatna; Maleb, Adil; Benlahlou, Yassine; Kassouati, Jalal; Doghmi, Nawfal; Bait, Abdelouahed; Haimeur, Charki; Louzi, Lhoussain; Ibrahimi, Azeddine

    2017-01-01

    Background Carbapenem-resistant Acinetobacter baumannii has recently been defined by the World Health Organization as a critical pathogen. The aim of this study was to compare clonal diversity and carbapenemase-encoding genes of A. baumannii isolates collected from colonized or infected patients and hospital environment in two intensive care units (ICUs) in Morocco. Methods The patient and environmental sampling was carried out in the medical and surgical ICUs of Mohammed V Military teaching ...

  8. The tomato I gene for Fusarium wilt resistance encodes an atypical leucine-rich repeat receptor-like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1.

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    Catanzariti, Ann-Maree; Do, Huong T T; Bru, Pierrick; de Sain, Mara; Thatcher, Louise F; Rep, Martijn; Jones, David A

    2017-03-01

    We have identified the tomato I gene for resistance to the Fusarium wilt fungus Fusarium oxysporum f. sp. lycopersici (Fol) and show that it encodes a membrane-anchored leucine-rich repeat receptor-like protein (LRR-RLP). Unlike most other LRR-RLP genes involved in plant defence, the I gene is not a member of a gene cluster and contains introns in its coding sequence. The I gene encodes a loopout domain larger than those in most other LRR-RLPs, with a distinct composition rich in serine and threonine residues. The I protein also lacks a basic cytosolic domain. Instead, this domain is rich in aromatic residues that could form a second transmembrane domain. The I protein recognises the Fol Avr1 effector protein, but, unlike many other LRR-RLPs, recognition specificity is determined in the C-terminal half of the protein by polymorphic amino acid residues in the LRRs just preceding the loopout domain and in the loopout domain itself. Despite these differences, we show that I/Avr1-dependent necrosis in Nicotiana benthamiana depends on the LRR receptor-like kinases (RLKs) SERK3/BAK1 and SOBIR1. Sequence comparisons revealed that the I protein and other LRR-RLPs involved in plant defence all carry residues in their last LRR and C-terminal LRR capping domain that are conserved with SERK3/BAK1-interacting residues in the same relative positions in the LRR-RLKs BRI1 and PSKR1. Tyrosine mutations of two of these conserved residues, Q922 and T925, abolished I/Avr1-dependent necrosis in N. benthamiana, consistent with similar mutations in BRI1 and PSKR1 preventing their interaction with SERK3/BAK1. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  9. Clonal diversity and detection of carbapenem resistance encoding genes among multidrug-resistantAcinetobacter baumanniiisolates recovered from patients and environment in two intensive care units in a Moroccan hospital.

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    Uwingabiye, Jean; Lemnouer, Abdelhay; Roca, Ignasi; Alouane, Tarek; Frikh, Mohammed; Belefquih, Bouchra; Bssaibis, Fatna; Maleb, Adil; Benlahlou, Yassine; Kassouati, Jalal; Doghmi, Nawfal; Bait, Abdelouahed; Haimeur, Charki; Louzi, Lhoussain; Ibrahimi, Azeddine; Vila, Jordi; Elouennass, Mostafa

    2017-01-01

    Carbapenem-resistant Acinetobacter baumannii has recently been defined by the World Health Organization as a critical pathogen. The aim of this study was to compare clonal diversity and carbapenemase-encoding genes of A. baumannii isolates collected from colonized or infected patients and hospital environment in two intensive care units (ICUs) in Morocco. The patient and environmental sampling was carried out in the medical and surgical ICUs of Mohammed V Military teaching hospital from March to August 2015. All A. baumannii isolates recovered from clinical and environmental samples, were identified using routine microbiological techniques and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using disc diffusion method. The carbapenemase-encoding genes were screened for by PCR. Clonal relatedness was analyzed by digestion of the DNA with low frequency restriction enzymes and pulsed field gel electrophoresis (PFGE) and the multi locus sequence typing (MLST) was performed on two selected isolates from two major pulsotypes. A total of 83 multidrug-resistant A. baumannii isolates were collected: 47 clinical isolates and 36 environmental isolates. All isolates were positive for the bla OXA51-like and bla OXA23-like genes. The coexistence of bla NDM-1 /bla OXA-23-like and bla OXA 24-like /bla OXA-23-like were detected in 27 (32.5%) and 2 (2.4%) of A. baumannii isolates, respectively. The environmental samples and the fecally-colonized patients were significantly identified ( p  distinct clusters with two major groups (0007 and 0008) containing up to 59% of the isolates. The pulsotype 0008 corresponds to sequence type (ST) 195 while pulsotype 0007 corresponds to ST 1089.The genetic similarity between the clinical and environmental isolates was observed in 80/83 = 96.4% of all isolates, belonging to 7 pulsotypes. This study shows that the clonal spread of environmental A. baumannii isolates

  10. Clonal diversity and detection of carbapenem resistance encoding genes among multidrug-resistant Acinetobacter baumannii isolates recovered from patients and environment in two intensive care units in a Moroccan hospital

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    Jean Uwingabiye

    2017-09-01

    Full Text Available Abstract Background Carbapenem-resistant Acinetobacter baumannii has recently been defined by the World Health Organization as a critical pathogen. The aim of this study was to compare clonal diversity and carbapenemase-encoding genes of A. baumannii isolates collected from colonized or infected patients and hospital environment in two intensive care units (ICUs in Morocco. Methods The patient and environmental sampling was carried out in the medical and surgical ICUs of Mohammed V Military teaching hospital from March to August 2015. All A. baumannii isolates recovered from clinical and environmental samples, were identified using routine microbiological techniques and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using disc diffusion method. The carbapenemase-encoding genes were screened for by PCR. Clonal relatedness was analyzed by digestion of the DNA with low frequency restriction enzymes and pulsed field gel electrophoresis (PFGE and the multi locus sequence typing (MLST was performed on two selected isolates from two major pulsotypes. Results A total of 83 multidrug-resistant A. baumannii isolates were collected: 47 clinical isolates and 36 environmental isolates. All isolates were positive for the bla OXA51-like and bla OXA23-like genes. The coexistence of bla NDM-1 /bla OXA-23-like and bla OXA 24-like /bla OXA-23-like were detected in 27 (32.5% and 2 (2.4% of A. baumannii isolates, respectively. The environmental samples and the fecally-colonized patients were significantly identified (p < 0.05 as the most common sites of isolation of NDM-1-harboring isolates. PFGE grouped all isolates into 9 distinct clusters with two major groups (0007 and 0008 containing up to 59% of the isolates. The pulsotype 0008 corresponds to sequence type (ST 195 while pulsotype 0007 corresponds to ST 1089.The genetic similarity between the clinical and environmental isolates

  11. Nonmotor regions encode path-related information during movements.

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    Breault, Macauley S; Sacre, Pierre; Johnson, Jacob J; Kerr, Matthew; Johnson, Matthew D; Bulacio, Juan; Gonzalez-Martinez, Jorge; Sarma, Sridevi V; Gale, John T

    2017-07-01

    Sensorimotor control and the involvement of motor brain regions has been extensively studied, but the role nonmotor brain regions play during movements has been overlooked. This is particularly due to the difficulty of recording from multiple regions in the brain during motor control. In this study, we utilize stereoelectroencephalography (SEEG) recording techniques to explore the role nonmotor brain areas have on the way we move. Nine humans were implanted with SEEG depth electrodes for clinical purposes, which rendered access to local field potential (LFP) activity in deep and peripheral nonmotor structures. Participants performed fast and slow arm reaching movements using a robotic manipulandum. In this study, we explored whether neural activity in a given nonmotor brain structure correlated to movement path metrics including: path length, path deviation, and path speed. Statistical analysis revealed correlations between averaged neural activity in middle temporal gyrus, supramarginal gyrus, and fusiform gyrus and our path metrics both within and across the subjects. Furthermore, we split trials across subjects into two groups: one group consisted of trials with high values of each path metric and the other with low values. We then found significant differences in LFP power in specific frequency bands (e.g. beta) during movement between each group. These results suggest that nonmotor regions may dynamically encode path-related information during movement.

  12. Brainstem Encoding of Aided Speech in Hearing Aid Users with Cochlear Dead Region(s

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    Hassaan, Mohammad Ramadan

    2016-02-01

    Full Text Available Introduction Neural encoding of speech begins with the analysis of the signal as a whole broken down into its sinusoidal components in the cochlea, which has to be conserved up to the higher auditory centers. Some of these components target the dead regions of the cochlea causing little or no excitation. Measuring aided speech-evoked auditory brainstem response elicited by speech stimuli with different spectral maxima can give insight into the brainstem encoding of aided speech with spectral maxima at these dead regions. Objective This research aims to study the impact of dead regions of the cochlea on speech processing at the brainstem level after a long period of hearing aid use. Methods This study comprised 30 ears without dead regions and 46 ears with dead regions at low, mid, or high frequencies. For all ears, we measured the aided speech-evoked auditory brainstem response using speech stimuli of low, mid, and high spectral maxima. Results Aided speech-evoked auditory brainstem response was producible in all subjects. Responses evoked by stimuli with spectral maxima at dead regions had longer latencies and smaller amplitudes when compared with the control group or the responses of other stimuli. Conclusion The presence of cochlear dead regions affects brainstem encoding of speech with spectral maxima perpendicular to these regions. Brainstem neuroplasticity and the extrinsic redundancy of speech can minimize the impact of dead regions in chronic hearing aid users.

  13. Identification of chromatin marks at TERRA promoter and encoding region.

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    Negishi, Yutaka; Kawaji, Hideya; Minoda, Aki; Usui, Kengo

    2015-11-27

    TERRA is a long non-coding RNA that is essential for telomere integrity. Although it is transcribed from subtelomeres and telomeres, how it is expressed in heterochromatic region is currently unknown. In this study, we focused our analysis on TERRA-encoding region TelBam3.4 and TelBam3.4-like sequences, and determined their transcription start sites, as well as enrichment of RNA polymerase II and histone modifications. We found that H3K4me3 and H3K9me3 are present at TERRA promoters, whereas H3K27ac and H3K9me3 are present at telomeric repeats. Consistently, we show that presence of active histone modifications H3K4me3 and H3K27ac are correlated to TERRA expression. These results mark an important step towards understanding telomere maintenance and transcription. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Commensal E. coli as an Important Reservoir of Resistance Encoding Genetic Elements

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    Azam Mahmoudi-Aznaveh

    2013-11-01

    Full Text Available Background: Diarrheagenic E. coli is the most important cause of diarrhea in children and is a public health concern in developing countries. A major public problem is acquisition and transmission of antimicrobial resistance via mobile genetic elements including plasmids, conjugative transposons, and integrons which may occur through horizontal gene transfer. Objectives: The aim of this study was to investigate the distribution of class 1 and 2 integrons among commensal and enteropathogenic E. coli isolates and assess the role of commensal E. coli population as a reservoir in the acquisition and transmission of antimicrobial resistance. Materials and Methods: Swabs were collected directly from stool samples of the children with diarrhea admitted to three hospitals in Tehran, Iran during July 2012 through October 2012. Antimicrobial susceptibility testing and PCR analysis were performed for analysis of the resistance pattern and integron content of isolates. Results: A total of 20 enteropathogenic E.coli (identified as eae+stx1-stx2- and 20 commensal E.coli were selected for analysis. The resistance pattern in commensal and pathogenic E.coli was very similar. In both groups a high rate of resistance was seen to tetracycline, streptomycin, cotrimoxazole, nalidixic acid, and minocycline. Of 20 EPEC strains, 3 strains (15 % and 1 strain (5% had positive results for int and hep genes, respectively. Among 20 commensal, 65% (13 strains and 10% (2 strains had positive results for int and hep genes, respectively. Conclusions: The higher rate of class 1 integron occurrence among commensal population proposes the commensal intestinal organisms as a potential reservoir of mobile resistance gene elements which could transfer the resistance gene cassettes to other pathogenic and/or nonpathogenic organisms in the intestinal lumen at different occasions.

  15. Trait-based food-cravings are encoded by regional homogeneity in the parahippocampal gyrus.

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    Chen, Shuaiyu; Dong, Debo; Jackson, Todd; Zhuang, Qian; Chen, Hong

    2017-07-01

    Food cravings can reflect an intense trait-like emotional-motivational desire to eat palatable food, often resulting in the failure of weight loss efforts. Studies have linked trait-based food-cravings to increased risk of overeating. However, little is known about resting-state neural mechanisms that underlie food cravings. We investigated this issue using resting-state functional magnetic resonance imaging (fMRI) to test the extent to which spontaneous neural activity occurs in regions implicated in emotional memory and reward motivation associated with food cravings. Spontaneous regional activity patterns correlating to food cravings were assessed among 65 young healthy women using regional homogeneity analysis to assess temporal synchronization of spontaneous activity. Analyses indicated that women with higher scores on the Food Cravings Questionnaire displayed increased local functional homogeneity in brain regions involved in emotional memory and visual attention processing (i.e., parahippocampal gyrus and fusiform gyrus) but not reward. In view of parahippocampal gyrus involvement in hedonic learning and incentive memory encoding, this study suggests that trait-based food cravings are encoded by emotional memory circuits. Copyright © 2017. Published by Elsevier Ltd.

  16. Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2 encoding secreted proteins

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    Mereghetti Laurent

    2011-04-01

    Full Text Available Abstract Background The genome of serotype M28 group A Streptococcus (GAS strain MGAS6180 contains a novel genetic element named Region of Difference 2 (RD2 that encodes seven putative secreted extracellular proteins. RD2 is present in all serotype M28 strains and strains of several other GAS serotypes associated with female urogenital infections. We show here that the GAS RD2 element is present in strain MGAS6180 both as an integrative chromosomal form and a circular extrachromosomal element. RD2-like regions were identified in publicly available genome sequences of strains representing three of the five major group B streptococcal serotypes causing human disease. Ten RD2-encoded proteins have significant similarity to proteins involved in conjugative transfer of Streptococcus thermophilus integrative chromosomal elements (ICEs. Results We transferred RD2 from GAS strain MGAS6180 (serotype M28 to serotype M1 and M4 GAS strains by filter mating. The copy number of the RD2 element was rapidly and significantly increased following treatment of strain MGAS6180 with mitomycin C, a DNA damaging agent. Using a PCR-based method, we also identified RD2-like regions in multiple group C and G strains of Streptococcus dysgalactiae subsp.equisimilis cultured from invasive human infections. Conclusions Taken together, the data indicate that the RD2 element has disseminated by lateral gene transfer to genetically diverse strains of human-pathogenic streptococci.

  17. Structured RNAs in the ENCODE selected regions of the human genome

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    Washietl, Stefan; Pedersen, Jakob Skou; Korbel, Jan O

    2007-01-01

    Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack...... with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz...

  18. The Saccharomyces cerevisiae enolase-related regions encode proteins that are active enolases.

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    Kornblatt, M J; Richard Albert, J; Mattie, S; Zakaib, J; Dayanandan, S; Hanic-Joyce, P J; Joyce, P B M

    2013-02-01

    In addition to two genes (ENO1 and ENO2) known to code for enolase (EC4.2.1.11), the Saccharomyces cerevisiae genome contains three enolase-related regions (ERR1, ERR2 and ERR3) which could potentially encode proteins with enolase function. Here, we show that products of these genes (Err2p and Err3p) have secondary and quaternary structures similar to those of yeast enolase (Eno1p). In addition, Err2p and Err3p can convert 2-phosphoglycerate to phosphoenolpyruvate, with kinetic parameters similar to those of Eno1p, suggesting that these proteins could function as enolases in vivo. To address this possibility, we overexpressed the ERR2 and ERR3 genes individually in a double-null yeast strain lacking ENO1 and ENO2, and showed that either ERR2 or ERR3 could complement the growth defect in this strain when cells are grown in medium with glucose as the carbon source. Taken together, these data suggest that the ERR genes in Saccharomyces cerevisiae encode a protein that could function in glycolysis as enolase. The presence of these enolase-related regions in Saccharomyces cerevisiae and their absence in other related yeasts suggests that these genes may play some unique role in Saccharomyces cerevisiae. Further experiments will be required to determine whether these functions are related to glycolysis or other cellular processes. Copyright © 2012 John Wiley & Sons, Ltd.

  19. Growth Factor Identity Is Encoded by Discrete Coiled-Coil Rotamers in the EGFR Juxtamembrane Region.

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    Doerner, Amy; Scheck, Rebecca; Schepartz, Alanna

    2015-06-18

    Binding of transforming growth factor α (TGF-α) to the epidermal growth factor receptor (EGFR) extracellular domain is encoded through the formation of a unique antiparallel coiled coil within the juxtamembrane segment. This new coiled coil is an "inside-out" version of the coiled coil formed in the presence of epidermal growth factor (EGF). A third, intermediary coiled-coil interface is formed in the juxtamembrane region when EGFR is stimulated with betacellulin. The seven growth factors that activate EGFR in mammalian systems (EGF, TGF-α, epigen, epiregulin, betacellulin, heparin-binding EGF, and amphiregulin) fall into distinct categories in which the structure of the coiled coil induced within the juxtamembrane region correlates with cell state. The observation that coiled-coil state tracks with the downstream signaling profiles for each ligand provides evidence for growth factor functional selectivity by EGFR. Encoding growth factor identity in alternative coiled-coil rotamers provides a simple and elegant method for communicating chemical information across the plasma membrane. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

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    Mignon A Keaton

    2011-03-01

    Full Text Available The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.

  1. Conserved sequences of BART and BHRF regions encoding viral microRNAs in Epstein-Barr virus-associated lymphoma.

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    Sunagawa, Keishin; Hishima, Tsunekazu; Fukumoto, Hitomi; Hasegawa, Hideki; Katano, Harutaka

    2017-07-14

    Epstein-Barr virus (EBV) encodes at least 25 pri-microRNAs (miRNAs) in two regions of its DNA genome, BART and BHRF. B95-8, an EBV reference strain, has a deletion in the BART region. However, no information is available on the deletions or mutations in the BART and BHRF regions in clinical samples of EBV-associated lymphoma. Nine DNA fragments encoding miR-BARTs and two coding miR-BHRF1s were amplified by PCR from DNA samples extracted from 16 cases of EBV-associated lymphoma. All the PCR products were sequenced directly. DNA fragments encoding miR-BARTs and miR-BHRF1-1 were successfully amplified from all samples. An adenine-to-guanine mutation in the DNA fragment encoding miR-BART2-3p was detected in four of the 16 cases, and a cytosine-to-thymidine mutation in the DNA fragment encoding miR-BART11-3p was detected in one of the 16 samples. These mutations were not associated with any histological categories of lymphoma. In conclusion, mutations were rarely observed in the DNA encoding viral miRNAs in cases of lymphoma. This suggests that the DNA sequences of EBV-encoded miR-BARTs and miR-BHRF1-1 are conserved in EBV-associated lymphoma.

  2. An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis

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    Wang, Ming; Fleming, Joy; Li, Zihui; Li, Chuanyou; Zhang, Hongtai; Xue, Yunxin; Chen, Maoshan; Zhang, Zongde; Zhang, Xian-En; Bi, Lijun

    2016-01-01

    Deep-sequencing of bacterial transcriptomes using RNA-Seq technology has made it possible to identify small non-coding RNAs, RNA molecules which regulate gene expression in response to changing environments, on a genome-wide scale in an ever-increasing range of prokaryotes. However, a simple and reliable automated method for identifying sRNA candidates in these large datasets is lacking. Here, after generating a transcriptome from an exponential phase culture of Mycobacterium tuberculosis H37Rv, we developed and validated an automated method for the genome-wide identification of sRNA candidate-containing regions within RNA-Seq datasets based on the analysis of the characteristics of reads coverage maps. We identified 192 novel candidate sRNA-encoding regions in intergenic regions and 664 RNA transcripts transcribed from regions antisense (as) to open reading frames (ORF), which bear the characteristics of asRNAs, and validated 28 of these novel sRNA-encoding regions by northern blotting. Our work has not only provided a simple automated method for genome-wide identification of candidate sRNA-encoding regions in RNA-Seq data, but has also uncovered many novel candidate sRNA-encoding regions in M. tuberculosis, reinforcing the view that the control of gene expression in bacteria is more complex than previously anticipated. PMID:27174874

  3. Regulatory elements in the promoter region of the rat gene encoding the acyl-CoA-binding protein

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    Elholm, M; Bjerking, G; Knudsen, J

    1996-01-01

    Acyl-CoA-binding protein (ACBP) is an ubiquitously expressed 10-kDa protein which is present in high amounts in cells involved in solute transport or secretion. Rat ACBP is encoded by a gene containing the typical hallmarks of a housekeeping gene. Analysis of the promoter region of the rat ACBP g...

  4. Transposon Tn5 encodes streptomycin resistance in nonenteric bacteria.

    OpenAIRE

    O'Neill, E A; Kiely, G M; Bender, R A

    1984-01-01

    Strains of Caulobacter crescentus, Pseudomonas putida, Acinetobacter calcoaceticus, Rhizobium meliloti, and Rhodopseudomonas sphaeroides carrying the kanamycin resistance-encoding transposon Tn5 were 15 to 500 times more resistant to streptomycin than transposon-free strains. The streptomycin resistance determinant, which is separable from the kanamycin resistance determinant of Tn5, was not expressed in Escherichia coli or Klebsiella aerogenes.

  5. Alternative exon-encoding regions of Locusta migratoria muscle myosin modulate the pH dependence of ATPase activity.

    Science.gov (United States)

    Li, J; Lu, Z; He, J; Chen, Q; Wang, X; Kang, L; Li, X-D

    2016-12-01

    Whereas the vertebrate muscle myosin heavy chains (MHCs) are encoded by a family of Mhc genes, most insects examined to date contain a single Mhc gene and produce all of the different MHC isoforms by alternative RNA splicing. Here, we found that the migratory locust, Locusta migratoria, has one Mhc gene, which contains 41 exons, including five alternative exclusive exons and one differently included penultimate exon, and potentially encodes 360 MHC isoforms. From the adult L. migratoria, we identified 14 MHC isoforms (including two identical isoforms): four from flight muscle (the thorax dorsal longitudinal muscle), three from jump muscle (the hind leg extensor tibiae muscle) and seven from the abdominal intersegmental muscle. We purified myosins from flight muscle and jump muscle and characterized their motor activities. At neutral pH, the flight and the jump muscle myosins displayed similar levels of in vitro actin-gliding activity, whereas the former had a slightly higher actin-activated ATPase activity than the latter. Interestingly, the pH dependences of the actin-activated ATPase activity of these two myosins are different. Because the dominant MHC isoforms in these two muscles are identical except for the two alternative exon-encoding regions, we propose that these two alternative regions modulate the pH dependence of L. migratoria muscle myosin. © 2016 The Royal Entomological Society.

  6. Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

    DEFF Research Database (Denmark)

    Rossin, Elizabeth J.; Hansen, Kasper Lage; Raychaudhuri, Soumya

    2011-01-01

    in rheumatoid arthritis (RA) and Crohn's disease (CD) GWAS, we build protein-protein interaction (PPI) networks for genes within associated loci and find abundant physical interactions between protein products of associated genes. We apply multiple permutation approaches to show that these networks are more...... that the RA and CD networks have predictive power by demonstrating that proteins in these networks, not encoded in the confirmed list of disease associated loci, are significantly enriched for association to the phenotypes in question in extended GWAS analysis. Finally, we test our method in 3 non...... evidence that, for many of the complex diseases studied here, common genetic associations implicate regions encoding proteins that physically interact in a preferential manner, in line with observations in Mendelian disease....

  7. Regional activation of the human medial temporal lobe during intentional encoding of objects and positions

    DEFF Research Database (Denmark)

    Ramsøy, T.Z.; Liptrot, Matthew George; Skimminge, A.

    2009-01-01

    The medial temporal lobe (MTL) consists of several regions thought to be involved in learning and memory. However, the degree of functional specialization among these regions remains unclear. Previous studies have demonstrated effects of both content and processing stage, but findings have been...

  8. Minor Threonine Dehydratase Encoded Within the Threonine Synthetic Region of Bacillus subtilis1

    Science.gov (United States)

    Vapnek, Daniel; Greer, Sheldon

    1971-01-01

    Challenging auxotrophs on metabolites that are precursors of a biosynthetic step involving a mutated enzyme has revealed a new class of suppressor mutations which act by derepressing a minor enzyme activity not normally detected in the wild-type strain. These indirect, partial suppressor mutations which allow isoleucine auxotrophs to grow on homoserine or threonine have been analyzed to determine their effect on enzymes involved in the biosynthesis of these amino acids. It has been found that one class of these suppressor mutations (sprA) leads to the derepression of homoserine kinase, homoserine dehydrogenase, and a minor threonine dehydratase that is not sufficiently active to be detected in the wild-type strain. The gene encoding this second threonine dehydratase activity has been found to be located between the structural genes for homoserine kinase and homoserine dehydrogenase. The results of these experiments indicate that plating of auxotrophs on precursors of a biosynthetic step involving mutated enzymes could prove to be a valuable method for the detection of regulatory mutants as well as a possible tool in studying the evolution of biochemical pathways. PMID:4997544

  9. A Legionella pneumophila effector protein encoded in a region of genomic plasticity binds to Dot/Icm-modified vacuoles.

    Directory of Open Access Journals (Sweden)

    Shira Ninio

    2009-01-01

    Full Text Available Legionella pneumophila is an opportunistic pathogen that can cause a severe pneumonia called Legionnaires' disease. In the environment, L. pneumophila is found in fresh water reservoirs in a large spectrum of environmental conditions, where the bacteria are able to replicate within a variety of protozoan hosts. To survive within eukaryotic cells, L. pneumophila require a type IV secretion system, designated Dot/Icm, that delivers bacterial effector proteins into the host cell cytoplasm. In recent years, a number of Dot/Icm substrate proteins have been identified; however, the function of most of these proteins remains unknown, and it is unclear why the bacterium maintains such a large repertoire of effectors to promote its survival. Here we investigate a region of the L. pneumophila chromosome that displays a high degree of plasticity among four sequenced L. pneumophila strains. Analysis of GC content suggests that several genes encoded in this region were acquired through horizontal gene transfer. Protein translocation studies establish that this region of genomic plasticity encodes for multiple Dot/Icm effectors. Ectopic expression studies in mammalian cells indicate that one of these substrates, a protein called PieA, has unique effector activities. PieA is an effector that can alter lysosome morphology and associates specifically with vacuoles that support L. pneumophila replication. It was determined that the association of PieA with vacuoles containing L. pneumophila requires modifications to the vacuole mediated by other Dot/Icm effectors. Thus, the localization properties of PieA reveal that the Dot/Icm system has the ability to spatially and temporally control the association of an effector with vacuoles containing L. pneumophila through activities mediated by other effector proteins.

  10. Two putative subunits of a peptide pump encoded in the human major histocompatability complex class 2 region

    International Nuclear Information System (INIS)

    Bahram, S.; Arnold, D.; Bresnahan, M.; Strominger, J.L.; Spies, T.

    1991-01-01

    The class 2 region of the human major histocompatibility complex (MHC) may encode several genes controlling the processing of endogenous antigen and the presentation of peptide epitopes by MHC class 1 molecules to cytotoxic T lymphocytes. A previously described peptide supply factor (PSF1) is a member of the multidrug-resistance family of transporters and may pump cytosolic peptides into the membrane-bound compartment where class 1 molecules assemble. A second transporter gene, PSF2, was identified 10 kilobases (kb) from PSF1, near the class 2 DOB gene. The complete sequences of PSF1 and PSF2 were determined from cDNA clones. The translation products are closely related in sequence and predicted secondary structure. Both contain a highly conserved ATP-binding fold and share 25% homology in a hydrophobic domain with a tentative number of eight membrane-spanning segments. Based on the principle dimeric organization of these two domains in other transporters, PSF1 and PSF2 may function as complementary subunits, independently as homodimers, or both. Taken together with previous genetic evidence, the coregulation of PSF1 and PSF2 by γ interferon and the to-some-degree coordinate transcription of these genes suggest a common role in peptide-loading of class 1 molecules, although a distinct function of PSF2 cannot be ruled out

  11. A Blumeria graminis gene family encoding proteins with a C-terminal variable region with homologues in pathogenic fungi.

    Science.gov (United States)

    Grell, Morten N; Mouritzen, Peter; Giese, Henriette

    2003-06-05

    In a study aimed at characterising, at the molecular level, the obligate biotrophic fungus Blumeria graminis f. sp. hordei (Bgh), we have identified a novel group of genes, the Egh16H genes, and shown that two of these are up-regulated during primary infection of barley leaves. The genes have partial homology to a previously characterised Bgh gene family, Egh16. Egh16 and Egh16H are subfamilies of a larger multigene family with presently about 15 members identified in Bgh. Egh16H has about ten members, and we show that five of these are expressed as highly conserved mRNAs that are predicted to encode proteins with a C-terminal variable region. Egh16H has high homology to sequences in Magnaporthe grisea and other plant pathogenic fungi, as well as sequences of both the insect pathogen Metarhizium anisopliae and the human pathogen Aspergillus fumigatus. No close homologues of Egh16H were found in the non-pathogenic fungi Neurospora crassa and Aspergillus nidulans. We predict that Egh16H plays a general role in the interaction between pathogenic fungi and their hosts. At present, the large number of gene family members with C-terminal variation appears to be unique for Bgh, and the Egh16/Egh16H gene family is to our knowledge the largest gene family so far characterised in this fungus.

  12. Class 1 Integron-Borne, Multiple-Antibiotic Resistance Encoded by a 150-Kilobase Conjugative Plasmid in Epidemic Vibrio cholerae O1 Strains Isolated in Guinea-Bissau

    OpenAIRE

    Dalsgaard, Anders; Forslund, Anita; Petersen, Andreas; Brown, Derek J.; Dias, Francisco; Monteiro, Serifo; Mølbak, Kåre; Aaby, Peter; Rodrigues, Amabelia; Sandström, Anita

    2000-01-01

    In the 1996–1997 cholera epidemic in Guinea-Bissau, surveillance for antimicrobial resistance showed the emergence of a multidrug-resistant strain of Vibrio cholerae O1 during the course of the epidemic. The strain was resistant to ampicillin, erythromycin, tetracycline, furazolidone, aminoglycosides, trimethoprim, and sulfamethoxazole. Concomitant with the emergence of this strain, we observed a resurgence in the number of registered cholera cases as well as an increase in the case fatality ...

  13. Chemical and serologic definition of two unique D region-encoded molecules in the wild-derived mouse strain B10.GAA37.

    Science.gov (United States)

    Lillehoj, E P; Walsh, W D; Potter, T; Lee, D R; Coligan, J E; Hansen, T H

    1984-12-01

    Detailed serologic and biochemical characterization of D region products of the wild-derived mouse strain B10.GAA37 (Dw16) were performed and compared with previous studies of the D region products of the H-2d,b, and q haplotypes. Serologic analysis revealed that the antigens encoded by the Dw16 region express a unique combination of specificities defined by monoclonal antibodies (mAb) with established activity for the Ld and Dd molecules. Two out of five anti-Ld-reactive mAb reacted with B10.GAA37 cells, whereas one of three anti-Dd mAb showed B10.GAA37 reactivity. Sequential immunoprecipitation of B10.GAA37 antigens demonstrated the existence of at least two antigenically distinct molecules (designated Dw16 and Lw16) encoded by genes associated with the Dw16 region. Peptide map comparisons of the Dw16 and Lw16 molecules defined multiple differences in their primary protein structure, suggesting they are products of separate genes. Structural comparisons of the Lw16 and Dw16 molecules with the Ld and Dd molecules implied a) that the Dw16 and Dd regions did not result from a recent evolutionary divergence of a common primordial haplotype, and b) that the Lw16 and Dw16 molecules are more structurally homologous to each other than the Ld and Dd molecules are. Comparison of these findings with our previous studies of antigens encoded by the D regions suggest that each of these haplotypes has unique properties in terms of the number of gene products expressed and/or the structural relatedness of products of the same region.

  14. Existence of mutations in the homeodomain-encoding region of NKX2.5 gene in Iranian patients with tetralogy of Fallot

    Science.gov (United States)

    Kheirollahi, Majid; Khosravi, Fereshteh; Ashouri, Saeideh; Ahmadi, Alireza

    2016-01-01

    Background: Tetralogy of Fallot (TOF), the most common cyanotic heart defect and one of the most common congenital heart diseases, occurs mostly sporadically and nonsyndromically. The underlying molecular genetic mechanism is not known. Therefore, the existence of mutations in the homeodomain-encoding region of NKX2.5 gene in Iranian patients with tetralogy of Fallot is evaluated. Materials and Methods: In the present study, we analyzed the peripheral blood samples of27 patients in order to find any mutation in the 180 bp homeodomain-encoding region of NKX2.5 gene, which is known to be involved in heart development and diseases. DNA was extracted and all the samples were amplified by polymerase chain reaction (PCR) and sequenced. Results: Twenty-seven patients were included in the study. Twenty-five of them were infants and children (6 days to 11 years of age), one was a teenager (14-years of age), and another was a 33-year-old man [mean ± standard deviation (SD): 5.80 ± 3.90 years]. Thirteen patents were males (mean ± SD: 6.587077 ± 5.02 years) and 14 were females (mean ± SD: 5.0726 ± 2.81 years). One synonymous variant, i.e., c.543G>A was identified in one patient. Conclusion: Mutations in the homeodomain-encoding region of NKX2.5 gene may not have an outstanding role in etiology of tetralogy of Fallot patients in Iran. PMID:27904570

  15. Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

    International Nuclear Information System (INIS)

    Flores, J.; Sears, J.; Schael, I.P.; White, L.; Garcia, D.; Lanata, C.; Kapikian, A.Z.

    1990-01-01

    We have synthesized 32 P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated from field studies

  16. Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

    Energy Technology Data Exchange (ETDEWEB)

    Flores, J.; Sears, J.; Schael, I.P.; White, L.; Garcia, D.; Lanata, C.; Kapikian, A.Z. (National Institutes of Health, Bethesda, MD (USA))

    1990-08-01

    We have synthesized {sup 32}P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated from field studies.

  17. Proximal Region of the Gene Encoding Cytadherence-Related Protein Permits Molecular Typing of Mycoplasma genitalium Clinical Strains by PCR-Restriction Fragment Length Polymorphism

    Science.gov (United States)

    Musatovova, Oxana; Herrera, Caleb; Baseman, Joel B.

    2006-01-01

    Restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified proximal region of the gene encoding cytadherence accessory protein P110 (MG192) revealed DNA sequence divergences among 54 Mycoplasma genitalium clinical strains isolated from the genitourinary tracts of women attending a sexually transmitted disease-related health clinic, plus one from the respiratory tract and one from synovial fluid. Seven of 56 (12.5%) strains exhibited RFLPs following digestion of the proximal region with restriction endonuclease MboI or RsaI, or both. No sequence variability was detected in the distal portion of the gene. PMID:16455921

  18. Analysis of viral protein-2 encoding gene of avian encephalomyelitis virus from field specimens in Central Java region, Indonesia

    Directory of Open Access Journals (Sweden)

    Aris Haryanto

    2016-01-01

    Full Text Available Aim: Avian encephalomyelitis (AE is a viral disease which can infect various types of poultry, especially chicken. In Indonesia, the incidence of AE infection in chicken has been reported since 2009, the AE incidence tends to increase from year to year. The objective of this study was to analyze viral protein 2 (VP-2 encoding gene of AE virus (AEV from various species of birds in field specimen by reverse transcription polymerase chain reaction (RT-PCR amplification using specific nucleotides primer for confirmation of AE diagnosis. Materials and Methods: A total of 13 AEV samples are isolated from various species of poultry which are serologically diagnosed infected by AEV from some areas in central Java, Indonesia. Research stage consists of virus samples collection from field specimens, extraction of AEV RNA, amplification of VP-2 protein encoding gene by RT-PCR, separation of RT-PCR product by agarose gel electrophoresis, DNA sequencing and data analysis. Results: Amplification products of the VP-2 encoding gene of AEV by RT-PCR methods of various types of poultry from field specimens showed a positive results on sample code 499/4/12 which generated DNA fragment in the size of 619 bp. Sensitivity test of RT-PCR amplification showed that the minimum concentration of RNA template is 127.75 ng/μl. The multiple alignments of DNA sequencing product indicated that positive sample with code 499/4/12 has 92% nucleotide homology compared with AEV with accession number AV1775/07 and 85% nucleotide homology with accession number ZCHP2/0912695 from Genbank database. Analysis of VP-2 gene sequence showed that it found 46 nucleotides difference between isolate 499/4/12 compared with accession number AV1775/07 and 93 nucleotides different with accession number ZCHP2/0912695. Conclusions: Analyses of the VP-2 encoding gene of AEV with RT-PCR method from 13 samples from field specimen generated the DNA fragment in the size of 619 bp from one sample with

  19. TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region

    Science.gov (United States)

    Wise, Carol A.; Chiang, Lydia C.; Paznekas, William A.; Sharma, Mridula; Musy, Maurice M.; Ashley, Jennifer A.; Lovett, Michael; Jabs, Ethylin W.

    1997-01-01

    Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development. PMID:9096354

  20. TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region.

    Science.gov (United States)

    Wise, C A; Chiang, L C; Paznekas, W A; Sharma, M; Musy, M M; Ashley, J A; Lovett, M; Jabs, E W

    1997-04-01

    Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

  1. The nuclear protein encoded by the Drosophila neurogenic gene mastermind is widely expressed and associates with specific chromosomal regions

    Energy Technology Data Exchange (ETDEWEB)

    Bettler, D.; Pearson, S.; Yedvobnick, B. [Emory Univ., Atlanta, GA (United States)

    1996-06-01

    The Drosophila neurogenic loci encode a diverse group of proteins that comprise an inhibitory signal transduction pathway. The pathway is used throughout development in numerous contexts. We have examined the distribution of the neurogenic locus mastermind protein (Mam). Mam is expressed through all germlayers during early embryogenesis, including ectodermal precursors to both neuroblasts and epidermoblasts. Mam is subsequently down-regulated within the nervous system and then reexpressed. It persists in the nervous system through late embryogenesis and postembryonically. Mam is ubiquitously expressed in wing and leg imaginal discs and is not down-regulated in sensory organ precursor cells of the wing margin or notum. In the eye disc, Mam shows most prominent expression posterior to the morphogenetic furrow. Expression of the protein during oogenesis appears limited to follicle cells. Immunohistochemical detection of Mam on polytene chromosomes revealed binding at >100 sites. Chromosome colocalization studies with RNA polymerase and the groucho corepressor protein implicate Mam in transcriptional regulation. 94 refs., 8 figs., 1 tab.

  2. Prophage-Encoded Staphylococcal Enterotoxin A: Regulation of Production in Staphylococcus aureus Strains Representing Different Sea Regions

    Directory of Open Access Journals (Sweden)

    Nikoleta Zeaki

    2015-12-01

    Full Text Available The present study investigates the nature of the link between the staphylococcal enterotoxin A (SEA gene and the lifecycle of Siphoviridae bacteriophages, including the origin of strain variation regarding SEA production after prophage induction. Five strains representing three different genetic lines of the sea region were studied under optimal and prophage-induced growth conditions and the Siphoviridae lifecycle was followed through the phage replicative form copies and transcripts of the lysogenic repressor, cro. The role of SOS response on prophage induction was addressed through recA transcription in a recA-disruption mutant. Prophage induction was found to increase the abundance of the phage replicative form, the sea gene copies and transcripts and enhance SEA production. Sequence analysis of the sea regions revealed that observed strain variances were related to strain capacity for prophage induction, rather than sequence differences in the sea region. The impact of SOS response activation on the phage lifecycle was demonstrated by the absence of phage replicative form copies in the recA-disruption mutant after prophage induction. From this study it emerges that all aspects of SEA-producing strain, the Siphoviridae phage and the food environment must be considered when evaluating SEA-related hazards.

  3. Hemispheric Asymmetries in Striatal Reward Responses Relate to Approach-Avoidance Learning and Encoding of Positive-Negative Prediction Errors in Dopaminergic Midbrain Regions.

    Science.gov (United States)

    Aberg, Kristoffer Carl; Doell, Kimberly C; Schwartz, Sophie

    2015-10-28

    Some individuals are better at learning about rewarding situations, whereas others are inclined to avoid punishments (i.e., enhanced approach or avoidance learning, respectively). In reinforcement learning, action values are increased when outcomes are better than predicted (positive prediction errors [PEs]) and decreased for worse than predicted outcomes (negative PEs). Because actions with high and low values are approached and avoided, respectively, individual differences in the neural encoding of PEs may influence the balance between approach-avoidance learning. Recent correlational approaches also indicate that biases in approach-avoidance learning involve hemispheric asymmetries in dopamine function. However, the computational and neural mechanisms underpinning such learning biases remain unknown. Here we assessed hemispheric reward asymmetry in striatal activity in 34 human participants who performed a task involving rewards and punishments. We show that the relative difference in reward response between hemispheres relates to individual biases in approach-avoidance learning. Moreover, using a computational modeling approach, we demonstrate that better encoding of positive (vs negative) PEs in dopaminergic midbrain regions is associated with better approach (vs avoidance) learning, specifically in participants with larger reward responses in the left (vs right) ventral striatum. Thus, individual dispositions or traits may be determined by neural processes acting to constrain learning about specific aspects of the world. Copyright © 2015 the authors 0270-6474/15/3514491-10$15.00/0.

  4. Size polymorphism of chicken major histocompatibility complex-encoded B-G molecules is due to length variation in the cytoplasmic heptad repeat region

    DEFF Research Database (Denmark)

    Kaufman, J; Salomonsen, J; Skjødt, K

    1990-01-01

    B-G antigens are cell-surface molecules encoded by a highly polymorphic multigene family located in the chicken major histocompatibility complex (MHC). Rabbit antisera to B-G molecules immunoprecipitate 3-6 bands from iodinated erythrocytes by sodium dodecyl sulfate (SDS) gels under reducing...... conditions. These are all B-G molecules because they all map to the B-G region of the chicken MHC in congenic and recombinant chickens, most are directly recognized by the antisera, most form disulfide-linked dimers, and none bear N-linked carbohydrate. Both apparent homodimers and heterodimers are found......, which bear intrachain disulfide bonds. All 3-6 bands have different mobilities in SDS gels between different haplotypes, ranging from 30 to 55 kDa. This size polymorphism is not affected by glycosidase treatment or addition of protease inhibitors. Partial proteolysis of cell surface-iodinated B-G...

  5. Molecular diversity of the coat protein-encoding region of Barley yellow dwarf virus-PAV and Barley yellow dwarf virus-MAV from Latvia and Sweden.

    Science.gov (United States)

    Bisnieks, M; Kvarnheden, A; Sigvald, R; Valkonen, J P T

    2004-04-01

    The sequence variability of Barley yellow dwarf virus-PAV (PAV) and Barley yellow dwarf virus-MAV (MAV) was studied by comparing 502 nucleotides from the coat protein-encoding region of six isolates from Latvia and four from Sweden. The diversity within MAV was low (>97% sequence identity), also when compared to isolates from USA and China. In contrast, the variability among PAV isolates was greater and phylogenetic analysis including isolates of a wide geographic origin detected two major clusters, of which both contained isolates from Latvia and Sweden. A new distinct variant of BYDV-PAV was discovered in Latvia, and because of the sequence difference it is proposed to belong to a new species (BYDV-OYV).

  6. Mapping to mouse chromosome 3 of the gene encoding latexin (Lxn) expressed in neocortical neurons in a region-specific manner

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Ming-hao; Uratani, Yoshihiko; Arimatsu, Yasuyoshi [Mitsubishi Kasei Institute of Life Sciences, Tokyo (Japan)

    1997-02-01

    Latexin was first found as a 29-kDa antigen expressed in a subset of neurons in infragranular layers of lateral, but not dorsal, neocortical areas in the rat using a monoclonal antibody PC3.1. It was found that the vast majority of latexin-expressing neurons in both layers V and VI within the lateral neocortex were generated concurrently at Embryonic Day 15, demonstrating a strict correlation between the molecular identity of neurons and the time of their generation. Since neurons expressing latexin are located in the restricted part of the neocortex, latexin has been used as a useful molecular marker to elucidate the mechanism underlying cortical regional specification. The latexin cDNA isolated from a cDNA library of the rat cerebral cortex encodes a protein composed of 223-amino-acid residues containing two potential Ca{sup 2+}/calmodulin-dependent protein kinase sites and one cGMP-dependent protein kinase phosphorylation site. The absence of any signal peptide or potential transmembrane domain is consistent with the apparent cytosolic localization of latexin in the rat brain. The transcripts of latexin were expressed in not only neutral but also nonneural tissues (e.g., lung, spleen, kidney, heart, and digestive tracts). Recently, it has been demonstrated that latexin purified from the rat brain has inhibitory activity against carboxypeptidase A1, carboxypeptidase A2, and mast cell carboxypeptidase A, with less carboxypeptidase B-inhibiting activity. The amino acid sequence deduced from the rat latexin cDNA has no strict homology to any sequences so far known. Genomic Southern blot analysis using a cDNA probe of rat latexin suggested that the gene encoding latexin in the rat has homologues in other mammalian species and in the chicken, but not in the nematode, fly, or frog. 9 refs., 1 fig.

  7. Organization of the gene encoding common acute lymphoblastic leukemia antigen (neutral endopeptidase 24.11): multiple miniexons and separate 5' untranslated regions.

    OpenAIRE

    D'Adamio, L; Shipp, M A; Masteller, E L; Reinherz, E L

    1989-01-01

    The common acute lymphoblastic leukemia antigen (CALLA) is a 749-amino acid type II integral membrane protein that has been identified recently as the neutral endopeptidase 24.11 [NEP (EC 3.4.24.11)]. Herein, we characterize the organization of the human CALLA/NEP gene and show that it spans more than 80 kilobases (kb) and is composed of 24 exons. Exons 1 and 2 encode 5' untranslated sequences; exon 3 [170 base pairs (bp)] encodes the initiation codon and transmembrane and cytoplasmic domain;...

  8. Genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pRet42a from Rhizobium etli CFN42 participate in modulating transfer and affect conjugation from different donors.

    Directory of Open Access Journals (Sweden)

    Susana eBrom

    2015-01-01

    Full Text Available Among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. In bacterial genomes, genes related to a similar function are often located in contiguous regions. The presence of genes encoding conserved hypothetical proteins (chp in such a region may suggest that they are related to that particular function. Plasmid pRet42a from Rhizobium etli CFN42 is a conjugative plasmid containing a segment of approximately 30 Kb encoding genes involved in conjugative transfer. In addition to genes responsible for Dtr (DNA transfer and replication, Mpf (Mating pair formation and regulation, it has two chp-encoding genes (RHE_PA00163 and RHE_PA00164 and a transcriptional regulator (RHE_PA00165. RHE_PA00163 encodes an uncharacterized protein conserved in bacteria that presents a COG4634 conserved domain, and RHE_PA00164 encodes an uncharacterized conserved protein with a DUF433 domain of unknown function. RHE_PA00165 presents a HTH_XRE domain, characteristic of DNA-binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Interestingly, genes similar to these are also present in transfer regions of plasmids from other bacteria. To determine if these genes participate in conjugative transfer, we mutagenized them and analyzed their conjugative phenotype. A mutant in RHE_PA00163 showed a slight (10 times but reproducible increase in transfer frequency from Rhizobium donors, while mutants in RHE_PA00164 and RHE_PA00165 lost their ability to transfer the plasmid from some Agrobacterium donors. Our results indicate that the chp-encoding genes located among conjugation genes are indeed related to this function. However, the participation of RHE_PA00164 and RHE_PA00165 is only revealed under very specific circumstances, and is not perceived when the plasmid is transferred from the original host. RHE_PA00163 seems to be a fine-tuning modulator for conjugative

  9. Peri-encoding predictors of memory encoding and consolidation.

    Science.gov (United States)

    Cohen, Noga; Pell, Liat; Edelson, Micah G; Ben-Yakov, Aya; Pine, Alex; Dudai, Yadin

    2015-03-01

    We review reports of brain activations that occur immediately prior to the onset or following the offset of to-be-remembered information and can predict subsequent mnemonic success. Memory-predictive pre-encoding processes, occurring from fractions of a second to minutes prior to event onset, are mainly associated with activations in the medial temporal lobe (MTL), amygdala and midbrain, and with enhanced theta oscillations. These activations may be considered as the neural correlates of one or more cognitive operations, including contextual processing, attention, and the engagement of distinct computational modes associated with prior encoding or retrieval. Post-encoding activations that correlate with subsequent memory performance are mainly observed in the MTL, sensory cortices and frontal regions. These activations may reflect binding of elements of the encoded information and initiation of memory consolidation. In all, the findings reviewed here illustrate the importance of brain states in the immediate peri-encoding time windows in determining encoding success. Understanding these brain states and their specific effects on memory may lead to optimization of the encoding of desired memories and mitigation of undesired ones. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Cloning and sequencing of cDNA encoding human DNA topoisomerase II and localization of the gene to chromosome region 17q21-22

    International Nuclear Information System (INIS)

    Tsai-Pflugfelder, M.; Liu, L.F.; Liu, A.A.; Tewey, K.M.; Whang-Peng, J.; Knutsen, T.; Huebner, K.; Croce, C.M.; Wang, J.C.

    1988-01-01

    Two overlapping cDNA clones encoding human DNA topoisomerase II were identified by two independent methods. In one, a human cDNA library in phage λ was screened by hybridization with a mixed oligonucleotide probe encoding a stretch of seven amino acids found in yeast and Drosophila DNA topoisomerase II; in the other, a different human cDNA library in a λgt11 expression vector was screened for the expression of antigenic determinants that are recognized by rabbit antibodies specific to human DNA topoisomerase II. The entire coding sequences of the human DNA topoisomerase II gene were determined from these and several additional clones, identified through the use of the cloned human TOP2 gene sequences as probes. Hybridization between the cloned sequences and mRNA and genomic DNA indicates that the human enzyme is encoded by a single-copy gene. The location of the gene was mapped to chromosome 17q21-22 by in situ hybridization of a cloned fragment to metaphase chromosomes and by hybridization analysis with a panel of mouse-human hybrid cell lines, each retaining a subset of human chromosomes

  11. A study of coagulase-negative staphylococci (CoNS isolated from bovine mastitis for the presence of penicillin and methicillin resistance-encoding genes in the north west of Iran

    Directory of Open Access Journals (Sweden)

    Dastmalchi Saei, H.

    2014-11-01

    Full Text Available Coagulase-negative staphylococci (CoNS are often associated with bovine mastitis and may be resistant to antimicrobial therapy. The aim of the current study was to investigate the presence of blaZ (responsible for penicillin resistance and mecA (responsible for methicillin resistance genes among 108 CoNS belonging to 9 different species isolated from bovine mastitis in seven dairy herds (H1-H7. Of 108 CoNS isolates, 44 were Staphylococcus haemolyticus, 17 S. chromogenes, 11 S. epidermidis, 11 S. warneri, 11 S. cohnii, 6 S. simulans, 4 S. hominis, 3 S. capitis, and 1 S. xylosus. The blaZ was detected in 65.7% (n=71 of all Staphylococcus spp. isolates. Five isolates were positive for the presence of mecA gene (4.6%, including 2 S. hominis, 1 S. haemolyticus, 1 S. epidermidis, and 1 S. warneri. All mecA-carrying CoNS were also positive for the blaZ gene and were recovered from two studied herds (H3 and H6. Some variations were also observed in distribution of both blaZ and mecA genes between CoNS species. This study demonstrates that CoNS from bovine mastitis can be reservoirs of blaZ gene. This study also provides evidence of the presence of methicillin resistant CoNS (MR-CoNS and emphasizes the need for their epidemiological monitoring, in order to prevent the risk of spread to human through direct contact and/or consumption of contaminated food.

  12. The multidrug resistance IncA/C transferable plasmid encodes a novel domain-swapped dimeric protein-disulfide isomerase.

    Science.gov (United States)

    Premkumar, Lakshmanane; Kurth, Fabian; Neyer, Simon; Schembri, Mark A; Martin, Jennifer L

    2014-01-31

    The multidrug resistance-encoding IncA/C conjugative plasmids disseminate antibiotic resistance genes among clinically relevant enteric bacteria. A plasmid-encoded disulfide isomerase is associated with conjugation. Sequence analysis of several IncA/C plasmids and IncA/C-related integrative and conjugative elements (ICE) from commensal and pathogenic bacteria identified a conserved DsbC/DsbG homolog (DsbP). The crystal structure of DsbP reveals an N-terminal domain, a linker region, and a C-terminal catalytic domain. A DsbP homodimer is formed through domain swapping of two DsbP N-terminal domains. The catalytic domain incorporates a thioredoxin-fold with characteristic CXXC and cis-Pro motifs. Overall, the structure and redox properties of DsbP diverge from the Escherichia coli DsbC and DsbG disulfide isomerases. Specifically, the V-shaped dimer of DsbP is inverted compared with EcDsbC and EcDsbG. In addition, the redox potential of DsbP (-161 mV) is more reducing than EcDsbC (-130 mV) and EcDsbG (-126 mV). Other catalytic properties of DsbP more closely resemble those of EcDsbG than EcDsbC. These catalytic differences are in part a consequence of the unusual active site motif of DsbP (CAVC); substitution to the EcDsbC-like (CGYC) motif converts the catalytic properties to those of EcDsbC. Structural comparison of the 12 independent subunit structures of DsbP that we determined revealed that conformational changes in the linker region contribute to mobility of the catalytic domain, providing mechanistic insight into DsbP function. In summary, our data reveal that the conserved plasmid-encoded DsbP protein is a bona fide disulfide isomerase and suggest that a dedicated oxidative folding enzyme is important for conjugative plasmid transfer.

  13. CsrA Represses Translation of sdiA, Which Encodes the N-Acylhomoserine-l-Lactone Receptor of Escherichia coli, by Binding Exclusively within the Coding Region of sdiA mRNA ▿ †

    Science.gov (United States)

    Yakhnin, Helen; Baker, Carol S.; Berezin, Igor; Evangelista, Michael A.; Rassin, Alisa; Romeo, Tony; Babitzke, Paul

    2011-01-01

    The RNA binding protein CsrA is the central component of a conserved global regulatory system that activates or represses gene expression posttranscriptionally. In every known example of CsrA-mediated translational control, CsrA binds to the 5′ untranslated region of target transcripts, thereby repressing translation initiation and/or altering the stability of the RNA. Furthermore, with few exceptions, repression by CsrA involves binding directly to the Shine-Dalgarno sequence and blocking ribosome binding. sdiA encodes the quorum-sensing receptor for N-acyl-l-homoserine lactone in Escherichia coli. Because sdiA indirectly stimulates transcription of csrB, which encodes a small RNA (sRNA) antagonist of CsrA, we further explored the relationship between sdiA and the Csr system. Primer extension analysis revealed four putative transcription start sites within 85 nucleotides of the sdiA initiation codon. Potential σ70-dependent promoters were identified for each of these primer extension products. In addition, two CsrA binding sites were predicted in the initially translated region of sdiA. Expression of chromosomally integrated sdiA′-′lacZ translational fusions containing the entire promoter and CsrA binding site regions indicates that CsrA represses sdiA expression. The results from gel shift and footprint studies demonstrate that tight binding of CsrA requires both of these sites. Furthermore, the results from toeprint and in vitro translation experiments indicate that CsrA represses translation of sdiA by directly competing with 30S ribosomal subunit binding. Thus, this represents the first example of CsrA preventing translation by interacting solely within the coding region of an mRNA target. PMID:21908661

  14. CsrA represses translation of sdiA, which encodes the N-acylhomoserine-L-lactone receptor of Escherichia coli, by binding exclusively within the coding region of sdiA mRNA.

    Science.gov (United States)

    Yakhnin, Helen; Baker, Carol S; Berezin, Igor; Evangelista, Michael A; Rassin, Alisa; Romeo, Tony; Babitzke, Paul

    2011-11-01

    The RNA binding protein CsrA is the central component of a conserved global regulatory system that activates or represses gene expression posttranscriptionally. In every known example of CsrA-mediated translational control, CsrA binds to the 5' untranslated region of target transcripts, thereby repressing translation initiation and/or altering the stability of the RNA. Furthermore, with few exceptions, repression by CsrA involves binding directly to the Shine-Dalgarno sequence and blocking ribosome binding. sdiA encodes the quorum-sensing receptor for N-acyl-l-homoserine lactone in Escherichia coli. Because sdiA indirectly stimulates transcription of csrB, which encodes a small RNA (sRNA) antagonist of CsrA, we further explored the relationship between sdiA and the Csr system. Primer extension analysis revealed four putative transcription start sites within 85 nucleotides of the sdiA initiation codon. Potential σ(70)-dependent promoters were identified for each of these primer extension products. In addition, two CsrA binding sites were predicted in the initially translated region of sdiA. Expression of chromosomally integrated sdiA'-'lacZ translational fusions containing the entire promoter and CsrA binding site regions indicates that CsrA represses sdiA expression. The results from gel shift and footprint studies demonstrate that tight binding of CsrA requires both of these sites. Furthermore, the results from toeprint and in vitro translation experiments indicate that CsrA represses translation of sdiA by directly competing with 30S ribosomal subunit binding. Thus, this represents the first example of CsrA preventing translation by interacting solely within the coding region of an mRNA target.

  15. Hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hood, E.E.; Helmer, G.L.; Fraley, R.T.; Chilton, M.D.

    1986-12-01

    A binary-vectory strategy was used to study the hypervirulence of Agrobacterium tumefaciens A281, an L,L-succinamopine strain. Strain A281 is hypervirulent on several solanaceous plants. Plasmids were constructed (pCS65 and pCS277) carrying either the transferred DNA (T-DNA) or the remainder of the tumor-inducing (Ti) plasmid (pEHA101) from this strain and tested each of these constructs were tested in trans with complementary each of regions from heterologous Ti plasmids. Hypervirulence on tobacco could be reconstructed in a bipartite strain with the L,L-succinamopine T-DNA and the vir region on separate plasmids. pEHA101 was able to complement octopine T-DNA to hypervirulence on tobacco and tomato plants. Nopaline T-DNA was complemented better on tomato plants by pEHA101 than it was by its own nopaline vir region, but not to hypervirulence. L,L-Succinamopine T-DNA could not be complemented to hypervirulence on tobacco and tomato plants with either heterologous vir region. From these results the authors suggest that the hypervirulence of strain A281 is due to non-T-DNA sequences on the Ti plasmid.

  16. The Ancestral Gene for Transcribed, Low-Copy Repeats in the Prader-Willi/Angleman Region Encodes a Large Protein Implicated in Protein Trafficking that is Deficient in Mice with Neuromuscular and

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Y.

    1999-01-01

    Transcribed, low-copy repeat elements are associated with the breakpoint regions of common deletions in Prader-Willi and Angelman syndromes. We report here the identification of the ancestral gene ( HERC2 ) and a family of duplicated, truncated copies that comprise these low-copy repeats. This gene encodes a highly conserved giant protein, HERC2, that is distantly related to p532 (HERC1), a guanine nucleotide exchange factor (GEF) implicated in vesicular trafficking. The mouse genome contains a single Herc2 locus, located in the jdf2 (juvenile development and fertility-2) interval of chromosome 7C. We have identified single nucleotide splice junction mutations in Herc2 in three independent N-ethyl-N-nitrosourea-induced jdf2 mutant alleles, each leading to exon skipping with premature termination of translation and/or deletion of conserved amino acids. Therefore, mutations in Herc2 lead to the neuromuscular secretory vesicle and sperm acrosome defects, other developmental abnormalities and juvenile lethality of jdf2 mice. Combined, these findings suggest that HERC2 is an important gene encoding a GEF involved in protein trafficking and degradation pathways in the cell.

  17. Functional isotypes are not encoded by the constant region genes of the beta subunit of the T cell receptor for antigen/major histocompatibility complex

    OpenAIRE

    1984-01-01

    Human T cell clones and a cDNA probe specific for constant regions of the beta subunit of the antigen/major histocompatibility complex (MHC) receptor, TiC beta 1 and TiC beta 2, were employed to determine whether these genes were differentially used by functional classes of T lymphocytes. DNA from 10 interleukin-2-dependent T cell clones including class I and class II MHC-specific cytotoxic T lymphocytes (n = 6), T4+ inducer T lymphocytes (n = 2), and T8+ suppressor T lymphocytes (n = 2) show...

  18. The putative imprinted locus D15S9 within the common deletion region for the Prader-Willi and Angelman syndromes encodes two overlapping mRNAs transcribed from opposite strands

    Energy Technology Data Exchange (ETDEWEB)

    Glenn, C.C.; Driscoll, D.J. [Univ. of Florida, Gainesville, FL (United States); Saitoh, S. [Case Western Reserve Univ., Cleveland, OH (United States)] [and others

    1994-09-01

    Prader-Willi syndrome is typically caused by a deletion of paternal 15q11-q13, or maternal uniparental disomy (UPD) of chromosome 15, while Angelman syndrome is caused by a maternal deletion or paternal UPD of the same region. Therefore, these two clinically distinct neurobehavioral syndromes result from differential expression of imprinted genes within 15q11-q13. A 3.1 kb cDNA, DN34, from the D15S9 locus within 15q11-q13 was isolated from a human fetal brain library. We showed previously that DN34 probe detects a DNA methylation imprint and therefore may represent a candidate imprinted gene. Isolation of genomic clones and DNA sequencing demonstrated that the gene segment encoding the partial cDNA DN34 was split by a 2 kb intron, but did not encode a substantial open reading frame (ORF). Preliminary analysis of expression by RT-PCR suggests that this gene is expressed in fetal but not in tested tissue types from the adult, and thus its imprinting status has not been possible to assess at present. Surprisingly, we found an ORF on the antisense strand of the DN34 cDNA. This ORF encodes a putative polypeptide of 505 amino acid residues containing a RING C{sub 3}HC{sub 4} zinc-finger motif and other features of nuclear proteins. Subsequent characterization of this gene, ZNF127, and a mouse homolog, demonstrated expression of 3.2 kb transcript from all tested fetal and adult tissues. Transcripts initiate from within a CpG-island, shown to be differentially methylated on parental alleles in the human. Interestingly, functional imprinting of the mouse homolog was subsequently demonstrated in an F{sub 1} cross by analyzing a VNTR polymorphism in the mRNA. The ZNF127 gene is intronless, has significant overlap with the DN34 gene on the antisense strand, and a 1 kb 3{prime} end within the 2 kb DN34 intron.

  19. A 22q11.2 amplification in the region encoding microRNA-650 correlates with the epithelial to mesenchymal transition in breast cancer primary cultures of Mexican patients.

    Science.gov (United States)

    Lango-Chavarría, M; Chimal-Ramírez, G K; Ruiz-Tachiquín, M E; Espinoza-Sánchez, N A; Suárez-Arriaga, M C; Fuentes-Pananá, E M

    2017-02-01

    Breast cancer ranks first in incidence and mortality in working age women. Cancer initiation and progression relies on accumulation of genetic and epigenetic aberrations that alter cellular processes, among them, epithelial to mesenchymal transition (EMT) denotes particularly aggressive neoplasias given its capacity to invade and metastasize. Several microRNAs (miRNA) have been found able to regulate gene expression at the core of EMT. In this study, the Affymetrix CytoScan HD array was used to analyze three different primary tumor cell isolates from Mexican breast cancer patients. We found an amplification in band 22q11.2 shared by the three samples, in the region that encodes miRNA-650. Overexpression of this miRNA has been associated with downregulation of tumor suppressors ING4 and NDRG2, which have been implicated in cancer progression. Using the Pathway Linker platform the ING4 and NDRG2 interaction networks showed a significant association with signaling pathways commonly deregulated in cancer. Also, several studies support their participation in the EMT. Supporting the latter, we found that the three primary isolates were E-cadherin negative, vimentin positive, presented a cancer stem cell-like phenotype CD44+CD24-/low and were invasive in Transwell invasion assays. This evidence suggests that the gain of region 22q11.2 contributes to trigger EMT. This is the first evidence linking miR-650 and breast cancer.

  20. Time-Encoded Imagers.

    Energy Technology Data Exchange (ETDEWEB)

    Marleau, Peter; Brubaker, Erik

    2014-11-01

    This report provides a short overview of the DNN R&D funded project, Time-Encoded Imagers. The project began in FY11 and concluded in FY14. The Project Description below provides the overall motivation and objectives for the project as well as a summary of programmatic direction. It is followed by a short description of each task and the resulting deliverables.

  1. Encoders and Fault Detection

    NARCIS (Netherlands)

    Persis, Claudio De

    2003-01-01

    Monitoring large-scale systems is of fundamental importance in modern infrastructures. Many of these large-scale systems are complex interconnections of sub-components which interact by means of communication channels with limited bandwidth. Therefore the information must be encoded in order to be

  2. Neural Semantic Encoders.

    Science.gov (United States)

    Munkhdalai, Tsendsuren; Yu, Hong

    2017-04-01

    We present a memory augmented neural network for natural language understanding: Neural Semantic Encoders. NSE is equipped with a novel memory update rule and has a variable sized encoding memory that evolves over time and maintains the understanding of input sequences through read , compose and write operations. NSE can also access multiple and shared memories. In this paper, we demonstrated the effectiveness and the flexibility of NSE on five different natural language tasks: natural language inference, question answering, sentence classification, document sentiment analysis and machine translation where NSE achieved state-of-the-art performance when evaluated on publically available benchmarks. For example, our shared-memory model showed an encouraging result on neural machine translation, improving an attention-based baseline by approximately 1.0 BLEU.

  3. Disorders of phonological encoding.

    Science.gov (United States)

    Butterworth, B

    1992-03-01

    Studies of phonological disturbances in aphasic speech are reviewed. It is argued that failure to test for error consistency in individual patients makes it generally improper to draw inferences about specific disorders of phonological encoding. A minimalist interpretation of available data on phonological errors is therefore proposed that involves variable loss of information in transmission between processing subsystems. Proposals for systematic loss or corruption of phonological information in lexical representations or in translation subsystems is shown to be inadequately grounded. The review concludes with some simple methodological prescriptions for future research.

  4. Isolation, cloning and characterisation of the abiI gene from Lactococcus lactis subsp. lactis M138 encoding abortive phage infection

    Science.gov (United States)

    Su, Ping; Harvey, Melissa; Im, Hee J.

    2010-01-01

    Plasmid pND852 (56 kb) encodes nisin resistance and was isolated from Lactococcus lactis ssp lactis (L. lactis) M138 by conjugation to L. lactis LM0230. It conferred strong resistance to the isometric-headed phage φ712 and partial resistance to the prolate-headed phage φc2. A 2.6 kb HpaII fragment encoding phage resistance was cloned into the streptococcal/Bacillus hybrid vector pGB301 to generate pND817. The mechanism of phage resistance encoded by pND817 involved abortive infection and this was illustrated by a reduction in burst size from 166 to 6 at 30°C and from 160 to 90 at 37°C. Partial resistance was therefore retained at 37°C. DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein. Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database. Frame shift mutation at the unique EcoRI site within the ORF resulted in loss of the Abi+ phenotype, confirming that the ORF is responsible for the encoded phage resistance. PMID:9195753

  5. Glucose-dependent turnover of the mRNAs encoding succinate dehydrogenase peptides in Saccharomyces cerevisiae: sequence elements in the 5' untranslated region of the Ip mRNA play a dominant role.

    Science.gov (United States)

    Cereghino, G P; Atencio, D P; Saghbini, M; Beiner, J; Scheffler, I E

    1995-09-01

    We have demonstrated previously that glucose repression of mitochondrial biogenesis in Saccharomyces cerevisiae involves the control of the turnover of mRNAs for the iron protein (Ip) and flavoprotein (Fp) subunits of succinate dehydrogenase (SDH). Their half-lives are > 60 min in the presence of a nonfermentable carbon source (YPG medium) and YPD medium). This is a rare example in yeast in which the half-lives are > 60 min in the presence of a nonfermentable carbon source (YPG medium) and YPD medium). This is a rare example in yeast in which the half-life of an mRNA can be controlled by manipulating external conditions. In our current studies, a series of Ip transcripts with internal deletions as well as chimeric transcripts with heterologous sequences (internally or at the ends) have been examined, and we established that the 5'-untranslated region (5' UTR) of the Ip mRNA contains a major determinant controlling its differential turnover in YPG and YPD. Furthermore, the 5' exonuclease encoded by the XRN1 gene is required for the rapid degradation of the Ip and Fp mRNAs upon the addition of glucose. In the presence of cycloheximide the nucleolytic degradation of the Ip mRNA can be slowed down by stalled ribosomes to allow the identification of intermediates. Such intermediates have lost their 5' ends but still retain their 3' UTRs. If protein synthesis is inhibited at an early initiation step by the use of a prt1 mutation (affecting the initiation factor eIF3), the Ip and Fp mRNAs are very rapidly degraded even in YPG. Significantly, the arrest of translation by the introduction of a stable hairpin loop just upstream of the initiation codon does not alter the differential stability of the transcript in YPG and YPD. These observations suggest that a signaling pathway exists in which the external carbon source can control the turnover of mRNAs of specific mitochondrial proteins. Factors must be present that control either the activity or more likely the access of a

  6. Sequence and functional conservation of the intergenic region between the head-to-head genes encoding the small heat shock proteins alphaB-crystallin and HspB2 in the mammalian lineage.

    NARCIS (Netherlands)

    Doerwald, L.; Rheede, T. van; Dirks, R.P.H.; Madsen, O.; Rexwinkel, R; Genesen, S.T. van; Martens, G.J.M.; Jong, W.W.W. de; Lubsen, N.H.

    2004-01-01

    An unexpected feature of the large mammalian genome is the frequent occurrence of closely linked head-to-head gene pairs. Close apposition of such gene pairs has been suggested to be due to sharing of regulatory elements. We show here that the head-to-head gene pair encoding two small heat shock

  7. Time encoded radiation imaging

    Science.gov (United States)

    Marleau, Peter; Brubaker, Erik; Kiff, Scott

    2014-10-21

    The various technologies presented herein relate to detecting nuclear material at a large stand-off distance. An imaging system is presented which can detect nuclear material by utilizing time encoded imaging relating to maximum and minimum radiation particle counts rates. The imaging system is integrated with a data acquisition system that can utilize variations in photon pulse shape to discriminate between neutron and gamma-ray interactions. Modulation in the detected neutron count rates as a function of the angular orientation of the detector due to attenuation of neighboring detectors is utilized to reconstruct the neutron source distribution over 360 degrees around the imaging system. Neutrons (e.g., fast neutrons) and/or gamma-rays are incident upon scintillation material in the imager, the photons generated by the scintillation material are converted to electrical energy from which the respective neutrons/gamma rays can be determined and, accordingly, a direction to, and the location of, a radiation source identified.

  8. Encoding the Factorisation Calculus

    Directory of Open Access Journals (Sweden)

    Reuben N. S. Rowe

    2015-08-01

    Full Text Available Jay and Given-Wilson have recently introduced the Factorisation (or SF- calculus as a minimal fundamental model of intensional computation. It is a combinatory calculus containing a special combinator, F, which is able to examine the internal structure of its first argument. The calculus is significant in that as well as being combinatorially complete it also exhibits the property of structural completeness, i.e. it is able to represent any function on terms definable using pattern matching on arbitrary normal forms. In particular, it admits a term that can decide the structural equality of any two arbitrary normal forms. Since SF-calculus is combinatorially complete, it is clearly at least as powerful as the more familiar and paradigmatic Turing-powerful computational models of Lambda Calculus and Combinatory Logic. Its relationship to these models in the converse direction is less obvious, however. Jay and Given-Wilson have suggested that SF-calculus is strictly more powerful than the aforementioned models, but a detailed study of the connections between these models is yet to be undertaken. This paper begins to bridge that gap by presenting a faithful encoding of the Factorisation Calculus into the Lambda Calculus preserving both reduction and strong normalisation. The existence of such an encoding is a new result. It also suggests that there is, in some sense, an equivalence between the former model and the latter. We discuss to what extent our result constitutes an equivalence by considering it in the context of some previously defined frameworks for comparing computational power and expressiveness.

  9. Exploring the influence of encoding format on subsequent memory.

    Science.gov (United States)

    Turney, Indira C; Dennis, Nancy A; Maillet, David; Rajah, M Natasha

    2017-05-01

    Distinctive encoding is greatly influenced by gist-based processes and has been shown to suffer when highly similar items are presented in close succession. Thus, elucidating the mechanisms underlying how presentation format affects gist processing is essential in determining the factors that influence these encoding processes. The current study utilised multivariate partial least squares (PLS) analysis to identify encoding networks directly associated with retrieval performance in a blocked and intermixed presentation condition. Subsequent memory analysis for successfully encoded items indicated no significant differences between reaction time and retrieval performance and presentation format. Despite no significant behavioural differences, behaviour PLS revealed differences in brain-behaviour correlations and mean condition activity in brain regions associated with gist-based vs. distinctive encoding. Specifically, the intermixed format encouraged more distinctive encoding, showing increased activation of regions associated with strategy use and visual processing (e.g., frontal and visual cortices, respectively). Alternatively, the blocked format exhibited increased gist-based processes, accompanied by increased activity in the right inferior frontal gyrus. Together, results suggest that the sequence that information is presented during encoding affects the degree to which distinctive encoding is engaged. These findings extend our understanding of the Fuzzy Trace Theory and the role of presentation format on encoding processes.

  10. Selecting Operations for Assembler Encoding

    Directory of Open Access Journals (Sweden)

    Tomasz Praczyk

    2010-04-01

    Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
    The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

  11. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Science.gov (United States)

    Sahoo, Dipak K; Abeysekara, Nilwala S; Cianzio, Silvia R; Robertson, Alison E; Bhattacharyya, Madan K

    2017-01-01

    Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  12. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Directory of Open Access Journals (Sweden)

    Dipak K Sahoo

    Full Text Available Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs (F7 families were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  13. Mutational analysis of the coding regions of the genes encoding protein kinase B-alpha and -beta, phosphoinositide-dependent protein kinase-1, phosphatase targeting to glycogen, protein phosphatase inhibitor-1, and glycogenin

    DEFF Research Database (Denmark)

    Hansen, L; Fjordvang, H; Rasmussen, S K

    1999-01-01

    for a genetic involvement in the disease. The mode of inheritance of the common forms of NIDDM is as yet unclear, but the prevailing hypothesis supports a polygenic model. In the present study, we tested the hypothesis that the putative inheritable defects of insulin-stimulated muscle glycogen synthesis might...... be caused by genetic variability in the genes encoding proteins shown by biochemical evidence to be involved in insulin-stimulated glycogen synthesis in skeletal muscle. In 70 insulin-resistant Danish NIDDM patients, mutational analysis by reverse transcription-polymerase chain reaction-single strand...... of silent variants were identified in some of the examined genes, we found no evidence for the hypothesis that the defective insulin-stimulated glycogen synthesis in skeletal muscle in NIDDM is caused by structural changes in the genes encoding the known components of the insulin-sensitive glycogen...

  14. LETM1, a novel gene encoding a putative EF-hand Ca(2+)-binding protein, flanks the Wolf-Hirschhorn syndrome (WHS) critical region and is deleted in most WHS patients.

    Science.gov (United States)

    Endele, S; Fuhry, M; Pak, S J; Zabel, B U; Winterpacht, A

    1999-09-01

    Deletions within human chromosome 4p16.3 cause Wolf-Hirschhorn syndrome (WHS), which is characterized by severe mental and developmental defects. It is thought that haploinsufficiency of more than one gene contributes to the complex phenotype. We have cloned and characterized a novel gene (LETM1) that is deleted in nearly all WHS patients. LETM1 encodes a putative member of the EF-hand family of Ca(2+)-binding proteins. The protein contains two EF-hands, a transmembrane domain, a leucine zipper, and several coiled-coil domains. On the basis of its possible Ca(2+)-binding property and involvement in Ca(2+) signaling and/or homeostasis, we propose that haploinsufficiency of LETM1 may contribute to the neuromuscular features of WHS patients. Copyright 1999 Academic Press.

  15. Peptide Signals Encode Protein Localization▿

    OpenAIRE

    Russell, Jay H.; Keiler, Kenneth C.

    2007-01-01

    Many bacterial proteins are localized to precise intracellular locations, but in most cases the mechanism for encoding localization information is not known. Screening libraries of peptides fused to green fluorescent protein identified sequences that directed the protein to helical structures or to midcell. These peptides indicate that protein localization can be encoded in 20-amino-acid peptides instead of complex protein-protein interactions and raise the possibility that the location of a ...

  16. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  17. Multidimensionally encoded magnetic resonance imaging.

    Science.gov (United States)

    Lin, Fa-Hsuan

    2013-07-01

    Magnetic resonance imaging (MRI) typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here, we propose the multidimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel radiofrequency coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled. Copyright © 2012 Wiley Periodicals, Inc.

  18. Fly Photoreceptors Encode Phase Congruency.

    Directory of Open Access Journals (Sweden)

    Uwe Friederich

    Full Text Available More than five decades ago it was postulated that sensory neurons detect and selectively enhance behaviourally relevant features of natural signals. Although we now know that sensory neurons are tuned to efficiently encode natural stimuli, until now it was not clear what statistical features of the stimuli they encode and how. Here we reverse-engineer the neural code of Drosophila photoreceptors and show for the first time that photoreceptors exploit nonlinear dynamics to selectively enhance and encode phase-related features of temporal stimuli, such as local phase congruency, which are invariant to changes in illumination and contrast. We demonstrate that to mitigate for the inherent sensitivity to noise of the local phase congruency measure, the nonlinear coding mechanisms of the fly photoreceptors are tuned to suppress random phase signals, which explains why photoreceptor responses to naturalistic stimuli are significantly different from their responses to white noise stimuli.

  19. Fly Photoreceptors Encode Phase Congruency.

    Science.gov (United States)

    Friederich, Uwe; Billings, Stephen A; Hardie, Roger C; Juusola, Mikko; Coca, Daniel

    2016-01-01

    More than five decades ago it was postulated that sensory neurons detect and selectively enhance behaviourally relevant features of natural signals. Although we now know that sensory neurons are tuned to efficiently encode natural stimuli, until now it was not clear what statistical features of the stimuli they encode and how. Here we reverse-engineer the neural code of Drosophila photoreceptors and show for the first time that photoreceptors exploit nonlinear dynamics to selectively enhance and encode phase-related features of temporal stimuli, such as local phase congruency, which are invariant to changes in illumination and contrast. We demonstrate that to mitigate for the inherent sensitivity to noise of the local phase congruency measure, the nonlinear coding mechanisms of the fly photoreceptors are tuned to suppress random phase signals, which explains why photoreceptor responses to naturalistic stimuli are significantly different from their responses to white noise stimuli.

  20. A user's guide to the encyclopedia of DNA elements (ENCODE).

    Science.gov (United States)

    2011-04-01

    The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

  1. Virally encoded 7TM receptors

    DEFF Research Database (Denmark)

    Rosenkilde, M M; Waldhoer, M; Lüttichau, H R

    2001-01-01

    expression of this single gene in certain lymphocyte cell lineages leads to the development of lesions which are remarkably similar to Kaposi's sarcoma, a human herpesvirus 8 associated disease. Thus, this and other virally encoded 7TM receptors appear to be attractive future drug targets....

  2. Frequency of conjugative transfer of plasmid-encoded ISEcp1 - blaCTX-M-15 and aac(6'-lb-cr genes in Enterobacteriaceae at a tertiary care center in Lebanon - role of transferases

    Directory of Open Access Journals (Sweden)

    Araj George F

    2010-07-01

    Full Text Available Abstract Background The frequency of transfer of genes encoding resistance to antimicrobial agents was determined by conjugation in ESBL-producing and/or fluoroquinolone or aminoglycoside resistant Enterobacteriaceae clinical isolates at a tertiary care center in Lebanon. In addition, the role of tra genes encoding transferases in mediating conjugation was assessed. Methods Conjugation experiments were done on 53 ESBL-producing and/or fluoroquinolone resistant E. coli and K. pneumoniae and ESBL-producing S. sonnei isolates. Antimicrobial susceptibility testing on parent and transconjugant isolates, and PCR amplifications on plasmid extracts of the resistance-encoding genes: blaCTX-M-15 with the ISEcp1 insertion sequence, the aac(6'-lb-cr and qnrS genes, as well as tra encoding transferases genes were done. Random amplified polymorphic DNA (RAPD analysis was performed to demonstrate whether conjugative isolates are clonal and whether they are linked epidemiologically to a particular source. Results Antimicrobial susceptibility testing on transconjugants revealed that 26 out of 53 (49% ESBL-producing Enterobacteriaceae were able to transfer antimicrobial resistance to the recipients. Transfer of high-level resistance to the transconjugants encoded by the blaCTX-M-15 gene downstream the ISEcp1 insertion sequence against 3rd generation cephalosporins, and of low-level resistance against ciprofloxacin, and variable levels of resistance against aminoglycosides encoded by aac(6'-lb-cr gene, were observed in transconjugants. tra encoding transferase genes were detected exclusively in conjugative isolates. Conclusion In conclusion, the frequency of transfer of antimicrobial resistance in non clonal Enterobacteriaceae at the tertiary care center by conjugation was 49%. Conjugation occurred in isolates expressing the tra encoding transferase genes. Multiple conjugative strains harboring the plasmid encoded antimicrobial resistant genes were circulating in

  3. Molecular detection of Acinetobacter species in lice and keds of domestic animals in Oromia Regional State, Ethiopia.

    Science.gov (United States)

    Kumsa, Bersissa; Socolovschi, Cristina; Parola, Philippe; Rolain, Jean-Marc; Raoult, Didier

    2012-01-01

    This study was conducted to determine the presence of Acinetobacter and Rickettsia species DNA in lice and Melophagus ovinus (sheep ked) of animals from Oromia Regional State in Ethiopia. From September through November 2011, a total of 207 cattle, 85 sheep, 47 dogs and 16 cats were examined for ectoparasites. Results of morphological identification revealed several species of ectoparasites: Linognathus vituli (L. vituli), Bovicola bovis (B. bovis) and Solenopotes capillatus (S. capillatus) on cattle; B. ovis and Melophagus ovinus (M. ovinus) on sheep; and Heterodoxus spiniger (H. spiniger) on dogs. There was a significantly (p≤0.0001) higher prevalence of L. vituli observed in cattle than both S. capillatus and B. bovis. Molecular identification of lice using an 18S rRNA gene analysis confirms the identified lice species by morphological methods. We detected different Acinetobacter species among lice (11.1%) and keds (86.4%) including A. soli in L. vituli of cattle, A. lowffii in M. ovinus of sheep, A. pittii in H. spiniger of dogs, 1 new Acinetobacter spp. in M. ovinus and 2 new Acinetobacter spp. in H. spiniger of dogs using partial rpoB gene sequence analysis. There was a significantly higher prevalence of Acinetobacter spp. in keds than in lice (p≤0.00001). Higher percentage of Acinetobacter spp. DNA was detected in H. spiniger than in both B. ovis and L. vituli (p≤0.00001). Carbapenemase resistance encoding genes for blaOXA-23, blaOXA-24, blaOXA-58, blaNDM-1 and blaOXA-51 were not found in any lice and keds. These findings suggest that synanthropic animals and their ectoparasites might increase the risk of human exposure to zoonotic pathogens and could be a source for Acinetobacter spp. infections in humans. However, additional epidemiological data are required to determine whether ectoparasites of animals can act as environmental reservoirs and play a role in spreading these bacteria to both animal and human hosts.

  4. Re-engaging with the past: recapitulation of encoding operations during retrieval

    Directory of Open Access Journals (Sweden)

    Alexa eMorcom

    2014-05-01

    Full Text Available Recollection of events is accompanied by selective reactivation of cortical regions which responded to specific sensory and cognitive dimensions of the original events. This reactivation is thought to reflect the reinstatement of stored memory representations and therefore to reflect memory content, but it may also reveal processes which support both encoding and retrieval. The present study used event-related functional magnetic resonance imaging (fMRI to investigate whether regions selectively engaged in encoding face and scene context with studied words are also re-engaged when the context is later retrieved. As predicted, encoding face and scene context with visually presented words elicited activity in distinct, context-selective regions. Retrieval of face and scene context also re-engaged some of the regions which had shown successful encoding effects. However, this recapitulation of encoding activity did not show the same context selectivity observed at encoding. Successful retrieval of both face and scene context re-engaged regions which had been associated with encoding of the other type of context, as well as those associated with encoding the same type of context. This recapitulation may reflect retrieval attempts which are not context-selective, but use shared retrieval cues to re-engage encoding operations in service of recollection.

  5. Encoding information into precipitation structures

    International Nuclear Information System (INIS)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-01-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A + + B – → C reaction–diffusion processes. Our main result, based on simulating the reaction–diffusion–precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm

  6. Mental reinstatement of encoding context improves episodic remembering.

    Science.gov (United States)

    Bramão, Inês; Karlsson, Anna; Johansson, Mikael

    2017-09-01

    This study investigates context-dependent memory retrieval. Previous work has shown that physically re-experiencing the encoding context at retrieval improves memory accessibility. The current study examined if mental reconstruction of the original encoding context would yield parallel memory benefits. Participants performed a cued-recall memory task, preceded either by a mental or by a physical context reinstatement task, and we manipulated whether the context reinstated at retrieval overlapped with the context of the target episode. Both behavioral and electrophysiological measures of brain activity showed strong encoding-retrieval (E-R) overlap effects, with facilitated episodic retrieval when the encoding and retrieval contexts overlapped. The electrophysiological E-R overlap effect was more sustained and involved more posterior regions when context was mentally compared with physically reinstated. Additionally, a time-frequency analysis revealed that context reinstatement alone engenders recollection of the target episode. However, while recollection of the target memory is readily prompted by a physical reinstatement, target recollection during mental reinstatement is delayed and depends on the gradual reconstruction of the context. Taken together, our results show facilitated episodic remembering also when mentally reinstating the encoding context; and that such benefits are supported by both shared and partially non-overlapping neural mechanisms when the encoding context is mentally reconstructed as compared with physically presented at the time of retrieval. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Isolation and characterization of the rat gene encoding glutamate dehydrogenase

    NARCIS (Netherlands)

    Das, A. T.; Arnberg, A. C.; Malingré, H.; Moerer, P.; Charles, R.; Moorman, A. F.; Lamers, W. H.

    1993-01-01

    The concentration of glutamate dehydrogenase (GDH) varies strongly between different organs and between different regions within organs. To permit further studies on the regulation of GDH expression, we isolated and characterized the rat gene encoding the GDH protein. This gene contains 13 exons and

  8. Direct encoding of orientation variance in the visual system.

    Science.gov (United States)

    Norman, Liam J; Heywood, Charles A; Kentridge, Robert W

    2015-01-01

    Our perception of regional irregularity, an example of which is orientation variance, seems effortless when we view two patches of texture that differ in this attribute. Little is understood, however, of how the visual system encodes a regional statistic like orientation variance, but there is some evidence to suggest that it is directly encoded by populations of neurons tuned broadly to high or low levels. The present study shows that selective adaptation to low or high levels of variance results in a perceptual aftereffect that shifts the perceived level of variance of a subsequently viewed texture in the direction away from that of the adapting stimulus (Experiments 1 and 2). Importantly, the effect is durable across changes in mean orientation, suggesting that the encoding of orientation variance is independent of global first moment orientation statistics (i.e., mean orientation). In Experiment 3 it was shown that the variance-specific aftereffect did not show signs of being encoded in a spatiotopic reference frame, similar to the equivalent aftereffect of adaptation to the first moment orientation statistic (the tilt aftereffect), which is represented in the primary visual cortex and exists only in retinotopic coordinates. Experiment 4 shows that a neuropsychological patient with damage to ventral areas of the cortex but spared intact early areas retains sensitivity to orientation variance. Together these results suggest that orientation variance is encoded directly by the visual system and possibly at an early cortical stage.

  9. Hall effect encoding of brushless dc motors

    Science.gov (United States)

    Berard, C. A.; Furia, T. J.; Goldberg, E. A.; Greene, R. C.

    1970-01-01

    Encoding mechanism integral to the motor and using the permanent magnets embedded in the rotor eliminates the need for external devices to encode information relating the position and velocity of the rotating member.

  10. Successful Scene Encoding in Presymptomatic Early-Onset Alzheimer's Disease.

    Science.gov (United States)

    Quiroz, Yakeel T; Willment, Kim Celone; Castrillon, Gabriel; Muniz, Martha; Lopera, Francisco; Budson, Andrew; Stern, Chantal E

    2015-01-01

    Brain regions critical to episodic memory are altered during the preclinical stages of Alzheimer's disease (AD). However, reliable means of identifying cognitively-normal individuals at higher risk to develop AD have not been established. To examine whether functional MRI can detect early functional changes associated with scene encoding in a group of presymptomatic presenilin-1 (PSEN1) E280A mutation carriers. Participants were 39 young, cognitively-normal individuals from an autosomal dominant early-onset AD kindred, located in Antioquia, Colombia. Participants performed a functional MRI scene encoding task and a post-scan subsequent memory test. PSEN1 mutation carriers exhibited hyperactivation within medial temporal lobe regions (hippocampus,parahippocampal formation) during successful scene encoding compared to age-matched non-carriers. Hyperactivation in medial temporal lobe regions during scene encoding is seen in individuals genetically-determined to develop AD years before their clinical onset. Our findings will guide future research with the ultimate goal of using functional neuroimaging in the early detection of preclinical AD.

  11. Splice variants of porcine PPHLN1 encoding periphilin-1

    DEFF Research Database (Denmark)

    Larsen, Knud Erik; Momeni, Jamal; Farajzadeh, Leila

    2017-01-01

    splice variants hereof. RT-PCR cloning using oligonucleotide primers derived from in silico sequences resulted in three PPHLN1 transcripts: a full-length mRNA and two transcript variant resulting in shorter proteins. The longest encoded periphilin-1, consisting of 373 amino acids, displays a high......The periphilin-1 protein is encoded by the PPHLN1 gene. Periphilin-1 is found in the cornified cell envelope during the terminal differentiation of keratinocyte at the outer layer of epidermis. In the current study we report on the cloning and characterization of the porcine PPHLN1 cDNA and two...... homology to the human periphilin-1 protein coded by the transcript variant 2 (91%). A shorter transcript variant (PPHLN1Sp1) contains a 1065-codon ORF, which is consistent with that of the authentic PPHLN1, but lacks a region of 57 bp spanning exon 7. Hence, the encoded polypeptide periphilin-1Sp1 consists...

  12. Effects of Modality on the Neural Correlates of Encoding Processes Supporting Recollection and Familiarity

    Science.gov (United States)

    Gottlieb, Lauren J.; Rugg, Michael D.

    2011-01-01

    Prior research has demonstrated that the neural correlates of successful encoding ("subsequent memory effects") partially overlap with neural regions selectively engaged by the on-line demands of the study task. The primary goal of the present experiment was to determine whether this overlap is associated solely with encoding processes supporting…

  13. Assessment of Low-Rate Turbo Encoding to Extend Coverage in WCDMA/HSDPA Systems

    DEFF Research Database (Denmark)

    Pérez Riverola, Ignasi; Sørensen, Troels Bundgaard; Kolding, T.E.

    2005-01-01

    a spectral efficiency loss compared to the use of dedicated low data rate encoding. In this paper we consider an alternative scheme with rate 1/5 turbo encoding and rate matching to achieve increased performance at the cell edge. We find a 1.2 dB link-gain in the coverage region, which in a data...

  14. Engineering Genetically Encoded FRET Sensors

    Science.gov (United States)

    Lindenburg, Laurens; Merkx, Maarten

    2014-01-01

    Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening. PMID:24991940

  15. SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

    Science.gov (United States)

    Hitz, Benjamin C; Rowe, Laurence D; Podduturi, Nikhil R; Glick, David I; Baymuradov, Ulugbek K; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Narayana, Aditi K; Onate, Kathrina C; Hilton, Jason; Ho, Marcus C; Lee, Brian T; Miyasato, Stuart R; Dreszer, Timothy R; Sloan, Cricket A; Strattan, J Seth; Tanaka, Forrest Y; Hong, Eurie L; Cherry, J Michael

    2017-01-01

    The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.

  16. SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

    Directory of Open Access Journals (Sweden)

    Benjamin C Hitz

    Full Text Available The Encyclopedia of DNA elements (ENCODE project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data has been released as a separate Python package.

  17. Optimal Achievable Encoding for Brain Machine Interface

    Science.gov (United States)

    2017-12-22

    AFRL-RH-WP-TP-2017-0001 Optimal Achievable Encoding for Brain- Machine Interface Eduardo Chichilnisky Leland Stanford Junior...Oct 2016 – 30 Sep 2017 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Optimal Achievable Encoding for Brain- Machine Interface 5b...required. First, we developed novel models of retinal encoding that improve upon the state of the art, by using machine learning methods to

  18. The ENCODE project: missteps overshadowing a success.

    Science.gov (United States)

    Eddy, Sean R

    2013-04-08

    Two clichés of science journalism have now played out around the ENCODE project. ENCODE's publicity first presented a misleading "all the textbooks are wrong" narrative about noncoding human DNA. Now several critiques of ENCODE's narrative have been published, and one was so vitriolic that it fueled "undignified academic squabble" stories that focused on tone more than substance. Neither story line does justice to our actual understanding of genomes, to ENCODE's results, or to the role of big science in biology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Encoder designed to work in harsh environments

    Energy Technology Data Exchange (ETDEWEB)

    Toop, L.

    2007-05-15

    Dynapar has developed the Acuro AX71 absolute encoder for use on offshore or land-based oil rig operations. It provides feedback on the operation of automated systems such as draw works, racking systems, rotary tables and top drives. By ensuring that automated systems function properly, this encoder responds to a need by the oil and gas industry to keep workers safe and improve efficiency, particularly for operations in rugged situations. The encoder provides feedback from motor systems to controllers, giving information about position and speed of downhole drill bits. This newly developed encoder is better than commonly used incremental encoders which are not precise in strong electrical noise environments. Rather, the absolute encoder uses a different method of reporting to the controller. A digital signal is transmitted constantly as the device operates. It is less susceptible to noise issues. It is highly accurate, tolerant of noise and is not affected by power outages. However, the absolute encoder is generally more delicate in drilling applications with high ambient temperatures and shock levels. Dynapar addressed this issue by developing compact stainless steel housing that is useful for corrosion resistance in marine applications. The AX71 absolute encoder can withstand up to 100 G of mechanical shock and ambient temperatures of up to 60 degrees C. The encoder is ATEX certified without barriers, and offers the high resolution feedback of 4,000 counts of multiturn rotation and 16,000 counts of position. 1 fig.

  20. Universal dynamic goniometer for rotary encoders

    Science.gov (United States)

    Smirnov, Nikolai V.; Latyev, Svjatoslav M.; Naumova, Anastasiia I.

    2017-06-01

    A novel dynamic goniometer for the accuracy of rotary encoders has been developed on the base of the method of comparison with the reference encoder. The set-up of the goniometer considers all constructive and informative characteristics of measured encoders. The novel goniometer construction uses the new compensating method of instrumental errors in automatic working process. The advantages of the dynamic goniometer in combination with an optical rotary encoder at the reduction of the measuring time and a simultaneous increase of the accuracy.

  1. Task-selective memory effects for successfully implemented encoding strategies.

    Directory of Open Access Journals (Sweden)

    Eric D Leshikar

    Full Text Available Previous behavioral evidence suggests that instructed strategy use benefits associative memory formation in paired associate tasks. Two such effective encoding strategies--visual imagery and sentence generation--facilitate memory through the production of different types of mediators (e.g., mental images and sentences. Neuroimaging evidence suggests that regions of the brain support memory reflecting the mental operations engaged at the time of study. That work, however, has not taken into account self-reported encoding task success (i.e., whether participants successfully generated a mediator. It is unknown, therefore, whether task-selective memory effects specific to each strategy might be found when encoding strategies are successfully implemented. In this experiment, participants studied pairs of abstract nouns under either visual imagery or sentence generation encoding instructions. At the time of study, participants reported their success at generating a mediator. Outside of the scanner, participants further reported the quality of the generated mediator (e.g., images, sentences for each word pair. We observed task-selective memory effects for visual imagery in the left middle occipital gyrus, the left precuneus, and the lingual gyrus. No such task-selective effects were observed for sentence generation. Intriguingly, activity at the time of study in the left precuneus was modulated by the self-reported quality (vividness of the generated mental images with greater activity for trials given higher ratings of quality. These data suggest that regions of the brain support memory in accord with the encoding operations engaged at the time of study.

  2. Superior memorizers employ different neural networks for encoding and recall.

    Science.gov (United States)

    Mallow, Johannes; Bernarding, Johannes; Luchtmann, Michael; Bethmann, Anja; Brechmann, André

    2015-01-01

    Superior memorizers often employ the method of loci (MoL) to memorize large amounts of information. The MoL, known since ancient times, relies on a complex process where information to be memorized is bound to landmarks along mental routes in a previously memorized environment. However, functional magnetic resonance imaging data on groups of trained superior memorizer are rare. Based on the memorizing strategy reported by superior memorizers, we developed a scheme of the processes successively employed during memorizing and recalling digits and relate these to brain activation that is specific for the encoding and recall period. In the examined superior memorizers several regions, suggested to be involved in mental navigation and digit-to-word processing, were specifically activated during encoding: bilateral early visual cortex, retrosplenial cortex, left parahippocampus, left visual cortex, and left superior parietal cortex. Although the scheme suggests that some steps during encoding and recall seem to be analog, none of the encoding areas were specifically activated during the recall. Instead, we found strong activation in left anterior superior temporal gyrus, which we relate to recalling the sequential order of the digits, and right motor cortex that may be related to reciting the digits.

  3. Comparative genomics of Shiga toxin encoding bacteriophages

    Directory of Open Access Journals (Sweden)

    Smith Darren L

    2012-07-01

    Full Text Available Abstract Background Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages. Results The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC, however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. Conclusions The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

  4. 47 CFR 11.32 - EAS Encoder.

    Science.gov (United States)

    2010-10-01

    ... encoder programming shall be protected by a lock or other security measures and be configured so that... for either manual or automatic operation. (2) Inputs. The encoder shall have two inputs, one for audio... initiating the automatic generation of the simultaneous tones shall be protected to prevent accidental...

  5. Effects of diazepam on encoding processes

    NARCIS (Netherlands)

    Gorissen, M.; Eling, P.; Luijtelaar, G. van; Coenen, A.

    1995-01-01

    Benzodiazepines are known to induce amnesic effects. To specify these effects more precisely, 40 healthy volunteers were given 15 mg diazepam or placebo. Effects on a chain of encoding operations were investigated: activation of memory representations, spreading of activation, semantic encoding and

  6. The Arabic Diatessaron Project: Digitalizing, Encoding, Lemmatization

    Directory of Open Access Journals (Sweden)

    Giuliano Lancioni

    2016-04-01

    Full Text Available The Arabic Diatessaron Project (henceforth ADP is an international research project in Digital Humanities that aims to collect, digitalise and encode all known manuscripts of the Arabic Diatessaron (henceforth AD, a text that has been relatively neglected in scholarly research. ADP’s final goal is to provide a number of tools that can enable scholars to effectively query, compare and investigate all known variants of the text that will be encoded as far as possible in compliance with the Text Encoding Initiative (TEI guidelines. The paper addresses a number of issues involved in the process of digitalising manuscripts included in the two existing editions (Ciasca 1888 and Marmardji 1935, adding variants in unedited manuscripts, encoding and lemmatising the text. Issues involved in the design of the ADP include presentation of variants, choice of the standard text, applicability of TEI guidelines, automatic translation between different encodings, cross-edition concordances and principles of lemmatisation.

  7. A model for visual memory encoding.

    Directory of Open Access Journals (Sweden)

    Rodolphe Nenert

    Full Text Available Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA. All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN. Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  8. A model for visual memory encoding.

    Science.gov (United States)

    Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

    2014-01-01

    Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA) with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA). All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions) and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN). Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s) of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  9. Identification and validation of human papillomavirus encoded microRNAs.

    Directory of Open Access Journals (Sweden)

    Kui Qian

    Full Text Available We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

  10. Encoding of coordination complexes with XML.

    Science.gov (United States)

    Vinoth, P; Sankar, P

    2017-09-01

    An in-silico system to encode structure, bonding and properties of coordination complexes is developed. The encoding is achieved through a semantic XML markup frame. Composition of the coordination complexes is captured in terms of central atom and ligands. Structural information of central atom is detailed in terms of electron status of valence electron orbitals. The ligands are encoded with specific reference to the electron environment of ligand centre atoms. Behaviour of ligands to form low or high spin complexes is accomplished by assigning a Ligand Centre Value to every ligand based on the electronic environment of ligand centre atom. Chemical ontologies are used for categorization purpose and to control different hybridization schemes. Complexes formed by the central atoms of transition metal, non-transition elements belonging to s-block, p-block and f-block are encoded with a generic encoding platform. Complexes of homoleptic, heteroleptic and bridged types are also covered by this encoding system. Utility of the encoded system to predict redox electron transfer reaction in the coordination complexes is demonstrated with a simple application. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Efficient reverse time migration with amplitude encoding

    Science.gov (United States)

    Hu, Jiangtao; Wang, Huazhong; Zhao, Lei; Shao, Yu; Wang, Meixia; Osen, Are

    2015-08-01

    Reverse time migration (RTM) is an accurate seismic imaging method for imaging the complex subsurface structure. Traditional common shot RTM suffers from low efficiency due to the large number of single shot gathers, especially for marine seismic data. Phase encoding is commonly used to reduce the computational cost of RTM. Phase encoding in the frequency domain is usually related to time shift in the time domain. Therefore, phase-encoding-based RTM needs time padding to avoid information loss which degrades the efficiency of the time-domain wavefield extrapolator. In this paper, an efficient time-domain RTM scheme based on the amplitude encoding is proposed. This scheme uses the orthogonal cosine basis as the encoding function, which has similar physical meaning to plane wave encoding (i.e. plane-wave components with different surface shooting angles). The proposed scheme can generate a qualified imaging result as well as common shot RTM but with less computational cost. Since this scheme does not need time padding, it is more efficient than the phase encoding schemes and can be conveniently implemented in the time domain. Numerical examples on the Sigsbee2a synthetic dataset demonstrate the feasibility of the proposed method.

  12. The olfactory tubercle encodes odor valence in behaving mice.

    Science.gov (United States)

    Gadziola, Marie A; Tylicki, Kate A; Christian, Diana L; Wesson, Daniel W

    2015-03-18

    Sensory information acquires meaning to adaptively guide behaviors. Despite odors mediating a number of vital behaviors, the components of the olfactory system responsible for assigning meaning to odors remain unclear. The olfactory tubercle (OT), a ventral striatum structure that receives monosynaptic input from the olfactory bulb, is uniquely positioned to transform odor information into behaviorally relevant neural codes. No information is available, however, on the coding of odors among OT neurons in behaving animals. In recordings from mice engaged in an odor discrimination task, we report that the firing rate of OT neurons robustly and flexibly encodes the valence of conditioned odors over identity, with rewarded odors evoking greater firing rates. This coding of rewarded odors occurs before behavioral decisions and represents subsequent behavioral responses. We predict that the OT is an essential region whereby odor valence is encoded in the mammalian brain to guide goal-directed behaviors. Copyright © 2015 the authors 0270-6474/15/354515-13$15.00/0.

  13. Evidence for cortical encoding specificity in episodic memory: memory-induced re-activation of picture processing areas.

    Science.gov (United States)

    Vaidya, Chandan J; Zhao, Margaret; Desmond, John E; Gabrieli, John D E

    2002-01-01

    Functional magnetic resonance imaging (fMRI) was used to examine whether neural pathways used to encode pictures into memory were re-activated during retrieval of those memories. At encoding, subjects semantically classified common objects presented as pictures or words. At retrieval, subjects performed yes/no recognition memory judgments on words that had been encoded as pictures or as words. The retrieval test probed memory for the encoded item, but not memory for the modality of the encoded item (picture/word). Results revealed that a subset of the brain regions involved specifically in encoding of pictures were also engaged during recognition memory for the encoded pictures. Specifically, encoding of pictures relative to words engaged bilateral extrastriate visual cortex, namely fusiform, lingual, middle occipital, and inferior temporal gyri (Broadman area (BA) 18/19/37). Recognition memory judgments about words that were encoded as pictures relative to those that were encoded as words activated fusiform and inferior temporal gyri primarily in the left hemisphere. Thus, cortical areas originally involved in perception of a visual experience become part of the long-term memory trace for that experience. These findings suggest a neural basis for encoding specificity and transfer appropriate processing in human memory.

  14. Novel adenovirus encoded virus-like particles displaying the placental malaria associated VAR2CSA antigen

    DEFF Research Database (Denmark)

    Andersson, Anne-Marie C; dos Santos Marques Resende, Mafalda; Salanti, Ali

    2017-01-01

    and the CSA binding region of VAR2CSA has been identified as a promising vaccine target against placental malaria. Here we designed adenovirus encoded virus-like particles (VLP) by co-encoding Simian Immunodeficiency Virus (SIV) gag and VAR2CSA. The VAR2CSA antigen was fused to the transmembrane (TM...... revealed a unique targeting of several epitopes in mice that had been primed with VAR2CSA HA TM-CT. Consequently, modification of VLP anchors is an important point of optimization in virus-encoded retroviral VLP-based vaccines, and adenovirus VLPs boosted by recombinant proteins offer hope of increasing...

  15. Using XML to encode TMA DES metadata.

    Science.gov (United States)

    Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

    2011-01-01

    The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

  16. Using XML to encode TMA DES metadata

    Directory of Open Access Journals (Sweden)

    Oliver Lyttleton

    2011-01-01

    Full Text Available Background: The Tissue Microarray Data Exchange Specification (TMA DES is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

  17. Encoder: a connectionist model of how learning to visually encode fixated text images improves reading fluency.

    Science.gov (United States)

    Martin, Gale L

    2004-07-01

    This article proposes that visual encoding learning improves reading fluency by widening the span over which letters are recognized from a fixated text image so that fewer fixations are needed to cover a text line. Encoder is a connectionist model that learns to convert images like the fixated text images human readers encode into the corresponding letter sequences. The computational theory of classification learning predicts that fixated text-image size makes this learning difficult but that reducing image variability and biasing learning should help. Encoder confirms these predictions. It fails to learn as image size increases but achieves humanlike visual encoding accuracy when image variability is reduced by regularities in fixation positions and letter sequences and when learning is biased to discover mapping functions based on the sequential, componential structure of text. After training, Encoder exhibits many humanlike text familiarity effects. ((c) 2004 APA, all rights reserved)

  18. Dissociation of the neural correlates of visual and auditory contextual encoding.

    Science.gov (United States)

    Gottlieb, Lauren J; Uncapher, Melina R; Rugg, Michael D

    2010-01-01

    The present study contrasted the neural correlates of encoding item-context associations according to whether the contextual information was visual or auditory. Subjects (N=20) underwent fMRI scanning while studying a series of visually presented pictures, each of which co-occurred with either a visually or an auditorily presented name. The task requirement was to judge whether the name corresponded to the presented object. In a subsequent memory test subjects judged whether test pictures were studied or unstudied and, for items judged as studied, indicated the presentation modality of the associated name. Dissociable cortical regions demonstrating increased activity for visual vs. auditory trials (and vice versa) were identified. A subset of these modality-selective regions also showed modality-selective subsequent source memory effects, that is, enhanced responses on trials associated with correct modality judgments relative to those for which modality or item memory later failed. These findings constitute direct evidence for the proposal that successful encoding of a contextual feature is associated with enhanced activity in the cortical regions engaged during the on-line processing of that feature. In addition, successful encoding of visual objects within auditory contexts was associated with more extensive engagement of the hippocampus and adjacent medial temporal cortex than was the encoding of such objects within visual contexts. This raises the possibility that the encoding of across-modality item-context associations places more demands on the hippocampus than does the encoding of within-modality associations.

  19. Fragments of a larger whole: retrieval cues constrain observed neural correlates of memory encoding.

    Science.gov (United States)

    Otten, Leun J

    2007-09-01

    Laying down a new memory involves activity in a number of brain regions. Here, it is shown that the particular regions associated with successful encoding depend on the way in which memory is probed. Event-related functional magnetic resonance imaging signals were acquired while subjects performed an incidental encoding task on a series of visually presented words denoting objects. A recognition memory test using the Remember/Know procedure to separate responses based on recollection and familiarity followed 1 day later. Critically, half of the studied objects were cued with a corresponding spoken word, and half with a corresponding picture. Regardless of cue, activity in prefrontal and hippocampal regions predicted subsequent recollection of a word. Type of retrieval cue modulated activity in prefrontal, temporal, and parietal cortices. Words subsequently recognized on the basis of a sense of familiarity were at study also associated with differential activity in a number of brain regions, some of which were probe dependent. Thus, observed neural correlates of successful encoding are constrained by type of retrieval cue, and are only fragments of all encoding-related neural activity. Regions exhibiting cue-specific effects may be sites that support memory through the degree of overlap between the processes engaged during encoding and those engaged during retrieval.

  20. An encyclopedia of mouse DNA elements (Mouse ENCODE).

    Science.gov (United States)

    Stamatoyannopoulos, John A; Snyder, Michael; Hardison, Ross; Ren, Bing; Gingeras, Thomas; Gilbert, David M; Groudine, Mark; Bender, Michael; Kaul, Rajinder; Canfield, Theresa; Giste, Erica; Johnson, Audra; Zhang, Mia; Balasundaram, Gayathri; Byron, Rachel; Roach, Vaughan; Sabo, Peter J; Sandstrom, Richard; Stehling, A Sandra; Thurman, Robert E; Weissman, Sherman M; Cayting, Philip; Hariharan, Manoj; Lian, Jin; Cheng, Yong; Landt, Stephen G; Ma, Zhihai; Wold, Barbara J; Dekker, Job; Crawford, Gregory E; Keller, Cheryl A; Wu, Weisheng; Morrissey, Christopher; Kumar, Swathi A; Mishra, Tejaswini; Jain, Deepti; Byrska-Bishop, Marta; Blankenberg, Daniel; Lajoie, Bryan R; Jain, Gaurav; Sanyal, Amartya; Chen, Kaun-Bei; Denas, Olgert; Taylor, James; Blobel, Gerd A; Weiss, Mitchell J; Pimkin, Max; Deng, Wulan; Marinov, Georgi K; Williams, Brian A; Fisher-Aylor, Katherine I; Desalvo, Gilberto; Kiralusha, Anthony; Trout, Diane; Amrhein, Henry; Mortazavi, Ali; Edsall, Lee; McCleary, David; Kuan, Samantha; Shen, Yin; Yue, Feng; Ye, Zhen; Davis, Carrie A; Zaleski, Chris; Jha, Sonali; Xue, Chenghai; Dobin, Alex; Lin, Wei; Fastuca, Meagan; Wang, Huaien; Guigo, Roderic; Djebali, Sarah; Lagarde, Julien; Ryba, Tyrone; Sasaki, Takayo; Malladi, Venkat S; Cline, Melissa S; Kirkup, Vanessa M; Learned, Katrina; Rosenbloom, Kate R; Kent, W James; Feingold, Elise A; Good, Peter J; Pazin, Michael; Lowdon, Rebecca F; Adams, Leslie B

    2012-08-13

    To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

  1. Cortical pattern separation and item-specific memory encoding.

    Science.gov (United States)

    Pidgeon, Laura M; Morcom, Alexa M

    2016-05-01

    Pattern separation and pattern completion are fundamental brain processes thought to be critical for episodic memory encoding and retrieval, and for discrimination between similar memories. These processes are best understood in the hippocampus, but are proposed to occur throughout the brain, in particular in sensory regions. Cortical, as well as hippocampal, pattern separation may therefore support formation of event-unique memory traces. Using fMRI, we investigated cortical pattern separation and pattern completion and their relationship to encoding activity predicting subsequent item-specific compared to gist memory. During scanning, participants viewed images of novel objects, repeated objects, and objects which were both perceptually and conceptually similar to previously presented images, while performing a size judgement task. In a later surprise recognition test, they judged whether test items were 'same' 'similar' or 'new' relative to studied items. Activity consistent with pattern separation - responses to similar items as if novel - was observed in bilateral occipito-temporal cortex. Activity consistent with pattern completion - responses to similar items as if repeated - was observed in left prefrontal cortex and hippocampus. Curve fitting analysis further revealed that graded responses to change in image conceptual and perceptual similarity in bilateral prefrontal and right parietal regions met specific computational predictions for pattern separation for one or both of these similarity dimensions. Functional overlap between encoding activity predicting subsequent item-specific recognition and pattern separation activity was also observed in left occipital cortex and bilateral inferior frontal cortex. The findings suggest that extrahippocampal regions including sensory and prefrontal cortex contribute to pattern separation and pattern completion of visual input, consistent with the proposal that cortical pattern separation contributes to formation of

  2. Multiple genes encode the major surface glycoprotein of Pneumocystis carinii

    DEFF Research Database (Denmark)

    Kovacs, J A; Powell, F; Edman, J C

    1993-01-01

    The major surface antigen of Pneumocystis carinii, a life-threatening opportunistic pathogen in human immunodeficiency virus-infected patients, is an abundant glycoprotein that functions in host-organism interactions. A monoclonal antibody to this antigen is protective in animals, and thus...... hydrophobic region at the carboxyl terminus. The presence of multiple related msg genes encoding the major surface glycoprotein of P. carinii suggests that antigenic variation is a possible mechanism for evading host defenses. Further characterization of this family of genes should allow the development...... of novel approaches to the control of this pathogen....

  3. Determining the Neural Substrate for Encoding a Memory of Human Pain and the Influence of Anxiety.

    Science.gov (United States)

    Tseng, Ming-Tsung; Kong, Yazhuo; Eippert, Falk; Tracey, Irene

    2017-12-06

    To convert a painful stimulus into a briefly maintainable construct when the painful stimulus is no longer accessible is essential to guide human behavior and avoid dangerous situations. Because of the aversive nature of pain, this encoding process might be influenced by emotional aspects and could thus vary across individuals, but we have yet to understand both the basic underlying neural mechanisms as well as potential interindividual differences. Using fMRI in combination with a delayed-discrimination task in healthy volunteers of both sexes, we discovered that brain regions involved in this working memory encoding process were dissociable according to whether the to-be-remembered stimulus was painful or not, with the medial thalamus and the rostral anterior cingulate cortex encoding painful and the primary somatosensory cortex encoding nonpainful stimuli. Encoding of painful stimuli furthermore significantly enhanced functional connectivity between the thalamus and medial prefrontal cortex (mPFC). With regards to emotional aspects influencing encoding processes, we observed that more anxious participants showed significant performance advantages when encoding painful stimuli. Importantly, only during the encoding of pain, the interindividual differences in anxiety were associated with the strength of coupling between medial thalamus and mPFC, which was furthermore related to activity in the amygdala. These results indicate not only that there is a distinct signature for the encoding of a painful experience in humans, but also that this encoding process involves a strong affective component. SIGNIFICANCE STATEMENT To convert the sensation of pain into a briefly maintainable construct is essential to guide human behavior and avoid dangerous situations. Although this working memory encoding process is implicitly contained in the majority of studies, the underlying neural mechanisms remain unclear. Using fMRI in a delayed-discrimination task, we found that the

  4. Molecular detection of Acinetobacter species in lice and keds of domestic animals in Oromia Regional State, Ethiopia.

    Directory of Open Access Journals (Sweden)

    Bersissa Kumsa

    Full Text Available This study was conducted to determine the presence of Acinetobacter and Rickettsia species DNA in lice and Melophagus ovinus (sheep ked of animals from Oromia Regional State in Ethiopia. From September through November 2011, a total of 207 cattle, 85 sheep, 47 dogs and 16 cats were examined for ectoparasites. Results of morphological identification revealed several species of ectoparasites: Linognathus vituli (L. vituli, Bovicola bovis (B. bovis and Solenopotes capillatus (S. capillatus on cattle; B. ovis and Melophagus ovinus (M. ovinus on sheep; and Heterodoxus spiniger (H. spiniger on dogs. There was a significantly (p≤0.0001 higher prevalence of L. vituli observed in cattle than both S. capillatus and B. bovis. Molecular identification of lice using an 18S rRNA gene analysis confirms the identified lice species by morphological methods. We detected different Acinetobacter species among lice (11.1% and keds (86.4% including A. soli in L. vituli of cattle, A. lowffii in M. ovinus of sheep, A. pittii in H. spiniger of dogs, 1 new Acinetobacter spp. in M. ovinus and 2 new Acinetobacter spp. in H. spiniger of dogs using partial rpoB gene sequence analysis. There was a significantly higher prevalence of Acinetobacter spp. in keds than in lice (p≤0.00001. Higher percentage of Acinetobacter spp. DNA was detected in H. spiniger than in both B. ovis and L. vituli (p≤0.00001. Carbapenemase resistance encoding genes for blaOXA-23, blaOXA-24, blaOXA-58, blaNDM-1 and blaOXA-51 were not found in any lice and keds. These findings suggest that synanthropic animals and their ectoparasites might increase the risk of human exposure to zoonotic pathogens and could be a source for Acinetobacter spp. infections in humans. However, additional epidemiological data are required to determine whether ectoparasites of animals can act as environmental reservoirs and play a role in spreading these bacteria to both animal and human hosts.

  5. Spatially dynamic recurrent information flow across long-range dorsal motor network encodes selective motor goals.

    Science.gov (United States)

    Yoo, Peter E; Hagan, Maureen A; John, Sam E; Opie, Nicholas L; Ordidge, Roger J; O'Brien, Terence J; Oxley, Thomas J; Moffat, Bradford A; Wong, Yan T

    2018-03-08

    Performing voluntary movements involves many regions of the brain, but it is unknown how they work together to plan and execute specific movements. We recorded high-resolution ultra-high-field blood-oxygen-level-dependent signal during a cued ankle-dorsiflexion task. The spatiotemporal dynamics and the patterns of task-relevant information flow across the dorsal motor network were investigated. We show that task-relevant information appears and decays earlier in the higher order areas of the dorsal motor network then in the primary motor cortex. Furthermore, the results show that task-relevant information is encoded in general initially, and then selective goals are subsequently encoded in specifics subregions across the network. Importantly, the patterns of recurrent information flow across the network vary across different subregions depending on the goal. Recurrent information flow was observed across all higher order areas of the dorsal motor network in the subregions encoding for the current goal. In contrast, only the top-down information flow from the supplementary motor cortex to the frontoparietal regions, with weakened recurrent information flow between the frontoparietal regions and bottom-up information flow from the frontoparietal regions to the supplementary cortex were observed in the subregions encoding for the opposing goal. We conclude that selective motor goal encoding and execution rely on goal-dependent differences in subregional recurrent information flow patterns across the long-range dorsal motor network areas that exhibit graded functional specialization. © 2018 Wiley Periodicals, Inc.

  6. Single echo acquisition MRI using RF encoding.

    Science.gov (United States)

    Wright, Steven M; McDougall, Mary Preston

    2009-11-01

    Encoding of spatial information in magnetic resonance imaging is conventionally accomplished by using magnetic field gradients. During gradient encoding, the position in k-space is determined by a time-integral of the gradient field, resulting in a limitation in imaging speed due to either gradient power or secondary effects such as peripheral nerve stimulation. Partial encoding of spatial information through the sensitivity patterns of an array of coils, known as parallel imaging, is widely used to accelerate the imaging, and is complementary to gradient encoding. This paper describes the one-dimensional limit of parallel imaging in which all spatial localization in one dimension is performed through encoding by the radiofrequency (RF) coil. Using a one-dimensional array of long and narrow parallel elements to localize the image information in one direction, an entire image is obtained from a single line of k-space, avoiding rapid or repeated manipulation of gradients. The technique, called single echo acquisition (SEA) imaging, is described, along with the need for a phase compensation gradient pulse to counteract the phase variation contained in the RF coil pattern which would otherwise cause signal cancellation in each imaging voxel. Image reconstruction and resolution enhancement methods compatible with the speed of the technique are discussed. MR movies at frame rates of 125 frames per second are demonstrated, illustrating the ability to monitor the evolution of transverse magnetization to steady state during an MR experiment as well as demonstrating the ability to image rapid motion. Because this technique, like all RF encoding approaches, relies on the inherent spatially varying pattern of the coil and is not a time-integral, it should enable new applications for MRI that were previously inaccessible due to speed constraints, and should be of interest as an approach to extending the limits of detection in MR imaging.

  7. Enhanced double patterning decomposition using lines encoding

    Directory of Open Access Journals (Sweden)

    Khaled M. Soradi

    2016-09-01

    Full Text Available Double patterning photolithography (DPL is considered one of the best solutions used for enabling 32 nm/22 nm technology. In this paper, we propose a new technique for double patterning post decomposition conflict resolution. The algorithm is based on lines positions encoding followed by code pattern matching. Experimental results show that the usage of encoded patterns decreases the time needed for pattern matching and increases the matching accuracy. The overall manual problem solution time is reduced to about 1%.

  8. Neural correlates of durable memories across the adult lifespan: brain activity at encoding and retrieval.

    Science.gov (United States)

    Vidal-Piñeiro, Didac; Sneve, Markus H; Storsve, Andreas B; Roe, James M; Walhovd, Kristine B; Fjell, Anders M

    2017-12-01

    Age-related effects on brain activity during encoding and retrieval of episodic memories are well documented. However, research typically tests memory only once, shortly after encoding. Retaining information over extended periods is critical, and there are reasons to expect age-related effects on the neural correlates of durable memories. Here, we tested whether age was associated with the activity elicited by durable memories. One hundred forty-three participants (22-78 years) underwent an episodic memory experiment where item-context relationships were encoded and tested twice. Participants were scanned during encoding and the first test. Memories retained after 90 minutes but later forgotten were classified as transient, whereas memories retained after 5 weeks were classified as durable. Durable memories were associated with greater encoding activity in inferior lateral parietal and posteromedial regions and greater retrieval activity in frontal and insular regions. Older adults exhibited lower posteromedial activity during encoding and higher frontal activity during retrieval, possibly reflecting greater involvement of control processes. This demonstrates that long-lasting memories are supported by specific patterns of cortical activity that are related to age. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. An Unusual Phage Repressor Encoded by Mycobacteriophage BPs.

    Directory of Open Access Journals (Sweden)

    Valerie M Villanueva

    Full Text Available Temperate bacteriophages express transcription repressors that maintain lysogeny by down-regulating lytic promoters and confer superinfection immunity. Repressor regulation is critical to the outcome of infection-lysogenic or lytic growth-as well as prophage induction into lytic replication. Mycobacteriophage BPs and its relatives use an unusual integration-dependent immunity system in which the phage attachment site (attP is located within the repressor gene (33 such that site-specific integration leads to synthesis of a prophage-encoded product (gp33103 that is 33 residues shorter at its C-terminus than the virally-encoded protein (gp33136. However, the shorter form of the repressor (gp33103 is stable and active in repression of the early lytic promoter PR, whereas the longer virally-encoded form (gp33136 is inactive due to targeted degradation via a C-terminal ssrA-like tag. We show here that both forms of the repressor bind similarly to the 33-34 intergenic regulatory region, and that BPs gp33103 is a tetramer in solution. The BPs gp33103 repressor binds to five regulatory regions spanning the BPs genome, and regulates four promoters including the early lytic promoter, PR. BPs gp33103 has a complex pattern of DNA recognition in which a full operator binding site contains two half sites separated by a variable spacer, and BPs gp33103 induces a DNA bend at the full operator site but not a half site. The operator site structure is unusual in that one half site corresponds to a 12 bp palindrome identified previously, but the other half site is a highly variable variant of the palindrome.

  10. In silicio search for genes encoding peroxisomal proteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Kal, A J; Hettema, E H; van den Berg, M; Koerkamp, M G; van Ijlst, L; Distel, B; Tabak, H F

    2000-01-01

    The biogenesis of peroxisomes involves the synthesis of new proteins that after, completion of translation, are targeted to the organelle by virtue of peroxisomal targeting signals (PTS). Two types of PTSs have been well characterized for import of matrix proteins (PTS1 and PTS2). Induction of the genes encoding these matrix proteins takes place in oleate-containing medium and is mediated via an oleate response element (ORE) present in the region preceding these genes. The authors have searched the yeast genome for OREs preceding open reading frames (ORFs), and for ORFs that contain either a PTS1 or PTS2. Of the ORFs containing an ORE, as well as either a PTS1 or a PTS2, many were known to encode bona fide peroxisomal matrix proteins. In addition, candidate genes were identified as encoding putative new peroxisomal proteins. For one case, subcellular location studies validated the in silicio prediction. This gene encodes a new peroxisomal thioesterase.

  11. KOGNAC : Efficient encoding of large knowledge graphs

    NARCIS (Netherlands)

    Urbani, Jacopo; Dutta, Sourav; Gurajada, Sairam; Weikum, Gerhard

    2016-01-01

    Many Web applications require efficient querying of large Knowledge Graphs (KGs). We propose KOGNAC, a dictionary-encoding algorithm designed to improve SPARQL querying with a judicious combination of statistical and semantic techniques. In KOGNAC, frequent terms are detected with a frequency

  12. Phenotypic and Molecular Characterization of Plasmid- Encoded ...

    African Journals Online (AJOL)

    Purpose: To investigate the distribution of plasmid-encoded extended spectrum beta-lacatamases (ESBLs) in Lahore, Pakistan using different phenotypic and molecular methods. Methods: Escherichia coli and Klebsiella spp were obtained over a period of nineteen months (June 2007 to December 2008). Both were tested ...

  13. in rice encoding a flavin monooxygenase

    Indian Academy of Sciences (India)

    Cloning, characterization and expression of OsFMO(t) in rice encoding a flavin monooxygenase. Jicai Yi, Lanna Liu, Youpei Cao, Jiazuo Li and Mantong Mei. J. Genet. 92, 471–480. Figure 1. Examples of PCR analysis of the presence of the genes for HPT and GUS in transgenic plants. Genomic DNA of putative.

  14. RNAi suppressors encoded by pathogenic human viruses

    NARCIS (Netherlands)

    de Vries, Walter; Berkhout, Ben

    2008-01-01

    RNA silencing or RNAi interference (RNAi) serves as an innate antiviral mechanism in plants, fungi and animals. Human viruses, like plant viruses, encode suppressor proteins or RNAs that block or modulate the RNAi pathway. This review summarizes the mechanisms by which pathogenic human viruses

  15. Visual Memory : The Price of Encoding Details

    NARCIS (Netherlands)

    Nieuwenstein, Mark; Kromm, Maria

    2017-01-01

    Studies on visual long-term memory have shown that we have a tremendous capacity for remembering pictures of objects, even at a highly detailed level. What remains unclear, however, is whether encoding objects at such a detailed level comes at any cost. In the current study, we examined how the

  16. Frequency encoded optical assessment of human retinal physiology

    Science.gov (United States)

    Leitgeb, Rainer A.; Michaely, Roland; Bachmann, Adrian; Lassner, Theo; Blatter, Cedric

    2008-02-01

    We demonstrate in-vivo functional imaging of the human retina with Fourier domain optical coherence tomography employing frequency encoding of an excitation pattern. The principle is based on projecting a modulated rectangular pattern across the foveal region and acquiring a time series of B-Scans at the same vertical position across the pattern. The idea is to modulate the excitation with a frequency that is distinct from the heartbeat and irregular motion artifacts. Fourier analysis of the time series at each transverse position in the B-scan series allows assessing the retinal response as change in the FDOCT reflectivity signal exactly at the pattern modulation frequency. We observe a change in retinal reflectivity within the region of the outer segment photoreceptor layer exactly at the pattern modulation frequency.

  17. Hippocampal PET activations of memory encoding and retrieval: the HIPER model.

    Science.gov (United States)

    Lepage, M; Habib, R; Tulving, E

    1998-01-01

    A meta-analysis of experimentally induced changes in blood flow ("activations") in positron emission tomography (PET) studies of memory has revealed an orderly functional anatomic pattern: Activations in the hippocampal region associated with episodic memory encoding are located primarily in the rostral portions of the region, whereas activations associated with episodic memory retrieval are located primarily in the caudal portions. These findings are based on an analysis of a sample of 54 "hippocampal encoding and retrieval" activations that were culled from an overall database consisting of 52 published PET studies of memory. We refer to this general pattern of rostrocaudal gradient of encoding and retrieval PET activations as the HIPER (Hippocampal Encoding/Retrieval) model. The model suggests a division of memory-related labor between the rostral and caudal portions of the hippocampal formation. Because functional anatomic pattern of encoding and retrieval activation that defines the HIPER model was unprecedented and unexpected, it is difficult to relate the model to what is already known or thought about functional neuroanatomy of episodic memory in the hippocampal regions. The model is interesting primarily because its exploration may yield fresh insights into the neural basis of human memory.

  18. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

    Science.gov (United States)

    Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; Liu, Shengyi

    2014-01-03

    Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome

  19. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.

    Science.gov (United States)

    Siggens, L; Ekwall, K

    2014-09-01

    The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease. © 2014 The Association for the Publication of the Journal of Internal Medicine.

  20. Implicit false memory in the DRM paradigm: effects of amnesia, encoding instructions, and encoding duration.

    Science.gov (United States)

    Van Damme, Ilse; d'Ydewalle, Géry

    2009-09-01

    Recent studies with the Deese/Roediger-McDermott (Deese 1959; Roediger & McDermott, 1995) paradigm have revealed that amnesic patients do not only show impaired veridical memory, but also diminished false memory for semantically related lure words. Due to the typically used explicit retrieval instructions, however, this finding may reflect problems at encoding, at recollection, or both. Therefore, the present experiments examined implicit as well as explicit false memory in patients suffering from Korsakoff's syndrome and controls. In Experiment 1, encoding instructions either focused on remembering individual list words, or on discovering semantic relationships among the words. In Experiment 2, different presentation durations were used. Results emphasize the distinction between automatic and intentional retrieval: Korsakoff patients' veridical and false memory scores were diminished when explicit recollection was required, but not when memory was tested implicitly. Encoding manipulations only significantly affected veridical memory: Priming was reduced with thematic encoding, and explicit retrieval was facilitated when given more study time.

  1. Configural face encoding and spatial frequency information.

    Science.gov (United States)

    Boutet, Isabelle; Collin, Charles; Faubert, Jocelyn

    2003-10-01

    Configural relations and a critical band of spatial frequencies (SFs) in the middle range are particularly important for face recognition. We report the results of four experiments in which the relationship between these two types of information was examined. In Experiments 1, 2A, and 2B, the face inversion effect (FIE) was used to probe configural face encoding. Recognition of upright and inverted faces and nonface objects was measured in four conditions: a no-filter condition and three SF conditions (low, medium, and high frequency). We found significant FIEs of comparable magnitudes for all frequency conditions. In Experiment 3, discrimination of faces on the basis of either configural or featural modifications was measured under the same four conditions. Although the ability to discriminate configural modifications was superior in the medium-frequency condition, so was the ability to discriminate featural modifications. We conclude that the band of SF that is critical for face recognition does not contribute preferentially to configural encoding.

  2. Bacillus caldolyticus prs gene encoding phosphoribosyldiphosphate synthase

    DEFF Research Database (Denmark)

    Krath, Britta N.; Hove-Jensen, Bjarne

    1996-01-01

    The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-l-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

  3. Storing data encoded DNA in living organisms

    Science.gov (United States)

    Wong,; Pak C. , Wong; Kwong K. , Foote; Harlan, P [Richland, WA

    2006-06-06

    Current technologies allow the generation of artificial DNA molecules and/or the ability to alter the DNA sequences of existing DNA molecules. With a careful coding scheme and arrangement, it is possible to encode important information as an artificial DNA strand and store it in a living host safely and permanently. This inventive technology can be used to identify origins and protect R&D investments. It can also be used in environmental research to track generations of organisms and observe the ecological impact of pollutants. Today, there are microorganisms that can survive under extreme conditions. As well, it is advantageous to consider multicellular organisms as hosts for stored information. These living organisms can provide as memory housing and protection for stored data or information. The present invention provides well for data storage in a living organism wherein at least one DNA sequence is encoded to represent data and incorporated into a living organism.

  4. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  5. A PILOT STUDY ON THE ENCODING OF A PERCEPTUAL LEARNING TASK FOLLOWING SLEEP DEPRIVATION.

    Science.gov (United States)

    McWhirter, Kelly K; Morrow, Anne S; Lee, Beth A; Bishu, Shrinivas; Zametkin, Alan J; Balkin, Thomas J; Smith, Carolyn B; Picchioni, Dante

    2015-08-01

    Memory encoding sometimes must occur during a period of sleep deprivation. The question was whether one night of sleep deprivation inhibits encoding on a perceptual learning task (the texture discrimination task). The sample was 18 human participants (M age=22.1 yr., SEM=0.5; 8 men). The participants were randomized to a sleep deprivation or sleep control condition and, after the manipulation, were given two administrations of the texture discrimination task. All participants were given an opportunity for a 90 min. nap between the two administrations. Performance was measured by the interpolated stimulus-to-mask-onset asynchrony (i.e., the inter-stimulus interval), at which the percentage of correct responses for the stimuli in the participant's peripheral vision fell below 80%. Offline consolidation was defined as a decrease in this index between the two administrations. Participants who were sleep deprived prior to encoding exhibited similar offline consolidation (M=-5.3 msec., SEM=2.3) compared to participants who were not sleep deprived prior to encoding (M=-6.2 msec., SEM=3.9); the two-way interaction between time and condition was not significant. In light of reports in the literature, these results indicate encoding following sleep deprivation may be influenced by both the type of task encoded and the brain regions involved in memory processing.

  6. An Intensional Concurrent Faithful Encoding of Turing Machines

    Directory of Open Access Journals (Sweden)

    Thomas Given-Wilson

    2014-10-01

    Full Text Available The benchmark for computation is typically given as Turing computability; the ability for a computation to be performed by a Turing Machine. Many languages exploit (indirect encodings of Turing Machines to demonstrate their ability to support arbitrary computation. However, these encodings are usually by simulating the entire Turing Machine within the language, or by encoding a language that does an encoding or simulation itself. This second category is typical for process calculi that show an encoding of lambda-calculus (often with restrictions that in turn simulates a Turing Machine. Such approaches lead to indirect encodings of Turing Machines that are complex, unclear, and only weakly equivalent after computation. This paper presents an approach to encoding Turing Machines into intensional process calculi that is faithful, reduction preserving, and structurally equivalent. The encoding is demonstrated in a simple asymmetric concurrent pattern calculus before generalised to simplify infinite terms, and to show encodings into Concurrent Pattern Calculus and Psi Calculi.

  7. Audio Cartography: Visual Encoding of Acoustic Parameters

    OpenAIRE

    Kornfeld, A.; Schiewe, J.; Dykes, J.

    2011-01-01

    Our sonic environment is the matter of subject in multiple domains which developed individual means of its description. As a result, it lacks an established visual language through which knowledge can be connected and insights shared. We provide a visual communication framework for the systematic and coherent documentation of sound in large-scale environments. This consists of visual encodings and mappings of acoustic parameters into distinct graphic variables that present plausible solutions...

  8. Toward Chemical Implementation of Encoded Combinatorial Libraries

    DEFF Research Database (Denmark)

    Nielsen, John; Janda, Kim D.

    1994-01-01

    The recent application of "combinatorial libraries" to supplement existing drug screening processes might simplify and accelerate the search for new lead compounds or drugs. Recently, a scheme for encoded combinatorial chemistry was put forward to surmount a number of the limitations possessed by...... by existing methodologies. Here we detail the synthesis of several matrices and the necessary chemistry to implement the conceptual scheme. In addition, we disclose how this novel technology permits a controlled ′dendritic" display of the chemical libraries....

  9. ISOLATION AND CHARACTERIZATION OF THE RAT GENE ENCODING GLUTAMATE-DEHYDROGENASE

    NARCIS (Netherlands)

    DAS, AT; ARNBERG, AC; MALINGRE, H; MOERER, P; CHARLES, R; MOORMAN, AFM; LAMERS, WH

    1993-01-01

    The concentration of glutamate dehydrogenase (GDH) varies strongly between different organs and between different regions within organs. To permit further studies on the regulation of GDH expression, we isolated and characterized the rat gene encoding the GDH protein. This gene contains 13 exons and

  10. The intersubject and intrasubject reproducibility of FMRI activation during three encoding tasks: implications for clinical applications

    Energy Technology Data Exchange (ETDEWEB)

    Harrington, Greg S. [Virginia Commonwealth University, Department of Radiology, Richmond, VA (United States); Tomaszewski Farias, Sarah [University of California at Davis, Department of Neurology, Sacramento (United States); Buonocore, Michael H. [University of California at Davis, Department of Radiology, Sacramento (United States); Yonelinas, Andrew P. [University of California at Davis, Department of Psychology, Davis (United States)

    2006-07-15

    The goal of the present study was to evaluate the inter- and intrasubject reproducibility of FMRI activation for three memory encoding tasks previously used in the context of presurgical functional mapping. The primary region of interest (ROI) was the medial temporal lobe (MTL). Comparative ROIs included the inferior frontal and fusiform gyri which are less affected by susceptibility-induced signal losses than the MTL regions. Eighteen subjects were scanned using three memory encoding paradigms: word-pair, pattern, and scene encoding. Nine subjects underwent repeat scanning. Intersubject reproducibility of FMRI activation was evaluated by examining the percent of subjects who showed activation within a given ROI and the range to which individual laterality indices (LIs) varied from the mean. Intrasubject test-retest reproducibility was evaluated by examining the LI test-retest correlation, the average difference between LIs from two separate imaging sessions, and concordance ratios of activation volumes (R{sub volume} and R{sub overlap}). For scene encoding the reproducibility of activation volume and LIs within the MTL were as good as or better than the reproducibility within the fusiform and inferior frontal ROIs. For pattern encoding and word-pair encoding, the reproducibility of activation volume and LIs within the MTL tended to be worse compared to the fusiform and inferior frontal ROIs. The differences in FMRI reproducibility appeared more dependent on the task than the susceptibility effects. The results of this study suggest that FMRI-based assessment of the neural substrates of memory using a scene encoding task may be a useful clinical tool. (orig.)

  11. The intersubject and intrasubject reproducibility of FMRI activation during three encoding tasks: implications for clinical applications

    International Nuclear Information System (INIS)

    Harrington, Greg S.; Tomaszewski Farias, Sarah; Buonocore, Michael H.; Yonelinas, Andrew P.

    2006-01-01

    The goal of the present study was to evaluate the inter- and intrasubject reproducibility of FMRI activation for three memory encoding tasks previously used in the context of presurgical functional mapping. The primary region of interest (ROI) was the medial temporal lobe (MTL). Comparative ROIs included the inferior frontal and fusiform gyri which are less affected by susceptibility-induced signal losses than the MTL regions. Eighteen subjects were scanned using three memory encoding paradigms: word-pair, pattern, and scene encoding. Nine subjects underwent repeat scanning. Intersubject reproducibility of FMRI activation was evaluated by examining the percent of subjects who showed activation within a given ROI and the range to which individual laterality indices (LIs) varied from the mean. Intrasubject test-retest reproducibility was evaluated by examining the LI test-retest correlation, the average difference between LIs from two separate imaging sessions, and concordance ratios of activation volumes (R volume and R overlap ). For scene encoding the reproducibility of activation volume and LIs within the MTL were as good as or better than the reproducibility within the fusiform and inferior frontal ROIs. For pattern encoding and word-pair encoding, the reproducibility of activation volume and LIs within the MTL tended to be worse compared to the fusiform and inferior frontal ROIs. The differences in FMRI reproducibility appeared more dependent on the task than the susceptibility effects. The results of this study suggest that FMRI-based assessment of the neural substrates of memory using a scene encoding task may be a useful clinical tool. (orig.)

  12. Object recognition memory: neurobiological mechanisms of encoding, consolidation and retrieval.

    Science.gov (United States)

    Winters, Boyer D; Saksida, Lisa M; Bussey, Timothy J

    2008-07-01

    Tests of object recognition memory, or the judgment of the prior occurrence of an object, have made substantial contributions to our understanding of the nature and neurobiological underpinnings of mammalian memory. Only in recent years, however, have researchers begun to elucidate the specific brain areas and neural processes involved in object recognition memory. The present review considers some of this recent research, with an emphasis on studies addressing the neural bases of perirhinal cortex-dependent object recognition memory processes. We first briefly discuss operational definitions of object recognition and the common behavioural tests used to measure it in non-human primates and rodents. We then consider research from the non-human primate and rat literature examining the anatomical basis of object recognition memory in the delayed nonmatching-to-sample (DNMS) and spontaneous object recognition (SOR) tasks, respectively. The results of these studies overwhelmingly favor the view that perirhinal cortex (PRh) is a critical region for object recognition memory. We then discuss the involvement of PRh in the different stages--encoding, consolidation, and retrieval--of object recognition memory. Specifically, recent work in rats has indicated that neural activity in PRh contributes to object memory encoding, consolidation, and retrieval processes. Finally, we consider the pharmacological, cellular, and molecular factors that might play a part in PRh-mediated object recognition memory. Recent studies in rodents have begun to indicate the remarkable complexity of the neural substrates underlying this seemingly simple aspect of declarative memory.

  13. Novel Intermode Prediction Algorithm for High Efficiency Video Coding Encoder

    Directory of Open Access Journals (Sweden)

    Chan-seob Park

    2014-01-01

    Full Text Available The joint collaborative team on video coding (JCT-VC is developing the next-generation video coding standard which is called high efficiency video coding (HEVC. In the HEVC, there are three units in block structure: coding unit (CU, prediction unit (PU, and transform unit (TU. The CU is the basic unit of region splitting like macroblock (MB. Each CU performs recursive splitting into four blocks with equal size, starting from the tree block. In this paper, we propose a fast CU depth decision algorithm for HEVC technology to reduce its computational complexity. In 2N×2N PU, the proposed method compares the rate-distortion (RD cost and determines the depth using the compared information. Moreover, in order to speed up the encoding time, the efficient merge SKIP detection method is developed additionally based on the contextual mode information of neighboring CUs. Experimental result shows that the proposed algorithm achieves the average time-saving factor of 44.84% in the random access (RA at Main profile configuration with the HEVC test model (HM 10.0 reference software. Compared to HM 10.0 encoder, a small BD-bitrate loss of 0.17% is also observed without significant loss of image quality.

  14. Encoding of reward expectation by monkey anterior insular neurons.

    Science.gov (United States)

    Mizuhiki, Takashi; Richmond, Barry J; Shidara, Munetaka

    2012-06-01

    The insula, a cortical brain region that is known to encode information about autonomic, visceral, and olfactory functions, has recently been shown to encode information during reward-seeking tasks in both single neuronal recording and functional magnetic resonance imaging studies. To examine the reward-related activation, we recorded from 170 single neurons in anterior insula of 2 monkeys during a multitrial reward schedule task, where the monkeys had to complete a schedule of 1, 2, 3, or 4 trials to earn a reward. In one block of trials a visual cue indicated whether a reward would or would not be delivered in the current trial after the monkey successfully detected that a red spot turned green, and in other blocks the visual cue was random with respect to reward delivery. Over one-quarter of 131 responsive neurons were activated when the current trial would (certain or uncertain) be rewarded if performed correctly. These same neurons failed to respond in trials that were certain, as indicated by the cue, to be unrewarded. Another group of neurons responded when the reward was delivered, similar to results reported previously. The dynamics of population activity in anterior insula also showed strong signals related to knowing when a reward is coming. The most parsimonious explanation is that this activity codes for a type of expected outcome, where the expectation encompasses both certain and uncertain rewards.

  15. Evidence for a Mechanism Encoding Audiovisual Spatial Separation

    Directory of Open Access Journals (Sweden)

    Emily Orchard-Mills

    2011-10-01

    Full Text Available Auditory and visual spatial representations are produced by distinct processes, drawing on separate neural inputs and occurring in different regions of the brain. We tested for a bimodal spatial representation using a spatial increment discrimination task. Discrimination thresholds for synchronously presented but spatially separated audiovisual stimuli were measured for base separations ranging from 0° to 45°. In a dark anechoic chamber, the spatial interval was defined by azimuthal separation of a white-noise burst from a speaker on a movable robotic arm and a checkerboard patch 5° wide projected onto an acoustically transparent screen. When plotted as a function of base interval, spatial increment thresholds exhibited a J-shaped pattern. Thresholds initially declined, the minimum occurring at base separations approximately equal to the individual observer's detection threshold and thereafter rose log-linearly according to Weber's law. This pattern of results, known as the ‘dipper function’, would be expected if the auditory and visual signals defining the spatial interval converged onto an early sensory filter encoding audiovisual space. This mechanism could be used to encode spatial separation of auditory and visual stimuli.

  16. Fast entrainment of human electroencephalogram to a theta-band photic flicker during successful memory encoding

    Directory of Open Access Journals (Sweden)

    Naoyuki eSato

    2013-05-01

    Full Text Available Theta band power (4-8Hz in the scalp electroencephalogram (EEG is thought to be stronger during memory encoding for subsequently remembered items than for forgotten items. According to simultaneous EEG-functional magnetic resonance imaging (fMRI measurements, the memory-dependent EEG theta is associated with multiple regions of the brain. This suggests that the multiple regions cooperate with EEG theta synchronization during successful memory encoding. However, a question still remains: What kind of neural dynamic organizes such a memory-dependent global network? In this study, the modulation of the EEG theta entrainment property during successful encoding was hypothesized to lead to EEG theta synchronization among a distributed network. Then, a transient response of EEG theta to a theta-band photic flicker with a short duration was evaluated during memory encoding. In the results, flicker-induced EEG power increased and decreased with a time constant of several hundred milliseconds following the onset and the offset of the flicker, respectively. Importantly, the offset response of EEG power was found to be significantly decreased during successful encoding. Moreover, the offset response of the phase locking index was also found to associate with memory performance. According to computational simulations, the results are interpreted as a smaller time constant (i.e., faster response of a driven harmonic oscillator rather than a change in the spontaneous oscillatory input. This suggests that the fast response of EEG theta forms a global EEG theta network among memory-related regions during successful encoding, and it contributes to a flexible formation of the network along the time course.

  17. Fast entrainment of human electroencephalogram to a theta-band photic flicker during successful memory encoding

    Science.gov (United States)

    Sato, Naoyuki

    2013-01-01

    Theta band power (4–8 Hz) in the scalp electroencephalogram (EEG) is thought to be stronger during memory encoding for subsequently remembered items than for forgotten items. According to simultaneous EEG-functional magnetic resonance imaging (fMRI) measurements, the memory-dependent EEG theta is associated with multiple regions of the brain. This suggests that the multiple regions cooperate with EEG theta synchronization during successful memory encoding. However, a question still remains: What kind of neural dynamic organizes such a memory-dependent global network? In this study, the modulation of the EEG theta entrainment property during successful encoding was hypothesized to lead to EEG theta synchronization among a distributed network. Then, a transient response of EEG theta to a theta-band photic flicker with a short duration was evaluated during memory encoding. In the results, flicker-induced EEG power increased and decreased with a time constant of several hundred milliseconds following the onset and the offset of the flicker, respectively. Importantly, the offset response of EEG power was found to be significantly decreased during successful encoding. Moreover, the offset response of the phase locking index was also found to associate with memory performance. According to computational simulations, the results are interpreted as a smaller time constant (i.e., faster response) of a driven harmonic oscillator rather than a change in the spontaneous oscillatory input. This suggests that the fast response of EEG theta forms a global EEG theta network among memory-related regions during successful encoding, and it contributes to a flexible formation of the network along the time course. PMID:23730282

  18. The self-pleasantness judgment modulates the encoding performance and the Default Mode Network activity

    Directory of Open Access Journals (Sweden)

    Perrone-Bertolotti eMarcela

    2016-03-01

    Full Text Available In this functional magnetic resonance imaging (fMRI study, we evaluated the effect of self-relevance on cerebral activity and behavioral performance during an incidental encoding task. Recent findings suggest that pleasantness judgments reliably induce self-oriented (internal thoughts and increase default mode network (DMN activity. We hypothesized that this increase in DMN activity would relate to increased memory recognition for pleasantly-judged stimuli (which depend on internally-oriented attention but decreased recognition for unpleasantly-judged items (which depend on externally-oriented attention. To test this hypothesis, brain activity was recorded from 21 healthy participants while they performed a pleasantness judgment requiring them to rate visual stimuli as pleasant or unpleasant. One hour later, participants performed a surprise memory recognition test outside of the scanner. Thus, we were able to evaluate the effects of pleasant and unpleasant judgments on cerebral activity and incidental encoding. The behavioral results showed that memory recognition was better for items rated as pleasant than items rated as unpleasant. The whole brain analysis indicated that successful encoding activates the inferior frontal and lateral temporal cortices, whereas unsuccessful encoding recruits two key medial posterior DMN regions, the posterior cingulate cortex and precuneus. A region of interest analysis including classic DMN areas, revealed significantly greater involvement of the medial Prefrontal Cortex in pleasant compared to unpleasant judgments, suggesting this region’s involvement in self-referential (i.e., internal processing. This area may be responsible for the greater recognition performance seen for pleasant stimuli. Furthermore, a significant interaction between the encoding performance (successful vs. unsuccessful and pleasantness was observed for the posterior cingulate cortex, precuneus and inferior frontal gyrus. Overall, our

  19. Multiple genes encode the major surface glycoprotein of Pneumocystis carinii

    DEFF Research Database (Denmark)

    Kovacs, J A; Powell, F; Edman, J C

    1993-01-01

    hydrophobic region at the carboxyl terminus. The presence of multiple related msg genes encoding the major surface glycoprotein of P. carinii suggests that antigenic variation is a possible mechanism for evading host defenses. Further characterization of this family of genes should allow the development......The major surface antigen of Pneumocystis carinii, a life-threatening opportunistic pathogen in human immunodeficiency virus-infected patients, is an abundant glycoprotein that functions in host-organism interactions. A monoclonal antibody to this antigen is protective in animals, and thus...... blot studies using chromosomal or restricted DNA, the major surface glycoproteins are the products of a multicopy family of genes. The predicted protein has an M(r) of approximately 123,000, is relatively rich in cysteine residues (5.5%) that are very strongly conserved, and contains a well conserved...

  20. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

    Science.gov (United States)

    Landt, Stephen G.; Marinov, Georgi K.; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E.; Bickel, Peter; Brown, James B.; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I.; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J.; Hoffman, Michael M.; Iyer, Vishwanath R.; Jung, Youngsook L.; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V.; Li, Qunhua; Liu, Tao; Liu, X. Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M.; Park, Peter J.; Pazin, Michael J.; Perry, Marc D.; Raha, Debasish; Reddy, Timothy E.; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A.; Tolstorukov, Michael Y.; White, Kevin P.; Xi, Simon; Farnham, Peggy J.; Lieb, Jason D.; Wold, Barbara J.; Snyder, Michael

    2012-01-01

    Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals. PMID:22955991

  1. Evaluating standard terminologies for encoding allergy information.

    Science.gov (United States)

    Goss, Foster R; Zhou, Li; Plasek, Joseph M; Broverman, Carol; Robinson, George; Middleton, Blackford; Rocha, Roberto A

    2013-01-01

    Allergy documentation and exchange are vital to ensuring patient safety. This study aims to analyze and compare various existing standard terminologies for representing allergy information. Five terminologies were identified, including the Systemized Nomenclature of Medical Clinical Terms (SNOMED CT), National Drug File-Reference Terminology (NDF-RT), Medication Dictionary for Regulatory Activities (MedDRA), Unique Ingredient Identifier (UNII), and RxNorm. A qualitative analysis was conducted to compare desirable characteristics of each terminology, including content coverage, concept orientation, formal definitions, multiple granularities, vocabulary structure, subset capability, and maintainability. A quantitative analysis was also performed to compare the content coverage of each terminology for (1) common food, drug, and environmental allergens and (2) descriptive concepts for common drug allergies, adverse reactions (AR), and no known allergies. Our qualitative results show that SNOMED CT fulfilled the greatest number of desirable characteristics, followed by NDF-RT, RxNorm, UNII, and MedDRA. Our quantitative results demonstrate that RxNorm had the highest concept coverage for representing drug allergens, followed by UNII, SNOMED CT, NDF-RT, and MedDRA. For food and environmental allergens, UNII demonstrated the highest concept coverage, followed by SNOMED CT. For representing descriptive allergy concepts and adverse reactions, SNOMED CT and NDF-RT showed the highest coverage. Only SNOMED CT was capable of representing unique concepts for encoding no known allergies. The proper terminology for encoding a patient's allergy is complex, as multiple elements need to be captured to form a fully structured clinical finding. Our results suggest that while gaps still exist, a combination of SNOMED CT and RxNorm can satisfy most criteria for encoding common allergies and provide sufficient content coverage.

  2. The ENCODE (ENCyclopedia Of DNA Elements) Project.

    Science.gov (United States)

    2004-10-22

    The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.

  3. Rapidly-Indexing Incremental-Angle Encoder

    Science.gov (United States)

    Christon, Philip R.; Meyer, Wallace W.

    1989-01-01

    Optoelectronic system measures relative angular position of shaft or other device to be turned, also measures absolute angular position after device turned through small angle. Relative angular position measured with fine resolution by optoelectronically counting finely- and uniformly-spaced light and dark areas on encoder disk as disk turns past position-sensing device. Also includes track containing coarsely- and nonuniformly-spaced light and dark areas, angular widths varying in proportion to absolute angular position. This second track provides gating and indexing signal.

  4. Successful scene encoding in presymptomatic early-onset Alzheimer’s disease

    Science.gov (United States)

    Quiroz, Yakeel T.; Willment, Kim Celone; Castrillon, Gabriel; Muniz, Martha; Lopera, Francisco; Budson, Andrew; Stern, Chantal E.

    2016-01-01

    Background Brain regions critical to episodic memory are altered during the preclinical stages of Alzheimer’s disease (AD). However, reliable means of identifying cognitively-normal individuals at higher risk to develop AD have not been established. Objective To examine whether fMRI can detect early functional changes associated with scene encoding in a group of presymptomatic Presenilin-1 (PSEN1) E280A mutation carriers. Methods Participants were 39 young, cognitively-normal individuals from an autosomal dominant early-onset AD kindred, located in Antioquia, Colombia. Participants performed an fMRI scene encoding task and a post-scan subsequent memory test. Results PSEN1 mutation carriers exhibited hyperactivation within medial temporal lobe regions during successful scene encoding (hippocampal formation, parahippocampal gyrus) compared to age-matched non-carriers. Conclusion Hyperactivation in medial temporal lobe regions during scene encoding is seen in individuals genetically-determined to develop AD years before their clinical onset. Our findings will guide future research with the ultimate goal of using functional neuroimaging in the early detection of preclinical AD. PMID:26401774

  5. Dual beam encoded extended fractional Fourier transform security ...

    Indian Academy of Sciences (India)

    This paper describes a simple method for making dual beam encoded extended fractional Fourier transform (EFRT) security holograms. The hologram possesses different stages of encoding so that security features are concealed and remain invisible to the counterfeiter. These concealed and encoded anticounterfeit ...

  6. Dual beam encoded extended fractional Fourier transform security ...

    Indian Academy of Sciences (India)

    Abstract. This paper describes a simple method for making dual beam encoded ex- tended fractional Fourier transform (EFRT) security holograms. The hologram possesses different stages of encoding so that security features are concealed and remain invisible to the counterfeiter. These concealed and encoded ...

  7. CDNA encoding a polypeptide including a hevein sequence

    Science.gov (United States)

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  8. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  9. How can survival processing improve memory encoding?

    Science.gov (United States)

    Luo, Meng; Geng, Haiyan

    2013-11-01

    We investigated the psychological mechanism of survival processing advantage from the perspective of false memory in two experiments. Using a DRM paradigm in combination with analysis based on signal detection theory, we were able to separately examine participants' utilization of verbatim representation and gist representation. Specifically, in Experiment 1, participants rated semantically related words in a survival scenario for a survival condition but rated pleasantness of words in the same DRM lists for a non-survival control condition. The results showed that participants demonstrated more gist processing in the survival condition than in the pleasantness condition; however, the degree of item-specific processing in the two encoding conditions did not significantly differ. In Experiment 2, the control task was changed to a category rating task, in which participants were asked to make category ratings of words in the category lists. We found that the survival condition involved more item-specific processing than did the category condition, but we found no significant difference between the two encoding conditions at the level of gist processing. Overall, our study demonstrates that survival processing can simultaneously promote gist and item-specific representations. When the control tasks only promoted either item-specific representation or gist representation, memory advantages of survival processing occurred.

  10. V123 Beam Synchronous Encoder Module

    International Nuclear Information System (INIS)

    Kerner, T.; Conkling, C. R.; Oerter, B.

    1999-01-01

    The V123 Synchronous Encoder Module transmits events to distributed trigger modules and embedded decoders around the RHIC rings where they are used to provide beam instrumentation triggers [1,2,3]. The RHIC beam synchronous event link hardware is mainly comprised of three VMEbus board designs, the central input modules (V201), and encoder modules (V123), and the distributed trigger modules (V124). Two beam synchronous links, one for each ring, are distributed via fiberoptic and fanned out via twisted wire pair cables. The V123 synchronizes with the RF system clock derived from the beam bucket frequency and a revolution fiducial pulse. The RF system clock is used to create the beam synchronous event link carrier and events are synchronized with the rotation fiducial. A low jitter RF clock is later recovered from this carrier by phase lock loops in the trigger modules. Prioritized hardware and software triggers fill up to 15 beam event code transmission slots per revolution while tracking the ramping RF acceleration frequency and storage frequency. The revolution fiducial event is always the first event transmitted which is used to synchronize the firing of the abort kicker and to locate the first bucket for decoders distributed about the ring

  11. Translating the ENCyclopedia Of DNA Elements Project findings to the clinic: ENCODE's implications for eye disease.

    Science.gov (United States)

    Sanfilippo, Paul G; Hewitt, Alex W

    2014-01-01

    Approximately 10 years after the Human Genome Project unravelled the sequence of our DNA, the ENCyclopedia Of DNA Elements (ENCODE) Project sought to interpret it. Data from the recently completed project have shed new light on the proportion of biologically active human DNA, assigning a biochemical role to much of the sequence previously considered to be 'junk'. Many of these newly catalogued functional elements represent epigenetic mechanisms involved in regulation of gene expression. Analogous to an Ishihara plate, a gene-coding region of DNA (target dots) only comes into context when the non-coding DNA (surrounding dots) is appreciated. In this review we provide an overview of the ENCODE project, discussing the significance of these data for ophthalmic research and eye disease. The novel insights afforded by the ENCODE project will in time allow for the development of new therapeutic strategies in the management of common blinding disorders. © 2013 Royal Australian and New Zealand College of Ophthalmologists.

  12. Mirror neurons differentially encode the peripersonal and extrapersonal space of monkeys.

    Science.gov (United States)

    Caggiano, Vittorio; Fogassi, Leonardo; Rizzolatti, Giacomo; Thier, Peter; Casile, Antonino

    2009-04-17

    Actions performed by others may have different relevance for the observer, and thus lead to different behavioral responses, depending on the regions of space in which they are executed. We found that in rhesus monkeys, the premotor cortex neurons activated by both the execution and the observation of motor acts (mirror neurons) are differentially modulated by the location in space of the observed motor acts relative to the monkey, with about half of them preferring either the monkey's peripersonal or extrapersonal space. A portion of these spatially selective mirror neurons encode space according to a metric representation, whereas other neurons encode space in operational terms, changing their properties according to the possibility that the monkey will interact with the object. These results suggest that a set of mirror neurons encodes the observed motor acts not only for action understanding, but also to analyze such acts in terms of features that are relevant to generating appropriate behaviors.

  13. Molecular cloning and functional expression in Lactobacillus plantarum 80 of xylT, encoding the D-xylose-H+ symporter of Lactobacillus brevis

    NARCIS (Netherlands)

    Chaillou, S.; Bor, Y.-C.; Batt, C.A.; Postma, P.W.; Pouwels, P.H.

    1998-01-01

    A 3-kb region, located downstream of the Lactobacillus brevis xylA gene (encoding D-xylose isomerase), was cloned in Escherichia coli TG1. The sequence revealed two open reading frames which could code for the D-xylulose kinase gene (xylB) and another gene (xylT) encoding a protein of 457 amino

  14. Negative base encoding in optical linear algebra processors

    Science.gov (United States)

    Perlee, C.; Casasent, D.

    1986-01-01

    In the digital multiplication by analog convolution algorithm, the bits of two encoded numbers are convolved to form the product of the two numbers in mixed binary representation; this output can be easily converted to binary. Attention is presently given to negative base encoding, treating base -2 initially, and then showing that the negative base system can be readily extended to any radix. In general, negative base encoding in optical linear algebra processors represents a more efficient technique than either sign magnitude or 2's complement encoding, when the additions of digitally encoded products are performed in parallel.

  15. Functional magnetic resonance imaging correlates of emotional word encoding and recognition in depression and anxiety disorders.

    Science.gov (United States)

    van Tol, Marie-José; Demenescu, Liliana R; van der Wee, Nic J A; Kortekaas, Rudie; Marjan M A, Nielen; Boer, J A Den; Renken, Remco J; van Buchem, Mark A; Zitman, Frans G; Aleman, André; Veltman, Dick J

    2012-04-01

    Major depressive disorder (MDD), panic disorder, and social anxiety disorder are among the most prevalent and frequently co-occurring psychiatric disorders in adults and may be characterized by a common deficiency in processing of emotional information. We used functional magnetic resonance imaging during the performance of an emotional word encoding and recognition paradigm in patients with MDD (n = 51), comorbid MDD and anxiety (n = 59), panic disorder and/or social anxiety disorder without comorbid MDD (n = 56), and control subjects (n = 49). In addition, we studied effects of illness severity, regional brain volume, and antidepressant use. Patients with MDD, prevalent anxiety disorders, or both showed a common hyporesponse in the right hippocampus during positive (>neutral) word encoding compared with control subjects. During negative encoding, increased insular activation was observed in both depressed groups (MDD and MDD + anxiety), whereas increased amygdala and anterior cingulate cortex activation during positive word encoding were observed as depressive state-dependent effects in MDD only. During recognition, anxiety patients showed increased inferior frontal gyrus activation. Overall, effects were unaffected by medication use and regional brain volume. Hippocampal blunting during positive word encoding is a generic effect in depression and anxiety disorders, which may constitute a common vulnerability factor. Increased insular and amygdalar involvement during negative word encoding may underlie heightened experience of, and an inability to disengage from, negative emotions in depressive disorders. Our results emphasize a common neurobiological deficiency in both MDD and anxiety disorders, which may mark a general insensitiveness to positive information. Copyright © 2012 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  16. Enterotoxin-encoding genes in Staphylococcus spp. from bulk goat milk.

    Science.gov (United States)

    Lyra, Daniele G; Sousa, Francisca G C; Borges, Maria F; Givisiez, Patrícia E N; Queiroga, Rita C R E; Souza, Evandro L; Gebreyes, Wondwossen A; Oliveira, Celso J B

    2013-02-01

    Although Staphylococcus aureus has been implicated as the main Staphylococcus species causing human food poisoning, recent studies have shown that coagulase-negative Staphylococcus could also harbor enterotoxin-encoding genes. Such organisms are often present in goat milk and are the most important mastitis-causing agents. Therefore, this study aimed to investigate the occurrence of enterotoxin-encoding genes among coagulase-positive (CoPS) and coagulase-negative (CoNS) staphylococci isolated from raw goat milk produced in the semi-arid region of Paraiba, the most important region for goat milk production in Brazil. Enterotoxin-encoding genes were screened in 74 staphylococci isolates (30 CoPS and 44 CoNS) by polymerase chain reaction targeting the genes sea, seb, sec, sed, see, seg, seh, and sei. Enterotoxin-encoding genes were found in nine (12.2%) isolates, and four different genes (sea, sec, seg, and sei) were identified amongst the isolates. The most frequent genes were seg and sei, which were often found simultaneously in 44.5% of the isolates. The gene sec was the most frequent among the classical genes, and sea was found only in one isolate. All CoPS isolates (n=7) harboring enterotoxigenic genes were identified as S. aureus. The two coagulase-negative isolates were S. haemolyticus and S. hominis subsp. hominis and they harbored sei and sec genes, respectively. A higher frequency of enterotoxin-encoding genes was observed amongst CoPS (23.3%) than CoNS (4.5%) isolates (pgoat milk should not be ignored because it has a higher occurrence in goat milk and enterotoxin-encoding genes were detected in some isolates.

  17. Neural activation patterns of successful episodic encoding: Reorganization during childhood, maintenance in old age

    Directory of Open Access Journals (Sweden)

    Yee Lee Shing

    2016-08-01

    Full Text Available The two-component framework of episodic memory (EM development posits that the contributions of medial temporal lobe (MTL and prefrontal cortex (PFC to successful encoding differ across the lifespan. To test the framework’s hypotheses, we compared subsequent memory effects (SME of 10–12 year-old children, younger adults, and older adults using functional magnetic resonance imaging (fMRI. Memory was probed by cued recall, and SME were defined as regional activation differences during encoding between subsequently correctly recalled versus omitted items. In MTL areas, children’s SME did not differ in magnitude from those of younger and older adults. In contrast, children’s SME in PFC were weaker than the corresponding SME in younger and older adults, in line with the hypothesis that PFC contributes less to successful encoding in childhood. Differences in SME between younger and older adults were negligible. The present results suggest that, among individuals with high memory functioning, the neural circuitry contributing to successful episodic encoding is reorganized from middle childhood to adulthood. Successful episodic encoding in later adulthood, however, is characterized by the ability to maintain the activation patterns that emerged in young adulthood.

  18. Effects of emotion and reward motivation on neural correlates of episodic memory encoding: a PET study.

    Science.gov (United States)

    Shigemune, Yayoi; Abe, Nobuhito; Suzuki, Maki; Ueno, Aya; Mori, Etsuro; Tashiro, Manabu; Itoh, Masatoshi; Fujii, Toshikatsu

    2010-05-01

    It is known that emotion and reward motivation promote long-term memory formation. It remains unclear, however, how and where emotion and reward are integrated during episodic memory encoding. In the present study, subjects were engaged in intentional encoding of photographs under four different conditions that were made by combining two factors (emotional valence, negative or neutral; and monetary reward value, high or low for subsequent successful recognition) during H2 15O positron emission tomography (PET) scanning. As for recognition performance, we found significant main effects of emotional valence (negative>neutral) and reward value (high value>low value), without an interaction between the two factors. Imaging data showed that the left amygdala was activated during the encoding conditions of negative pictures relative to neutral pictures, and the left orbitofrontal cortex was activated during the encoding conditions of high reward pictures relative to low reward pictures. In addition, conjunction analysis of these two main effects detected right hippocampal activation. Although we could not find correlations between recognition performance and activity of these three regions, we speculate that the right hippocampus may integrate the effects of emotion (processed in the amygdala) and monetary reward (processed in the orbitofrontal cortex) on episodic memory encoding. 2010 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

  19. ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

    Science.gov (United States)

    Hazarika, Rashmi R; De Coninck, Barbara; Yamamoto, Lidia R; Martin, Laura R; Cammue, Bruno P A; van Noort, Vera

    2017-01-17

    Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides. To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.

  20. A New Quantum Gray-Scale Image Encoding Scheme

    Science.gov (United States)

    Naseri, Mosayeb; Abdolmaleky, Mona; Parandin, Fariborz; Fatahi, Negin; Farouk, Ahmed; Nazari, Reza

    2018-02-01

    In this paper, a new quantum images encoding scheme is proposed. The proposed scheme mainly consists of four different encoding algorithms. The idea behind of the scheme is a binary key generated randomly for each pixel of the original image. Afterwards, the employed encoding algorithm is selected corresponding to the qubit pair of the generated randomized binary key. The security analysis of the proposed scheme proved its enhancement through both randomization of the generated binary image key and altering the gray-scale value of the image pixels using the qubits of randomized binary key. The simulation of the proposed scheme assures that the final encoded image could not be recognized visually. Moreover, the histogram diagram of encoded image is flatter than the original one. The Shannon entropies of the final encoded images are significantly higher than the original one, which indicates that the attacker can not gain any information about the encoded images. Supported by Kermanshah Branch, Islamic Azad University, Kermanshah, IRAN

  1. Compensating for Language Deficits in Amnesia II: H.M.’s Spared versus Impaired Encoding Categories

    Directory of Open Access Journals (Sweden)

    Chris Hadley

    2013-03-01

    Full Text Available Although amnesic H.M. typically could not recall where or when he met someone, he could recall their topics of conversation after long interference-filled delays, suggesting impaired encoding for some categories of novel events but not others. Similarly, H.M. successfully encoded into internal representations (sentence plans some novel linguistic structures but not others in the present language production studies. For example, on the Test of Language Competence (TLC, H.M. produced uncorrected errors when encoding a wide range of novel linguistic structures, e.g., violating reliably more gender constraints than memory-normal controls when encoding referent-noun, pronoun-antecedent, and referent-pronoun anaphora, as when he erroneously and without correction used the gender-inappropriate pronoun “her” to refer to a man. In contrast, H.M. never violated corresponding referent-gender constraints for proper names, suggesting that his mechanisms for encoding proper name gender-agreement were intact. However, H.M. produced no more dysfluencies, off-topic comments, false starts, neologisms, or word and phonological sequencing errors than controls on the TLC. Present results suggest that: (a frontal mechanisms for retrieving and sequencing word, phrase, and phonological categories are intact in H.M., unlike in category-specific aphasia; (b encoding mechanisms in the hippocampal region are category-specific rather than item-specific, applying to, e.g., proper names rather than words; (c H.M.’s category-specific mechanisms for encoding referents into words, phrases, and propositions are impaired, with the exception of referent gender, person, and number for encoding proper names; and (d H.M. overuses his intact proper name encoding mechanisms to compensate for his impaired mechanisms for encoding other functionally equivalent linguistic information.

  2. Premotor and Motor Cortices Encode Reward.

    Directory of Open Access Journals (Sweden)

    Pavan Ramkumar

    Full Text Available Rewards associated with actions are critical for motivation and learning about the consequences of one's actions on the world. The motor cortices are involved in planning and executing movements, but it is unclear whether they encode reward over and above limb kinematics and dynamics. Here, we report a categorical reward signal in dorsal premotor (PMd and primary motor (M1 neurons that corresponds to an increase in firing rates when a trial was not rewarded regardless of whether or not a reward was expected. We show that this signal is unrelated to error magnitude, reward prediction error, or other task confounds such as reward consumption, return reach plan, or kinematic differences across rewarded and unrewarded trials. The availability of reward information in motor cortex is crucial for theories of reward-based learning and motivational influences on actions.

  3. Encoding !-tensors as !-graphs with neighbourhood orders

    Directory of Open Access Journals (Sweden)

    David Quick

    2015-11-01

    Full Text Available Diagrammatic reasoning using string diagrams provides an intuitive language for reasoning about morphisms in a symmetric monoidal category. To allow working with infinite families of string diagrams, !-graphs were introduced as a method to mark repeated structure inside a diagram. This led to !-graphs being implemented in the diagrammatic proof assistant Quantomatic. Having a partially automated program for rewriting diagrams has proven very useful, but being based on !-graphs, only commutative theories are allowed. An enriched abstract tensor notation, called !-tensors, has been used to formalise the notion of !-boxes in non-commutative structures. This work-in-progress paper presents a method to encode !-tensors as !-graphs with some additional structure. This will allow us to leverage the existing code from Quantomatic and quickly provide various tools for non-commutative diagrammatic reasoning.

  4. Radiofrequency encoded angular-resolved light scattering

    DEFF Research Database (Denmark)

    Buckley, Brandon W.; Akbari, Najva; Diebold, Eric D.

    2015-01-01

    The sensitive, specific, and label-free classification of microscopic cells and organisms is one of the outstanding problems in biology. Today, instruments such as the flow cytometer use a combination of light scatter measurements at two distinct angles to infer the size and internal complexity...... of cells at rates of more than 10,000 per second. However, by examining the entire angular light scattering spectrum it is possible to classify cells with higher resolution and specificity. Current approaches to performing these angular spectrum measurements all have significant throughput limitations...... Encoded Angular-resolved Light Scattering (REALS), this technique multiplexes angular light scattering in the radiofrequency domain, such that a single photodetector captures the entire scattering spectrum from a particle over approximately 100 discrete incident angles on a single shot basis. As a proof...

  5. Brain Circuits Encoding Reward from Pain Relief.

    Science.gov (United States)

    Navratilova, Edita; Atcherley, Christopher W; Porreca, Frank

    2015-11-01

    Relief from pain in humans is rewarding and pleasurable. Primary rewards, or reward-predictive cues, are encoded in brain reward/motivational circuits. While considerable advances have been made in our understanding of reward circuits underlying positive reinforcement, less is known about the circuits underlying the hedonic and reinforcing actions of pain relief. We review findings from electrophysiological, neuroimaging, and behavioral studies supporting the concept that the rewarding effect of pain relief requires opioid signaling in the anterior cingulate cortex (ACC), activation of midbrain dopamine neurons, and the release of dopamine in the nucleus accumbens (NAc). Understanding of circuits that govern the reward of pain relief may allow the discovery of more effective and satisfying therapies for patients with acute or chronic pain.

  6. Measurement strategy for spatially encoded photonic qubits

    International Nuclear Information System (INIS)

    Solis-Prosser, M. A.; Neves, L.

    2010-01-01

    We propose a measurement strategy which can, probabilistically, reproduce the statistics of any observable for spatially encoded photonic qubits. It comprises the implementation of a two-outcome positive operator-valued measure followed by a detection in a fixed transverse position, making the displacement of the detection system unnecessary, unlike previous methods. This strategy generalizes a scheme recently demonstrated by one of us and co-workers, restricted to measurement of observables with equatorial eigenvectors only. The method presented here can be implemented with the current technology of programmable multipixel liquid-crystal displays. In addition, it can be straightforwardly extended to high-dimensional qudits and may be a valuable tool in optical implementations of quantum information protocols with spatial qubits and qudits.

  7. Ultrathin Nonlinear Metasurface for Optical Image Encoding.

    Science.gov (United States)

    Walter, Felicitas; Li, Guixin; Meier, Cedrik; Zhang, Shuang; Zentgraf, Thomas

    2017-05-10

    Security of optical information is of great importance in modern society. Many cryptography techniques based on classical and quantum optics have been widely explored in the linear optical regime. Nonlinear optical encryption in which encoding and decoding involve nonlinear frequency conversions represents a new strategy for securing optical information. Here, we demonstrate that an ultrathin nonlinear photonic metasurface, consisting of meta-atoms with 3-fold rotational symmetry, can be used to hide optical images under illumination with a fundamental wave. However, the hidden image can be read out from second harmonic generation (SHG) waves. This is achieved by controlling the destructive and constructive interferences of SHG waves from two neighboring meta-atoms. In addition, we apply this concept to obtain gray scale SHG imaging. Nonlinear metasurfaces based on space variant optical interference open new avenues for multilevel image encryption, anticounterfeiting, and background free image reconstruction.

  8. Encoding by synchronization in the primate striatum.

    Science.gov (United States)

    Adler, Avital; Finkes, Inna; Katabi, Shiran; Prut, Yifat; Bergman, Hagai

    2013-03-13

    Information is encoded in the nervous system through the discharge and synchronization of single neurons. The striatum, the input stage of the basal ganglia, is divided into three territories: the putamen, the caudate, and the ventral striatum, all of which converge onto the same motor pathway. This parallel organization suggests that there are multiple and competing systems in the basal ganglia network controlling behavior. To explore which mechanism(s) enables the different striatal domains to encode behavioral events and to control behavior, we compared the neural activity of phasically active neurons [medium spiny neurons (MSNs), presumed projection neurons] and tonically active neurons (presumed cholinergic interneurons) across striatal territories from monkeys during the performance of a well practiced task. Although neurons in all striatal territories displayed similar spontaneous discharge properties and similar temporal modulations of their discharge rates to the behavioral events, their correlation structure was profoundly different. The distributions of signal and noise correlation of pairs of putamen MSNs were strongly shifted toward positive correlations and these two measures were correlated. In contrast, MSN pairs in the caudate and ventral striatum displayed symmetrical, near-zero signal and noise correlation distributions. Furthermore, only putamen MSN pairs displayed different noise correlation dynamics to rewarding versus neutral/aversive cues. Similarly, the noise correlation between tonically active neuron pairs was stronger in the putamen than in the caudate. We suggest that the level of synchronization of the neuronal activity and its temporal dynamics differentiate the striatal territories and may thus account for the different roles that striatal domains play in behavioral control.

  9. Encoding and Decoding Models in Cognitive Electrophysiology.

    Science.gov (United States)

    Holdgraf, Christopher R; Rieger, Jochem W; Micheli, Cristiano; Martin, Stephanie; Knight, Robert T; Theunissen, Frederic E

    2017-01-01

    Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of "Encoding" models, in which stimulus features are used to model brain activity, and "Decoding" models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyter notebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aim is to provide a practical understanding of predictive modeling of human brain data and to propose best-practices in conducting these analyses.

  10. Comparison of the neural correlates of encoding item-item and item-context associations

    Directory of Open Access Journals (Sweden)

    Jenny X Wong

    2013-08-01

    Full Text Available fMRI was employed to investigate the role of the left inferior frontal gyrus (LIFG in the encoding of item-item and item-context associations. On each of a series of study trials subjects viewed a picture that was presented either to the left or right of fixation, along with a subsequently presented word that appeared at fixation. Memory was tested in a subsequent memory test that took place outside of the scanner. On each test trial one of two forced choice judgments was required. For the associative test, subjects chose between the word paired with the picture at study and a word studied on a different trial. For the source test, the judgment was whether the picture had been presented on the left or right. Successful encoding of associative information was accompanied by subsequent memory effects in several cortical regions, including much of the LIFG. By contrast, successful source encoding was selectively associated with a subsequent memory effect in right fusiform cortex. The finding that the LIFG was enhanced during successful associative, but not source, encoding is interpreted in light of the proposal that subsequent memory effects are localized to cortical regions engaged by the on-line demands of the study task.

  11. Linking mathematical modeling with human neuroimaging to segregate verbal working memory maintenance processes from stimulus encoding.

    Science.gov (United States)

    McKenna, Benjamin S; Brown, Gregory G; Drummond, Sean P A; Turner, Travis H; Mano, Quintino R

    2013-03-01

    A fundamental dissociation for most working memory (WM) theories involves the separation of sensory-perceptual encoding of stimulus information from the maintenance of this information. The present paper reports tests of this separability hypothesis for visually presented pseudowords at both mathematical and neuroimaging levels of analysis. Levels of analysis were linked by two experimental manipulations-visual degradation and pseudoword length variation-that coupled findings from a mathematical modeling study of WM performed in a separate sample to findings from an event-related functional MRI (fMRI) study reported in the present paper. Results from the mathematical modeling study generated parametric signatures of stimulus encoding and WM rehearsal and displacement. These signatures led to specific predictions about neurophysiological responses to study manipulations in a priori regions of interest (ROI). Results demonstrated predicted dissociations of activation signatures in several ROIs. Significant patterns of brain response mirroring the encode signature were observed only during the task encode interval and only in the visual cortex and posterior fusiform gyrus. In contrast, significant brain response mirroring the rehearsal/displacement signature was observed only in the dorsolateral prefrontal cortex, inferior frontal gyrus, and supramarginal gyrus. Present findings support the separability hypothesis insofar as brain regions that underlie sensory-perceptual processes demonstrated encode signatures whereas brain regions that support WM maintenance demonstrated the rehearsal/displacement signature. These results also provide evidence for the utility of combining mathematical modeling with fMRI to integrate information across cognitive and neural levels of analysis. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  12. Use of the integration elements encoded by the temperate lactococcal bacteriophage TP901-1

    DEFF Research Database (Denmark)

    Brøndsted, Lone; Hammer, Karin

    1999-01-01

    Previously we showed that only one phage-expressed protein (Orf1), a 425-bp region upstream of the orf1 gene (presumably encoding a promoter), and the attP region are necessary and also sufficient for integration of the bacteriophage TP901-1 genome into the chromosome of Lactococcus lactis subsp......P region seem to be necessary for site-specific integration of the temperate bacteriophage TP901-1. By use of the integrative elements (attP and orf1) expressed by the temperate lactococcal bacteriophage TP901-1, a system for obtaining stable chromosomal single-copy transcriptional fusions in L. lactis...

  13. Characterization of a cDNA encoding cottonseed catalase.

    Science.gov (United States)

    Ni, W; Turley, R B; Trelease, R N

    1990-06-21

    A 1.7 kb cDNA clone was isolated from our lambda gt11 library constructed from poly(A) RNA of 24-h-old cotyledons. The cDNA encodes a full-length catalase peptide (492 amino acid residues). The calculated molecular mass is 56,800, similar to that determined for purified enzyme (57,000 SDS-PAGE). Among higher plant catalases, this cotton catalase shows the highest amino acid sequence identity (85%) to the subunit of homotetrameric maize CAT 1, a developmental counterpart to the homotetrameric CAT A isoform of cotton seeds. Comparison of sequences from cotton, sweet potato, maize CAT 1, and yeast with bovine catalase revealed that the amino acid residues and regions that are involved in catalytic activity and/or required to maintain basic catalase structure, are highly conserved. The C-terminus region, which has the lowest nucleotide sequence identity between plant and mammalian catalases, does not terminate with a tripeptide, S-K/R/H-L, a putative targeting signal for peroxisomal proteins.

  14. Modular verification of chemical reaction network encodings via serializability analysis

    Science.gov (United States)

    Lakin, Matthew R.; Stefanovic, Darko; Phillips, Andrew

    2015-01-01

    Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a “commit reaction” that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of “extra tolerance”, which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited. PMID:27325906

  15. Modular verification of chemical reaction network encodings via serializability analysis.

    Science.gov (United States)

    Lakin, Matthew R; Stefanovic, Darko; Phillips, Andrew

    2016-06-13

    Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a "commit reaction" that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of "extra tolerance", which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited.

  16. Identification and characterization of two putative microRNAs encoded by Bombyx mori cypovirus.

    Science.gov (United States)

    Pan, Zhong-Hua; Wu, Ping; Gao, Kun; Hou, Cheng-Xiang; Qin, Guang-Xing; Geng, Tao; Guo, Xi-Jie

    2017-04-02

    Viral microRNAs (miRNAs) have been demonstrated to play important roles in virus-host interactions. Some RNA virus-encoded miRNAs have been reported to promote viral replication and may be used as potential drug targets. Bombyx mori cypovirus (BmCPV), an important pathogen of silkworm, is a double-stranded RNA virus frequently causing serious damages in sericulture. Research on miRNA encoded by BmCPV may be useful to elucidate the BmCPV-host interaction and to develop new anti-viral methods. In our previous study, small RNA libraries of the midgut of BmCPV-infected silkworm have been generated by deep sequencing and several BmCPV-encoded putative miRNAs were predicted. In this study, two putative miRNAs encoded by BmCPV were identified and then validated by stem-loop qRT-PCR and northern blot. They are BmCPV-miR-3 encoded by the third genomic RNA segment of BmCPV (478-497bp) and BmCPV-miR-5 encoded by the fifth genomic RNA segment (2481-2500bp), both are 20bp and encoded by ORF regions. miRNA expression could be detected as early as 5h after BmCPV infection, and the expression level of BmCPV-miR-3 is much higher than that of BmCPV-miR-5 in the course of infection. Three potential target genes were predicted in the host genome, two for BmCPV-miR-3 and one for BmCPV-miR-5, but just one in the virus genome for BmCPV-miR-3 only, with the binding sites all in coding regions. Dual luciferase assay and qRT-PCR indicated that BmCPV-miR-3 could down-regulate the expression of both its two target genes, but no regulatory effect by BmCPV-miR-5 on its target gene was detected. In contrast, BmCPV-miR-3 could up-regulate the viral target. This is the first report that an insect double stranded RNA virus may generate miRNAs and the results obtained will benefit the future study of the functions of BmCPV-encoded miRNAs on viral replication and virus-host interaction. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Hippocampal Contribution to Context Encoding across Development Is Disrupted following Early-Life Adversity.

    Science.gov (United States)

    Lambert, Hilary K; Sheridan, Margaret A; Sambrook, Kelly A; Rosen, Maya L; Askren, Mary K; McLaughlin, Katie A

    2017-02-15

    Context can drastically influence responses to environmental stimuli. For example, a gunshot should provoke a different response at a public park than a shooting range. Little is known about how contextual processing and neural correlates change across human development or about individual differences related to early environmental experiences. Children ( N = 60; 8-19 years, 24 exposed to interpersonal violence) completed a context encoding task during fMRI scanning using a delayed match-to-sample design with neutral, happy, and angry facial cues embedded in realistic background scenes. Outside the scanner, participants completed a memory test for context-face pairings. Context memory and neural correlates of context encoding did not vary with age. Larger hippocampal volume was associated with better context memory. Posterior hippocampus was recruited during context encoding, and greater activation in this region predicted better memory for contexts paired with angry faces. Children exposed to violence had poor memory of contexts paired with angry faces, reduced hippocampal volume, and atypical neural recruitment on encoding trials with angry faces, including reduced hippocampal activation and greater functional connectivity between hippocampus and ventrolateral prefrontal cortex (vlPFC). Greater hippocampus-vlPFC connectivity was associated with worse memory for contexts paired with angry faces. Posterior hippocampus appears to support context encoding, a process that does not exhibit age-related variation from middle childhood to late adolescence. Exposure to dangerous environments in childhood is associated with poor context encoding in the presence of threat, likely due to greater vlPFC-dependent attentional narrowing on threat cues at the expense of hippocampus-dependent processing of the broader context. SIGNIFICANCE STATEMENT The ability to use context to guide reactions to environmental stimuli promotes flexible behavior. Remarkably little research has

  18. ENCODE whole-genome data in the UCSC Genome Browser

    Science.gov (United States)

    Rosenbloom, Kate R.; Dreszer, Timothy R.; Pheasant, Michael; Barber, Galt P.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Wang, Ting; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Learned, Katrina; Rhead, Brooke; Smith, Kayla E.; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

    2010-01-01

    The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. PMID:19920125

  19. Role of Virus-Encoded microRNAs in Avian Viral Diseases

    Directory of Open Access Journals (Sweden)

    Yongxiu Yao

    2014-03-01

    Full Text Available With total dependence on the host cell, several viruses have adopted strategies to modulate the host cellular environment, including the modulation of microRNA (miRNA pathway through virus-encoded miRNAs. Several avian viruses, mostly herpesviruses, have been shown to encode a number of novel miRNAs. These include the highly oncogenic Marek’s disease virus-1 (26 miRNAs, avirulent Marek’s disease virus-2 (36 miRNAs, herpesvirus of turkeys (28 miRNAs, infectious laryngotracheitis virus (10 miRNAs, duck enteritis virus (33 miRNAs and avian leukosis virus (2 miRNAs. Despite the closer antigenic and phylogenetic relationship among some of the herpesviruses, miRNAs encoded by different viruses showed no sequence conservation, although locations of some of the miRNAs were conserved within the repeat regions of the genomes. However, some of the virus-encoded miRNAs showed significant sequence homology with host miRNAs demonstrating their ability to serve as functional orthologs. For example, mdv1-miR-M4-5p, a functional ortholog of gga-miR-155, is critical for the oncogenicity of Marek’s disease virus. Additionally, we also describe the potential association of the recently described avian leukosis virus subgroup J encoded E (XSR miRNA in the induction of myeloid tumors in certain genetically-distinct chicken lines. In this review, we describe the advances in our understanding on the role of virus-encoded miRNAs in avian diseases.

  20. Visual working memory encoding in schizophrenia and first-degree relatives: neurofunctional abnormalities and impaired consolidation.

    Science.gov (United States)

    Stäblein, Michael; Storchak, Helena; Ghinea, Denisa; Kraft, Dominik; Knöchel, Christian; Prvulovic, David; Bittner, Robert A; Reif, Andreas; Oertel-Knöchel, Viola

    2018-03-09

    Working memory (WM) deficits in schizophrenia (SCZ) have been linked to impairments in the encoding phase that are associated with aberrant neuronal functioning. Similar abnormalities have been observed in unaffected first-degree relatives (REL) and are thus discussed as candidate endophenotypes. The process of WM consolidation - i.e. the formation of durable WM representations - is assumed to be impaired in SCZ, but no study has investigated WM consolidation and neuronal correlates of visual WM encoding in REL before. We examined whole-brain activation during the encoding phase with an event-related functional magnetic resonance imaging study design in 25 SCZ subjects, 22 REL subjects, and 25 healthy controls. Subjects performed a visual masked change detection task that assessed WM performance and consolidation. SCZ showed deficient WM performance indicating an impairment consolidation process, accompanied by broad neuronal hypoactivation, most prominently in frontal brain regions, as well as increased activity of the anterior cingulate during the encoding phase. REL showed decreased neuronal activity in the middle and medial frontal gyrus and increased activity in the precentral gyrus and insula during encoding, but no significant behavioral deficits were observed. In respect of given consolidation times, REL showed a shift from decreased frontal activity at short time intervals to increased frontal activity at longer time intervals. Findings suggest WM consolidation may be slowed in REL so that the deployment of compensatory neuronal resources during encoding is needed to assure proper WM performance. This supports the view of WM-related neuronal dysfunctions as a potential endophenotypic marker.

  1. Three-dimensional MRI with independent slab excitation and encoding.

    Science.gov (United States)

    Eissa, Amir; Wilman, Alan H

    2012-02-01

    Three-dimensional MRI is typically performed with the same orientation for radiofrequency slab excitation and slab select phase encoding. We introduce independent slab excitation and encoding to create a new degree of freedom in three-dimensional MRI, which is the angular relationship between the prescribed excitation volume and the voxel encoding grid. By separating the directions of slab excitation and slab phase encoding, the independent slab excitation and encoding method allows choice of optimal voxel orientation, while maintaining volume excitation based on anatomic landmarks. The method requires simple pulse sequence modifications and uses standard image reconstruction followed by removal of aliasing and image reformatting. The independent slab excitation and encoding method enables arbitrary oblique angle imaging using fixed voxel encoding gradients to maintain similar eddy current, concomitant field, or magnetic dipole effects independent of the oblique angle of excitation. We apply independent slab excitation and encoding to phase and susceptibility-weighted imaging using fixed voxel encoding aligned with the main magnetic field to demonstrate its value in both standardizing and improving image contrast, when using arbitrary oblique imaging volumes. Copyright © 2011 Wiley Periodicals, Inc.

  2. An optimal dissipative encoder for the toric code

    Science.gov (United States)

    Dengis, John; König, Robert; Pastawski, Fernando

    2014-01-01

    We consider the problem of preparing specific encoded resource states for the toric code by local, time-independent interactions with a memoryless environment. We propose the construction of such a dissipative encoder which converts product states to topologically ordered ones while preserving logical information. The corresponding Liouvillian is made up of four local Lindblad operators. For a qubit lattice of size L × L, we show that this process prepares encoded states in time O(L), which is optimal. This scaling compares favorably with known local unitary encoders for the toric code which take time of order Ω(L2) and require active time-dependent control.

  3. Temporal encoding in a nervous system.

    Directory of Open Access Journals (Sweden)

    Zane N Aldworth

    2011-05-01

    Full Text Available We examined the extent to which temporal encoding may be implemented by single neurons in the cercal sensory system of the house cricket Acheta domesticus. We found that these neurons exhibit a greater-than-expected coding capacity, due in part to an increased precision in brief patterns of action potentials. We developed linear and non-linear models for decoding the activity of these neurons. We found that the stimuli associated with short-interval patterns of spikes (ISIs of 8 ms or less could be predicted better by second-order models as compared to linear models. Finally, we characterized the difference between these linear and second-order models in a low-dimensional subspace, and showed that modification of the linear models along only a few dimensions improved their predictive power to parity with the second order models. Together these results show that single neurons are capable of using temporal patterns of spikes as fundamental symbols in their neural code, and that they communicate specific stimulus distributions to subsequent neural structures.

  4. Dynamical encoding of looming, receding, and focussing

    Science.gov (United States)

    Longtin, Andre; Clarke, Stephen Elisha; Maler, Leonard; CenterNeural Dynamics Collaboration

    This talk will discuss a non-conventional neural coding task that may apply more broadly to many senses in higher vertebrates. We ask whether and how a non-visual sensory system can focus on an object. We present recent experimental and modeling work that shows how the early sensory circuitry of electric sense can perform such neuronal focusing that is manifested behaviorally. This sense is the main one used by weakly electric fish to navigate, locate prey and communicate in the murky waters of their natural habitat. We show that there is a distance at which the Fisher information of a neuron's response to a looming and receding object is maximized, and that this distance corresponds to a behaviorally relevant one chosen by these animals. Strikingly, this maximum occurs at a bifurcation between tonic firing and bursting. We further discuss how the invariance of this distance to signal attributes can arise, a process that first involves power-law spike frequency adaptation. The talk will also highlight the importance of expanding the classic dual neural encoding of contrast using ON and OFF cells in the context of looming and receding stimuli. The authors acknowledge support from CIHR and NSERC.

  5. Holographic encoding of universality in corner spectra

    Science.gov (United States)

    Huang, Ching-Yu; Wei, Tzu-Chieh; Orús, Román

    2017-05-01

    In numerical simulations of classical and quantum lattice systems, 2D corner transfer matrices (CTMs) and 3D corner tensors (CTs) are a useful tool to compute approximate contractions of infinite-size tensor networks. In this paper we show how the numerical CTMs and CTs can be used, additionally, to extract universal information from their spectra. We provide examples of this for classical and quantum systems, in 1D, 2D, and 3D. Our results provide, in particular, practical evidence for a wide variety of models of the correspondence between d -dimensional quantum and (d +1 ) -dimensional classical spin systems. We show also how corner properties can be used to pinpoint quantum phase transitions, topological or not, without the need for observables. Moreover, for a chiral topological PEPS we show by examples that corner tensors can be used to extract the entanglement spectrum of half a system, with the expected symmetries of the S U (2) k Wess-Zumino-Witten model describing its gapless edge for k =1 ,2 . We also review the theory behind the quantum-classical correspondence for spin systems and provide a numerical scheme for quantum state renormalization in 2D using CTs. Our results show that bulk information of a lattice system is encoded holographically in efficiently-computable properties of its corners.

  6. Peafowl antipredator calls encode information about signalers.

    Science.gov (United States)

    Yorzinski, Jessica L

    2014-02-01

    Animals emit vocalizations that convey information about external events. Many of these vocalizations, including those emitted in response to predators, also encode information about the individual that produced the call. The relationship between acoustic features of antipredator calls and information relating to signalers (including sex, identity, body size, and social rank) were examined in peafowl (Pavo cristatus). The "bu-girk" antipredator calls of male and female peafowl were recorded and 20 acoustic parameters were automatically extracted from each call. Both the bu and girk elements of the antipredator call were individually distinctive and calls were classified to the correct signaler with over 90% and 70% accuracy in females and males, respectively. Females produced calls with a higher fundamental frequency (F0) than males. In both females and males, body size was negatively correlated with F0. In addition, peahen rank was related to the duration, end mean frequency, and start harmonicity of the bu element. Peafowl antipredator calls contain detailed information about the signaler and can potentially be used by receivers to respond to dangerous situations.

  7. Electrophysiological Anomalies in Face–Name Memory Encoding in Young Binge Drinkers

    Directory of Open Access Journals (Sweden)

    Rocío Folgueira-Ares

    2017-11-01

    Full Text Available A growing body of evidence indicates that the intake of large amounts of alcohol during one session may have structural and functional effects on the still-maturing brains of young people. These effects are particularly pronounced in prefrontal and hippocampal regions, which appear to be especially sensitive to the neurotoxic effects of alcohol. However, to date, few studies have used the event-related potentials (ERPs technique to analyze the relationship between binge drinking (BD and associative memory. The objective of this study was to examine brain activity during memory encoding using the Subsequent memory paradigm in subjects who have followed a BD pattern of alcohol consumption for at least 2 years. A total of 50 undergraduate students (mean age = 20.6 years, i.e., 25 controls (12 females and 25 binge drinkers (BDs; 11 females, with no personal or family history of alcoholism or psychopathological disorders, performed a visual face–name association memory task. The task used enables assessment of the Difference due to memory effect (Dm, a measure of memory encoding based on comparison of the neural activity associated with subsequent successful and unsuccessful retrieval. In ERP studies, study items that are subsequently remembered elicit larger positive amplitudes at midline parieto-frontal sites than those items that are subsequently forgotten. The Dm effect generally appears in the latency range of about 300–800 ms. The results showed a Dm effect in posterior regions in the 350–650 ms latency range in the Control group. However, in the BD group, no significant differences were observed in the electrophysiological brain activity between remembered and forgotten items during the encoding process. No differences between groups were found in behavioral performance. These findings show that young BDs display abnormal pattern of ERP brain activity during the encoding phase of a visual face–name association task

  8. Building on prior knowledge: schema-dependent encoding processes relate to academic performance.

    Science.gov (United States)

    van Kesteren, Marlieke T R; Rijpkema, Mark; Ruiter, Dirk J; Morris, Richard G M; Fernández, Guillén

    2014-10-01

    The acquisition and retention of conceptual knowledge is more effective in well-structured curricula that provide an optimal conceptual framework for learning new material. However, the neural mechanisms by which preexisting conceptual schemas facilitate learning are not yet well understood despite their fundamental importance. A preexisting schema has been shown to enhance memory by influencing the balance between activity within the medial-temporal lobe and the medial pFC during mnemonic processes such as encoding, consolidation, and retrieval. Specifically, correctly encoding and retrieving information that is related to preexisting schemas appears rather related to medial prefrontal processing, whereas information unrelated or inconsistent with preexisting schemas rather relates to enhanced medial temporal processing and enhanced interaction between these structures. To further investigate interactions between these regions during conceptual encoding in a real-world university setting, we probed human brain activity and connectivity using fMRI during educationally relevant conceptual encoding carefully embedded within two course programs. Early second-year undergraduate biology and education students were scanned while encoding new facts that were either related or unrelated to the preexisting conceptual knowledge they had acquired during their first year of study. Subsequently, they were tested on their knowledge of these facts 24 hr later. Memory scores were better for course-related information, and this enhancement was associated with larger medial-prefrontal, but smaller medial-temporal subsequent memory effects. These activity differences went along with decreased functional interactions between these regions. Furthermore, schema-related medial-prefrontal subsequent memory effects measured during this experiment were found to be predictive of second-year course performance. These results, obtained in a real-world university setting, reveal brain

  9. Evidence for anomalous network connectivity during working memory encoding in schizophrenia: an ICA based analysis.

    Directory of Open Access Journals (Sweden)

    Shashwath A Meda

    2009-11-01

    Full Text Available Numerous neuroimaging studies report abnormal regional brain activity during working memory performance in schizophrenia, but few have examined brain network integration as determined by "functional connectivity" analyses.We used independent component analysis (ICA to identify and characterize dysfunctional spatiotemporal networks in schizophrenia engaged during the different stages (encoding and recognition of a Sternberg working memory fMRI paradigm. 37 chronic schizophrenia and 54 healthy age/gender-matched participants performed a modified Sternberg Item Recognition fMRI task. Time series images preprocessed with SPM2 were analyzed using ICA. Schizophrenia patients showed relatively less engagement of several distinct "normal" encoding-related working memory networks compared to controls. These encoding networks comprised 1 left posterior parietal-left dorsal/ventrolateral prefrontal cortex, cingulate, basal ganglia, 2 right posterior parietal, right dorsolateral prefrontal cortex and 3 default mode network. In addition, the left fronto-parietal network demonstrated a load-dependent functional response during encoding. Network engagement that differed between groups during recognition comprised the posterior cingulate, cuneus and hippocampus/parahippocampus. As expected, working memory task accuracy differed between groups (p<0.0001 and was associated with degree of network engagement. Functional connectivity within all three encoding-associated functional networks correlated significantly with task accuracy, which further underscores the relevance of abnormal network integration to well-described schizophrenia working memory impairment. No network was significantly associated with task accuracy during the recognition phase.This study extends the results of numerous previous schizophrenia studies that identified isolated dysfunctional brain regions by providing evidence of disrupted schizophrenia functional connectivity using ICA within

  10. Remembering with gains and losses: effects of monetary reward and punishment on successful encoding activation of source memories.

    Science.gov (United States)

    Shigemune, Yayoi; Tsukiura, Takashi; Kambara, Toshimune; Kawashima, Ryuta

    2014-05-01

    The motivation of getting rewards or avoiding punishments reinforces learning behaviors. Although the neural mechanisms underlying the effect of rewards on episodic memory have been demonstrated, there is little evidence of the effect of punishments on this memory. Our functional magnetic resonance imaging (fMRI) study investigated the effects of monetary rewards and punishments on activation during the encoding of source memories. During encoding, participants memorized words (item) and locations of presented words (source) under 3 conditions (Reward, Punishment, and Control). During retrieval, participants retrieved item and source memories of the words and were rewarded or penalized according to their performance. Source memories encoded with rewards or punishments were remembered better than those without such encoding. fMRI data demonstrated that the ventral tegmental area and substantia nigra and nucleus accumbens activations reflected both the processes of reward and punishment, whereas insular activation increased as a linear function of punishment. Activation in the hippocampus and parahippocampal cortex predicted subsequent retrieval success of source memories. Additionally, correlations between these reward/punishment-related regions and the hippocampus were significant. The successful encoding of source memories could be enhanced by punishments and rewards, and interactions between reward/punishment-related regions and memory-related regions could contribute to memory enhancement by reward and/or punishment.

  11. Age Differences in Self-Referencing: Evidence for Common and Distinct Encoding Strategies

    Science.gov (United States)

    Gutchess, Angela H.; Sokal, Rebecca; Coleman, Jennifer A.; Gotthilf, Gina; Grewal, Lauren; Rosa, Nicole

    2014-01-01

    Although engagement of medial prefrontal cortex (MPFC) underlies self-referencing of information for younger and older adults, the region has not consistently been implicated across age groups for the encoding of self-referenced information. We sought to determine whether making judgments about others as well as the self influenced findings in the previous study. During an fMRI session, younger and older adults encoded adjectives using only a self-reference task. For items later remembered compared to those later forgotten, both age groups robustly recruited medial prefrontal cortex, indicating common neural regions support encoding across younger and older adults when participants make only self-reference judgments. Focal age differences emerged in regions related to emotional processing and cognitive control, though these differences are more limited than in tasks in which judgments also are made about others. We conclude that making judgments about another person differently affects the ways that younger and older adults make judgments about the self, with results of a follow-up behavioral study supporting this interpretation. PMID:25223905

  12. Stress as a mnemonic filter: Interactions between medial temporal lobe encoding processes and post-encoding stress.

    Science.gov (United States)

    Ritchey, Maureen; McCullough, Andrew M; Ranganath, Charan; Yonelinas, Andrew P

    2017-01-01

    Acute stress has been shown to modulate memory for recently learned information, an effect attributed to the influence of stress hormones on medial temporal lobe (MTL) consolidation processes. However, little is known about which memories will be affected when stress follows encoding. One possibility is that stress interacts with encoding processes to selectively protect memories that had elicited responses in the hippocampus and amygdala, two MTL structures important for memory formation. There is limited evidence for interactions between encoding processes and consolidation effects in humans, but recent studies of consolidation in rodents have emphasized the importance of encoding "tags" for determining the impact of consolidation manipulations on memory. Here, we used functional magnetic resonance imaging in humans to test the hypothesis that the effects of post-encoding stress depend on MTL processes observed during encoding. We found that changes in stress hormone levels were associated with an increase in the contingency of memory outcomes on hippocampal and amygdala encoding responses. That is, for participants showing high cortisol reactivity, memories became more dependent on MTL activity observed during encoding, thereby shifting the distribution of recollected events toward those that had elicited relatively high activation. Surprisingly, this effect was generally larger for neutral, compared to emotionally negative, memories. The results suggest that stress does not uniformly enhance memory, but instead selectively preserves memories tagged during encoding, effectively acting as mnemonic filter. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. Olfactory bulb encoding during learning under anaesthesia

    Directory of Open Access Journals (Sweden)

    Alister U Nicol

    2014-06-01

    Full Text Available Neural plasticity changes within the olfactory bulb are important for olfactory learning, although how neural encoding changes support new associations with specific odours and whether they can be investigated under anaesthesia, remain unclear. Using the social transmission of food preference olfactory learning paradigm in mice in conjunction with in vivo microdialysis sampling we have shown firstly that a learned preference for a scented food odour smelled on the breath of a demonstrator animal occurs under isofluorane anaesthesia. Furthermore, subsequent exposure to this cued odour under anaesthesia promotes the same pattern of increased release of glutamate and GABA in the olfactory bulb as previously found in conscious animals following olfactory learning, and evoked GABA release was positively correlated with the amount of scented food eaten. In a second experiment, multiarray (24 electrodes electrophysiological recordings were made from olfactory bulb mitral cells under isofluorane anaesthesia before, during and after a novel scented food odour was paired with carbon disulfide. Results showed significant increases in overall firing frequency to the cued-odour during and after learning and decreases in response to an uncued odour. Analysis of patterns of changes in individual neurons revealed that a substantial proportion (>50% of them significantly changed their response profiles during and after learning with most of those previously inhibited becoming excited. A large number of cells exhibiting no response to the odours prior to learning were either excited or inhibited afterwards. With the uncued odour many previously responsive cells became unresponsive or inhibited. Learning associated changes only occurred in the posterior part of the olfactory bulb. Thus olfactory learning under anaesthesia promotes extensive, but spatially distinct, changes in mitral cell networks to both cued and uncued odours as well as in evoked glutamate and

  14. Olfactory bulb encoding during learning under anesthesia

    Science.gov (United States)

    Nicol, Alister U.; Sanchez-Andrade, Gabriela; Collado, Paloma; Segonds-Pichon, Anne; Kendrick, Keith M.

    2014-01-01

    Neural plasticity changes within the olfactory bulb are important for olfactory learning, although how neural encoding changes support new associations with specific odors and whether they can be investigated under anesthesia, remain unclear. Using the social transmission of food preference olfactory learning paradigm in mice in conjunction with in vivo microdialysis sampling we have shown firstly that a learned preference for a scented food odor smelled on the breath of a demonstrator animal occurs under isofluorane anesthesia. Furthermore, subsequent exposure to this cued odor under anesthesia promotes the same pattern of increased release of glutamate and gamma-aminobutyric acid (GABA) in the olfactory bulb as previously found in conscious animals following olfactory learning, and evoked GABA release was positively correlated with the amount of scented food eaten. In a second experiment, multiarray (24 electrodes) electrophysiological recordings were made from olfactory bulb mitral cells under isofluorane anesthesia before, during and after a novel scented food odor was paired with carbon disulfide. Results showed significant increases in overall firing frequency to the cued-odor during and after learning and decreases in response to an uncued odor. Analysis of patterns of changes in individual neurons revealed that a substantial proportion (>50%) of them significantly changed their response profiles during and after learning with most of those previously inhibited becoming excited. A large number of cells exhibiting no response to the odors prior to learning were either excited or inhibited afterwards. With the uncued odor many previously responsive cells became unresponsive or inhibited. Learning associated changes only occurred in the posterior part of the olfactory bulb. Thus olfactory learning under anesthesia promotes extensive, but spatially distinct, changes in mitral cell networks to both cued and uncued odors as well as in evoked glutamate and GABA

  15. Encoding and Decoding Models in Cognitive Electrophysiology

    Directory of Open Access Journals (Sweden)

    Christopher R. Holdgraf

    2017-09-01

    Full Text Available Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of “Encoding” models, in which stimulus features are used to model brain activity, and “Decoding” models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyter notebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aim is to provide a practical understanding of predictive modeling of human brain data and to propose best-practices in conducting these analyses.

  16. Stereoscopic radiographic images with gamma source encoding

    International Nuclear Information System (INIS)

    Strocovsky, S.G.; Otero, D

    2012-01-01

    Conventional radiography with X-ray tube has several drawbacks, as the compromise between the size of the focal spot and the fluence. The finite dimensions of the focal spot impose a limit to the spatial resolution. Gamma radiography uses gamma-ray sources which surpass in size, portability and simplicity to X-ray tubes. However, its low intrinsic fluence forces to use extended sources that also degrade the spatial resolution. In this work, we show the principles of a new radiographic technique that overcomes the limitations associated with the finite dimensions of X-ray sources, and that offers additional benefits to conventional techniques. The new technique called coding source imaging (CSI), is based on the use of extended sources, edge-encoding of radiation and differential detection. The mathematical principles and the method of images reconstruction with the new proposed technique are explained in the present work. Analytical calculations were made to determine the maximum spatial resolution and the variables on which it depends. The CSI technique was tested by means of Monte Carlo simulations with sets of spherical objects. We show that CSI has stereoscopic capabilities and it can resolve objects smaller than the source size. The CSI decoding algorithm reconstructs simultaneously four different projections from the same object, while conventional radiography produces only one projection per acquisition. Projections are located in separate image fields on the detector plane. Our results show it is possible to apply an extremely simple radiographic technique with extended sources, and get 3D information of the attenuation coefficient distribution for simple geometry objects in a single acquisition. The results are promising enough to evaluate the possibility of future research with more complex objects typical of medical diagnostic radiography and industrial gamma radiography (author)

  17. Recency effects in HIV-associated dementia are characterized by deficient encoding.

    Science.gov (United States)

    Scott, J Cobb; Woods, Steven Paul; Patterson, Katherine A; Morgan, Erin E; Heaton, Robert K; Grant, Igor; Marcotte, Thomas D

    2006-01-01

    The aim of the present study was to investigate the nature and cognitive mechanisms of serial position learning effects in HIV-associated dementia (HAD). Participants were 16 persons with HAD, 50 non-demented persons with HIV-infection, and 50 demographically comparable HIV-seronegative participants. HAD participants, relative to both comparison groups, exhibited reduced middle region (precency region (pprimacy region effect (p>0.10). On recognition testing, the HAD group was impaired in discriminating targets from distractors (p0.10) within these same regions. In sum, HAD participants relied disproportionately on recency regions of the list, indicating a passive recall style of echoing only the words within their auditory attention span. Interestingly, HAD participants did not evidence significant improvement on measures of recognition, a finding that suggests that the serial position effects are most consistent with a primary encoding deficit.

  18. PREVALENCE OF TOXIN ENCODING GENES IN ESCHERICHIACOLI ISOLATES FROM URINARY TRACT INFECTIONS INSLOVENIA

    Directory of Open Access Journals (Sweden)

    Marjanca Starčič-Erjavec

    2008-06-01

    Full Text Available Methods 110 uropathogenic Escherichia coli strains (UPEC obtained from the Institute of Microbiology and Immunology of the Medical Faculty in Ljubljana were screened by PCR withprimers specific for the following toxin encoding genes: hlyA (haemolysin, cnf1 (cytotoxicnecrotising factor 1, usp (uropathogenic specific protein USP and ibeA (invasin. Dotblot hybridisation experiments were performed to validate the PCR assays.Results In 44% of the strains usp gene sequences were detected. The prevalence of hlyA and cnf1was 25% and 23%, respectively. Only 9% of the strains harbored ibeA. The majority of thetested toxin encoding genes was found in strains belonging to the B2 phylogenetic group.Conclusions The toxin encoding genes hlyA, cnf1 and usp were strongly co-associated. Further, we founda statistically significant co-association of ibeA and usp. The prevalence of the testedtoxin encoding genes in E. coli strains from urinary tract infections isolated in Slovenia iscomparable to those from studies in other geographic regions.

  19. Age-related influences of prior sleep on brain activation during verbal encoding

    Directory of Open Access Journals (Sweden)

    Michelle B Jonelis

    2012-04-01

    Full Text Available Disrupted sleep is more common in older adults (OA than younger adults (YA, often co-morbid with other conditions. How these sleep disturbances affect cognitive performance is an area of active study. We examined whether brain activation during verbal encoding correlates with sleep quantity and quality the night before testing in a group of healthy OA and YA. Twenty-seven OA (ages 59-82 and twenty-seven YA (ages 19-36 underwent one night of standard polysomnography. Twelve hours post-awakening, subjects performed a verbal encoding task while undergoing functional MRI. Analyses examined the group (OA vs. YA by prior sleep quantity (Total Sleep Time (TST or quality (Sleep Efficiency (SE interaction on cerebral activation, controlling for performance. Longer TST promoted higher levels of activation in the bilateral anterior parahippocampi in OA and lower activation levels in the left anterior parahippocampus in YA. Greater SE promoted higher activation levels in the left posterior parahippocampus and right inferior frontal gyrus in YA, but not in OA. The roles of these brain regions in verbal encoding suggest, in OA, longer sleep duration may facilitate functional compensation during cognitive challenges. By contrast, in YA, shorter sleep duration may necessitate functional compensation to maintain cognitive performance, similar to what is seen following acute sleep deprivation. Additionally, in YA, better sleep quality may improve semantic retrieval processes, thereby aiding encoding.

  20. W-band radio-over-fiber propagation of two optically encoded wavelength channels

    Science.gov (United States)

    Eghbal, Morad Khosravi; Shadaram, Mehdi

    2018-01-01

    We propose a W-band wavelength-division multiplexing (WDM)-over-optical code-division multiple access radio-over-fiber system. This system offers capacity expansion by increasing the working frequency to millimeter wave region and by introducing optical encoding and multiwavelength multiplexing. The system's functionality is investigated by software modeling, and the results are presented. The generated signals are data modulated at 10 Gb/s and optically encoded for two wavelength channels and transmitted with a 20-km length of fiber. The received signals are optically decoded and detected. Also, encoding has improved the bit error rate (BER) versus the received optical power margin for the WDM setting by about 4 dB. In addition, the eye-diagram shows that the difference between received optical power levels at the BER of 10-12 to 10-3 is about 1.3% between two encoded channels. This method of capacity improvement is significantly important for the next generation of mobile communication, where millimeter wave signals will be widely used to deliver data to small cells.

  1. Encoding the identity and location of objects in human LOC.

    Science.gov (United States)

    Cichy, Radoslaw Martin; Chen, Yi; Haynes, John-Dylan

    2011-02-01

    We are able to recognize objects independent of their location in the visual field. At the same time, we also keep track of the location of objects to orient ourselves and to interact with the environment. The lateral occipital complex (LOC) has been suggested as the prime cortical region for representation of object identity. However, the extent to which LOC also represents object location has remained debated. In this study we used high-resolution fMRI in combination with multivoxel pattern classification to investigate the cortical encoding of three object exemplars from four different categories presented in two different locations. This approach allowed us to study location-tolerant object information and object-tolerant location information in LOC, both at the level of categories and exemplars. We found evidence for both location-tolerant object information and object-tolerant location information in LOC at the level of categories and exemplars. Our results further highlight the mixing of identity and location information in the ventral visual pathway. Copyright © 2010 Elsevier Inc. All rights reserved.

  2. Impact of anxiety on prefrontal cortex encoding of cognitive flexibility.

    Science.gov (United States)

    Park, Junchol; Moghaddam, Bita

    2017-03-14

    Anxiety often is studied as a stand-alone construct in laboratory models. But in the context of coping with real-life anxiety, its negative impacts extend beyond aversive feelings and involve disruptions in ongoing goal-directed behaviors and cognitive functioning. Critical examples of cognitive constructs affected by anxiety are cognitive flexibility and decision making. In particular, anxiety impedes the ability to shift flexibly between strategies in response to changes in task demands, as well as the ability to maintain a strategy in the presence of distractors. The brain region most critically involved in behavioral flexibility is the prefrontal cortex (PFC), but little is known about how anxiety impacts PFC encoding of internal and external events that are critical for flexible behavior. Here we review animal and human neurophysiological and neuroimaging studies implicating PFC neural processing in anxiety-induced deficits in cognitive flexibility. We then suggest experimental and analytical approaches for future studies to gain a better mechanistic understanding of impaired cognitive inflexibility in anxiety and related disorders. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Encoded Archival Description: An Introduction and Overview | Pitti ...

    African Journals Online (AJOL)

    Encoded Archival Description (EAD) is an emerging standard used internationally in an increasing number of archives and manuscripts libraries to encode data describing corporate records and personal papers. The individual descriptions are variously called finding aids, guides, handlists, or catalogues. While archival ...

  4. On The Designed And Constructed Feedback Shift-Register Encoder

    African Journals Online (AJOL)

    An encoder capable of cyclical shifting of data, and which can therefore be used for Bose-Chaudhuri and Hocquenghem (BCH) coding, has been designed and constructed using discrete components. It comprises basically four bistable multivibrators and an exclusive-OR device. On completion, the encoder performed ...

  5. What is a "good" encoding of guarded choice?

    DEFF Research Database (Denmark)

    Nestmann, Uwe

    2000-01-01

    into the latter that preserves divergence-freedom and symmetries. This paper argues that there are nevertheless "good" encodings between these calculi. In detail, we present a series of encodings for languages with (1) input-guarded choice, (2) both input and output-guarded choice, and (3) mixed-guarded choice...

  6. Polypeptides having laccase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Tang, Lan; Duan, Junxin; Zhang, Yu

    2017-08-22

    The present invention relates to isolated polypeptides having laccase activity and polynucleotides encoding the polypeptides and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  7. On The Designed And Constructed Feedback Shift-Register Encoder

    African Journals Online (AJOL)

    Information transmission in noisy channels can be achieved with vanishingly small probability of error by proper coding of the information as long as the encoding rate is less than the channel capacity. An encoder capable of cyclical shifting of data, and which can therefore be used for Bose-Chaudhuri and Hocquenghem ...

  8. A SSVEP Stimuli Encoding Method Using Trinary Frequency-Shift Keying Encoded SSVEP (TFSK-SSVEP

    Directory of Open Access Journals (Sweden)

    Xing Zhao

    2017-06-01

    Full Text Available SSVEP is a kind of BCI technology with advantage of high information transfer rate. However, due to its nature, frequencies could be used as stimuli are scarce. To solve such problem, a stimuli encoding method which encodes SSVEP signal using Frequency Shift–Keying (FSK method is developed. In this method, each stimulus is controlled by a FSK signal which contains three different frequencies that represent “Bit 0,” “Bit 1” and “Bit 2” respectively. Different to common BFSK in digital communication, “Bit 0” and “Bit 1” composited the unique identifier of stimuli in binary bit stream form, while “Bit 2” indicates the ending of a stimuli encoding. EEG signal is acquired on channel Oz, O1, O2, Pz, P3, and P4, using ADS1299 at the sample rate of 250 SPS. Before original EEG signal is quadrature demodulated, it is detrended and then band-pass filtered using FFT-based FIR filtering to remove interference. Valid peak of the processed signal is acquired by calculating its derivative and converted into bit stream using window method. Theoretically, this coding method could implement at least 2n−1 (n is the length of bit command stimulus while keeping the ITR the same. This method is suitable to implement stimuli on a monitor and where the frequency and phase could be used to code stimuli is limited as well as implementing portable BCI devices which is not capable of performing complex calculations.

  9. What is a "good" encoding of guarded choice?

    DEFF Research Database (Denmark)

    Nestmann, Uwe

    2000-01-01

    The pi-calculus with synchronous output and mixed-guarded choices is strictly more expressive than the pi-calculus with asynchronous output and no choice. This result was recently proved by C. Palamidessi and, as a corollary, she showed that there is no fully compositional encoding from the former...... into the latter that preserves divergence-freedom and symmetries. This paper argues that there are nevertheless "good" encodings between these calculi. In detail, we present a series of encodings for languages with (1) input-guarded choice, (2) both input and output-guarded choice, and (3) mixed-guarded choice......, and investigate them with respect to compositionality and divergence-freedom. The first and second encoding satisfy all of the above criteria, but various "good" candidates for the third encoding-inspired by an existing distributed implementation-invalidate one or the other criterion, While essentially confirming...

  10. Convolutional over Recurrent Encoder for Neural Machine Translation

    Directory of Open Access Journals (Sweden)

    Dakwale Praveen

    2017-06-01

    Full Text Available Neural machine translation is a recently proposed approach which has shown competitive results to traditional MT approaches. Standard neural MT is an end-to-end neural network where the source sentence is encoded by a recurrent neural network (RNN called encoder and the target words are predicted using another RNN known as decoder. Recently, various models have been proposed which replace the RNN encoder with a convolutional neural network (CNN. In this paper, we propose to augment the standard RNN encoder in NMT with additional convolutional layers in order to capture wider context in the encoder output. Experiments on English to German translation demonstrate that our approach can achieve significant improvements over a standard RNN-based baseline.

  11. Absolute scale-based imaging position encoder with submicron accuracy

    Science.gov (United States)

    Anisimov, Andrey G.; Pantyushin, Anton V.; Lashmanov, Oleg U.; Vasilev, A. S.; Timofeev, Alexander N.; Korotaev, Valery V.; Gordeev, Sergey V.

    2013-04-01

    Study is devoted to experimental research and development of absolute imaging position encoder based on standard calibrated scale of invar alloy with 1 mm spacing. The encoder uses designed imaging system as a vernier and absolute magnetic encoder as a rough indication. The features of optical design, choice and use of imaging system as long as indexes images processing algorithm are described. A shadow method was implemented: indexes images on a CCD array are formed by the lens focused at the scale surface; the laser module lights up the scale through a beam-splitting prism by a parallel beam. Further dark indexes images on a light scale background are detected and analyzed to estimate the encoder position. Full range of experimental tests was set to calibrate the encoder and to estimate the accuracy. As a result, accuracy close to 1 μm at 1 m was achieved.

  12. Review of Random Phase Encoding in Volume Holographic Storage

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    Wei-Chia Su

    2012-09-01

    Full Text Available Random phase encoding is a unique technique for volume hologram which can be applied to various applications such as holographic multiplexing storage, image encryption, and optical sensing. In this review article, we first review and discuss diffraction selectivity of random phase encoding in volume holograms, which is the most important parameter related to multiplexing capacity of volume holographic storage. We then review an image encryption system based on random phase encoding. The alignment of phase key for decryption of the encoded image stored in holographic memory is analyzed and discussed. In the latter part of the review, an all-optical sensing system implemented by random phase encoding and holographic interconnection is presented.

  13. Role of sleep for encoding of emotional memory.

    Science.gov (United States)

    Kaida, Kosuke; Niki, Kazuhisa; Born, Jan

    2015-05-01

    Total sleep deprivation (TSD) has been consistently found to impair encoding of information during ensuing wakefulness, probably through suppressing NonREM (non-rapid eye movement) sleep. However, a possible contribution of missing REM sleep to this encoding impairment after TSD has so far not been systematically examined in humans, although such contribution might be suspected in particular for emotional information. Here, in two separate experiments in young healthy men, we compared effects of TSD and of selective REM sleep deprivation (REMD), relative to respective control conditions of undisturbed sleep, on the subsequent encoding of neutral and emotional pictures. The pictures were presented in conjunction with colored frames to also assess related source memory. REMD was achieved by tones presented contingently upon initial signs of REM sleep. Encoding capabilities were examined in the evening (18:00h) after the experimental nights, by a picture recognition test right after encoding. TSD significantly decreased both the rate of correctly recognized pictures and of recalled frames associated with the pictures. The TSD effect was robust and translated into an impaired long term memory formation, as it was likewise observed on a second recognition testing one week after the encoding phase. Contrary to our expectation, REMD did not affect encoding in general, or particularly of emotional pictures. Also, REMD did not affect valence ratings of the encoded pictures. However, like TSD, REMD distinctly impaired vigilance at the time of encoding. Altogether, these findings indicate an importance of NonREM rather than REM sleep for the encoding of information that is independent of the emotionality of the materials. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. High-resolution MRI encoding using radiofrequency phase gradients.

    Science.gov (United States)

    Sharp, Jonathan C; King, Scott B; Deng, Qunli; Volotovskyy, Vyacheslav; Tomanek, Boguslaw

    2013-11-01

    Although MRI offers highly diagnostic medical imagery, patient access to this modality worldwide is very limited when compared with X-ray or ultrasound. One reason for this is the expense and complexity of the equipment used to generate the switched magnetic fields necessary for MRI encoding. These field gradients are also responsible for intense acoustic noise and have the potential to induce nerve stimulation. We present results with a new MRI encoding principle which operates entirely without the use of conventional B0 field gradients. This new approach--'Transmit Array Spatial Encoding' (TRASE)--uses only the resonant radiofrequency (RF) field to produce Fourier spatial encoding equivalent to conventional MRI. k-space traversal (image encoding) is achieved by spin refocusing with phase gradient transmit fields in spin echo trains. A transmit coil array, driven by just a single transmitter channel, was constructed to produce four phase gradient fields, which allows the encoding of two orthogonal spatial axes. High-resolution two-dimensional-encoded in vivo MR images of hand and wrist were obtained at 0.2 T. TRASE exploits RF field phase gradients, and offers the possibility of very low-cost diagnostics and novel experiments exploiting unique capabilities, such as imaging without disturbance of the main B0 magnetic field. Lower field imaging (moving through k space, there are many close analogies between it and conventional B0 -encoded techniques. TRASE is compatible with both B0 gradient encoding and parallel imaging, and so hybrid sequences containing all three spatial encoding approaches are possible. Copyright © 2013 John Wiley & Sons, Ltd.

  15. What makes deeply encoded items memorable? Insights into the levels of processing framework from neuroimaging and neuromodulation

    Directory of Open Access Journals (Sweden)

    Giulia eGalli

    2014-05-01

    Full Text Available When we form new memories, their mnestic fate largely depends upon the cognitive operations set in train during encoding. A typical observation in experimental as well as everyday life settings is that if we learn an item using semantic or deep operations, such as attending to its meaning, memory will be better than if we learn the same item using more shallow operations, such as attending to its structural features. In the psychological literature, this phenomenon has been conceptualised within the levels of processing framework and has been consistently replicated since its original proposal by Craik and Lockhart in 1972. However, the exact mechanisms underlying the memory advantage for deeply encoded items are not yet entirely understood. A cognitive neuroscience perspective can add to this field by clarifying the nature of the processes involved in effective deep and shallow encoding and how they are instantiated in the brain, but so far there has been little work to systematically integrate findings from the literature. This work aims to fill this gap by reviewing, first, some of the key neuroimaging findings on the neural correlates of deep and shallow episodic encoding and second, emerging evidence from studies using neuromodulatory approaches such as psychopharmacology and non invasive brain stimulation. Taken together, these studies help further our understanding of levels of processing. In addition, by showing that deep encoding can be modulated by acting upon specific brain regions or systems, the reviewed studies pave the way for selective enhancements of episodic encoding processes

  16. What makes deeply encoded items memorable? Insights into the levels of processing framework from neuroimaging and neuromodulation.

    Science.gov (United States)

    Galli, Giulia

    2014-01-01

    When we form new memories, their mnestic fate largely depends upon the cognitive operations set in train during encoding. A typical observation in experimental as well as everyday life settings is that if we learn an item using semantic or "deep" operations, such as attending to its meaning, memory will be better than if we learn the same item using more "shallow" operations, such as attending to its structural features. In the psychological literature, this phenomenon has been conceptualized within the "levels of processing" framework and has been consistently replicated since its original proposal by Craik and Lockhart in 1972. However, the exact mechanisms underlying the memory advantage for deeply encoded items are not yet entirely understood. A cognitive neuroscience perspective can add to this field by clarifying the nature of the processes involved in effective deep and shallow encoding and how they are instantiated in the brain, but so far there has been little work to systematically integrate findings from the literature. This work aims to fill this gap by reviewing, first, some of the key neuroimaging findings on the neural correlates of deep and shallow episodic encoding and second, emerging evidence from studies using neuromodulatory approaches such as psychopharmacology and non-invasive brain stimulation. Taken together, these studies help further our understanding of levels of processing. In addition, by showing that deep encoding can be modulated by acting upon specific brain regions or systems, the reviewed studies pave the way for selective enhancements of episodic encoding processes.

  17. Can natural selection encode Bayesian priors?

    Science.gov (United States)

    Ramírez, Juan Camilo; Marshall, James A R

    2017-08-07

    The evolutionary success of many organisms depends on their ability to make decisions based on estimates of the state of their environment (e.g., predation risk) from uncertain information. These decision problems have optimal solutions and individuals in nature are expected to evolve the behavioural mechanisms to make decisions as if using the optimal solutions. Bayesian inference is the optimal method to produce estimates from uncertain data, thus natural selection is expected to favour individuals with the behavioural mechanisms to make decisions as if they were computing Bayesian estimates in typically-experienced environments, although this does not necessarily imply that favoured decision-makers do perform Bayesian computations exactly. Each individual should evolve to behave as if updating a prior estimate of the unknown environment variable to a posterior estimate as it collects evidence. The prior estimate represents the decision-maker's default belief regarding the environment variable, i.e., the individual's default 'worldview' of the environment. This default belief has been hypothesised to be shaped by natural selection and represent the environment experienced by the individual's ancestors. We present an evolutionary model to explore how accurately Bayesian prior estimates can be encoded genetically and shaped by natural selection when decision-makers learn from uncertain information. The model simulates the evolution of a population of individuals that are required to estimate the probability of an event. Every individual has a prior estimate of this probability and collects noisy cues from the environment in order to update its prior belief to a Bayesian posterior estimate with the evidence gained. The prior is inherited and passed on to offspring. Fitness increases with the accuracy of the posterior estimates produced. Simulations show that prior estimates become accurate over evolutionary time. In addition to these 'Bayesian' individuals, we also

  18. Cloning and characterization of human liver cDNA encoding a protein S precursor

    International Nuclear Information System (INIS)

    Hoskins, J.; Norman, D.K.; Beckmann, R.J.; Long, G.L.

    1987-01-01

    Human liver cDNA encoding a protein S precursor was isolated from two cDNA libraries by two different techniques. Based upon the frequency of positive clones, the abundance of mRNA for protein S is ≅ 0.01%. Blot hybridization of electrophoretically fractionated poly(A) + RNA revealed a major mRNA ≅ 4 kilobases long and two minor forms of ≅ 3.1 and ≅ 2.6 kilobases. One of the cDNA clones contains a segment encoding a 676 amino acid protein S precursor, as well as 108 and 1132 nucleotides of 5' and 3' noncoding sequence, respectively, plus a poly(A) region at the 3' end. The cDNAs are adenosine plus thymidine-rich (60%) except for the 5' noncoding region, where 78% of the nucleotides are guanosine or cytosine. The protein precursor consists of a 41 amino acid leader peptide followed by 635 amino acids corresponding to mature protein S. Comparison of the mature protein region with homologous vitamin K-dependent plasma proteins shows that it is composed of the following domains: an amino-terminal γ-carboxyglutamic acid-rich region of 37 amino acids; a 36 amino acid linker region rich in hydroxy amino acids; four epidermal growth factor-like segments, each ≅ 45 amino acids long; and a 387 amino acid carboxyl-terminal domain of unrecognized structure and unknown function

  19. Segmentation of tumor ultrasound image in HIFU therapy based on texture and boundary encoding

    International Nuclear Information System (INIS)

    Zhang, Dong; Xu, Menglong; Quan, Long; Yang, Yan; Qin, Qianqing; Zhu, Wenbin

    2015-01-01

    It is crucial in high intensity focused ultrasound (HIFU) therapy to detect the tumor precisely with less manual intervention for enhancing the therapy efficiency. Ultrasound image segmentation becomes a difficult task due to signal attenuation, speckle effect and shadows. This paper presents an unsupervised approach based on texture and boundary encoding customized for ultrasound image segmentation in HIFU therapy. The approach oversegments the ultrasound image into some small regions, which are merged by using the principle of minimum description length (MDL) afterwards. Small regions belonging to the same tumor are clustered as they preserve similar texture features. The mergence is completed by obtaining the shortest coding length from encoding textures and boundaries of these regions in the clustering process. The tumor region is finally selected from merged regions by a proposed algorithm without manual interaction. The performance of the method is tested on 50 uterine fibroid ultrasound images from HIFU guiding transducers. The segmentations are compared with manual delineations to verify its feasibility. The quantitative evaluation with HIFU images shows that the mean true positive of the approach is 93.53%, the mean false positive is 4.06%, the mean similarity is 89.92%, the mean norm Hausdorff distance is 3.62% and the mean norm maximum average distance is 0.57%. The experiments validate that the proposed method can achieve favorable segmentation without manual initialization and effectively handle the poor quality of the ultrasound guidance image in HIFU therapy, which indicates that the approach is applicable in HIFU therapy. (paper)

  20. Segmentation of tumor ultrasound image in HIFU therapy based on texture and boundary encoding

    Science.gov (United States)

    Zhang, Dong; Xu, Menglong; Quan, Long; Yang, Yan; Qin, Qianqing; Zhu, Wenbin

    2015-02-01

    It is crucial in high intensity focused ultrasound (HIFU) therapy to detect the tumor precisely with less manual intervention for enhancing the therapy efficiency. Ultrasound image segmentation becomes a difficult task due to signal attenuation, speckle effect and shadows. This paper presents an unsupervised approach based on texture and boundary encoding customized for ultrasound image segmentation in HIFU therapy. The approach oversegments the ultrasound image into some small regions, which are merged by using the principle of minimum description length (MDL) afterwards. Small regions belonging to the same tumor are clustered as they preserve similar texture features. The mergence is completed by obtaining the shortest coding length from encoding textures and boundaries of these regions in the clustering process. The tumor region is finally selected from merged regions by a proposed algorithm without manual interaction. The performance of the method is tested on 50 uterine fibroid ultrasound images from HIFU guiding transducers. The segmentations are compared with manual delineations to verify its feasibility. The quantitative evaluation with HIFU images shows that the mean true positive of the approach is 93.53%, the mean false positive is 4.06%, the mean similarity is 89.92%, the mean norm Hausdorff distance is 3.62% and the mean norm maximum average distance is 0.57%. The experiments validate that the proposed method can achieve favorable segmentation without manual initialization and effectively handle the poor quality of the ultrasound guidance image in HIFU therapy, which indicates that the approach is applicable in HIFU therapy.

  1. Glucose Administration Enhances fMRI Brain Activation and Connectivity Related to Episodic Memory Encoding for Neutral and Emotional Stimuli

    Science.gov (United States)

    Parent, Marise B.; Krebs-Kraft, Desiree L.; Ryan, John P.; Wilson, Jennifer S.; Harenski, Carla; Hamann, Stephan

    2011-01-01

    Glucose enhances memory in a variety of species. In humans, glucose administration enhances episodic memory encoding, although little is known regarding the neural mechanisms underlying these effects. Here we examined whether elevating blood glucose would enhance functional MRI (fMRI) activation and connectivity in brain regions associated with…

  2. Mutations in the gene encoding epsilon-sarcoglycan cause myoclonus-dystonia syndrome.

    Science.gov (United States)

    Zimprich, A; Grabowski, M; Asmus, F; Naumann, M; Berg, D; Bertram, M; Scheidtmann, K; Kern, P; Winkelmann, J; Müller-Myhsok, B; Riedel, L; Bauer, M; Müller, T; Castro, M; Meitinger, T; Strom, T M; Gasser, T

    2001-09-01

    The dystonias are a common clinically and genetically heterogeneous group of movement disorders. More than ten loci for inherited forms of dystonia have been mapped, but only three mutated genes have been identified so far. These are DYT1, encoding torsin A and mutant in the early-onset generalized form, GCH1 (formerly known as DYT5), encoding GTP-cyclohydrolase I and mutant in dominant dopa-responsive dystonia, and TH, encoding tyrosine hydroxylase and mutant in the recessive form of the disease. Myoclonus-dystonia syndrome (MDS; DYT11) is an autosomal dominant disorder characterized by bilateral, alcohol-sensitive myoclonic jerks involving mainly the arms and axial muscles. Dystonia, usually torticollis and/or writer's cramp, occurs in most but not all affected patients and may occasionally be the only symptom of the disease. In addition, patients often show prominent psychiatric abnormalities, including panic attacks and obsessive-compulsive behavior. In most MDS families, the disease is linked to a locus on chromosome 7q21 (refs. 11-13). Using a positional cloning approach, we have identified five different heterozygous loss-of-function mutations in the gene for epsilon-sarcoglycan (SGCE), which we mapped to a refined critical region of about 3.2 Mb. SGCE is expressed in all brain regions examined. Pedigree analysis shows a marked difference in penetrance depending on the parental origin of the disease allele. This is indicative of a maternal imprinting mechanism, which has been demonstrated in the mouse epsilon-sarcoglycan gene.

  3. Reward modulation of hippocampal subfield activation during successful associative encoding and retrieval

    Science.gov (United States)

    Wolosin, Sasha M.; Zeithamova, Dagmar; Preston, Alison R.

    2012-01-01

    Emerging evidence suggests that motivation enhances episodic memory formation through interactions between medial temporal lobe (MTL) structures and dopaminergic midbrain. In addition, recent theories propose that motivation specifically facilitates hippocampal associative binding processes, resulting in more detailed memories that are readily reinstated from partial input. Here, we used high-resolution functional magnetic resonance imaging to determine how motivation influences associative encoding and retrieval processes within human MTL subregions and dopaminergic midbrain. Participants intentionally encoded object associations under varying conditions of reward and performed a retrieval task during which studied associations were cued from partial input. Behaviorally, cued recall performance was superior for high-value relative to low-value associations; however, participants differed in the degree to which rewards influenced memory. The magnitude of behavioral reward modulation was associated with reward-related activation changes in dentate gyrus/CA2,3 during encoding and enhanced functional connectivity between dentate gyrus/CA2,3 and dopaminergic midbrain during both the encoding and retrieval phases of the task. These findings suggests that within the hippocampus, reward-based motivation specifically enhances dentate gyrus/CA2,3 associative encoding mechanisms through interactions with dopaminergic midbrain. Furthermore, within parahippocampal cortex and dopaminergic midbrain regions, activation associated with successful memory formation was modulated by reward across the group. During the retrieval phase, we also observed enhanced activation in hippocampus and dopaminergic midbrain for high-value associations that occurred in the absence of any explicit cues to reward. Collectively, these findings shed light on fundamental mechanisms through which reward impacts associative memory formation and retrieval through facilitation of MTL and VTA/SN processing

  4. Complete Nucleotide Sequences of Two VIM-1-Encoding Plasmids from Klebsiella pneumoniae and Leclercia adecarboxylata Isolates of Czech Origin.

    Science.gov (United States)

    Papousek, Ivo; Papagiannitsis, Costas C; Medvecky, Matej; Hrabak, Jaroslav; Dolejska, Monika

    2017-05-01

    Two multidrug resistance (MDR) plasmids, carrying the VIM-1-encoding integron In110, were characterized. Plasmid pLec-476cz (311,758 bp), from a Leclercia adecarboxylata isolate, consisted of an IncHI1 backbone, a MDR region, and two accessory elements. Plasmid pKpn-431cz (142,876 bp), from a sequence type 323 (ST323) Klebsiella pneumoniae isolate, comprised IncFII Y -derived and pKPN3-like sequences and a mosaic region. A 40,400-bp sequence of pKpn-431cz was identical to the MDR region of pLec-476cz, indicating the en bloc acquisition of the VIM-1-encoding region from one plasmid by the other. Copyright © 2017 American Society for Microbiology.

  5. Development of a reflective optical encoder with submicron accuracy

    Science.gov (United States)

    Ye, Guoyong; Liu, Hongzhong; Ban, Yaowen; Shi, Yongsheng; Yin, Lei; Lu, Bingheng

    2018-03-01

    Signal distortion is a key issue that limits the measurement resolution and accuracy of optical encoders. In this paper, an optical encoder based on generalized grating imaging using a two-dimensional index grating is presented. The general expression of intensity distribution for generalized grating imaging including the relative displacement between the scale grating and the reading head is derived, and the formation of the signal distortion of the optical encoder is analyzed. Then, a two-dimensional index grating, which consists of multiple grating tracks with defined offsets, is proposed to suppress the dominant third and fifth order harmonic signals. The operating principle of the two-dimensional index grating is explained in detail and a reflective optical encoder is developed. In the experiment, approximately ideal Lissajous figure of the encoder signals is obtained. Fourier analysis of the encoder signals shows that both the third and fifth order harmonic distortions are below 0.6%. Experimental results show that the interpolation error of the optical encoder is within ± 0 . 18 μm, and the accuracy is better than ± 0 . 3 μm over 255 mm travel range with a maximum variation of 0.136 μm.

  6. High-Efficient Parallel CAVLC Encoders on Heterogeneous Multicore Architectures

    Directory of Open Access Journals (Sweden)

    H. Y. Su

    2012-04-01

    Full Text Available This article presents two high-efficient parallel realizations of the context-based adaptive variable length coding (CAVLC based on heterogeneous multicore processors. By optimizing the architecture of the CAVLC encoder, three kinds of dependences are eliminated or weaken, including the context-based data dependence, the memory accessing dependence and the control dependence. The CAVLC pipeline is divided into three stages: two scans, coding, and lag packing, and be implemented on two typical heterogeneous multicore architectures. One is a block-based SIMD parallel CAVLC encoder on multicore stream processor STORM. The other is a component-oriented SIMT parallel encoder on massively parallel architecture GPU. Both of them exploited rich data-level parallelism. Experiments results show that compared with the CPU version, more than 70 times of speedup can be obtained for STORM and over 50 times for GPU. The implementation of encoder on STORM can make a real-time processing for 1080p @30fps and GPU-based version can satisfy the requirements for 720p real-time encoding. The throughput of the presented CAVLC encoders is more than 10 times higher than that of published software encoders on DSP and multicore platforms.

  7. Datacube Interoperability, Encoding Independence, and Analytics

    Science.gov (United States)

    Baumann, Peter; Hirschorn, Eric; Maso, Joan

    2017-04-01

    representations. Further, CIS 1.1 offers a unified model for any kind of regular and irregular grids, also allowing sensor models as per SensorML. Encodings include ASCII formats like GML, JSON, RDF as well as binary formats like GeoTIFF, NetCDF, JPEG2000, and GRIB2; further, a container concept allows mixed representations within one coverage file utilizing zip or other convenient package formats. Through the tight integration with the Sensor Web Enablement (SWE), a lossless "transport" from sensor into coverage world is ensured. The corresponding service model of WCS supports datacube operations ranging from simple data extraction to complex ad-hoc analytics with WPCS. Notably, W3C is working has set out on a coverage model as well; it has been designed relatively independently from the abovementioned standards, but there is informal agreement to link it into the CIS universe (which allows for different, yet interchangeable representations). Particularly interesting in the W3C proposal is the detailed semantic modeling of metadata; as CIS 1.1 supports RDF, a tight coupling seems feasible.

  8. Wavelength-encoded OCDMA system using opto-VLSI processors

    Science.gov (United States)

    Aljada, Muhsen; Alameh, Kamal

    2007-07-01

    We propose and experimentally demonstrate a 2.5 Gbits/sper user wavelength-encoded optical code-division multiple-access encoder-decoder structure based on opto-VLSI processing. Each encoder and decoder is constructed using a single 1D opto-very-large-scale-integrated (VLSI) processor in conjunction with a fiber Bragg grating (FBG) array of different Bragg wavelengths. The FBG array spectrally and temporally slices the broadband input pulse into several components and the opto-VLSI processor generates codewords using digital phase holograms. System performance is measured in terms of the autocorrelation and cross-correlation functions as well as the eye diagram.

  9. pENCODE: a plant encyclopedia of DNA elements.

    Science.gov (United States)

    Lane, Amanda K; Niederhuth, Chad E; Ji, Lexiang; Schmitz, Robert J

    2014-01-01

    ENCODE projects exist for many eukaryotes, including humans, but as of yet no defined project exists for plants. A plant ENCODE would be invaluable to the research community and could be more readily produced than its metazoan equivalents by capitalizing on the preexisting infrastructure provided from similar projects. Collecting and normalizing plant epigenomic data for a range of species will facilitate hypothesis generation, cross-species comparisons, annotation of genomes, and an understanding of epigenomic functions throughout plant evolution. Here, we discuss the need for such a project, outline the challenges it faces, and suggest ways forward to build a plant ENCODE.

  10. Integrated source and channel encoded digital communications system design study

    Science.gov (United States)

    Huth, G. K.

    1974-01-01

    Studies on the digital communication system for the direct communication links from ground to space shuttle and the links involving the Tracking and Data Relay Satellite (TDRS). Three main tasks were performed:(1) Channel encoding/decoding parameter optimization for forward and reverse TDRS links,(2)integration of command encoding/decoding and channel encoding/decoding; and (3) modulation coding interface study. The general communication environment is presented to provide the necessary background for the tasks and to provide an understanding of the implications of the results of the studies.

  11. Wavelength-encoded OCDMA system using opto-VLSI processors.

    Science.gov (United States)

    Aljada, Muhsen; Alameh, Kamal

    2007-07-01

    We propose and experimentally demonstrate a 2.5 Gbits/sper user wavelength-encoded optical code-division multiple-access encoder-decoder structure based on opto-VLSI processing. Each encoder and decoder is constructed using a single 1D opto-very-large-scale-integrated (VLSI) processor in conjunction with a fiber Bragg grating (FBG) array of different Bragg wavelengths. The FBG array spectrally and temporally slices the broadband input pulse into several components and the opto-VLSI processor generates codewords using digital phase holograms. System performance is measured in terms of the autocorrelation and cross-correlation functions as well as the eye diagram.

  12. Latency Performance of Encoding with Random Linear Network Coding

    DEFF Research Database (Denmark)

    Nielsen, Lars; Hansen, René Rydhof; Lucani Rötter, Daniel Enrique

    2018-01-01

    In this paper, we present a performance study of the impact of generation and symbol sizes on latency for encoding with Random Linear Network Coding (RLNC). This analysis is important for low latency applications of RLNC as well as data storage applications that use large blocks of data, where...... the encoding process can be parallelized based on system requirements to reduce data access time within the system. Using a counting argument, we focus on predicting the effect of changes of generation (number of original packets) and symbol size (number of bytes per data packet) configurations on the encoding...

  13. Isolation and sequence analysis of the gene encoding triose phosphate isomerase from Zygosaccharomyces bailii.

    Science.gov (United States)

    Merico, A; Rodrigues, F; Côrte-Real, M; Porro, D; Ranzi, B M; Compagno, C

    2001-06-30

    The ZbTPI1 gene encoding triose phosphate isomerase (TIM) was cloned from a Zygosaccharomyces bailii genomic library by complementation of the Saccharomyces cerevisiae tpi1 mutant strain. The nucleotide sequence of a 1.5 kb fragment showed an open reading frame (ORF) of 746 bp, encoding a protein of 248 amino acid residues. The deduced amino acid sequence shares a high degree of homology with TIMs from other yeast species, including some highly conserved regions. The analysis of the promoter sequence of the ZbTPI1 revealed the presence of putative motifs known to have regulatory functions in S. cerevisiae. The GenBank Accession No. of ZbTPI1 is AF325852. Copyright 2001 John Wiley & Sons, Ltd.

  14. Molecular cloning and chromosome mapping of the human gene encoding protein phosphotyrosyl phosphatase 1B

    International Nuclear Information System (INIS)

    Brown-Shimer, S.; Johnson, K.A.; Bruskin, A.; Green, N.R.; Hill, D.E.; Lawrence, J.B.; Johnson, C.

    1990-01-01

    The inactivation of growth suppressor genes appears to play a major role in the malignant process. To assess whether protein phosphotyrosyl phosphatases function as growth suppressors, the authors have isolated a cDNA clone encoding human protein phosphotyrosyl phosphatase 1B for structural and functional characterization. The translation product deduced from the 1,305-nucleotide open reading frame predicts a protein containing 435 amino acids and having a molecular mass of 49,966 Da. The amino-terminal 321 amino acids deduced from the cDNA sequence are identical to the empirically determined sequence of protein phosphotyrosyl phosphatase 1B. A genomic clone has been isolated and used in an in situ hybridization to banded metaphase chromosomes to determine that the gene encoding protein phosphotyrosyl phosphatase 1B maps as a single-copy gene to the long arm of chromosome 20 in the region q13.1-q13.2

  15. The gene encoding topoisomerase I from the human malaria parasite Plasmodium falciparum.

    Science.gov (United States)

    Tosh, K; Kilbey, B

    1995-09-22

    Part of the topoisomerase I (TopoI)-encoding gene from Plasmodium falciparum (Pf) was isolated by PCR from cDNA using oligodeoxyribonucleotides modelled on the highly conserved regions of sequence from other species. The entire TopoI gene was obtained by screening a Pf K1 HindIII-EcoRI genomic library in lambda NM1149 with a random-labeled heterologous probe from the Saccharomyces cerevisiae TopoI gene. DNA sequence analysis revealed an open reading frame of 2520 nt encoding a deduced protein of 839 amino acids (aa) with no detectable introns. The Pf TopoI aa sequence has about 40% identity with most eukaryotic TopoI homologues. The gene is located as a single copy on chromosome 5 and Northern analysis identified a transcript of 3.8 kb.

  16. IQCJ-SCHIP1, a novel fusion transcript encoding a calmodulin-binding IQ motif protein

    International Nuclear Information System (INIS)

    Kwasnicka-Crawford, Dorota A.; Carson, Andrew R.; Scherer, Stephen W.

    2006-01-01

    The existence of transcripts that span two adjacent, independent genes is considered rare in the human genome. This study characterizes a novel human fusion gene named IQCJ-SCHIP1. IQCJ-SCHIP1 is the longest isoform of a complex transcriptional unit that bridges two separate genes that encode distinct proteins, IQCJ, a novel IQ motif containing protein and SCHIP1, a schwannomin interacting protein that has been previously shown to interact with the Neurofibromatosis type 2 (NF2) protein. IQCJ-SCHIP1 is located on the chromosome 3q25 and comprises a 1692-bp transcript encompassing 11 exons spanning 828 kb of the genomic DNA. We show that IQCJ-SCHIP1 mRNA is highly expressed in the brain. Protein encoded by the IQCJ-SCHIP1 gene was localized to cytoplasm and actin-rich regions and in differentiated PC12 cells was also seen in neurite extensions

  17. Led into temptation? Rewarding brand logos bias the neural encoding of incidental economic decisions.

    Directory of Open Access Journals (Sweden)

    Carsten Murawski

    Full Text Available Human decision-making is driven by subjective values assigned to alternative choice options. These valuations are based on reward cues. It is unknown, however, whether complex reward cues, such as brand logos, may bias the neural encoding of subjective value in unrelated decisions. In this functional magnetic resonance imaging (fMRI study, we subliminally presented brand logos preceding intertemporal choices. We demonstrated that priming biased participants' preferences towards more immediate rewards in the subsequent temporal discounting task. This was associated with modulations of the neural encoding of subjective values of choice options in a network of brain regions, including but not restricted to medial prefrontal cortex. Our findings demonstrate the general susceptibility of the human decision making system to apparently incidental contextual information. We conclude that the brain incorporates seemingly unrelated value information that modifies decision making outside the decision-maker's awareness.

  18. Led into temptation? Rewarding brand logos bias the neural encoding of incidental economic decisions.

    Science.gov (United States)

    Murawski, Carsten; Harris, Philip G; Bode, Stefan; Domínguez D, Juan F; Egan, Gary F

    2012-01-01

    Human decision-making is driven by subjective values assigned to alternative choice options. These valuations are based on reward cues. It is unknown, however, whether complex reward cues, such as brand logos, may bias the neural encoding of subjective value in unrelated decisions. In this functional magnetic resonance imaging (fMRI) study, we subliminally presented brand logos preceding intertemporal choices. We demonstrated that priming biased participants' preferences towards more immediate rewards in the subsequent temporal discounting task. This was associated with modulations of the neural encoding of subjective values of choice options in a network of brain regions, including but not restricted to medial prefrontal cortex. Our findings demonstrate the general susceptibility of the human decision making system to apparently incidental contextual information. We conclude that the brain incorporates seemingly unrelated value information that modifies decision making outside the decision-maker's awareness.

  19. Stimulus-invariant auditory cortex threat encoding during fear conditioning with simple and complex sounds.

    Science.gov (United States)

    Staib, Matthias; Bach, Dominik R

    2018-02-01

    Learning to predict threat depends on amygdala plasticity and does not require auditory cortex (ACX) when threat predictors (conditioned stimuli, CS) are simple sine tones. However, ACX is required in rodents to learn from some naturally occurring CS. Yet, the precise function of ACX, and whether it differs for different CS types, is unknown. Here, we address how ACX encodes threat predictions during human fear conditioning using functional magnetic resonance imaging (fMRI) with multivariate pattern analysis. As in previous rodent work, CS+ and CS- were defined either by direction of frequency modulation (complex) or by frequency of pure tones (simple). In an instructed non-reinforcement context, different sets of simple and complex sounds were always presented without reinforcement (neutral sounds, NS). Threat encoding was measured by separation of fMRI response patterns induced by CS+/CS-, or similar NS1/NS2 pairs. We found that fMRI patterns in Heschl's gyrus encoded threat prediction over and above encoding the physical stimulus features also present in NS, i.e. CS+/CS- could be separated better than NS1/NS2. This was the case both for simple and complex CS. Furthermore, cross-prediction demonstrated that threat representations were similar for simple and complex CS, and thus unlikely to emerge from stimulus-specific top-down, or learning-induced, receptive field plasticity. Searchlight analysis across the entire ACX demonstrated further threat representations in a region including BA22 and BA42. However, in this region, patterns were distinct for simple and complex sounds, and could thus potentially arise from receptive field plasticity. Strikingly, across participants, individual size of Heschl's gyrus predicted strength of fear learning for complex sounds. Overall, our findings suggest that ACX represents threat predictions, and that Heschl's gyrus contains a threat representation that is invariant across physical stimulus categories. Copyright © 2017 The

  20. The Drosophila homologue of vertebrate myogenic-determination genes encodes a transiently expressed nuclear protein marking primary myogenic cells.

    OpenAIRE

    Paterson, B M; Walldorf, U; Eldridge, J; Dübendorfer, A; Frasch, M; Gehring, W J

    1991-01-01

    We have isolated a cDNA clone, called Dmyd for Drosophila myogenic-determination gene, that encodes a protein with structural and functional characteristics similar to the members of the vertebrate MyoD family. Dmyd clone encodes a polypeptide of 332 amino acids with 82% identity to MyoD in the 41 amino acids of the putative helix-loop-helix region and 100% identity in the 13 amino acids of the basic domain proposed to contain the essential recognition code for muscle-specific gene activation...

  1. Effects of modality on the neural correlates of encoding processes supporting recollection and familiarity

    Science.gov (United States)

    Gottlieb, Lauren J.; Rugg, Michael D.

    2011-01-01

    Prior research has demonstrated that the neural correlates of successful encoding (“subsequent memory effects”) partially overlap with neural regions selectively engaged by the on-line demands of the study task. The primary goal of the present experiment was to determine whether this overlap is associated solely with encoding processes supporting later recollection, or whether overlapping subsequent memory and study condition effects are also evident when later memory is familiarity-based. Subjects (N = 17) underwent fMRI scanning while studying a series of visually and auditorily presented words. Memory for the words was subsequently tested with a modified Remember/Know procedure. Auditorily selective subsequent familiarity effects were evident in bilateral temporal regions that also responded preferentially to auditory items. Although other interpretations are possible, these findings suggest that overlap between study condition-selective subsequent memory effects and regions selectively sensitive to study demands is not uniquely associated with later recollection. In addition, modality-independent subsequent memory effects were identified in several cortical regions. In every case, the effects were greatest for later recollected items, and smaller for items later recognized on the basis of familiarity. The implications of this quantitative dissociation for dual-process models of recognition memory are discussed. PMID:21852431

  2. Universal Quantum Computing with Arbitrary Continuous-Variable Encoding.

    Science.gov (United States)

    Lau, Hoi-Kwan; Plenio, Martin B

    2016-09-02

    Implementing a qubit quantum computer in continuous-variable systems conventionally requires the engineering of specific interactions according to the encoding basis states. In this work, we present a unified formalism to conduct universal quantum computation with a fixed set of operations but arbitrary encoding. By storing a qubit in the parity of two or four qumodes, all computing processes can be implemented by basis state preparations, continuous-variable exponential-swap operations, and swap tests. Our formalism inherits the advantages that the quantum information is decoupled from collective noise, and logical qubits with different encodings can be brought to interact without decoding. We also propose a possible implementation of the required operations by using interactions that are available in a variety of continuous-variable systems. Our work separates the "hardware" problem of engineering quantum-computing-universal interactions, from the "software" problem of designing encodings for specific purposes. The development of quantum computer architecture could hence be simplified.

  3. Polypeptides having catalase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Duan, Junxin; Zhang, Yu; Tang, Lan

    2017-05-02

    Provided are isolated polypeptides having catalase activity and polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Statistical Characterization of MP3 Encoders for Steganalysis: 'CHAMP3'

    National Research Council Canada - National Science Library

    Westfeld, Andreas

    2004-01-01

    ...). As detailed in the technical proposal the research consists of three parts. The first task is to survey the discipline to identify the available MP3 encoders and generate a data pool for analysis...

  5. Two Genes Encoding Uracil Phosphoribosyltransferase Are Present in Bacillus subtilis

    DEFF Research Database (Denmark)

    Martinussen, Jan; Glaser, Philippe; Andersen, Paal S.

    1995-01-01

    Uracil phosphoribosyltransferase (UPRTase) catalyzes the key reaction in the salvage of uracil in many microorganisms. Surprisingly, two genes encoding UPRTase activity were cloned from Bacillus subtilis by complementation of an Escherichia coli mutant. The genes were sequenced, and the putative...

  6. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Science.gov (United States)

    Spodsberg, Nikolaj

    2015-07-14

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  7. Noise and neuronal populations conspire to encode simple waveforms reliably

    Science.gov (United States)

    Parnas, B. R.

    1996-01-01

    Sensory systems rely on populations of neurons to encode information transduced at the periphery into meaningful patterns of neuronal population activity. This transduction occurs in the presence of intrinsic neuronal noise. This is fortunate. The presence of noise allows more reliable encoding of the temporal structure present in the stimulus than would be possible in a noise-free environment. Simulations with a parallel model of signal processing at the auditory periphery have been used to explore the effects of noise and a neuronal population on the encoding of signal information. The results show that, for a given set of neuronal modeling parameters and stimulus amplitude, there is an optimal amount of noise for stimulus encoding with maximum fidelity.

  8. Hybrid polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Shaghasi, Tarana

    2016-11-01

    The present invention provides hybrid polypeptides having cellobiohydrolase activity. The present invention also provides polynucleotides encoding the hybrid polypeptides; nucleic acid constructs, vectors and host cells comprising the polynucleotides; and processes of using the hybrid polypeptides.

  9. Polypeptides having beta-xylosidase activity and polynucleotides encoding same

    Science.gov (United States)

    Liu, Ye; Tang, Lan; Zhang, Yu; Duan, Junxin

    2017-04-18

    Provided are isolated polypeptides having beta-xylosidase activity and polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Duan, Junxin; Zhang, Yu; Tang, Lan

    2017-09-26

    Provided are isolated polypeptides having beta-glucosidase activity and polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  11. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2016-06-28

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2016-12-13

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2017-11-21

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Liu, Ye; Duan, Junxin; Tang, Lan

    2017-07-18

    Provided are isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  15. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Science.gov (United States)

    Spodsberg, Nikolaj

    2015-11-17

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  16. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Tang, Lan; Henriksen, Svend Hostgaard Bang

    2016-05-17

    The present invention provides isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polypeptides having xylanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2017-05-02

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  18. Polypeptides having cellobiohydrolase activitiy and polynucleotides encoding same

    Science.gov (United States)

    Liu, Ye; Tang, Lan; Duan, Junxin

    2015-12-15

    The present invention provides isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  19. Polypeptides having xylanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2018-02-06

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Isolated menthone reductase and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  1. Spatial working memory encoding type modulates prefrontal cortical activity.

    Science.gov (United States)

    Oi, Yuhei; Kita, Yosuke; Suzuki, Kota; Okumura, Yasuko; Okuzumi, Hideyuki; Shinoda, Haruo; Inagaki, Masumi

    2017-05-03

    Spatial working memory (SWM) involves both simultaneous and sequential encoding, but the differences in their neural correlates are unclear. We investigated the differences in prefrontal cortex activity related to these SWM encoding types. We also examined the patterns of brain activity influencing individual visuospatial abilities (VSA). We conducted SWM tasks with two different conditions, sequential and simultaneous encoding, and examined hemodynamic activity in 39 healthy adults using near-infrared spectroscopy. The bilateral dorsolateral prefrontal cortex was activated more strongly in the sequential condition compared with the simultaneous condition. This suggests that prefrontal cortex activity underlying SWM is modulated by the type of encoding. We also found that individuals with high VSA showed weaker activation in the right-dorsolateral prefrontal cortex compared with those with lower VSA during the simultaneous condition. This hypoactivation is thought to reflect neural efficiency in the individuals with high ability. These findings are expected to lead to a better understanding of neural substrates for SWM.

  2. Multiple-stage pure phase encoding with biometric information

    Science.gov (United States)

    Chen, Wen

    2018-01-01

    In recent years, many optical systems have been developed for securing information, and optical encryption/encoding has attracted more and more attention due to the marked advantages, such as parallel processing and multiple-dimensional characteristics. In this paper, an optical security method is presented based on pure phase encoding with biometric information. Biometric information (such as fingerprint) is employed as security keys rather than plaintext used in conventional optical security systems, and multiple-stage phase-encoding-based optical systems are designed for generating several phase-only masks with biometric information. Subsequently, the extracted phase-only masks are further used in an optical setup for encoding an input image (i.e., plaintext). Numerical simulations are conducted to illustrate the validity, and the results demonstrate that high flexibility and high security can be achieved.

  3. Neonatal intramuscular injection of plasmid encoding glucagon-like ...

    Indian Academy of Sciences (India)

    Prakash

    -A) was significantly elevated in GP rats. These results suggest that neonatal intramuscular injection of plasmid DNA encoding GLP-1 affects anxiety behaviour in adolescent rats, probably through NGFI-A-activated upregulation of hippocampal ...

  4. Perbandingan Kinerja Algoritma Fixed Length Binary Encoding (FLBE) Dengan Variable Length Binary Encoding (VLBE) Dalam Kompresi Text File

    OpenAIRE

    Viliana, Debora

    2014-01-01

    This study aims to design a computer application that can compress text files and compare the performance of the algorithm. Compression is done with a text file using a text encoding algorithms Fixed Length Binary Encoding (FLBE) and Variable Length Binary Encoding algorithm, then do the compression process.The end result are a compression of the file extension *. flbe and *.vlbe which can be decompressed. The output of the decompression is a new file that consists of a file header and body f...

  5. Encoding of aversion by dopamine and the nucleus accumbens

    Directory of Open Access Journals (Sweden)

    James Edgar Mccutcheon

    2012-09-01

    Full Text Available Adaptive motivated behavior requires rapid discrimination between beneficial and harmful stimuli. Such discrimination leads to the generation of either an approach or rejection response, as appropriate, and enables organisms to maximize reward and minimize punishment. Classically, the nucleus accumbens (NAc and the dopamine projection to it are considered an integral part of the brain’s reward circuit, i.e., they direct approach and consumption behaviors and underlie positive reinforcement. This reward-centered framing ignores important evidence about the role of this system in encoding aversive events. One reason for bias towards reward is the difficulty in designing experiments in which animals repeatedly experience punishments; another is the challenge in dissociating the response to an aversive stimulus itself from the reward/relief experienced when an aversive stimulus is terminated. Here, we review studies that employ techniques with sufficient time resolution to measure responses in ventral tegmental area (VTA and NAc to aversive stimuli as they are delivered. We also present novel findings showing that the same stimulus – intraoral infusion of sucrose – has differing effects on NAc shell dopamine release depending on the prior experience. Here, for some rats, sucrose was rendered aversive by explicitly pairing it with malaise in a conditioned taste aversion paradigm. Thereafter, sucrose infusions led to a suppression of dopamine with a similar magnitude and time course to intra-oral infusions of a bitter quinine solution. The results are discussed in the context of regional differences in dopamine signaling and the implications of a pause in phasic dopamine release within the NAc shell. Together with our data, the emerging literature suggests an important role for differential phasic dopamine signaling in aversion versus reward.

  6. Data encoding using periodic nano-optical features

    OpenAIRE

    Vosoogh-Grayli, Siamack

    2012-01-01

    Successful trials have been made through a designed algorithm to quantize, compress and optically encode unsigned 8 bit integer values in the form of images using Nano optical features. The periodicity of the Nano-scale features (Nano-gratings) have been designed and investigated both theoretically and experimentally to create distinct states of variation (three on states and one off state). The use of easy to manufacture and machine readable encoded data in secured authentication media has b...

  7. Hybrid image encoding based on wavelet transform and DPCM

    Science.gov (United States)

    Tian, Jinwen; Liu, Bin; Liu, Jianguo

    1998-09-01

    In this paper, our purposes are image compression code by wavelet transformation, and develop a novel encoding algorithm structure of DPCM/WT on the basis of the DPCM/DCT. We have proposed a new encoding algorithm structure of DPCM/WT based on object driving and data flow driving, the novel algorithm in property is superior to DPCM/DCT in compression ratio, fidelity and real time processing.

  8. Permutations as a means to encode order in word space

    OpenAIRE

    Sahlgren, Magnus; Holst, Anders; Kanerva, Pentti

    2008-01-01

    We show that sequence information can be encoded into high-dimensional fixed-width vectors using permutations of coordinates. Computational models of language often represent words with high-dimensional semantic vectors compiled from word-use statistics. A word's semantic vector usually encodes the contexts in which the word appears in a large body of text but ignores word order. However, word order often signals a word's grammatical role in a sentence and thus tells of the word's meaning. Jo...

  9. An Optimal Dissipative Encoder for the Toric Code

    Science.gov (United States)

    2014-01-16

    corresponding Liouvillian is made up of four local Lindblad operators . For a qubit lattice of size L × L , we show that this process prepares encoded...this work may be used under the terms of the Creative Commons Attribution 3.0 licence . Any further distribution of this work must maintain attribution to...associated correction operations . For the toric code, an encoding procedure of this form was given [7]. It involves active error correction operations

  10. Mnemonic Encoding and Cortical Organization in Parietal and Prefrontal Cortices.

    Science.gov (United States)

    Masse, Nicolas Y; Hodnefield, Jonathan M; Freedman, David J

    2017-06-21

    Persistent activity within the frontoparietal network is consistently observed during tasks that require working memory. However, the neural circuit mechanisms underlying persistent neuronal encoding within this network remain unresolved. Here, we ask how neural circuits support persistent activity by examining population recordings from posterior parietal (PPC) and prefrontal (PFC) cortices in two male monkeys that performed spatial and motion direction-based tasks that required working memory. While spatially selective persistent activity was observed in both areas, robust selective persistent activity for motion direction was only observed in PFC. Crucially, we find that this difference between mnemonic encoding in PPC and PFC is associated with the presence of functional clustering: PPC and PFC neurons up to ∼700 μm apart preferred similar spatial locations, and PFC neurons up to ∼700 μm apart preferred similar motion directions. In contrast, motion-direction tuning similarity between nearby PPC neurons was much weaker and decayed rapidly beyond ∼200 μm. We also observed a similar association between persistent activity and functional clustering in trained recurrent neural network models embedded with a columnar topology. These results suggest that functional clustering facilitates mnemonic encoding of sensory information. SIGNIFICANCE STATEMENT Working memory refers to our ability to temporarily store and manipulate information. Numerous studies have observed that, during working memory, neurons in higher cortical areas, such as the parietal and prefrontal cortices, mnemonically encode the remembered stimulus. However, several recent studies have failed to observe mnemonic encoding during working memory, raising the question as to why mnemonic encoding is observed during some, but not all, conditions. In this study, we show that mnemonic encoding occurs when a cortical area is organized such that nearby neurons preferentially respond to the same

  11. Security enhanced BioEncoding for protecting iris codes

    Science.gov (United States)

    Ouda, Osama; Tsumura, Norimichi; Nakaguchi, Toshiya

    2011-06-01

    Improving the security of biometric template protection techniques is a key prerequisite for the widespread deployment of biometric technologies. BioEncoding is a recently proposed template protection scheme, based on the concept of cancelable biometrics, for protecting biometric templates represented as binary strings such as iris codes. The main advantage of BioEncoding over other template protection schemes is that it does not require user-specific keys and/or tokens during verification. Besides, it satisfies all the requirements of the cancelable biometrics construct without deteriorating the matching accuracy. However, although it has been shown that BioEncoding is secure enough against simple brute-force search attacks, the security of BioEncoded templates against more smart attacks, such as record multiplicity attacks, has not been sufficiently investigated. In this paper, a rigorous security analysis of BioEncoding is presented. Firstly, resistance of BioEncoded templates against brute-force attacks is revisited thoroughly. Secondly, we show that although the cancelable transformation employed in BioEncoding might be non-invertible for a single protected template, the original iris code could be inverted by correlating several templates used in different applications but created from the same iris. Accordingly, we propose an important modification to the BioEncoding transformation process in order to hinder attackers from exploiting this type of attacks. The effectiveness of adopting the suggested modification is validated and its impact on the matching accuracy is investigated empirically using CASIA-IrisV3-Interval dataset. Experimental results confirm the efficacy of the proposed approach and show that it preserves the matching accuracy of the unprotected iris recognition system.

  12. Molecular cloning and functional analysis of the gene encoding ...

    African Journals Online (AJOL)

    Here we report for the first time the cloning of a full-length cDNA encoding GGPPS (Jc-GGPPS) from Jatropha curcas L. The full-length cDNA was 1414 base pair (bp), with an 1110-bp open reading frame (ORF) encoding a 370- amino-acids polypeptide. Bioinformatic analysis revealed that Jc-GGPPS is a member of the ...

  13. Theory of multisource crosstalk reduction by phase-encoded statics

    KAUST Repository

    Schuster, Gerard T.

    2011-03-01

    Formulas are derived that relate the strength of the crosstalk noise in supergather migration images to the variance of time, amplitude and polarity shifts in encoding functions. A supergather migration image is computed by migrating an encoded supergather, where the supergather is formed by stacking a large number of encoded shot gathers. Analysis reveals that for temporal source static shifts in each shot gather, the crosstalk noise is exponentially reduced with increasing variance of the static shift and the square of source frequency. This is not too surprising because larger time shifts lead to less correlation between traces in different shot gathers, and so should tend to reduce the crosstalk noise. Analysis also reveals that combining both polarity and time statics is a superior encoding strategy compared to using either polarity statics or time statics alone. Signal-to-noise (SNR) estimates show that for a standard migration image and for an image computed by migrating a phase-encoded supergather; here, G is the number of traces in a shot gather, I is the number of stacking iterations in the supergather and S is the number of encoded/blended shot gathers that comprise the supergather. If the supergather can be uniformly divided up into Q unique sub-supergathers, then the resulting SNR of the final image is, which means that we can enhance image quality but at the expense of Q times more cost. The importance of these formulas is that they provide a precise understanding between different phase encoding strategies and image quality. Finally, we show that iterative migration of phase-encoded supergathers is a special case of passive seismic interferometry. We suggest that the crosstalk noise formulas can be helpful in designing optimal strategies for passive seismic interferometry and efficient extraction of Green\\'s functions from simulated supergathers. © 2011 The Authors Geophysical Journal International © 2011 RAS.

  14. The Encyclopedia of DNA elements (ENCODE): data portal update.

    Science.gov (United States)

    Davis, Carrie A; Hitz, Benjamin C; Sloan, Cricket A; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Hilton, Jason A; Jain, Kriti; Baymuradov, Ulugbek K; Narayanan, Aditi K; Onate, Kathrina C; Graham, Keenan; Miyasato, Stuart R; Dreszer, Timothy R; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest Y; Cherry, J Michael

    2018-01-04

    The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Secret key rates for an encoded quantum repeater

    Science.gov (United States)

    Bratzik, Sylvia; Kampermann, Hermann; Bruß, Dagmar

    2014-03-01

    We investigate secret key rates for the quantum repeater using encoding [L. Jiang et al., Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325] and compare them to the standard repeater scheme by Briegel, Dür, Cirac, and Zoller. The former scheme has the advantage of a minimal consumption of classical communication. We analyze the trade-off in the secret key rate between the communication time and the required resources. For this purpose we introduce an error model for the repeater using encoding which allows for input Bell states with a fidelity smaller than one, in contrast to the model given by L. Jiang et al. [Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325]. We show that one can correct additional errors in the encoded connection procedure of this repeater and develop a suitable decoding algorithm. Furthermore, we derive the rate of producing entangled pairs for the quantum repeater using encoding and give the minimal parameter values (gate quality and initial fidelity) for establishing a nonzero secret key. We find that the generic quantum repeater is optimal regarding the secret key rate per memory per second and show that the encoded quantum repeater using the simple three-qubit repetition code can even have an advantage with respect to the resources compared to other recent quantum repeater schemes with encoding.

  16. Analysis of Program Obfuscation Schemes with Variable Encoding Technique

    Science.gov (United States)

    Fukushima, Kazuhide; Kiyomoto, Shinsaku; Tanaka, Toshiaki; Sakurai, Kouichi

    Program analysis techniques have improved steadily over the past several decades, and software obfuscation schemes have come to be used in many commercial programs. A software obfuscation scheme transforms an original program or a binary file into an obfuscated program that is more complicated and difficult to analyze, while preserving its functionality. However, the security of obfuscation schemes has not been properly evaluated. In this paper, we analyze obfuscation schemes in order to clarify the advantages of our scheme, the XOR-encoding scheme. First, we more clearly define five types of attack models that we defined previously, and define quantitative resistance to these attacks. Then, we compare the security, functionality and efficiency of three obfuscation schemes with encoding variables: (1) Sato et al.'s scheme with linear transformation, (2) our previous scheme with affine transformation, and (3) the XOR-encoding scheme. We show that the XOR-encoding scheme is superior with regard to the following two points: (1) the XOR-encoding scheme is more secure against a data-dependency attack and a brute force attack than our previous scheme, and is as secure against an information-collecting attack and an inverse transformation attack as our previous scheme, (2) the XOR-encoding scheme does not restrict the calculable ranges of programs and the loss of efficiency is less than in our previous scheme.

  17. Low Complexity HEVC Encoder for Visual Sensor Networks

    Directory of Open Access Journals (Sweden)

    Zhaoqing Pan

    2015-12-01

    Full Text Available Visual sensor networks (VSNs can be widely applied in security surveillance, environmental monitoring, smart rooms, etc. However, with the increased number of camera nodes in VSNs, the volume of the visual information data increases significantly, which becomes a challenge for storage, processing and transmitting the visual data. The state-of-the-art video compression standard, high efficiency video coding (HEVC, can effectively compress the raw visual data, while the higher compression rate comes at the cost of heavy computational complexity. Hence, reducing the encoding complexity becomes vital for the HEVC encoder to be used in VSNs. In this paper, we propose a fast coding unit (CU depth decision method to reduce the encoding complexity of the HEVC encoder for VSNs. Firstly, the content property of the CU is analyzed. Then, an early CU depth decision method and a low complexity distortion calculation method are proposed for the CUs with homogenous content. Experimental results show that the proposed method achieves 71.91% on average encoding time savings for the HEVC encoder for VSNs.

  18. A deep learning method for lincRNA detection using auto-encoder algorithm.

    Science.gov (United States)

    Yu, Ning; Yu, Zeng; Pan, Yi

    2017-12-06

    RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions. The two evidences give the reasoning for adopting knowledge-based deep learning methods in lincRNA detection. Similar to coding region transcription, non-coding regions are split at transcriptional sites. However, regulatory RNAs rather than message RNAs are generated. That is, the transcribed RNAs participate the biological process as regulatory units instead of generating proteins. Identifying these transcriptional regions from non-coding regions is the first step towards lincRNA recognition. The auto-encoder method achieves 100% and 92.4% prediction accuracy on transcription sites over the putative data sets. The experimental results also show the excellent performance of predictive deep neural network on the lincRNA data sets compared with support vector machine and traditional neural network. In addition, it is validated through the newly discovered lincRNA data set and one unreported transcription site is found by feeding the whole annotated sequences through the deep learning machine, which indicates that deep learning method has the extensive ability for lincRNA prediction. The transcriptional sequences of lincRNAs are collected from the annotated human DNA genome data. Subsequently, a two-layer deep neural network is developed for the lincRNA detection, which adopts the auto-encoder algorithm and utilizes different encoding schemes to obtain the best performance over intergenic DNA sequence data. Driven by those newly

  19. TARM1 Is a Novel Leukocyte Receptor Complex-Encoded ITAM Receptor That Costimulates Proinflammatory Cytokine Secretion by Macrophages and Neutrophils

    DEFF Research Database (Denmark)

    Radjabova, Valeria; Mastroeni, Piero; Skjødt, Karsten

    2015-01-01

    We identified a novel, evolutionarily conserved receptor encoded within the human leukocyte receptor complex and syntenic region of mouse chromosome 7, named T cell-interacting, activating receptor on myeloid cells-1 (TARM1). The transmembrane region of TARM1 contained a conserved arginine residu...

  20. Effects of Age on Negative Subsequent Memory Effects Associated with the Encoding of Item and Item–Context Information

    Science.gov (United States)

    Mattson, Julia T.; Wang, Tracy H.; de Chastelaine, Marianne; Rugg, Michael D.

    2014-01-01

    It has consistently been reported that “negative” subsequent memory effects—lower study activity for later remembered than later forgotten items—are attenuated in older individuals. The present functional magnetic resonance imaging study investigated whether these findings extend to subsequent memory effects associated with successful encoding of item–context information. Older (n = 25) and young (n = 17) subjects were scanned while making 1 of 2 encoding judgments on a series of pictures. Memory was assessed for the study item and, for items judged old, the item's encoding task. Both memory judgments were made using confidence ratings, permitting item and source memory strength to be unconfounded and source confidence to be equated across age groups. Replicating prior findings, negative item effects in regions of the default mode network in young subjects were reversed in older subjects. Negative source effects, however, were invariant with respect to age and, in both age groups, the magnitude of the effects correlated with source memory performance. It is concluded that negative item effects do not reflect processes necessary for the successful encoding of item–context associations in older subjects. Negative source effects, in contrast, appear to reflect the engagement of processes that are equally important for successful episodic encoding in older and younger individuals. PMID:23904464

  1. Effects of age on negative subsequent memory effects associated with the encoding of item and item-context information.

    Science.gov (United States)

    Mattson, Julia T; Wang, Tracy H; de Chastelaine, Marianne; Rugg, Michael D

    2014-12-01

    It has consistently been reported that "negative" subsequent memory effects--lower study activity for later remembered than later forgotten items--are attenuated in older individuals. The present functional magnetic resonance imaging study investigated whether these findings extend to subsequent memory effects associated with successful encoding of item-context information. Older (n = 25) and young (n = 17) subjects were scanned while making 1 of 2 encoding judgments on a series of pictures. Memory was assessed for the study item and, for items judged old, the item's encoding task. Both memory judgments were made using confidence ratings, permitting item and source memory strength to be unconfounded and source confidence to be equated across age groups. Replicating prior findings, negative item effects in regions of the default mode network in young subjects were reversed in older subjects. Negative source effects, however, were invariant with respect to age and, in both age groups, the magnitude of the effects correlated with source memory performance. It is concluded that negative item effects do not reflect processes necessary for the successful encoding of item-context associations in older subjects. Negative source effects, in contrast, appear to reflect the engagement of processes that are equally important for successful episodic encoding in older and younger individuals. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. FMRI activity during associative encoding is correlated with cardiorespiratory fitness and source memory performance in older adults

    Science.gov (United States)

    Hayes, Scott M.; Hayes, Jasmeet P.; Williams, Victoria J.; Liu, Huiting; Verfaellie, Mieke

    2017-01-01

    Older adults (OA), relative to young adults (YA), exhibit age-related alterations in functional Magnetic Resonance Imaging (fMRI) activity during associative encoding, which contributes to deficits in source memory. Yet, there are remarkable individual differences in brain health and memory performance among OA. Cardiorespiratory fitness (CRF) is one individual difference factor that may attenuate brain aging, and thereby contribute to enhanced source memory in OA. To examine this possibility, 26 OA and 31 YA completed a treadmill-based exercise test to evaluate CRF (peak VO2) and fMRI to examine brain activation during a face-name associative encoding task. Our results indicated that in OA, peak VO2 was positively associated with fMRI activity during associative encoding in multiple regions including bilateral prefrontal cortex, medial frontal cortex, bilateral thalamus and left hippocampus. Next, a conjunction analysis was conducted to assess whether CRF influenced age-related differences in fMRI activation. We classified OA as high or low CRF and compared their activation to YA. High fit OA (HFOA) showed fMRI activation more similar to YA than low fit OA (LFOA) (i.e., reduced age-related differences) in multiple regions including thalamus, posterior and prefrontal cortex. Conversely, in other regions, primarily in prefrontal cortex, HFOA, but not LFOA, demonstrated greater activation than YA (i.e., increased age-related differences). Further, fMRI activity in these brain regions was positively associated with source memory among OA, with a mediation model demonstrating that associative encoding activation in medial frontal cortex indirectly influenced the relationship between peak VO2 and subsequent source memory performance. These results indicate that CRF may contribute to neuroplasticity among OA, reducing age-related differences in some brain regions, consistent with the brain maintenance hypothesis, but accentuating age-differences in other regions

  3. FMRI activity during associative encoding is correlated with cardiorespiratory fitness and source memory performance in older adults.

    Science.gov (United States)

    Hayes, Scott M; Hayes, Jasmeet P; Williams, Victoria J; Liu, Huiting; Verfaellie, Mieke

    2017-06-01

    Older adults (OA), relative to young adults (YA), exhibit age-related alterations in functional Magnetic Resonance Imaging (fMRI) activity during associative encoding, which contributes to deficits in source memory. Yet, there are remarkable individual differences in brain health and memory performance among OA. Cardiorespiratory fitness (CRF) is one individual difference factor that may attenuate brain aging, and thereby contribute to enhanced source memory in OA. To examine this possibility, 26 OA and 31 YA completed a treadmill-based exercise test to evaluate CRF (peak VO 2 ) and fMRI to examine brain activation during a face-name associative encoding task. Our results indicated that in OA, peak VO 2 was positively associated with fMRI activity during associative encoding in multiple regions including bilateral prefrontal cortex, medial frontal cortex, bilateral thalamus and left hippocampus. Next, a conjunction analysis was conducted to assess whether CRF influenced age-related differences in fMRI activation. We classified OA as high or low CRF and compared their activation to YA. High fit OA (HFOA) showed fMRI activation more similar to YA than low fit OA (LFOA) (i.e., reduced age-related differences) in multiple regions including thalamus, posterior and prefrontal cortex. Conversely, in other regions, primarily in prefrontal cortex, HFOA, but not LFOA, demonstrated greater activation than YA (i.e., increased age-related differences). Further, fMRI activity in these brain regions was positively associated with source memory among OA, with a mediation model demonstrating that associative encoding activation in medial frontal cortex indirectly influenced the relationship between peak VO 2 and subsequent source memory performance. These results indicate that CRF may contribute to neuroplasticity among OA, reducing age-related differences in some brain regions, consistent with the brain maintenance hypothesis, but accentuating age-differences in other regions

  4. Ready...go: Amplitude of the FMRI signal encodes expectation of cue arrival time.

    Directory of Open Access Journals (Sweden)

    Xu Cui

    2009-08-01

    Full Text Available What happens when the brain awaits a signal of uncertain arrival time, as when a sprinter waits for the starting pistol? And what happens just after the starting pistol fires? Using functional magnetic resonance imaging (fMRI, we have discovered a novel correlate of temporal expectations in several brain regions, most prominently in the supplementary motor area (SMA. Contrary to expectations, we found little fMRI activity during the waiting period; however, a large signal appears after the "go" signal, the amplitude of which reflects learned expectations about the distribution of possible waiting times. Specifically, the amplitude of the fMRI signal appears to encode a cumulative conditional probability, also known as the cumulative hazard function. The fMRI signal loses its dependence on waiting time in a "countdown" condition in which the arrival time of the go cue is known in advance, suggesting that the signal encodes temporal probabilities rather than simply elapsed time. The dependence of the signal on temporal expectation is present in "no-go" conditions, demonstrating that the effect is not a consequence of motor output. Finally, the encoding is not dependent on modality, operating in the same manner with auditory or visual signals. This finding extends our understanding of the relationship between temporal expectancy and measurable neural signals.

  5. Distinct medial temporal networks encode surprise during motivation by reward versus punishment.

    Science.gov (United States)

    Murty, Vishnu P; LaBar, Kevin S; Adcock, R Alison

    2016-10-01

    Adaptive motivated behavior requires predictive internal representations of the environment, and surprising events are indications for encoding new representations of the environment. The medial temporal lobe memory system, including the hippocampus and surrounding cortex, encodes surprising events and is influenced by motivational state. Because behavior reflects the goals of an individual, we investigated whether motivational valence (i.e., pursuing rewards versus avoiding punishments) also impacts neural and mnemonic encoding of surprising events. During functional magnetic resonance imaging (fMRI), participants encountered perceptually unexpected events either during the pursuit of rewards or avoidance of punishments. Despite similar levels of motivation across groups, reward and punishment facilitated the processing of surprising events in different medial temporal lobe regions. Whereas during reward motivation, perceptual surprises enhanced activation in the hippocampus, during punishment motivation surprises instead enhanced activation in parahippocampal cortex. Further, we found that reward motivation facilitated hippocampal coupling with ventromedial PFC, whereas punishment motivation facilitated parahippocampal cortical coupling with orbitofrontal cortex. Behaviorally, post-scan testing revealed that reward, but not punishment, motivation resulted in greater memory selectivity for surprising events encountered during goal pursuit. Together these findings demonstrate that neuromodulatory systems engaged by anticipation of reward and punishment target separate components of the medial temporal lobe, modulating medial temporal lobe sensitivity and connectivity. Thus, reward and punishment motivation yield distinct neural contexts for learning, with distinct consequences for how surprises are incorporated into predictive mnemonic models of the environment. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Hierarchical assembly of viral nanotemplates with encoded microparticles via nucleic acid hybridization.

    Science.gov (United States)

    Tan, Wui Siew; Lewis, Christina L; Horelik, Nicholas E; Pregibon, Daniel C; Doyle, Patrick S; Yi, Hyunmin

    2008-11-04

    We demonstrate hierarchical assembly of tobacco mosaic virus (TMV)-based nanotemplates with hydrogel-based encoded microparticles via nucleic acid hybridization. TMV nanotemplates possess a highly defined structure and a genetically engineered high density thiol functionality. The encoded microparticles are produced in a high throughput microfluidic device via stop-flow lithography (SFL) and consist of spatially discrete regions containing encoded identity information, an internal control, and capture DNAs. For the hybridization-based assembly, partially disassembled TMVs were programmed with linker DNAs that contain sequences complementary to both the virus 5' end and a selected capture DNA. Fluorescence microscopy, atomic force microscopy (AFM), and confocal microscopy results clearly indicate facile assembly of TMV nanotemplates onto microparticles with high spatial and sequence selectivity. We anticipate that our hybridization-based assembly strategy could be employed to create multifunctional viral-synthetic hybrid materials in a rapid and high-throughput manner. Additionally, we believe that these viral-synthetic hybrid microparticles may find broad applications in high capacity, multiplexed target sensing.

  7. Distinct medial temporal networks encode surprise during motivation by reward versus punishment

    Science.gov (United States)

    Murty, Vishnu P.; LaBar, Kevin S.; Adcock, R. Alison

    2016-01-01

    Adaptive motivated behavior requires predictive internal representations of the environment, and surprising events are indications for encoding new representations of the environment. The medial temporal lobe memory system, including the hippocampus and surrounding cortex, encodes surprising events and is influenced by motivational state. Because behavior reflects the goals of an individual, we investigated whether motivational valence (i.e., pursuing rewards versus avoiding punishments) also impacts neural and mnemonic encoding of surprising events. During functional magnetic resonance imaging (fMRI), participants encountered perceptually unexpected events either during the pursuit of rewards or avoidance of punishments. Despite similar levels of motivation across groups, reward and punishment facilitated the processing of surprising events in different medial temporal lobe regions. Whereas during reward motivation, perceptual surprises enhanced activation in the hippocampus, during punishment motivation surprises instead enhanced activation in parahippocampal cortex. Further, we found that reward motivation facilitated hippocampal coupling with ventromedial PFC, whereas punishment motivation facilitated parahippocampal cortical coupling with orbitofrontal cortex. Behaviorally, post-scan testing revealed that reward, but not punishment, motivation resulted in greater memory selectivity for surprising events encountered during goal pursuit. Together these findings demonstrate that neuromodulatory systems engaged by anticipation of reward and punishment target separate components of the medial temporal lobe, modulating medial temporal lobe sensitivity and connectivity. Thus, reward and punishment motivation yield distinct neural contexts for learning, with distinct consequences for how surprises are incorporated into predictive mnemonic models of the environment. PMID:26854903

  8. Alternative mRNA splicing creates transcripts encoding soluble proteins from most LILR genes.

    Science.gov (United States)

    Jones, Des C; Roghanian, Ali; Brown, Damien P; Chang, Chiwen; Allen, Rachel L; Trowsdale, John; Young, Neil T

    2009-11-01

    Leucocyte Ig-like receptors (LILR) are a family of innate immune receptors expressed on myeloid and lymphoid cells that influence adaptive immune responses. We identified a common mechanism of alternative mRNA splicing, which generates transcripts that encode soluble protein isoforms of the majority of human LILR. These alternative splice variants lack transmembrane and cytoplasmic encoding regions, due to the transcription of a cryptic stop codon present in an intron 5' of the transmembrane encoding exon. The alternative LILR transcripts were detected in cell types that express their membrane-associated isoforms. Expression of the alternative LILRB1 transcript in transfected cells resulted in the release of a soluble approximately 65 Kd LILRB1 protein into culture supernatants. Soluble LILRB1 protein was also detected in the culture supernatants of monocyte-derived DC. In vitro assays suggested that soluble LILRB1 could block the interaction between membrane-associated LILRB1 and HLA-class I. Soluble LILRB1 may act as a dominant negative regulator of HLA-class I-mediated LILRB1 inhibition. Soluble isoforms of the other LILR may function in a comparable way.

  9. Cloning and characterization of largemouth bass ( Micropterus salmoides) myostatin encoding gene and its promoter

    Science.gov (United States)

    Li, Shengjie; Bai, Junjie; Wang, Lin

    2008-08-01

    Myostatin or GDF-8, a member of the transforming growth factor-β (TGF-β) superfamily, has been demonstrated to be a negative regulator of skeletal muscle mass in mammals. In the present study, we obtained a 5.64 kb sequence of myostatin encoding gene and its promoter from largemouth bass ( Micropterus salmoides). The myostatin encoding gene consisted of three exons (488 bp, 371 bp and 1779 bp, respectively) and two introns (390 bp and 855 bp, respectively). The intron-exon boundaries were conservative in comparison with those of mammalian myostatin encoding genes, whereas the size of introns was smaller than that of mammals. Sequence analysis of 1.569 kb of the largemouth bass myostatin gene promoter region revealed that it contained two TATA boxes, one CAAT box and nine putative E-boxes. Putative muscle growth response elements for myocyte enhancer factor 2 (MEF2), serum response factor (SRF), activator protein 1 (AP1), etc., and muscle-specific Mt binding site (MTBF) were also detected. Some of the transcription factor binding sites were conserved among five teleost species. This information will be useful for studying the transcriptional regulation of myostatin in fish.

  10. Quantum control mechanism analysis through field based Hamiltonian encoding

    International Nuclear Information System (INIS)

    Mitra, Abhra; Rabitz, Herschel

    2006-01-01

    Optimal control of quantum dynamics in the laboratory is proving to be increasingly successful. The control fields can be complex, and the mechanisms by which they operate have often remained obscure. Hamiltonian encoding (HE) has been proposed as a method for understanding mechanisms in quantum dynamics. In this context mechanism is defined in terms of the dominant quantum pathways leading to the final state of the controlled system. HE operates by encoding a special modulation into the Hamiltonian and decoding its signature in the dynamics to determine the dominant pathway amplitudes. Earlier work encoded the modulation directly into the Hamiltonian operators. This present work introduces the alternative scheme of field based HE, where the modulation is encoded into the control field and not directly into the Hamiltonian operators. This distinct form of modulation yields a new perspective on mechanism and is computationally faster than the earlier approach. Field based encoding is also an important step towards a laboratory based algorithm for HE as it is the only form of encoding that may be experimentally executed. HE is also extended to cover systems with noise and uncertainty and finally, a hierarchical algorithm is introduced to reveal mechanism in a stepwise fashion of ever increasing detail as desired. This new hierarchical algorithm is an improvement over earlier approaches to HE where the entire mechanism was determined in one stroke. The improvement comes from the use of less complex modulation schemes, which leads to fewer evaluations of Schroedinger's equation. A number of simulations are presented on simple systems to illustrate the new field based encoding technique for mechanism assessment

  11. Cell type-specific transcriptional regulation of the gene encoding importin-α1

    International Nuclear Information System (INIS)

    Kamikawa, Yasunao; Yasuhara, Noriko; Yoneda, Yoshihiro

    2011-01-01

    Importin-α1 belongs to a receptor family that recognizes classical nuclear localization signals. Encoded by Kpna2, this receptor subtype is highly expressed in mouse embryonic stem (ES) cells. In this study, we identified a critical promoter region in Kpna2 and showed that the expression of this gene is differentially regulated in ES cells and NIH3T3 cells. Conserved CCAAT boxes are required for Kpna2 promoter activity in both ES and NIH3T3 cells. Interestingly, deletion of the region from nucleotide position - 251 to - 179 bp resulted in a drastic reduction in Kpna2 transcriptional activity only in ES cells. This region contains Krueppel-like factor (Klf) binding sequences and is responsible for transactivation of the gene by Klf2 and Klf4. Accordingly, endogenous Kpna2 mRNA levels decreased in response to depletion of Klf2 and Klf4 in ES cells. Our results suggest that Klf2 and Klf4 function redundantly to drive high level of Kpna2 expression in ES cells. -- Research Highlights: → We showed the cell type-specific transcriptional regulation of Kpna2 encoding importin-al. → NF-Y binds the CCAAT boxes to activate Kpna2 transcription in NIH3T3 cells. → Klf2 and Klf4 redundantly activate the expression of Kpna2 in ES cells.

  12. Escherichia coli kgtP encodes an alpha-ketoglutarate transporter.

    OpenAIRE

    Seol, W; Shatkin, A J

    1991-01-01

    The witA gene located between pss and rrnG on the Escherichia coli chromosome encodes a 432-amino acid protein. It is homologous to a human hepatoma glucose transporter and to E. coli membrane proteins that transport citrate (CitA), arabinose (AraE), and xylose (XylE), and, like these carrier proteins, WitA also contains 12 highly hydrophobic putative membrane-spanning regions. Gene disruption mutants constructed in two E. coli strains grew slowly or not at all, depending on genetic backgroun...

  13. Cloning and sequencing of dolphinfish (Coryphaena hippurus, Coryphaenidae) growth hormone-encoding cDNA.

    Science.gov (United States)

    Peduel, A D; Elizur, A; Knibb, W

    1994-01-01

    The cDNA encoding the preprotein growth hormone from the dolphinfish (Coryphaena hippurus) has been cloned and sequenced. The cDNA was derived by reverse transcription of RNA from the pituitary of a young fish using the method known as Rapid Amplification of cDNA Ends (RACE). An oligonucleotide primer corresponding to the 5' region of Pagrus major and the universal RACE primer enabled amplification using the Polymerase Chain Reaction (PCR). The dolphinfish and yellow-tail, Seriola quineqeradiata, are both members of the sub-order Percoidei (Perciforme) and their GH sequences show a high level of homology.

  14. Storage of polarization-encoded cluster states in an atomic system

    Science.gov (United States)

    Yuan, Chun-Hua; Chen, Li-Qing; Zhang, Weiping

    2009-05-01

    We present a scheme for entanglement of macroscopic atomic ensembles which are four spatially separate regions of an atomic cloud using cluster-correlated beams. We show that the cluster-type polarization-encoded entanglement could be mapped onto the long-lived collective ground state of the atomic ensembles, and the stored entanglement could be retrieved based on the technique of electromagnetically induced transparency. We also discuss the efficiency of, the lifetime of, and some quantitative restrictions to the proposed quantum memory.

  15. Encoding an Optical Signal using a Wireless Radio-Freqency Signal

    DEFF Research Database (Denmark)

    2011-01-01

    Source: US2012148252A The present invention provides a method for modulating an optical signal in a semiconductor device. A wireless radio frequency modulation signal is used to provide a time-dependent electric field in a semiconductor nanostructure region, which causes a change in the absorption...... in the semiconductor device. An optical signal propagating in the semiconductor device will be modulated in accordance with the properties of the wireless radio frequency modulation signal, thus providing a method for encoding information from a wireless radio frequency signal onto an optical carrier....

  16. Two Pathways to Stimulus Encoding in Category Learning?

    Science.gov (United States)

    Davis, Tyler; Love, Bradley C.; Maddox, W. Todd

    2008-01-01

    Category learning theorists tacitly assume that stimuli are encoded by a single pathway. Motivated by theories of object recognition, we evaluate a dual-pathway account of stimulus encoding. The part-based pathway establishes mappings between sensory input and symbols that encode discrete stimulus features, whereas the image-based pathway applies holistic templates to sensory input. Our experiments use rule-plus-exception structures in which one exception item in each category violates a salient regularity and must be distinguished from other items. In Experiment 1, we find that discrete representations are crucial for recognition of exceptions following brief training. Experiments 2 and 3 involve multi-session training regimens designed to encourage either part or image-based encoding. We find that both pathways are able to support exception encoding, but have unique characteristics. We speculate that one advantage of the part-based pathway is the ability to generalize across domains, whereas the image-based pathway provides faster and more effortless recognition. PMID:19460948

  17. Emotion suppression reduces hippocampal activity during successful memory encoding.

    Science.gov (United States)

    Binder, Julia; de Quervain, Dominique J-F; Friese, Malte; Luechinger, Roger; Boesiger, Peter; Rasch, Björn

    2012-10-15

    People suppressing their emotions while facing an emotional event typically remember it less well. However, the neural mechanisms underlying the impairing effect of emotion suppression on successful memory encoding are not well understood. Because successful memory encoding relies on the hippocampus and the amygdala, we hypothesized that memory impairments due to emotion suppression are associated with down-regulated activity in these brain areas. 59 healthy females were instructed either to simply watch the pictures or to down-regulate their emotions by using a response-focused emotion suppression strategy. Brain activity was recorded using functional magnetic resonance imaging (fMRI), and free recall of pictures was tested afterwards. As expected, suppressing one's emotions resulted in impaired recall of the pictures. On the neural level, the memory impairments were associated with reduced activity in the right hippocampus during successful encoding. No significant effects were observed in the amygdala. In addition, functional connectivity between the hippocampus and the right dorsolateral prefrontal cortex was strongly reduced during emotion suppression, and these reductions predicted free-recall performance. Our results indicate that emotion suppression interferes with memory encoding on the hippocampal level, possibly by decoupling hippocampal and prefrontal encoding processes, suggesting that response-focused emotion suppression might be an adaptive strategy for impairing hippocampal memory formation in highly arousing situations. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Graph Regularized Auto-Encoders for Image Representation.

    Science.gov (United States)

    Yiyi Liao; Yue Wang; Yong Liu

    2017-06-01

    Image representation has been intensively explored in the domain of computer vision for its significant influence on the relative tasks such as image clustering and classification. It is valuable to learn a low-dimensional representation of an image which preserves its inherent information from the original image space. At the perspective of manifold learning, this is implemented with the local invariant idea to capture the intrinsic low-dimensional manifold embedded in the high-dimensional input space. Inspired by the recent successes of deep architectures, we propose a local invariant deep nonlinear mapping algorithm, called graph regularized auto-encoder (GAE). With the graph regularization, the proposed method preserves the local connectivity from the original image space to the representation space, while the stacked auto-encoders provide explicit encoding model for fast inference and powerful expressive capacity for complex modeling. Theoretical analysis shows that the graph regularizer penalizes the weighted Frobenius norm of the Jacobian matrix of the encoder mapping, where the weight matrix captures the local property in the input space. Furthermore, the underlying effects on the hidden representation space are revealed, providing insightful explanation to the advantage of the proposed method. Finally, the experimental results on both clustering and classification tasks demonstrate the effectiveness of our GAE as well as the correctness of the proposed theoretical analysis, and it also suggests that GAE is a superior solution to the current deep representation learning techniques comparing with variant auto-encoders and existing local invariant methods.

  19. A genomic region of lactococcal temperate bacteriophage TP901-1 encoding major virion proteins

    DEFF Research Database (Denmark)

    Johnsen, Mads G.; Appel, Karen Fuglede; Madsen, Hans Peter Lynge

    1996-01-01

    Two major structural proteins, MHP (major head protein) and MTP (major tail protein), from the lactococcal temperate phage TP901-1 were sequenced at their amino acid termini, and derived degenerate oligonucleotides were used to locate the corresponding genes in the phage genome. This genomic regi...

  20. Identification of glycosaminoglycan binding regions in the Plasmodium falciparum encoded placental sequestration ligand, VAR2CSA

    DEFF Research Database (Denmark)

    Resende, Mafalda; Nielsen, Morten A.; Dahlbaeck, Madeleine

    2008-01-01

    Background: Pregnancy malaria is caused by Plasmodium falciparum-infected erythrocytes binding the placental receptor chondroitin sulfate A (CSA). This results in accumulation of parasites in the placenta with severe clinical consequences for the mother and her unborn child. Women become resistan...

  1. Validation of a Real-time AVS Encoder on FPGA

    Directory of Open Access Journals (Sweden)

    Qun Fang Yuan

    2014-01-01

    Full Text Available A whole I frame AVS real-time video encoder is designed and implemented on FPGA platform in this paper. The system uses the structure of the flow calculation, coupled with a dual-port RAM memory between/among the various functional modules. Reusable design and pipeline design are used to optimize various encoding module and to ensure the efficient operation of the pipeline. Through the simulation of ISE software and the verification of Xilinx Vritex-4 pro platform, it can be seen that the highest working frequency can be up to 110 MHz, meeting the requirements of the whole I frame real- time encoding of AVS in CIF resolution.

  2. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

    Directory of Open Access Journals (Sweden)

    Li Shen

    2013-06-01

    Full Text Available A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE, recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

  3. Encoding, training and retrieval in ferroelectric tunnel junctions

    Science.gov (United States)

    Xu, Hanni; Xia, Yidong; Xu, Bo; Yin, Jiang; Yuan, Guoliang; Liu, Zhiguo

    2016-05-01

    Ferroelectric tunnel junctions (FTJs) are quantum nanostructures that have great potential in the hardware basis for future neuromorphic applications. Among recently proposed possibilities, the artificial cognition has high hopes, where encoding, training, memory solidification and retrieval constitute a whole chain that is inseparable. However, it is yet envisioned but experimentally unconfirmed. The poor retention or short-term store of tunneling electroresistance, in particular the intermediate states, is still a key challenge in FTJs. Here we report the encoding, training and retrieval in BaTiO3 FTJs, emulating the key features of information processing in terms of cognitive neuroscience. This is implemented and exemplified through processing characters. Using training inputs that are validated by the evolution of both barrier profile and domain configuration, accurate recalling of encoded characters in the retrieval stage is demonstrated.

  4. Distinctiveness and encoding effects in online sentence comprehension

    Directory of Open Access Journals (Sweden)

    Philip eHofmeister

    2014-12-01

    Full Text Available In explicit memory recall and recognition tasks, elaboration and contextual isolation both facilitate memory performance. Here, we investigate these effects in the context of sentence processing: targets for retrieval during online sentence processing of English object relative clause constructions differ in the amount of elaboration associated with the target noun phrase, or the homogeneity of superficial features (text color. Experiment 1 shows that greater elaboration for targets during the encoding phase reduces reading times at retrieval sites, but elaboration of non-targets has considerably weaker effects. Experiment 2 illustrates that processing isolated superficial features of target noun phrases --- here, a green word in a sentence with words colored white --- does not lead to enhanced memory performance, despite triggering longer encoding times. These results are interpreted in the light of the memory models of Nairne 1990, 2001, 2006, which state that encoding remnants contribute to the set of retrieval cues that provide the basis for similarity-based interference effects.

  5. Enzymes and Enzyme Activity Encoded by Nonenveloped Viruses.

    Science.gov (United States)

    Azad, Kimi; Banerjee, Manidipa; Johnson, John E

    2017-09-29

    Viruses are obligate intracellular parasites that rely on host cell machineries for their replication and survival. Although viruses tend to make optimal use of the host cell protein repertoire, they need to encode essential enzymatic or effector functions that may not be available or accessible in the host cellular milieu. The enzymes encoded by nonenveloped viruses-a group of viruses that lack any lipid coating or envelope-play vital roles in all the stages of the viral life cycle. This review summarizes the structural, biochemical, and mechanistic information available for several classes of enzymes and autocatalytic activity encoded by nonenveloped viruses. Advances in research and development of antiviral inhibitors targeting specific viral enzymes are also highlighted.

  6. Deep Marginalized Sparse Denoising Auto-Encoder for Image Denoising

    Science.gov (United States)

    Ma, Hongqiang; Ma, Shiping; Xu, Yuelei; Zhu, Mingming

    2018-01-01

    Stacked Sparse Denoising Auto-Encoder (SSDA) has been successfully applied to image denoising. As a deep network, the SSDA network with powerful data feature learning ability is superior to the traditional image denoising algorithms. However, the algorithm has high computational complexity and slow convergence rate in the training. To address this limitation, we present a method of image denoising based on Deep Marginalized Sparse Denoising Auto-Encoder (DMSDA). The loss function of Sparse Denoising Auto-Encoder is marginalized so that it satisfies both sparseness and marginality. The experimental results show that the proposed algorithm can not only outperform SSDA in the convergence speed and training time, but also has better denoising performance than the current excellent denoising algorithms, including both the subjective and objective evaluation of image denoising.

  7. Subversion of cytokine networks by virally encoded decoy receptors.

    Science.gov (United States)

    Epperson, Megan L; Lee, Chung A; Fremont, Daved H

    2012-11-01

    During the course of evolution, viruses have captured or created a diverse array of open reading frames, which encode for proteins that serve to evade and sabotage the host innate and adaptive immune responses that would otherwise lead to their elimination. These viral genomes are some of the best textbooks of immunology ever written. The established arsenal of immunomodulatory proteins encoded by viruses is large and growing, and includes specificities for virtually all known inflammatory pathways and targets. The focus of this review is on herpes and poxvirus-encoded cytokine and chemokine-binding proteins that serve to undermine the coordination of host immune surveillance. Structural and mechanistic studies of these decoy receptors have provided a wealth of information, not only about viral pathogenesis but also about the inner workings of cytokine signaling networks. © 2012 John Wiley & Sons A/S.

  8. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing.

    Science.gov (United States)

    Polizzi, Karen M; Kontoravdi, Cleo

    2015-02-01

    With the current wealth of transcriptomic data, it is possible to design genetically-encoded biosensors for the detection of stress responses and apply these to high-throughput bioprocess development and monitoring of cellular health. Such biosensors can sense extrinsic factors such as nutrient or oxygen deprivation and shear stress, as well as intrinsic stress factors like oxidative damage and unfolded protein accumulation. Alongside, there have been developments in biosensing hardware and software applicable to the field of genetically-encoded biosensors in the near future. This review discusses the current state-of-the-art in biosensors for monitoring cultures during biological manufacturing and the future challenges for the field. Connecting the individual achievements into a coherent whole will enable the application of genetically-encoded biosensors in industry. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Performance study of large area encoding readout MRPC

    Science.gov (United States)

    Chen, X. L.; Wang, Y.; Chen, G.; Han, D.; Wang, X.; Zeng, M.; Zeng, Z.; Zhao, Z.; Guo, B.

    2018-02-01

    Muon tomography system built by the 2-D readout high spatial resolution Multi-gap Resistive Plate Chamber (MRPC) detector is a project of Tsinghua University. An encoding readout method based on the fine-fine configuration has been used to minimize the number of the readout electronic channels resulting in reducing the complexity and the cost of the system. In this paper, we provide a systematic comparison of the MRPC detector performance with and without fine-fine encoding readout. Our results suggest that the application of the fine-fine encoding readout leads us to achieve a detecting system with slightly worse spatial resolution but dramatically reduce the number of electronic channels.

  10. Prefrontal activity and impaired memory encoding strategies in schizophrenia.

    Science.gov (United States)

    Guimond, Synthia; Hawco, Colin; Lepage, Martin

    2017-08-01

    Schizophrenia patients have significant memory difficulties that have far-reaching implications in their daily life. These impairments are partly attributed to an inability to self-initiate effective memory encoding strategies, but its core neurobiological correlates remain unknown. The current study addresses this critical gap in our knowledge of episodic memory impairments in schizophrenia. Schizophrenia patients (n = 35) and healthy controls (n = 23) underwent a Semantic Encoding Memory Task (SEMT) during an fMRI scan. Brain activity was examined for conditions where participants were a) prompted to use semantic encoding strategies, or b) not prompted but required to self-initiate such strategies. When prompted to use semantic encoding strategies, schizophrenia patients exhibited similar recognition performance and brain activity as healthy controls. However, when required to self-initiate these strategies, patients had significant reduced recognition performance and brain activity in the left dorsolateral prefrontal cortex, as well as in the left temporal gyrus, left superior parietal lobule, and cerebellum. When patients were divided based on performance on the SEMT, the subgroup with more severe deficits in self-initiation also showed greater reduction in left dorsolateral prefrontal activity. These results suggest that impaired self-initiation of elaborative encoding strategies is a driving feature of memory deficits in schizophrenia. We also identified the neural correlates of impaired self-initiation of semantic encoding strategies, in which a failure to activate the left dorsolateral prefrontal cortex plays a key role. These findings provide important new targets in the development of novel treatments aiming to improve memory and ultimately patients' outcome. Copyright © 2017. Published by Elsevier Ltd.

  11. THE RELATIONSHIP BETWEEN ENCODING ABILITY AND AGGRESSIVE BEHAVIOR.

    Science.gov (United States)

    Tsamis, Vasiliki J; Rebok, George W; Montague, David R

    2009-03-26

    While past research efforts have reported a relationship between encoding ability and aggressive behavior in children, the relationship between encoding ability and adult aggressiveness has not been examined. Encoding, an element of attention, refers to the ability to recall and reorder information stored in memory. Using selected cognitive tests and a self-report measure of aggressive behavior in a sample of community college students (n=55), this study investigated the relationship between encoding ability and aggressive behavior, (i.e., physical aggression, verbal aggression, anger, hostility, indirect aggression, and total aggression). Aggressive behavior was assessed by the Aggression Questionnaire of the Buss-Durkee Hostility Inventory, a widely-used measure of aggressive behavior. Encoding was measured using the WAIS-III Digit Span and Arithmetic subtests. Initial analyses showed no significant correlations between the cognitive measures and the five scales of aggressive behavior. However, there was a significant age-related association between scores on the cognitive measures and the indices of aggressive behavior. Two groups were created, those who reported attention problems and those who did not report attention problems. When the two groups were compared, participants who had a history of attention problems were verbally more aggressive than participants with a negative history of attention problems, and they were generally more aggressive. A composite score, called an "encoding score," was related to scores on the aggressive behavior scales. Moreover, the age-related relationship between these two variables suggests that the relationship is maturational and may disappear as an individual ages. Concerning the latter, participants in the current study were enrolled in junior college. Therefore, persons who had attention problems and were aggressive may not have pursued higher education.

  12. Negative affect promotes encoding of and memory for details at the expense of the gist: affect, encoding, and false memories.

    Science.gov (United States)

    Storbeck, Justin

    2013-01-01

    I investigated whether negative affective states enhance encoding of and memory for item-specific information reducing false memories. Positive, negative, and neutral moods were induced, and participants then completed a Deese-Roediger-McDermott (DRM) false-memory task. List items were presented in unique spatial locations or unique fonts to serve as measures for item-specific encoding. The negative mood conditions had more accurate memories for item-specific information, and they also had fewer false memories. The final experiment used a manipulation that drew attention to distinctive information, which aided learning for DRM words, but also promoted item-specific encoding. For the condition that promoted item-specific encoding, false memories were reduced for positive and neutral mood conditions to a rate similar to that of the negative mood condition. These experiments demonstrated that negative affective cues promote item-specific processing reducing false memories. People in positive and negative moods encode events differently creating different memories for the same event.

  13. CAG-encoded polyglutamine length polymorphism in the human genome

    Directory of Open Access Journals (Sweden)

    Hayden Michael R

    2007-05-01

    Full Text Available Abstract Background Expansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority of individuals clinically diagnosed with spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to be caused by this common mutational mechanism. We set out to determine the length distributions of CAG-polyglutamine tracts for the entire human genome in a set of healthy individuals in order to characterize the nature of polyglutamine repeat length variation across the human genome, to establish the background against which pathogenic repeat expansions can be detected, and to prioritize candidate genes for repeat expansion disorders. Results We found that repeats, including those in known disease genes, have unique distributions of glutamine tract lengths, as measured by fragment analysis of PCR-amplified repeat regions. This emphasizes the need to characterize each distribution and avoid making generalizations between loci. The best predictors of known disease genes were occurrence of a long CAG-tract uninterrupted by CAA codons in their reference genome sequence, and high glutamine tract length variance in the normal population. We used these parameters to identify eight priority candidate genes for polyglutamine expansion disorders. Twelve CAG-polyglutamine repeats were invariant and these can likely be excluded as candidates. We outline some confusion in the literature about this type of data, difficulties in comparing such data between publications, and its application to studies of disease prevalence in different populations. Analysis of Gene Ontology-based functions of CAG-polyglutamine-containing genes provided a visual framework for interpretation of these genes' functions. All nine known disease genes were involved in DNA

  14. Hybrid architecture for encoded measurement-based quantum computation.

    Science.gov (United States)

    Zwerger, M; Briegel, H J; Dür, W

    2014-06-20

    We present a hybrid scheme for quantum computation that combines the modular structure of elementary building blocks used in the circuit model with the advantages of a measurement-based approach to quantum computation. We show how to construct optimal resource states of minimal size to implement elementary building blocks for encoded quantum computation in a measurement-based way, including states for error correction and encoded gates. The performance of the scheme is determined by the quality of the resource states, where within the considered error model a threshold of the order of 10% local noise per particle for fault-tolerant quantum computation and quantum communication.

  15. Signal Encoding and Telemetry Systems for Space Vehicles.

    Science.gov (United States)

    1983-05-01

    first application in which this design encoder was flown on two Brazilian Sonda III rockets. These encoders were programmed for the following operating...State University (OSU). The depletion sensing vehicles will be Sonda III rockets and will be instrumented by Northeastern University. The experiments...Preamp. Gain 400 Polarization Loss 3 dB Safety Factor 3 dB Xmtr. Power 3, 5 or 8 W RESULTS Xmtr. Power CNR at IF 3 watts 9.7 dB 5 12.0 8 14.0 Sonda III

  16. Ordering of diagnostic information in encoded medical images. Accuracy progression

    Science.gov (United States)

    Przelaskowski, A.; Jóźwiak, R.; Krzyżewski, T.; Wróblewska, A.

    2008-03-01

    A concept of diagnostic accuracy progression for embedded coding of medical images was presented. Implementation of JPEG2000 encoder with a modified PCRD optimization algorithm was realized and initially verified as a tool for accurate medical image streaming. Mean square error as a distortion measure was replaced by other numerical measures to revise quality progression according to diagnostic importance of successively encoded image information. A faster increment of image diagnostic importance during reconstruction of initial packets of code stream was reached. Modified Jasper code was initially tested on a set of mammograms containing clusters of microcalcifications and malignant masses, and other radiograms. Teleradiologic applications were considered as the first area of interests.

  17. Accelerated radial Fourier-velocity encoding using compressed sensing

    International Nuclear Information System (INIS)

    Hilbert, Fabian; Han, Dietbert

    2014-01-01

    Purpose:Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. Materials and Methods:We imaged the femoral artery of healthy volunteers with ECG - triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Results:Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6 - fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Conclusion: Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity

  18. Accelerated radial Fourier-velocity encoding using compressed sensing.

    Science.gov (United States)

    Hilbert, Fabian; Wech, Tobias; Hahn, Dietbert; Köstler, Herbert

    2014-09-01

    Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. We imaged the femoral artery of healthy volunteers with ECG-triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6-fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity distribution in vessels in the order of the voxel size. Thus

  19. Accelerated radial Fourier-velocity encoding using compressed sensing

    Energy Technology Data Exchange (ETDEWEB)

    Hilbert, Fabian; Han, Dietbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wech, Tobias; Koestler, Herbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wuerzburg Univ. (Germany). Comprehensive Heart Failure Center (CHFC)

    2014-10-01

    Purpose:Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. Materials and Methods:We imaged the femoral artery of healthy volunteers with ECG - triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Results:Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6 - fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Conclusion: Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity

  20. Straight to the point: how people encode linear discontinuations

    Directory of Open Access Journals (Sweden)

    Rodrigo I. Mora

    2012-12-01

    Full Text Available Spatial discontinuations, as those found in cities and buildings, are everyday events. But, how do we encode and classify such misalignments? This is the topic of this paper. Twenty participants were asked to classify a total of 51 icons showing an upward-moving line being misaligned to the right, left and straight down. The results show that subjects were very sensitive to slight discontinuations occurring to vertical lines and that there was not exact symmetry between the left and right axis, meaning that the pieces slightly misaligned to the left were encoded differently than those misaligned to the right

  1. Solving traveling salesman problems with DNA molecules encoding numerical values.

    Science.gov (United States)

    Lee, Ji Youn; Shin, Soo-Yong; Park, Tai Hyun; Zhang, Byoung-Tak

    2004-12-01

    We introduce a DNA encoding method to represent numerical values and a biased molecular algorithm based on the thermodynamic properties of DNA. DNA strands are designed to encode real values by variation of their melting temperatures. The thermodynamic properties of DNA are used for effective local search of optimal solutions using biochemical techniques, such as denaturation temperature gradient polymerase chain reaction and temperature gradient gel electrophoresis. The proposed method was successfully applied to the traveling salesman problem, an instance of optimization problems on weighted graphs. This work extends the capability of DNA computing to solving numerical optimization problems, which is contrasted with other DNA computing methods focusing on logical problem solving.

  2. submitter Linear encoder based low frequency inertial sensor

    CERN Document Server

    Hellegouarch, Sylvain; Artoos, Kurt; Lambert, Pierre; Collette, Christophe

    2016-01-01

    In this article, we present a novel concept of inertial sensor, based on a linear encoder. Compared to other interferometric sensors, the encoder is much more easy to mount, and the calibration more stable. A prototype has been built and validated experimentally by comparison with a commercial seismometer. It has a resolution of about 10 pm/√Hz. In order to further improve the resolution, two concepts of mechanical amplifiers have been studied and compared. One of them is shown to be extremely promising, provided that the amplifier does not stiffen the sensor.

  3. Authentication of gold nanoparticle encoded pharmaceutical tablets using polarimetric signatures.

    Science.gov (United States)

    Carnicer, Artur; Arteaga, Oriol; Suñé-Negre, Josep M; Javidi, Bahram

    2016-10-01

    The counterfeiting of pharmaceutical products represents concerns for both industry and the safety of the general public. Falsification produces losses to companies and poses health risks for patients. In order to detect fake pharmaceutical tablets, we propose producing film-coated tablets with gold nanoparticle encoding. These coated tablets contain unique polarimetric signatures. We present experiments to show that ellipsometric optical techniques, in combination with machine learning algorithms, can be used to distinguish genuine and fake samples. To the best of our knowledge, this is the first report using gold nanoparticles encoded with optical polarimetric classifiers to prevent the counterfeiting of pharmaceutical products.

  4. Blocking of irrelevant memories by posterior alpha activity boosts memory encoding.

    Science.gov (United States)

    Park, Hyojin; Lee, Dong Soo; Kang, Eunjoo; Kang, Hyejin; Hahm, Jarang; Kim, June Sic; Chung, Chun Kee; Jensen, Ole

    2014-08-01

    In our daily lives, we are confronted with a large amount of information. Because only a small fraction can be encoded in long-term memory, the brain must rely on powerful mechanisms to filter out irrelevant information. To understand the neuronal mechanisms underlying the gating of information into long-term memory, we employed a paradigm where the encoding was directed by a "Remember" or a "No-Remember" cue. We found that posterior alpha activity increased prior to the "No-Remember" stimuli, whereas it decreased prior to the "Remember" stimuli. The sources were localized in the parietal cortex included in the dorsal attention network. Subjects with a larger cue-modulation of the alpha activity had better memory for the to-be-remembered items. Interestingly, alpha activity reflecting successful inhibition following the "No-Remember" cue was observed in the frontal midline structures suggesting preparatory inhibition was mediated by anterior parts of the dorsal attention network. During the presentation of the memory items, there was more gamma activity for the "Remember" compared to the "No-Remember" items in the same regions. Importantly, the anticipatory alpha power during cue predicted the gamma power during item. Our findings suggest that top-down controlled alpha activity reflects attentional inhibition of sensory processing in the dorsal attention network, which then finally gates information to long-term memory. This gating is achieved by inhibiting the processing of visual information reflected by neuronal synchronization in the gamma band. In conclusion, the functional architecture revealed by region-specific changes in the alpha activity reflects attentional modulation which has consequences for long-term memory encoding. Copyright © 2014 Wiley Periodicals, Inc.

  5. The multiscale classification system and grid encoding mode of ecological land in China

    Science.gov (United States)

    Wang, Jing; Liu, Aixia; Lin, Yifan

    2017-10-01

    Ecological land provides goods and services that have direct or indirect benefic to eco-environment and human welfare. In recent years, researches on ecological land have become important in the field of land changes and ecosystem management. In the study, a multi-scale classification scheme of ecological land was developed for land management based on combination of the land-use classification and the ecological function zoning in China, including eco-zone, eco-region, eco-district, land ecosystem, and ecological land-use type. The geographical spatial unit leads toward greater homogeneity from macro to micro scale. The term "ecological land-use type" is the smallest one, being important to maintain the key ecological processes in land ecosystem. Ecological land-use type was categorized into main-functional and multi-functional ecological land-use type according to its ecological function attributes and production function attributes. Main-functional type was defined as one kind of land-use type mainly providing ecological goods and function attributes, such as river, lake, swampland, shoaly land, glacier and snow, while multi-functional type not only providing ecological goods and function attributes but also productive goods and function attributes, such as arable land, forestry land, and grassland. Furthermore, a six-level grid encoding mode was proposed for modern management of ecological land and data update under cadastral encoding. The six-level irregular grid encoding from macro to micro scale included eco-zone, eco-region, eco-district, cadastral area, land ecosystem, land ownership type, ecological land-use type, and parcel. Besides, the methodologies on ecosystem management were discussed for integrated management of natural resources in China.

  6. Cholinergic Enhancement of Brain Activation in Mild Cognitive Impairment (MCI during Episodic Memory Encoding

    Directory of Open Access Journals (Sweden)

    Shannon L Risacher

    2013-09-01

    Full Text Available Objective: To determine the physiological impact of treatment with donepezil (Aricept on neural circuitry supporting episodic memory encoding in patients with amnestic mild cognitive impairment (MCI using functional MRI (fMRI. Methods: 18 patients with MCI and 20 age-matched healthy controls (HC were scanned twice while performing an event-related verbal episodic encoding task. MCI participants were scanned before treatment and after approximately 3 months on donepezil; HC were untreated but rescanned at the same interval. Voxel-level analyses assessed treatment effects in activation profile relative to retest changes in non-treated HC. Changes in task-related connectivity in medial temporal circuitry were also evaluated, as were associations between brain activation pattern, task-related functional connectivity, task performance, and clinical measures of cognition.Results: At baseline, the MCI group showed reduced activation during encoding relative to HC in the right medial temporal lobe (MTL; hippocampal/parahippocampal and additional regions, as well as attenuated task-related deactivation, relative to rest, in a medial parietal lobe cluster. After treatment, the MCI group showed normalized MTL activation and improved parietal deactivation. These changes were associated with cognitive performance. After treatment, the MCI group also demonstrated increased task-related functional connectivity from the right MTL cluster seed region to a network of other sites including the basal nucleus/caudate and bilateral frontal lobes. Increased functional connectivity was associated with improved task performance.Conclusions: Pharmacologic enhancement of cholinergic function in amnestic MCI is associated with changes in brain activation pattern and functional connectivity during episodic memory processing which are in turn related to increased cognitive performance. fMRI is a promising biomarker for assessing treatment related changes in brain function.

  7. Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.

    Science.gov (United States)

    Pickard, Derek; Wain, John; Baker, Stephen; Line, Alexandra; Chohan, Sonia; Fookes, Maria; Barron, Andrew; Gaora, Peadar O; Chabalgoity, José A; Thanky, Niren; Scholes, Christoph; Thomson, Nicholas; Quail, Michael; Parkhill, Julian; Dougan, Gordon

    2003-09-01

    Vi capsular polysaccharide production is encoded by the viaB locus, which has a limited distribution in Salmonella enterica serovars. In S. enterica serovar Typhi, viaB is encoded on a 134-kb pathogenicity island known as SPI-7 that is located between partially duplicated tRNA(pheU) sites. Functional and bioinformatic analysis suggests that SPI-7 has a mosaic structure and may have evolved as a consequence of several independent insertion events. Analysis of viaB-associated DNA in Vi-positive S. enterica serovar Paratyphi C and S. enterica serovar Dublin isolates revealed the presence of similar SPI-7 islands. In S. enterica serovars Paratyphi C and Dublin, the SopE bacteriophage and a 15-kb fragment adjacent to the intact tRNA(pheU) site were absent. In S. enterica serovar Paratyphi C only, a region encoding a type IV pilus involved in the adherence of S. enterica serovar Typhi to host cells was missing. The remainder of the SPI-7 islands investigated exhibited over 99% DNA sequence identity in the three serovars. Of 30 other Salmonella serovars examined, 24 contained no insertions at the equivalent tRNA(pheU) site, 2 had a 3.7-kb insertion, and 4 showed sequence variation at the tRNA(pheU)-phoN junction, which was not analyzed further. Sequence analysis of the SPI-7 region from S. enterica serovar Typhi strain CT18 revealed significant synteny with clusters of genes from a variety of saprophytic bacteria and phytobacteria, including Pseudomonas aeruginosa and Xanthomonas axonopodis pv. citri. This analysis suggested that SPI-7 may be a mobile element, such as a conjugative transposon or an integrated plasmid remnant.

  8. Selective attention to phonology dynamically modulates initial encoding of auditory words within the left hemisphere.

    Science.gov (United States)

    Yoncheva, Yuliya; Maurer, Urs; Zevin, Jason D; McCandliss, Bruce D

    2014-08-15

    Selective attention to phonology, i.e., the ability to attend to sub-syllabic units within spoken words, is a critical precursor to literacy acquisition. Recent functional magnetic resonance imaging evidence has demonstrated that a left-lateralized network of frontal, temporal, and posterior language regions, including the visual word form area, supports this skill. The current event-related potential (ERP) study investigated the temporal dynamics of selective attention to phonology during spoken word perception. We tested the hypothesis that selective attention to phonology dynamically modulates stimulus encoding by recruiting left-lateralized processes specifically while the information critical for performance is unfolding. Selective attention to phonology was captured by manipulating listening goals: skilled adult readers attended to either rhyme or melody within auditory stimulus pairs. Each pair superimposed rhyming and melodic information ensuring identical sensory stimulation. Selective attention to phonology produced distinct early and late topographic ERP effects during stimulus encoding. Data-driven source localization analyses revealed that selective attention to phonology led to significantly greater recruitment of left-lateralized posterior and extensive temporal regions, which was notably concurrent with the rhyme-relevant information within the word. Furthermore, selective attention effects were specific to auditory stimulus encoding and not observed in response to cues, arguing against the notion that they reflect sustained task setting. Collectively, these results demonstrate that selective attention to phonology dynamically engages a left-lateralized network during the critical time-period of perception for achieving phonological analysis goals. These findings suggest a key role for selective attention in on-line phonological computations. Furthermore, these findings motivate future research on the role that neural mechanisms of attention may

  9. Encoding of natural sounds at multiple spectral and temporal resolutions in the human auditory cortex.

    Directory of Open Access Journals (Sweden)

    Roberta Santoro

    2014-01-01

    Full Text Available Functional neuroimaging research provides detailed observations of the response patterns that natural sounds (e.g. human voices and speech, animal cries, environmental sounds evoke in the human brain. The computational and representational mechanisms underlying these observations, however, remain largely unknown. Here we combine high spatial resolution (3 and 7 Tesla functional magnetic resonance imaging (fMRI with computational modeling to reveal how natural sounds are represented in the human brain. We compare competing models of sound representations and select the model that most accurately predicts fMRI response patterns to natural sounds. Our results show that the cortical encoding of natural sounds entails the formation of multiple representations of sound spectrograms with different degrees of spectral and temporal resolution. The cortex derives these multi-resolution representations through frequency-specific neural processing channels and through the combined analysis of the spectral and temporal modulations in the spectrogram. Furthermore, our findings suggest that a spectral-temporal resolution trade-off may govern the modulation tuning of neuronal populations throughout the auditory cortex. Specifically, our fMRI results suggest that neuronal populations in posterior/dorsal auditory regions preferably encode coarse spectral information with high temporal precision. Vice-versa, neuronal populations in anterior/ventral auditory regions preferably encode fine-grained spectral information with low temporal precision. We propose that such a multi-resolution analysis may be crucially relevant for flexible and behaviorally-relevant sound processing and may constitute one of the computational underpinnings of functional specialization in auditory cortex.

  10. Isolation of genomic DNA encoding transcription factor TFIID from Acanthamoeba castellanii: characterization of the promoter.

    Science.gov (United States)

    Wong, J M; Liu, F; Bateman, E

    1992-01-01

    We have isolated a genomic clone encoding Acanthamoeba castellanii TFIID. The clone contains the entire TFIID gene, 300 bp of 5' promoter sequences and several hundred base pairs of 3' non-coding sequence. The coding region is interrupted by two short introns, but is otherwise identical to Acanthamoeba TFIID cDNA. Comparisons between forty four Acanthamoeba intron 5' and 3' boundaries suggest a 5' splice site consensus of GTACG(T/C) and a 3' consensus of CAG. We determined the position of the transcription initiation site used in vivo, and show that the same site is used in vitro by homologous nuclear extracts. Deletion analysis of the promoter region shows that the minimal promoter required for efficient expression in vitro is located between -97 and +4 relative to the transcription start site. Three regions within the promoter are important for transcription in vitro; sequences between -97 and -35, the TATAAA box and the initiation region. The initiation region is dispensable but appears to position the transcription start site relative to the TATAAA box. The TATAAA box is absolutely required for transcription initiation whereas the upstream region stimulates transcription approximately five-fold. Images PMID:1408796

  11. Brain Activation during Memory Encoding in Type 2 Diabetes Mellitus: A Discordant Twin Pair Study

    Directory of Open Access Journals (Sweden)

    Amanda G. Wood

    2016-01-01

    Full Text Available Type 2 diabetes mellitus increases the risk of dementia and neuronal dysfunction may occur years before perceptible cognitive decline. We aimed to study the impact of type 2 diabetes on brain activation during memory encoding in middle-aged people, controlling for age, sex, genes, and early-shared environment. Twenty-two twin pairs discordant for type 2 diabetes mellitus (mean age 60.9 years without neurological disease were recruited from the Australian Twin Registry (ATR and underwent functional magnetic resonance imaging (fMRI during a memory encoding task, cognitive tests, and structural MRI. Type 2 diabetes was associated with significantly reduced activation in left hemisphere temporoparietal regions including angular gyrus, supramarginal gyrus, and middle temporal gyrus and significantly increased activation in bilateral posteriorly distributed regions. These findings were present in the absence of within-pair differences in standard cognitive test scores, brain volumes, or vascular lesion load. Differences in activation were more pronounced among monozygotic (MZ pairs, with MZ individuals with diabetes also displaying greater frontal activation. These results provide evidence for preclinical memory-related neuronal dysfunction in type 2 diabetes. They support the search for modifiable later-life environmental factors or epigenetic mechanisms linking type 2 diabetes and cognitive decline.

  12. Cloning, sequencing and expression of the gene encoding the extracellular metalloprotease of Aeromonas caviae.

    Science.gov (United States)

    Kawakami, K; Toma, C; Honma, Y

    2000-01-01

    A gene (apk) encoding the extracellular protease of Aeromonas caviae Ae6 has been cloned and sequenced. For cloning the gene, the DNA genomic library was screened using skim milk LB agar. One clone harboring plasmid pKK3 was selected for sequencing. Nucleotide sequencing of the 3.5 kb region of pKK3 revealed a single open reading frame (ORF) of 1,785 bp encoding 595 amino acids. The deduced polypeptide contained a putative 16-amino acid signal peptide followed by a large propeptide. The N-terminal amino acid sequence of purified recombinant protein (APK) was consistent with the DNA sequence. This result suggested a mature protein of 412 amino acids with a molecular mass of 44 kDa. However, the molecular mass of purified recombinant APK revealed 34 kDa by SDS-PAGE, suggesting that further processing at the C-terminal region took place. The 2 motifs of zinc binding sites deduced are highly conserved in the APK as well as in other zinc metalloproteases including Vibrio proteolyticus neutral protease, Emp V from Vibrio vulnificus, HA/P from Vibrio cholerae, and Pseudomonas aeruginosa elastase. Proteolytic activity was inhibited by EDTA, Zincov, 1,10-phenanthroline and tetraethylenepentamine while unaffected by the other inhibitors tested. The protease showed maximum activity at pH 7.0 and was inactivated by heating at 80 C for 15 min. These results together suggest that APK belongs to the thermolysin family of metalloendopeptidases.

  13. Four phosphoproteins with common amino termini are encoded by human cytomegalovirus AD169

    International Nuclear Information System (INIS)

    Wright, D.A.; Staprans, S.I.; Spector, D.H.

    1988-01-01

    In this report, the authors identify the proteins encoded by the 2.2-kilobase class of early transcripts arising from a region of the strain AD169 human cytomegalovirus genome (map units 0.682 to 0.713) which contains cell-related sequences. These transcripts, encoded by adjacent EcoRI fragments R and d, have a complex spliced structure with 5' and 3' coterminal ends. Antiserum directed against a synthetic 11-amino-acid peptide corresponding to the predicted amino terminus of the proteins was generated and found to immunoprecipitate four-infected-cell proteins of 84, 50, 43, and 34 kilodaltons. These proteins were phosphorylated and were associated predominantly with the nuclei of infected cells. The 43-kilodalton protein was the most abundant of the four proteins, and its level of expression remained relatively constant throughout the infection. Expression of the other proteins increased as the infection progressed. Pulse-chase analysis failed to show a precursor-product relationship between any of the proteins. A comparison of the [ 35 S]methionine-labeled tryptic peptide maps of the four proteins from infected cells and an in vitro-generated polypeptide derived from the putative first exon showed that all four infected-cell proteins were of viral origin and contained a common amino-terminal region

  14. FGF-2 antisense RNA encodes a nuclear protein with MutT-like antimutator activity.

    Science.gov (United States)

    Li, A W; Too, C K; Knee, R; Wilkinson, M; Murphy, P R

    1997-10-20

    Bidirectional transcription of the basic fibroblast growth factor (FGF-2) gene gives rise to multiple polyadenylated sense mRNAs and a unique 1.5 kb antisense transcript (FGF-AS) which is complementary to the 3'-untranslated region of the FGF-2 mRNA. The rat FGF-AS cDNA encodes a novel 35 kDa nuclear protein (GFG) with homology to the MutT family of antimutator NTPases. Antibodies against the deduced amino acid sequence of GFG detected intense immunoreactivity in the nuclei of adult rat hepatocytes. Subcellular fractionation and Western blotting confirmed the presence of a 35 kDa immunoreactive protein in the nuclear fraction and, to a lesser extent, in the mitochondrial fractions of rat liver homogenates. Recombinant GFG suppressed the spontaneous mutation rate of MutT-deficient E. coli in a complementation assay. In-frame deletion of the 53 amino acids encompassing the MutT domain eliminated this activity, confirming the catalytic function of this region in the FGF antisense gene product. These findings demonstrate for the first time that the FGF-AS transcript encodes a functional nuclear protein with MutT-related enzymatic activity.

  15. Segregated encoding of reward-identity and stimulus-reward associations in human orbitofrontal cortex.

    Science.gov (United States)

    Klein-Flügge, Miriam Cornelia; Barron, Helen Catharine; Brodersen, Kay Henning; Dolan, Raymond J; Behrens, Timothy Edward John

    2013-02-13

    A dominant focus in studies of learning and decision-making is the neural coding of scalar reward value. This emphasis ignores the fact that choices are strongly shaped by a rich representation of potential rewards. Here, using fMRI adaptation, we demonstrate that responses in the human orbitofrontal cortex (OFC) encode a representation of the specific type of food reward predicted by a visual cue. By controlling for value across rewards and by linking each reward with two distinct stimuli, we could test for representations of reward-identity that were independent of associative information. Our results show reward-identity representations in a medial-caudal region of OFC, independent of the associated predictive stimulus. This contrasts with a more rostro-lateral OFC region encoding reward-identity representations tied to the predicate stimulus. This demonstration of adaptation in OFC to reward specific representations opens an avenue for investigation of more complex decision mechanisms that are not immediately accessible in standard analyses, which focus on correlates of average activity.

  16. Beta-glucosidase variants and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Wogulis, Mark; Harris, Paul; Osborn, David

    2017-06-27

    The present invention relates to beta-glucosidase variants, e.g. beta-glucosidase variants of a parent Family GH3A beta-glucosidase from Aspergillus fumigatus. The present invention also relates to polynucleotides encoding the beta-glucosidase variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the beta-glucosidase variants.

  17. Method of implementing frequency-encoded NOT, OR and NOR ...

    Indian Academy of Sciences (India)

    2015-11-27

    Nov 27, 2015 ... Home; Journals; Pramana – Journal of Physics; Volume 73; Issue 5. Method of implementing frequency-encoded NOT, OR and NOR logic operations using lithium niobate waveguide and reflecting semiconductor optical amplifiers. Sisir Kumar Garai Sourangshu Mukhopadhyay. Volume 73 Issue 5 ...

  18. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2012-02-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  19. A spoonful of sugar: encoding and publishing in the classroom

    NARCIS (Netherlands)

    Spadini, E.

    2017-01-01

    This paper pursues the use of text encoding and digital publication in teaching textual criticism. A number of concepts and rules of textual criticism can be put into practice during a course thanks to the use of digital resources and tools. In dealing with original materials (text sources), the

  20. Practical Programming with Higher-Order Encodings and Dependent Types

    DEFF Research Database (Denmark)

    Poswolsky, Adam; Schürmann, Carsten

    2008-01-01

    utilizing HOAS free the programmer from concerns of handling explicit contexts and substitutions, our system permits programming over such encodings without making these constructs explicit, leading to concise and elegant programs. To this end our system distinguishes bindings of variables intended...

  1. Robust EPI Nyquist ghost elimination via spatial and temporal encoding.

    Science.gov (United States)

    Hoge, W Scott; Tan, Huan; Kraft, Robert A

    2010-12-01

    Nyquist ghosts are an inherent artifact in echo planar imaging acquisitions. An approach to robustly eliminate Nyquist ghosts is presented that integrates two previous Nyquist ghost correction techniques: temporal domain encoding (phase labeling for additional coordinate encoding: PLACE and spatial domain encoding (phased array ghost elimination: PAGE). Temporal encoding modulates the echo planar imaging acquisition trajectory from frame to frame, enabling one to interleave data to remove inconsistencies that occur between sampling on positive and negative gradient readouts. With PLACE, one can coherently combine the interleaved data to cancel residual Nyquist ghosts. If the level of ghosting varies significantly from image to image, however, the signal cancellation that occurs with PLACE can adversely affect SNR-sensitive applications such as perfusion imaging with arterial spin labeling. This work proposes integrating PLACE into a PAGE-based reconstruction process to yield significantly better Nyquist ghost correction that is more robust than PLACE or PAGE alone. The robustness of this method is demonstrated in the presence of magnetic field drift with an in-vivo arterial spin labeling perfusion experiment. Copyright © 2010 Wiley-Liss, Inc.

  2. Neurospora crassa fmf-1 encodes the homologue of the ...

    Indian Academy of Sciences (India)

    Neurospora crassa fmf-1 encodes the homologue of the. Schizosaccharomyces pombe Ste11p regulator of sexual development. Srividhya V. Iyer, Mukund Ramakrishnan and Durgadas P. Kasbekar. J. Genet. 88, 33–39. Figure 1. Sequence at the junction of the proximal breakpoint of T(AR173) has homology with Cen-VII ...

  3. Extraordinarily adaptive properties of the genetically encoded amino acids.

    Science.gov (United States)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves, H James

    2015-03-24

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or "chemistry space." Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

  4. Polypeptides having xylanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj; Shaghasi, Tarana

    2017-06-20

    The present invention relates to polypeptides having xylanase activity, catalytic domains, and carbohydrate binding domains, and polynucleotides encoding the polypeptides, catalytic domains, and carbohydrate binding domains. The present invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, and carbohydrate binding domains.

  5. The ternary-encoded fuzzy-neural networks

    OpenAIRE

    Semenova, Olena; Semenov, Andriy; Koval, Kostyantyn; Galka, Andriy

    2012-01-01

    When combining fuzzy logic and neural networks it is possible to get a hybrid system that can process uncertain values and can be trained. Fuzzy logic elements can be regarded as fuzzy-neural networks. In order to present a set of fuzzy values the ternary encoding is used.

  6. A Permutation Encoding Technique Applied to Genetic Algorithm ...

    African Journals Online (AJOL)

    In this paper, a permutation chromosome encoding scheme is proposed for obtaining solution to resource constrained project scheduling problem. The proposed chromosome coding method is applied to Genetic algorithm procedure and implemented through object oriented programming. The method is applied to a ...

  7. A CNOT gate between multiphoton qubits encoded in two cavities.

    Science.gov (United States)

    Rosenblum, S; Gao, Y Y; Reinhold, P; Wang, C; Axline, C J; Frunzio, L; Girvin, S M; Jiang, Liang; Mirrahimi, M; Devoret, M H; Schoelkopf, R J

    2018-02-13

    Entangling gates between qubits are a crucial component for performing algorithms in quantum computers. However, any quantum algorithm must ultimately operate on error-protected logical qubits encoded in high-dimensional systems. Typically, logical qubits are encoded in multiple two-level systems, but entangling gates operating on such qubits are highly complex and have not yet been demonstrated. Here we realize a controlled NOT (CNOT) gate between two multiphoton qubits in two microwave cavities. In this approach, we encode a qubit in the high-dimensional space of a single cavity mode, rather than in multiple two-level systems. We couple two such encoded qubits together through a transmon, which is driven by an RF pump to apply the gate within 190 ns. This is two orders of magnitude shorter than the decoherence time of the transmon, enabling a high-fidelity gate operation. These results are an important step towards universal algorithms on error-corrected logical qubits.

  8. RNAi-based silencing of genes encoding the vacuolar- ATPase ...

    African Journals Online (AJOL)

    RNAi-based silencing of genes encoding the vacuolar- ATPase subunits a and c in pink bollworm (Pectinophora gossypiella). Ahmed M. A. Mohammed. Abstract. RNA interference is a post- transcriptional gene regulation mechanism that is predominantly found in eukaryotic organisms. RNAi demonstrated a successful ...

  9. Encoding Requests to Web Service Compositions as Constraints

    NARCIS (Netherlands)

    Lazovik, Alexander; Aiello, Marco; Gennari, Rosella; van Beek, P.

    2005-01-01

    Interacting with a web service enabled marketplace in order to achieve a complex task involves sequencing a set of individual service operations, gathering information from the services, and making choices. We propose to encode the problem of issuing requests to a composition of web services as a

  10. The Role of Specificity in the Lexical Encoding of Participants

    Science.gov (United States)

    Conklin, Kathy; Koenig, Jean-Pierre; Mauner, Gail

    2004-01-01

    In addition to information about phonology, morphology and syntax, lexical entries contain semantic information about participants (e.g., Agent). However, the traditional criteria for determining how much participant information is lexically encoded have proved unreliable. We have proposed two semantic criteria (obligatoriness and selectivity)…

  11. Cytotoxic Escherichia coli strains encoding colibactin colonize 1 laboratory mice

    Science.gov (United States)

    García, Alexis; Mannion, Anthony; Feng, Yan; Madden, Carolyn M.; Bakthavatchalu, Vasudevan; Shen, Zeli; Ge, Zhongming; Fox, James G.

    2016-01-01

    Escherichia coli strains have not been fully characterized in laboratory mice and are not currently excluded from mouse colonies. Colibactin (Clb), a cytotoxin, has been associated with inflammation and cancer in humans and animals. We performed bacterial cultures utilizing rectal swab, fecal, and extra intestinal samples from clinically unaffected or affected laboratory mice. Fifty-one E. coli were isolated from 45 laboratory mice, identified biochemically, and selected isolates were serotyped. The 16S rRNA gene was amplified and sequenced for specific isolates, PCR used for clbA and clbQ gene amplification, and phylogenetic group identification was performed on all 51 E. coli strains. Clb genes were sequenced and selected E. coli isolates were characterized using a HeLa cell cytotoxicity assay. Forty-five of the 51 E. coli isolates (88 %) encoded clbA and clbQ and belonged to phylogenetic group B2. Mouse E. coli serotypes included: O2:H6, O−:H−, OM:H+, and O22:H−. Clb-encoding O2:H6 mouse E. coli isolates were cytotoxic in vitro. A Clb-encoding E. coli was isolated from a clinically affected genetically modified mouse with cystic endometrial hyperplasia. Our findings suggest that Clb-encoding E. coli colonize laboratory mice and may induce clinical and subclinical diseases that may impact experimental mouse models. PMID:27480057

  12. Encoded Extended Spectrum Beta-Lactamases Produced by ...

    African Journals Online (AJOL)

    Purpose: To investigate the distribution of plasmid-encoded extended spectrum beta-lacatamases. (ESBLs) in Lahore, Pakistan using different phenotypic and molecular methods. Methods: Escherichia coli and Klebsiella spp were obtained over a period of nineteen months (June. 2007 to December 2008). Both were tested ...

  13. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Science.gov (United States)

    Spodsberg, Nikolaj

    2016-02-23

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Science.gov (United States)

    Schnorr, Kirk; Kramer, Randall

    2016-04-05

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  15. Practical Programming with Higher-Order Encodings and Dependent Types

    DEFF Research Database (Denmark)

    Poswolsky, Adam; Schürmann, Carsten

    2008-01-01

    , tedious, and error-prone. In this paper, we describe the underlying calculus of Delphin. Delphin is a fully implemented functional-programming language supporting reasoning over higher-order encodings and dependent types, while maintaining the benefits of HOAS. More specifically, just as representations...

  16. Multiplexed Sequence Encoding: A Framework for DNA Communication

    Science.gov (United States)

    Zakeri, Bijan; Carr, Peter A.; Lu, Timothy K.

    2016-01-01

    Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication—data encoding, data transfer & data extraction—and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system—Multiplexed Sequence Encoding (MuSE)—that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA. PMID:27050646

  17. Learning from Number Board Games: You Learn What You Encode

    Science.gov (United States)

    Laski, Elida V.; Siegler, Robert S.

    2014-01-01

    We tested the hypothesis that encoding the numerical-spatial relations in a number board game is a key process in promoting learning from playing such games. Experiment 1 used a microgenetic design to examine the effects on learning of the type of counting procedure that children use. As predicted, having kindergartners count-on from their current…

  18. Topological quantum error correction with optimal encoding rate

    International Nuclear Information System (INIS)

    Bombin, H.; Martin-Delgado, M. A.

    2006-01-01

    We prove the existence of topological quantum error correcting codes with encoding rates k/n asymptotically approaching the maximum possible value. Explicit constructions of these topological codes are presented using surfaces of arbitrary genus. We find a class of regular toric codes that are optimal. For physical implementations, we present planar topological codes

  19. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    Science.gov (United States)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

    2015-01-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

  20. How Does Intentionality of Encoding Affect Memory for Episodic Information?

    Science.gov (United States)

    Craig, Michael; Butterworth, Karla; Nilsson, Jonna; Hamilton, Colin J.; Gallagher, Peter; Smulders, Tom V.

    2016-01-01

    Episodic memory enables the detailed and vivid recall of past events, including target and wider contextual information. In this paper, we investigated whether/how encoding intentionality affects the retention of target and contextual episodic information from a novel experience. Healthy adults performed (1) a "What-Where-When"…

  1. Encoding, Memory, and Transcoding Deficits in Childhood Apraxia of Speech

    Science.gov (United States)

    Shriberg, Lawrence D.; Lohmeier, Heather L.; Strand, Edythe A.; Jakielski, Kathy J.

    2012-01-01

    A central question in Childhood Apraxia of Speech (CAS) is whether the core phenotype is limited to transcoding (planning/programming) deficits or if speakers with CAS also have deficits in auditory-perceptual "encoding" (representational) and/or "memory" (storage and retrieval of representations) processes. We addressed this and other questions…

  2. PROTOTIPE KOMPRESI LOSSLESS AUDIO CODEC MENGGUNAKAN ENTROPY ENCODING

    OpenAIRE

    Andreas Soegandi

    2010-01-01

    The purpose of this study was to perform lossless compression on the uncompress audio file audio to minimize file size without reducing the quality. The application is developed using the entropy encoding compression method with rice coding technique. For the result, the compression ratio is good enough and easy to be developed because the algorithm is quite simple. 

  3. Prototipe Kompresi Lossless Audio Codec Menggunakan Entropy Encoding

    Directory of Open Access Journals (Sweden)

    Andreas Soegandi

    2010-12-01

    Full Text Available The purpose of this study was to perform lossless compression on the uncompress audio file audio to minimize file size without reducing the quality. The application is developed using the entropy encoding compression method with rice coding technique. For the result, the compression ratio is good enough and easy to be developed because the algorithm is quite simple. 

  4. Overexpression of BrSAC1 encoding a phosphoinositide ...

    African Journals Online (AJOL)

    This study demonstrates the isolation and characterization of cDNA encoding a phosphoinositide phosphatase (PIP) from a stem cell cDNA library of Chinese cabbage (Brassica rapa) seedling. The full length gene (BrSAC1; GenBank accession no., GU434275) contained 1999 base pairs (bp), with an open reading frame of ...

  5. Transcriptional modulation of genes encoding nitrate reductase in ...

    African Journals Online (AJOL)

    2016-10-26

    Oct 26, 2016 ... The free aluminum (Al) content in soil can reach levels that are toxic to plants, and this has frequently limited increased productivity of cultures. Four genes encoding nitrate reductase (NR) were identified, named ZmNR1–4. With the aim of evaluating NR activity and the transcriptional modulation of the.

  6. Transcriptional modulation of genes encoding nitrate reductase in ...

    African Journals Online (AJOL)

    The free aluminum (Al) content in soil can reach levels that are toxic to plants, and this has frequently limited increased productivity of cultures. Four genes encoding nitrate reductase (NR) were identified, named ZmNR1–4. With the aim of evaluating NR activity and the transcriptional modulation of the ZmNR1, ZmNR2, ...

  7. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    Science.gov (United States)

    Harris, Paul; Golightly, Elizabeth

    2007-07-17

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  8. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Schnorr, Kirk; Kramer, Randall

    2017-08-08

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having beta-xylosidase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Liu, Ye; Duan, Junxin; Tang, Lan; McBrayer, Brett

    2017-07-04

    The present invention relates to isolated polypeptides having beta-xylosidase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Polypeptides having xylanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Lopez de Leon, Alfredo; Rey, Michael

    2017-09-26

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  11. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Tang, Lan; Duan, Junxin

    2017-02-07

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding the same

    Science.gov (United States)

    Duan, Junxin; Schnorr, Kirk Matthew; Wu, Wenping

    2013-11-19

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Chimeric polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Science.gov (United States)

    Wogulis, Mark; Sweeney, Matthew; Heu, Tia

    2017-06-14

    The present invention relates to chimeric GH61 polypeptides having cellulolytic enhancing activity. The present invention also relates to polynucleotides encoding the chimeric GH61 polypeptides; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the chimeric GH61 polypeptides.

  14. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Stringer, Mary Ann; McBrayer, Brett

    2016-11-29

    The present invention relates to isolated polypeptides having cellobiohydrolase activity, catalytic domains, and cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains, and cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, or cellulose binding domains.

  15. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Joergensen, Christian; Kramer, Randall

    2016-11-29

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  16. Polypeptides having xylanase activity and polynucleotides encoding same

    Science.gov (United States)

    Tang, Lan; Liu, Ye; Duan, Junxin; Hanshu, Ding

    2012-10-30

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polynucleotides encoding polypeptides having beta-glucosidase activity

    Science.gov (United States)

    Harris, Paul; Golightly, Elizabeth

    2010-03-02

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  18. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Science.gov (United States)

    Maiyuran, Suchindra; Kramer, Randall; Harris, Paul

    2013-10-29

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  19. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2016-11-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Science.gov (United States)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2012-10-16

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  1. Polypeptides having xylanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Lopez de Leon, Alfredo; Rey, Michael

    2016-05-31

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2016-06-14

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  3. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Lan; Liu, Ye; Duan, Junxin; Wu, Wenping; Kramer, Randall

    2017-09-19

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj; Shagasi, Tarana

    2017-05-30

    The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.

  5. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Science.gov (United States)

    Harris, Paul; Lopez de Leon, Alfredo; Rey, Michael; Ding, Hanshu; Vlasenko, Elena

    2010-11-02

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  6. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  7. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2017-09-05

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  8. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Schnorr, Kirk; Kramer, Randall

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having xylanase activity and polynucleotides encoding the same

    Science.gov (United States)

    Spodsberg, Nikolaj [Bagsvaed, DK

    2014-01-07

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The inventino also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Neural Activity during Encoding Predicts False Memories Created by Misinformation

    Science.gov (United States)

    Okado, Yoko; Stark, Craig E. L.

    2005-01-01

    False memories are often demonstrated using the misinformation paradigm, in which a person's recollection of a witnessed event is altered after exposure to misinformation about the event. The neural basis of this phenomenon, however, remains unknown. The authors used fMRI to investigate encoding processes during the viewing of an event and…

  11. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    Science.gov (United States)

    Morant, Marc Dominique

    2014-10-14

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Measurement of safety rod trajectory using digital optical encoder

    International Nuclear Information System (INIS)

    Milovanovic, S.; Pesic, M.; Milovanovic, T.

    1996-01-01

    In this paper a rod drop position - time function z(t) is measured using new method - with a digital displacement transducer and digital optical incremental encoder connected to a serial communication port of a personal computer. Some improvements, comparing to the previously proposed method are explained. Also, some possible applications in analysis of reactor dynamics and kinetics are proposed. (author)

  13. Assessment of a DNA Vaccine Encoding Burkholderia pseudomallei Bacterioferritin

    Science.gov (United States)

    2007-08-01

    excised by restriction enzyme digestion with Xba I and subcloned into the mammalian expression vector pcDNA3.1start, to create the DNA vaccine...Lewis, J. T. August, and E. T. Marques. 2006. DNA Encoding an HIV -1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad

  14. EGVI endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2008-04-01

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  15. EGVII endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2009-05-05

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  16. Amsacta moorei entomopoxvirus encodes a functional DNA photolyase (AMV025)

    NARCIS (Netherlands)

    Nalcacioglu, R.; Dizman, Y.A.; Vlak, J.M.; Demirbag, Z.; Oers, van M.M.

    2010-01-01

    The major damage induced in DNA by ultraviolet light is the induction of cyclobutane pyrimidine dimers (CPDs). Amsacta moorei entomopoxvirus (AMEV) encodes a CPD photolyase (AMV025) with a putative role in converting these dimers back into monomers. In infected Lymantria dispar cells transcription

  17. Cloning, expression and characterisation of a novel gene encoding ...

    African Journals Online (AJOL)

    Cloning, expression and characterisation of a novel gene encoding a chemosensory protein from Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) ... The BtabCSP amino acid residues deduced from the respective full-length cDNA shares four conserved cysteine motifs with known CSPs from other insects. Homology ...

  18. RNAi-based silencing of genes encoding the vacuolar- ATPase ...

    African Journals Online (AJOL)

    2016-11-09

    Nov 9, 2016 ... Spodoptera exigua larval development by silencing chitin synthase gene with RNA interference. Bull. Entomol. Res. 98:613-619. Dow JAT (1999). The Multifunctional Drosophila melanogaster V-. ATPase is encoded by a multigene family. J. Bioenerg. Biomembr. 31:75-83. Fire A, Xu SQ, Montgomery MK, ...

  19. EGVII endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2013-07-16

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  20. EGVI endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-06-06

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  1. EGVIII endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-23

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl8, and the corresponding EGVIII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVIII, recombinant EGVIII proteins and methods for producing the same.

  2. Molecular cloning and characterization of a gene encoding RING ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    Molecular cloning and characterization of a gene encoding RING zinc finger ankyrin protein from drought-tolerant Artemisia desertorum. XIUHONG YANG, CHAO SUN, YUANLEI HU and ZHONGPING LIN. *. College of Life Sciences, National Key Laboratory of Protein Engineering and Plant Genetic Engineering, Peking.

  3. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Liu, Ye; Duan, Junxin; Tang, Lan

    2018-01-30

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. A MPEG-4 encoder based on TMS320C6416

    Science.gov (United States)

    Li, Gui-ju; Liu, Wei-ning

    2013-08-01

    Engineering and products need to achieve real-time video encoding by DSP, but the high computational complexity and huge amount of data requires that system has high data throughput. In this paper, a real-time MPEG-4 video encoder is designed based on TMS320C6416 platform. The kernel is the DSP of TMS320C6416T and FPGA chip f as the organization and management of video data. In order to control the flow of input and output data. Encoded stream is output using the synchronous serial port. The system has the clock frequency of 1GHz and has up to 8000 MIPS speed processing capacity when running at full speed. Due to the low coding efficiency of MPEG-4 video encoder transferred directly to DSP platform, it is needed to improve the program structure, data structures and algorithms combined with TMS320C6416T characteristics. First: Design the image storage architecture by balancing the calculation spending, storage space cost and EDMA read time factors. Open up a more buffer in memory, each buffer cache 16 lines of video data to be encoded, reconstruction image and reference image including search range. By using the variable alignment mode of the DSP, modifying the definition of structure variables and change the look-up table which occupy larger space with a direct calculation array to save memory space. After the program structure optimization, the program code, all variables, buffering buffers and the interpolation image including the search range can be placed in memory. Then, as to the time-consuming process modules and some functions which are called many times, the corresponding modules are written in parallel assembly language of TMS320C6416T which can increase the running speed. Besides, the motion estimation algorithm is improved by using a cross-hexagon search algorithm, The search speed can be increased obviously. Finally, the execution time, signal-to-noise ratio and compression ratio of a real-time image acquisition sequence is given. The experimental

  5. Structural region

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Structural region. The two groups had 4 substitutions similar to Yawat strain. The Yawat strain had 5 unique mutations. 3 in the E2 region and 2 in the E1 region. The mutation, I702V (E2), though different from all the recent Indian and Reunion sequences was similar ...

  6. Human visual system automatically encodes sequential regularities of discrete events.

    Science.gov (United States)

    Kimura, Motohiro; Schröger, Erich; Czigler, István; Ohira, Hideki

    2010-06-01

    For our adaptive behavior in a dynamically changing environment, an essential task of the brain is to automatically encode sequential regularities inherent in the environment into a memory representation. Recent studies in neuroscience have suggested that sequential regularities embedded in discrete sensory events are automatically encoded into a memory representation at the level of the sensory system. This notion is largely supported by evidence from investigations using auditory mismatch negativity (auditory MMN), an event-related brain potential (ERP) correlate of an automatic memory-mismatch process in the auditory sensory system. However, it is still largely unclear whether or not this notion can be generalized to other sensory modalities. The purpose of the present study was to investigate the contribution of the visual sensory system to the automatic encoding of sequential regularities using visual mismatch negativity (visual MMN), an ERP correlate of an automatic memory-mismatch process in the visual sensory system. To this end, we conducted a sequential analysis of visual MMN in an oddball sequence consisting of infrequent deviant and frequent standard stimuli, and tested whether the underlying memory representation of visual MMN generation contains only a sensory memory trace of standard stimuli (trace-mismatch hypothesis) or whether it also contains sequential regularities extracted from the repetitive standard sequence (regularity-violation hypothesis). The results showed that visual MMN was elicited by first deviant (deviant stimuli following at least one standard stimulus), second deviant (deviant stimuli immediately following first deviant), and first standard (standard stimuli immediately following first deviant), but not by second standard (standard stimuli immediately following first standard). These results are consistent with the regularity-violation hypothesis, suggesting that the visual sensory system automatically encodes sequential

  7. Electroencephalographic brain dynamics of memory encoding in emotionally arousing context

    Directory of Open Access Journals (Sweden)

    Carlos Enrique eUribe

    2011-06-01

    Full Text Available Emotional content/context enhances declarative memory through modulation of encoding and retrieval mechanisms. At encoding, neurophysiological data have consistently demonstrated the subsequent memory effect in theta and gamma oscillations. Yet, the existing studies were focused on the emotional content effect and let the emotional context effect unexplored. We hypothesized that theta and gamma oscillations show higher evoked/induced activity during the encoding of visual stimuli when delivered in an emotionally arousing context. Twenty-five healthy volunteers underwent evoked potentials recordings using a 21 scalp electrodes montage. They attended to an audiovisual test of emotional declarative memory being randomly assigned to either emotionally arousing or neutral context. Visual stimulus presentation was used as the time-locking event. Grand-averages of the evoked potentials and evoked spectral perturbations were calculated for each volunteer. Evoked potentials showed a higher negative deflection from 80 to 140 ms for the emotional condition. Such effect was observed over central, frontal and prefrontal locations bilaterally. Evoked theta power was higher in left parietal, central, frontal and prefrontal electrodes from -50 to 300 ms in the emotional condition. Evoked gamma power was higher in the emotional condition with a spatial distribution that overlapped at some points with the theta topography. The early theta power increase could be related to expectancy induced by auditory information processing that facilitates visual encoding in emotional contexts. Together, our results suggest that declarative memory enhancement for both emotional content and emotional context are supported by similar neural mechanisms at encoding, and offer new evidence about the brain processing of relevant environmental stimuli.

  8. [ENCODE apophenia or a panglossian analysis of the human genome].

    Science.gov (United States)

    Casane, Didier; Fumey, Julien; Laurenti, Patrick

    2015-01-01

    In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world. © 2015 médecine/sciences – Inserm.

  9. Polypeptide structure and encoding location of the adenovirus serotype 2 late, nonstructural 33K protein

    International Nuclear Information System (INIS)

    Oosterom-Dragon, E.A.; Anderson, C.W.

    1983-01-01

    Radiochemical microsequence analysis of selected tryptic peptides of the adenovirus type 2 33K nonstructural protein has revealed the precise region of the genomic nucleotide sequence that encodes this protein. The initiation codon for the 33K protein lies 606 nucleotides to the right of the EcoRI restriction site at 70.7 map units and 281 nucleotides to the left of the postulated carboxyterminal codon of the adenovirus 100K protein. The coding regions for these two proteins thus overlap; however, the 33K protein is derived from the +1 frame with respect to the postulated 100K reading frame. Our results contradict an earlier published report suggesting that these two proteins share extensive amino acid sequence homology. The published nucleotide sequence of the Ad2 EcoRI-F fragment (70.7 to 75.9 map units) cannot accomodate in a single reading frame the peptide sequences of the 33K protein that we have determined. Sequence analysis of DNA fragments derived from virus has confirmed the published nucleotide sequence in all critical regions with respect to the coding region for the 33K protein. Consequently, our data are only consistent with the existence of an mRNA splice within the coding for 33K. Consensus donor and acceptor splice sequences have been located that would predict the removal of 202 nucleotides from the transcripts for the 33K protein. Removal of these nucleotides would explain the structure of a peptide that cannot otherwise be directly encoded by the EcoRI-F fragment. Identification of the precise splice points by peptide sequencing has permitted a prediction of the complete amino acid sequence for the 33K protein

  10. Genomic cloning and characterization of a PPA gene encoding a mannose-binding lectin from Pinellia pedatisecta.

    Science.gov (United States)

    Lin, Juan; Zhou, Xuanwei; Fei, Jiong; Liao, Zhihua; Jin, Wang; Sun, Xiaofen; Tang, Kexuan

    2006-04-01

    A gene encoding a mannose-binding lectin, Pinellia pedatisecta agglutinin (PPA), was isolated from leaves of Pinellia pedatisecta using genomic walker technology. The ppa contained an 1140-bp 5'-upstream region, a 771-bp open reading frame (ORF) and an 829-bp 3'-downstream region. The ORF encoded a precursor polypeptide of 256 amino acid residues with a 24-amino acid signal peptide. There were one putative TATA box and six possible CAAT boxes lying in the 5'-upstream region of ppa. The ppa showed significant similarity at the nucleic acid level with genes encoding mannose-binding lectins from other Araceae species such as Pinellia ternata, Arisaema hererophyllum, Colocasia esculenta and Arum maculatum. At the amino acid level, PPA also shared varying homology (ranging from 40% to 85%) with mannose-binding lectins from other plant species, such as those from Araceae, Alliaceae, Iridaceae, Lillaceae, Amaryllidaceae and Bromeliaceae. The cloning of the ppa gene not only provides a basis for further investigation of PPA's structure, expression and regulation mechanism, but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into tobacco and rice in the future.

  11. Occipitoparietal contributions to recognition memory: stimulus encoding prompted by verbal instructions and operant contingencies

    Directory of Open Access Journals (Sweden)

    Schlund Michael W

    2007-08-01

    Full Text Available Abstract Background Many human neuroimaging investigations on recognition memory employ verbal instructions to direct subject's attention to a stimulus attribute. But do the same or a similar neurophysiological process occur during nonverbal experiences, such as those involving contingency-shaped responses? Establishing the spatially distributed neural network underlying recognition memory for instructed stimuli and operant, contingency-shaped (i.e., discriminative stimuli would extend the generality of contemporary domain-general views of recognition memory and clarify the involvement of declarative memory processes in human operant behavior. Methods Fifteen healthy adults received equivalent amounts of exposure to three different stimulus sets prior to neuroimaging. Encoding of one stimulus set was prompted using instructions that emphasized memorizing stimuli (Instructed. In contrast, encoding of two additional stimulus sets was prompted using a GO/NO-GO operant task, in which contingencies shaped appropriate GO and NO-GO responding. During BOLD functional MRI, subjects completed two recognition tasks. One required passive viewing of stimuli. The second task required recognizing whether a presented stimulus was a GO/NO-GO stimulus, an Instructed stimulus, or novel (NEW stimulus. Retrieval success related to recognition memory was isolated by contrasting activation from each stimulus set to a novel stimulus (i.e., an OLD > NEW contrast. To explore differences potentially related to source memory, separate contrasts were performed between stimulus sets. Results No regions reached supralevel thresholds during the passive viewing task. However, a relatively similar set of regions was activated during active recognition regardless of the methods and included dorsolateral and ventrolateral prefrontal cortex, right inferior and posterior parietal regions and the occipitoparietal region, precuneus, lingual, fusiform gyri and cerebellum. Results also

  12. Tape measuring system using linear encoder and digital camera

    Science.gov (United States)

    Eom, Tae Bong; Jeong, Don Young; Kim, Myung Soon; Kim, Jae Wan; Kim, Jong Ahn

    2013-04-01

    We have designed and constructed the calibration system of line standards such as tape and rule for the secondary calibration laboratories. The system consists of the main body with linear stage and linear encoder, the optical microscope with digital camera, and the computer. The base of the system is a aluminum profile with 2.9 m length, 0.09 m height and 0.18 m width. The linear stage and the linear encoder are fixed on the aluminum profile. The micro-stage driven by micrometer is fixed on the carriage of the long linear stage, and the optical microscope with digital camera and the tablet PC are on the this stage. The linear encoder counts the moving distance of the linear stage with resolution of 1 μm and its counting value is transferred to the tablet PC. The image of the scale mark of the tape is captured by the CCD camera of optical microscope and transferred to the PC through USB interface. The computer automatically determines the center of the scale mark by image processing technique and at the same time reads the moving distance of the linear stage. As a result, the computer can calculate the interval between the scale marks of the tape. In order to achieve the high accuracy, the linear encoder should be calibrated using the laser interferometer or the rigid steel rule. This calibration data of the linear encoder is stored at the computer and the computer corrects the reading value of the linear encoder. In order to determine the center of the scale mark, we use three different algorithms. First, the image profile over specified threshold level is fitted in even order polynomial and the axis of the polynomial is used as the center of the line. Second, the left side and right side areas at the center of the image profile are calculated so that two areas are same. Third, the left and right edges of the image profile are determined at every intensity level of the image and the center of the graduation is calculated as an average of the centers of the left

  13. Identification of functional elements and regulatory circuits by Drosophila modENCODE

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V.; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L.; Landolin, Jane M.; Bristow, Christopher A.; Ma, Lijia; Lin, Michael F.; Washietl, Stefan; Arshinoff, Bradley I.; Ay, Ferhat; Meyer, Patrick E.; Robine, Nicolas; Washington, Nicole L.; Stefano, Luisa Di; Berezikov, Eugene; Brown, Christopher D.; Candeias, Rogerio; Carlson, Joseph W.; Carr, Adrian; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Tolstorukov, Michael Y.; Will, Sebastian; Alekseyenko, Artyom A.; Artieri, Carlo; Booth, Benjamin W.; Brooks, Angela N.; Dai, Qi; Davis, Carrie A.; Duff, Michael O.; Feng, Xin; Gorchakov, Andrey A.; Gu, Tingting; Henikoff, Jorja G.; Kapranov, Philipp; Li, Renhua; MacAlpine, Heather K.; Malone, John; Minoda, Aki; Nordman, Jared; Okamura, Katsutomo; Perry, Marc; Powell, Sara K.; Riddle, Nicole C.; Sakai, Akiko; Samsonova, Anastasia; Sandler, Jeremy E.; Schwartz, Yuri B.; Sher, Noa; Spokony, Rebecca; Sturgill, David; van Baren, Marijke; Wan, Kenneth H.; Yang, Li; Yu, Charles; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca; Ahmad, Kami; Andrews, Justen; Berger, Bonnie; Brenner, Steven E.; Brent, Michael R.; Cherbas, Lucy; Elgin, Sarah C. R.; Gingeras, Thomas R.; Grossman, Robert; Hoskins, Roger A.; Kaufman, Thomas C.; Kent, William; Kuroda, Mitzi I.; Orr-Weaver, Terry; Perrimon, Norbert; Pirrotta, Vincenzo; Posakony, James W.; Ren, Bing; Russell, Steven; Cherbas, Peter; Graveley, Brenton R.; Lewis, Suzanna; Micklem, Gos; Oliver, Brian; Park, Peter J.; Celniker, Susan E.; Henikoff, Steven; Karpen, Gary H.; Lai, Eric C.; MacAlpine, David M.; Stein, Lincoln D.; White, Kevin P.; Kellis, Manolis

    2010-12-22

    of {approx}40% of the protein and nonprotein-coding genes [FlyBase 5.12 (4)] have been determined from cDNA collections (5, 6), manual curation of gene models (7), gene mutations and comprehensive genome-wide RNA interference screens (8-10), and comparative genomic analyses (11, 12). The Drosophila modENCODE project has generated more than 700 data sets that profile transcripts, histone modifications and physical nucleosome properties, general and specific transcription factors (TFs), and replication programs in cell lines, isolated tissues, and whole organisms across several developmental stages (Fig. 1). Here, we computationally integrate these data sets and report (i) improved and additional genome annotations, including full-length proteincoding genes and peptides as short as 21 amino acids; (ii) noncoding transcripts, including 132 candidate structural RNAs and 1608 nonstructural transcripts; (iii) additional Argonaute (Ago)-associated small RNA genes and pathways, including new microRNAs (miRNAs) encoded within protein-coding exons and endogenous small interfering RNAs (siRNAs) from 3-inch untranslated regions; (iv) chromatin 'states' defined by combinatorial patterns of 18 chromatin marks that are associated with distinct functions and properties; (v) regions of high TF occupancy and replication activity with likely epigenetic regulation; (vi)mixed TF and miRNA regulatory networks with hierarchical structure and enriched feed-forward loops; (vii) coexpression- and co-regulation-based functional annotations for nearly 3000 genes; (viii) stage- and tissue-specific regulators; and (ix) predictive models of gene expression levels and regulator function.

  14. A transcription unit at the ken and barbie gene locus encodes a novel Drosophila zinc finger protein.

    Science.gov (United States)

    Kühnlein, R P; Chen, C K; Schuh, R

    1998-12-01

    We describe a novel Drosophila transcription unit, located in chromosome region 60A. It encodes a zinc finger protein that is expressed in distinct spatial and temporal patterns during embryogenesis. Its initial expression occurs in a stripe at the anterior and the posterior trunk boundary, respectively. The two stripes are activated and spatially controlled by gap-gene activities. The P-element of the enhancer trap line l(2)02970 is inserted in the 5'-region of the transcript and causes a ken and barbie (ken) phenotype, associated with malformation of male genital structures.

  15. Analysis of single nucleotide polymorphisms in uridine/cytidine kinase gene encoding metabolic enzyme of 3'-ethynylcytidine.

    Science.gov (United States)

    Hasegawa, Takako; Futagami, Michiko; Kim, Hey-Sook; Matsuda, Akira; Wataya, Yusuke

    2002-01-01

    We investigated single nucleotide polymorphisms (SNPs) in uck2 gene encoding metabolic enzyme of 3'-ethynylcytidine (ECyd) which were associated with drug response of ECyd, and the newly synthesized antitumor ribonucleoside analog. We analized that on exon-intron junction and exon region to affect the qualitative alteration of gene product directly in ECyd sensitive and resistant human cancer cell lines. As the results, cSNP and sSNP were detected in exon 4. In the promoter region, 3 SNPs were detected. Our data seem to be able to give an important knowledge, when ECyd is applied clinically.

  16. REGIONAL COMPETITIVENESS

    OpenAIRE

    Krželj-Čolović, Zorica

    2015-01-01

    Individual city and regional authorities in many countries have themselves taken up the issue of “competitiveness” as part of their own economic development agendas: competitiveness has come to be regarded as critical for understanding and promoting local economic performance. Like their national counterparts, regional and city policy-makers have become preoccupied with knowing the relative competitive standing of their local economies compared with others, not just other regions and cities w...

  17. Znojmo Region

    OpenAIRE

    SANALLA, Merkéta

    2014-01-01

    This paper presents the main findings which are focusing interdisciplinary on contemporary trends in the regional policy in Central Europe. These findings are illustrated on regional policy activities in Znojmo region which is a pioneer in so called paradiplomacy activities. These deal consequents upon geographical emplacement on the border of the former Eastern Bloc which constitute area of renewed relations in united central Europe nowadays. These results are obtained by using classical the...

  18. Neural Correlates of Early Sound Encoding and their Relationship to Speech-in-Noise Perception.

    Science.gov (United States)

    Coffey, Emily B J; Chepesiuk, Alexander M P; Herholz, Sibylle C; Baillet, Sylvain; Zatorre, Robert J

    2017-01-01

    Speech-in-noise (SIN) perception is a complex cognitive skill that affects social, vocational, and educational activities. Poor SIN ability particularly affects young and elderly populations, yet varies considerably even among healthy young adults with normal hearing. Although SIN skills are known to be influenced by top-down processes that can selectively enhance lower-level sound representations, the complementary role of feed-forward mechanisms and their relationship to musical training is poorly understood. Using a paradigm that minimizes the main top-down factors that have been implicated in SIN performance such as working memory, we aimed to better understand how robust encoding of periodicity in the auditory system (as measured by the frequency-following response) contributes to SIN perception. Using magnetoencephalograpy, we found that the strength of encoding at the fundamental frequency in the brainstem, thalamus, and cortex is correlated with SIN accuracy. The amplitude of the slower cortical P2 wave was previously also shown to be related to SIN accuracy and FFR strength; we use MEG source localization to show that the P2 wave originates in a temporal region anterior to that of the cortical FFR. We also confirm that the observed enhancements were related to the extent and timing of musicianship. These results are consistent with the hypothesis that basic feed-forward sound encoding affects SIN perception by providing better information to later processing stages, and that modifying this process may be one mechanism through which musical training might enhance the auditory networks that subserve both musical and language functions.

  19. How does the sparse memory "engram" neurons encode the memory of a spatial-temporal event?

    Directory of Open Access Journals (Sweden)

    Ji-Song Guan

    2016-08-01

    Full Text Available Episodic memory in human brain is not a fixed 2-D picture but a highly dynamic movie serial, integrating information at both the temporal and the spatial domains. Recent studies in neuroscience reveal that memory storage and recall are closely related to the activities in discrete memory engram (trace neurons within the dentate gyrus region of hippocampus and the layer 2/3 of neocortex. More strikingly, optogenetic reactivation of those memory trace neurons is able to trigger the recall of naturally encoded memory. It is still unknown how the discrete memory traces encode and reactivate the memory. Considering a particular memory normally represents a natural event, which consists of information at both the temporal and spatial domains, it is unknown how the discrete trace neurons could reconstitute such enriched information in the brain. Furthermore, as the optogenetic-stimuli induced recall of memory did not depend on firing pattern of the memory traces, it is most likely that the spatial activation pattern, but not the temporal activation pattern of the discrete memory trace neurons encodes the memory in the brain. How does the neural circuit convert the activities in the spatial domain into the temporal domain to reconstitute memory of a natural event? By reviewing the literature, here we present how the memory engram (trace neurons are selected and consolidated in the brain. Then, we will discuss the main challenges in the memory trace theory. In the end, we will provide a plausible model of memory trace cell network, underlying the conversion of neural activities between the spatial domain and the temporal domain. We will also discuss on how the activation of sparse memory trace neurons might trigger the replay of neural activities in specific temporal patterns.

  20. Neural Correlates of Early Sound Encoding and their Relationship to Speech-in-Noise Perception

    Directory of Open Access Journals (Sweden)

    Emily B. J. Coffey

    2017-08-01

    Full Text Available Speech-in-noise (SIN perception is a complex cognitive skill that affects social, vocational, and educational activities. Poor SIN ability particularly affects young and elderly populations, yet varies considerably even among healthy young adults with normal hearing. Although SIN skills are known to be influenced by top-down processes that can selectively enhance lower-level sound representations, the complementary role of feed-forward mechanisms and their relationship to musical training is poorly understood. Using a paradigm that minimizes the main top-down factors that have been implicated in SIN performance such as working memory, we aimed to better understand how robust encoding of periodicity in the auditory system (as measured by the frequency-following response contributes to SIN perception. Using magnetoencephalograpy, we found that the strength of encoding at the fundamental frequency in the brainstem, thalamus, and cortex is correlated with SIN accuracy. The amplitude of the slower cortical P2 wave was previously also shown to be related to SIN accuracy and FFR strength; we use MEG source localization to show that the P2 wave originates in a temporal region anterior to that of the cortical FFR. We also confirm that the observed enhancements were related to the extent and timing of musicianship. These results are consistent with the hypothesis that basic feed-forward sound encoding affects SIN perception by providing better information to later processing stages, and that modifying this process may be one mechanism through which musical training might enhance the auditory networks that subserve both musical and language functions.

  1. Local Patch Vectors Encoded by Fisher Vectors for Image Classification

    Directory of Open Access Journals (Sweden)

    Shuangshuang Chen

    2018-02-01

    Full Text Available The objective of this work is image classification, whose purpose is to group images into corresponding semantic categories. Four contributions are made as follows: (i For computational simplicity and efficiency, we directly adopt raw image patch vectors as local descriptors encoded by Fisher vector (FV subsequently; (ii For obtaining representative local features within the FV encoding framework, we compare and analyze three typical sampling strategies: random sampling, saliency-based sampling and dense sampling; (iii In order to embed both global and local spatial information into local features, we construct an improved spatial geometry structure which shows good performance; (iv For reducing the storage and CPU costs of high dimensional vectors, we adopt a new feature selection method based on supervised mutual information (MI, which chooses features by an importance sorting algorithm. We report experimental results on dataset STL-10. It shows very promising performance with this simple and efficient framework compared to conventional methods.

  2. Power calculation of linear and angular incremental encoders

    Science.gov (United States)

    Prokofev, Aleksandr V.; Timofeev, Aleksandr N.; Mednikov, Sergey V.; Sycheva, Elena A.

    2016-04-01

    Automation technology is constantly expanding its role in improving the efficiency of manufacturing and testing processes in all branches of industry. More than ever before, the mechanical movements of linear slides, rotary tables, robot arms, actuators, etc. are numerically controlled. Linear and angular incremental photoelectric encoders measure mechanical motion and transmit the measured values back to the control unit. The capabilities of these systems are undergoing continual development in terms of their resolution, accuracy and reliability, their measuring ranges, and maximum speeds. This article discusses the method of power calculation of linear and angular incremental photoelectric encoders, to find the optimum parameters for its components, such as light emitters, photo-detectors, linear and angular scales, optical components etc. It analyzes methods and devices that permit high resolutions in the order of 0.001 mm or 0.001°, as well as large measuring lengths of over 100 mm. In linear and angular incremental photoelectric encoders optical beam is usually formulated by a condenser lens passes through the measuring unit changes its value depending on the movement of a scanning head or measuring raster. Past light beam is converting into an electrical signal by the photo-detecter's block for processing in the electrical block. Therefore, for calculating the energy source is a value of the desired value of the optical signal at the input of the photo-detecter's block, which reliably recorded and processed in the electronic unit of linear and angular incremental optoelectronic encoders. Automation technology is constantly expanding its role in improving the efficiency of manufacturing and testing processes in all branches of industry. More than ever before, the mechanical movements of linear slides, rotary tables, robot arms, actuators, etc. are numerically controlled. Linear and angular incremental photoelectric encoders measure mechanical motion and

  3. Context dependent prediction and category encoding for DPCM image compression

    Science.gov (United States)

    Beaudet, Paul R.

    1989-01-01

    Efficient compression of image data requires the understanding of the noise characteristics of sensors as well as the redundancy expected in imagery. Herein, the techniques of Differential Pulse Code Modulation (DPCM) are reviewed and modified for information-preserving data compression. The modifications include: mapping from intensity to an equal variance space; context dependent one and two dimensional predictors; rationale for nonlinear DPCM encoding based upon an image quality model; context dependent variable length encoding of 2x2 data blocks; and feedback control for constant output rate systems. Examples are presented at compression rates between 1.3 and 2.8 bits per pixel. The need for larger block sizes, 2D context dependent predictors, and the hope for sub-bits-per-pixel compression which maintains spacial resolution (information preserving) are discussed.

  4. Intonational speech prosody encoding in the human auditory cortex.

    Science.gov (United States)

    Tang, C; Hamilton, L S; Chang, E F

    2017-08-25

    Speakers of all human languages regularly use intonational pitch to convey linguistic meaning, such as to emphasize a particular word. Listeners extract pitch movements from speech and evaluate the shape of intonation contours independent of each speaker's pitch range. We used high-density electrocorticography to record neural population activity directly from the brain surface while participants listened to sentences that varied in intonational pitch contour, phonetic content, and speaker. Cortical activity at single electrodes over the human superior temporal gyrus selectively represented intonation contours. These electrodes were intermixed with, yet functionally distinct from, sites that encoded different information about phonetic features or speaker identity. Furthermore, the representation of intonation contours directly reflected the encoding of speaker-normalized relative pitch but not absolute pitch. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  5. Enhanced tactile encoding and memory recognition in congenital blindness.

    Science.gov (United States)

    D'Angiulli, Amedeo; Waraich, Paul

    2002-06-01

    Several behavioural studies have shown that early-blind persons possess superior tactile skills. Since neurophysiological data show that early-blind persons recruit visual as well as somatosensory cortex to carry out tactile processing (cross-modal plasticity), blind persons' sharper tactile skills may be related to cortical re-organisation resulting from loss of vision early in their life. To examine the nature of blind individuals' tactile superiority and its implications for cross-modal plasticity, we compared the tactile performance of congenitally totally blind, low-vision and sighted children on raised-line picture identification test and re-test, assessing effects of task familiarity, exploratory strategy and memory recognition. What distinguished the blind from the other children was higher memory recognition and higher tactile encoding associated with efficient exploration. These results suggest that enhanced perceptual encoding and recognition memory may be two cognitive correlates of cross-modal plasticity in congenital blindness.

  6. A Novel Audio Cryptosystem Using Chaotic Maps and DNA Encoding

    Directory of Open Access Journals (Sweden)

    S. J. Sheela

    2017-01-01

    Full Text Available Chaotic maps have good potential in security applications due to their inherent characteristics relevant to cryptography. This paper introduces a new audio cryptosystem based on chaotic maps, hybrid chaotic shift transform (HCST, and deoxyribonucleic acid (DNA encoding rules. The scheme uses chaotic maps such as two-dimensional modified Henon map (2D-MHM and standard map. The 2D-MHM which has sophisticated chaotic behavior for an extensive range of control parameters is used to perform HCST. DNA encoding technology is used as an auxiliary tool which enhances the security of the cryptosystem. The performance of the algorithm is evaluated for various speech signals using different encryption/decryption quality metrics. The simulation and comparison results show that the algorithm can achieve good encryption results and is able to resist several cryptographic attacks. The various types of analysis revealed that the algorithm is suitable for narrow band radio communication and real-time speech encryption applications.

  7. Advanced Encoding for Multilingual Access in a Terminological Data Base

    DEFF Research Database (Denmark)

    Leroyer, Patrick; L'Homme, Marie-Claude; Robichaud, Benoît

    2010-01-01

    This paper describes new functionalities implemented in a terminological database (TDB) in order to allow efficient editing of and access to multilingual data. The functionalities are original in the sense that they allow users of the database to retrieve the equivalents not only of headwords......, but also of semantically related terms (especially collocations) that appear within the articles. The methods we developed are based on a formal encoding of lexical relationships, namely lexical functions (LFs). Since LFs are language-independent and are designed to capture semantic distinctions, links...... between equivalents can be established automatically. Examples are taken from the fields of computing and the Internet and focus on English and French. However, the model can easily be extended to other fields and languages provided that the data is available and encoded properly....

  8. The encoding complexity of two dimensional range minimum data structures

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Brodnik, Andrej; Davoodi, Pooya

    2013-01-01

    In the two-dimensional range minimum query problem an input matrix A of dimension m ×n, m ≤ n, has to be preprocessed into a data structure such that given a query rectangle within the matrix, the position of a minimum element within the query range can be reported. We consider the space complexity...... of the encoding variant of the problem where queries have access to the constructed data structure but can not access the input matrix A, i.e. all information must be encoded in the data structure. Previously it was known how to solve the problem with space O(mn min {m,logn}) bits (and with constant query time...

  9. Encoded diffractive optics for full-spectrum computational imaging

    KAUST Repository

    Heide, Felix

    2016-09-16

    Diffractive optical elements can be realized as ultra-thin plates that offer significantly reduced footprint and weight compared to refractive elements. However, such elements introduce severe chromatic aberrations and are not variable, unless used in combination with other elements in a larger, reconfigurable optical system. We introduce numerically optimized encoded phase masks in which different optical parameters such as focus or zoom can be accessed through changes in the mechanical alignment of a ultra-thin stack of two or more masks. Our encoded diffractive designs are combined with a new computational approach for self-calibrating imaging (blind deconvolution) that can restore high-quality images several orders of magnitude faster than the state of the art without pre-calibration of the optical system. This co-design of optics and computation enables tunable, full-spectrum imaging using thin diffractive optics.

  10. Ensemble encoding of nociceptive stimulus intensity in the rat medial and lateral pain systems

    Directory of Open Access Journals (Sweden)

    Woodward Donald J

    2011-08-01

    Full Text Available Abstract Background The ability to encode noxious stimulus intensity is essential for the neural processing of pain perception. It is well accepted that the intensity information is transmitted within both sensory and affective pathways. However, it remains unclear what the encoding patterns are in the thalamocortical brain regions, and whether the dual pain systems share similar responsibility in intensity coding. Results Multichannel single-unit recordings were used to investigate the activity of individual neurons and neuronal ensembles in the rat brain following the application of noxious laser stimuli of increasing intensity to the hindpaw. Four brain regions were monitored, including two within the lateral sensory pain pathway, namely, the ventral posterior lateral thalamic nuclei and the primary somatosensory cortex, and two in the medial pathway, namely, the medial dorsal thalamic nuclei and the anterior cingulate cortex. Neuron number, firing rate, and ensemble spike count codings were examined in this study. Our results showed that the noxious laser stimulation evoked double-peak responses in all recorded brain regions. Significant correlations were found between the laser intensity and the number of responsive neurons, the firing rates, as well as the mass spike counts (MSCs. MSC coding was generally more efficient than the other two methods. Moreover, the coding capacities of neurons in the two pathways were comparable. Conclusion This study demonstrated the collective contribution of medial and lateral pathway neurons to the noxious intensity coding. Additionally, we provide evidence that ensemble spike count may be the most reliable method for coding pain intensity in the brain.

  11. Parallel H.263 Encoder in Normal Coding Mode

    OpenAIRE

    Cosmas, J; Paker, Y; Pearmain, A

    1998-01-01

    A parallel H.263 video encoder, which utilises spatial para1 elism, has been modelled using a multi-threaded program. Spatial parallelism is a technique where an image is subdivided into equal parts (as far as physically possible) and each part is proces!;ed by a separate processor by computing motion and texture mding with all processors cach acting on a different part of thc ]mag. This method leads to a performance increase, which is roughly in proportion to the number ...

  12. Wavelength encoding technique for particle analyses in hematology analyzer

    Science.gov (United States)

    Rongeat, Nelly; Brunel, Patrick; Gineys, Jean-Philippe; Cremien, Didier; Couderc, Vincent; Nérin, Philippe

    2011-07-01

    The aim of this study is to combine multiple excitation wavelengths in order to improve accuracy of fluorescence characterization of labeled cells. The experimental demonstration is realized with a hematology analyzer based on flow cytometry and a CW laser source emitting two visible wavelengths. A given optical encoding associated to each wavelength allows fluorescence identification coming from specific fluorochromes and avoiding the use of noisy compensation method.

  13. Exhaustive search of linear information encoding protein-peptide recognition.

    Science.gov (United States)

    Kelil, Abdellali; Dubreuil, Benjamin; Levy, Emmanuel D; Michnick, Stephen W

    2017-04-01

    High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition. However, these methods are limited in number of peptides, sequence variation, and length of peptides that can be explored, and often produce solutions that are not found in the cell. Despite the large number of methods developed to attempt addressing these issues, the exhaustive search of linear information encoding protein-peptide recognition has been so far physically unfeasible. Here, we describe a strategy, called DALEL, for the exhaustive search of linear sequence information encoded in proteins that bind to a common partner. We applied DALEL to explore binding specificity of SH3 domains in the budding yeast Saccharomyces cerevisiae. Using only the polypeptide sequences of SH3 domain binding proteins, we succeeded in identifying the majority of known SH3 binding sites previously discovered either in vitro or in vivo. Moreover, we discovered a number of sites with both non-canonical sequences and distinct properties that may serve ancillary roles in peptide recognition. We compared DALEL to a variety of state-of-the-art algorithms in the blind identification of known binding sites of the human Grb2 SH3 domain. We also benchmarked DALEL on curated biological motifs derived from the ELM database to evaluate the effect of increasing/decreasing the enrichment of the motifs. Our strategy can be applied in conjunction with experimental data of proteins interacting with a common partner to identify binding sites among them. Yet, our strategy can also be applied to any group of proteins of interest to identify enriched linear motifs or to exhaustively explore the space of linear information encoded in a polypeptide sequence. Finally, we have developed a webserver located at http://michnick.bcm.umontreal.ca/dalel, offering user-friendly interface and providing different scenarios utilizing DALEL.

  14. Tetrahydrocannabinol (THC) impairs encoding but not retrieval of verbal information.

    Science.gov (United States)

    Ranganathan, Mohini; Radhakrishnan, Rajiv; Addy, Peter H; Schnakenberg-Martin, Ashley M; Williams, Ashley H; Carbuto, Michelle; Elander, Jacqueline; Pittman, Brian; Andrew Sewell, R; Skosnik, Patrick D; D'Souza, Deepak Cyril

    2017-10-03

    Cannabis and agonists of the brain cannabinoid receptor (CB 1 R) produce acute memory impairments in humans. However, the extent to which cannabinoids impair the component processes of encoding and retrieval has not been established in humans. The objective of this analysis was to determine whether the administration of Δ 9 -Tetrahydrocannabinol (THC), the principal psychoactive constituent of cannabis, impairs encoding and/or retrieval of verbal information. Healthy subjects were recruited from the community. Subjects were administered the Rey-Auditory Verbal Learning Test (RAVLT) either before administration of THC (experiment #1) (n=38) or while under the influence of THC (experiment #2) (n=57). Immediate and delayed recall on the RAVLT was compared. Subjects received intravenous THC, in a placebo-controlled, double-blind, randomized manner at doses known to produce behavioral and subjective effects consistent with cannabis intoxication. Total immediate recall, short delayed recall, and long delayed recall were reduced in a statistically significant manner only when the RAVLT was administered to subjects while they were under the influence of THC (experiment #2) and not when the RAVLT was administered prior. THC acutely interferes with encoding of verbal memory without interfering with retrieval. These data suggest that learning information prior to the use of cannabis or cannabinoids is not likely to disrupt recall of that information. Future studies will be necessary to determine whether THC impairs encoding of non-verbal information, to what extent THC impairs memory consolidation, and the role of other cannabinoids in the memory-impairing effects of cannabis. Cannabinoids, Neural Synchrony, and Information Processing (THC-Gamma) http://clinicaltrials.gov/ct2/show/study/NCT00708994 NCT00708994 Pharmacogenetics of Cannabinoid Response http://clinicaltrials.gov/ct2/show/NCT00678730 NCT00678730. Copyright © 2017. Published by Elsevier Inc.

  15. Designing waveforms for temporal encoding using a frequency sampling method

    DEFF Research Database (Denmark)

    Gran, Fredrik; Jensen, Jørgen Arendt

    2007-01-01

    In this paper a method for designing waveforms for temporal encoding in medical ultrasound imaging is described. The method is based on least squares optimization and is used to design nonlinear frequency modulated signals for synthetic transmit aperture imaging. By using the proposed design method...... are shown for both methods, wherein the common carotid artery on a 27-year-old healthy male was scanned...

  16. Role of local field potentials in encoding hand movement kinematics.

    Science.gov (United States)

    Witte, Matthias

    2011-10-01

    How the brain orchestrates the musculoskeletal system to produce complex three-dimensional movements is still poorly understood. Despite first promising results in brain-machine interfaces that translate cortical activity to control output, there is an ongoing debate about which brain signals provide richest information related to movement planning and execution. Novel results by Bansal and colleagues (2011) now suggest that neuronal spiking and local field potentials jointly encode kinematics during skilled reach and grasp movements.

  17. Gene cluster encoding cholate catabolism in Rhodococcus spp.

    Science.gov (United States)

    Mohn, William W; Wilbrink, Maarten H; Casabon, Israël; Stewart, Gordon R; Liu, Jie; van der Geize, Robert; Eltis, Lindsay D

    2012-12-01

    Bile acids are highly abundant steroids with important functions in vertebrate digestion. Their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. We found that Rhodococcus jostii RHA1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. The transcriptome of RHA1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. Reverse transcriptase quantitative PCR confirmed that selected genes in the cluster were upregulated 10-fold on cholate versus on cholesterol. One of these genes, kshA3, encoding a putative 3-ketosteroid-9α-hydroxylase, was deleted and found essential for growth on cholate. Two coenzyme A (CoA) synthetases encoded in the cluster, CasG and CasI, were heterologously expressed. CasG was shown to transform cholate to cholyl-CoA, thus initiating side chain degradation. CasI was shown to form CoA derivatives of steroids with isopropanoyl side chains, likely occurring as degradation intermediates. Orthologous gene clusters were identified in all available Rhodococcus genomes, as well as that of Thermomonospora curvata. Moreover, Rhodococcus equi 103S, Rhodococcus ruber Chol-4 and Rhodococcus erythropolis SQ1 each grew on cholate. In contrast, several mycolic acid bacteria lacking the gene cluster were unable to grow on cholate. Our results demonstrate that the above-mentioned gene cluster encodes cholate catabolism and is distinct from a more widely occurring gene cluster encoding cholesterol catabolism.

  18. Polarization encoded all-optical multi-valued shift operators

    Science.gov (United States)

    Roy, Jitendra Nath; Bhowmik, Panchatapa

    2014-08-01

    Polarization encoded multi-valued (both ternary and quaternary logic) shift operators have been designed using linear optical devices only. There are six ternary and 24 quaternary shift operators in multi-valued system. These are also known as reversible literals. This circuit will be useful in future all-optical multi-valued logic based information processing system. Different states of polarization of light are taken as different logic states.

  19. Sparse encoding of automatic visual association in hippocampal networks

    DEFF Research Database (Denmark)

    Hulme, Oliver J; Skov, Martin; Chadwick, Martin J

    2014-01-01

    by these stimuli. Using multivariate Bayesian decoding, we show that human hippocampal and temporal neocortical structures host sparse associative representations that are automatically triggered by visual input. Furthermore, as predicted theoretically, there was a significant increase in sparsity in the Cornu...... for the sparse encoding of associative density. In the absence of reportability or attentional confounds, this charts a distribution of visual associative representations within hippocampal populations and their temporal lobe afferent fields, and demonstrates the viability of retrospective associative sampling...

  20. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney Bruce [Pullman, WA; Burke, Charles Cullen [Moscow, ID

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  1. A deep auto-encoder model for gene expression prediction.

    Science.gov (United States)

    Xie, Rui; Wen, Jia; Quitadamo, Andrew; Cheng, Jianlin; Shi, Xinghua

    2017-11-17

    Gene expression is a key intermediate level that genotypes lead to a particular trait. Gene expression is affected by various factors including genotypes of genetic variants. With an aim of delineating the genetic impact on gene expression, we build a deep auto-encoder model to assess how good genetic variants will contribute to gene expression changes. This new deep learning model is a regression-based predictive model based on the MultiLayer Perceptron and Stacked Denoising Auto-encoder (MLP-SAE). The model is trained using a stacked denoising auto-encoder for feature selection and a multilayer perceptron framework for backpropagation. We further improve the model by introducing dropout to prevent overfitting and improve performance. To demonstrate the usage of this model, we apply MLP-SAE to a real genomic datasets with genotypes and gene expression profiles measured in yeast. Our results show that the MLP-SAE model with dropout outperforms other models including Lasso, Random Forests and the MLP-SAE model without dropout. Using the MLP-SAE model with dropout, we show that gene expression quantifications predicted by the model solely based on genotypes, align well with true gene expression patterns. We provide a deep auto-encoder model for predicting gene expression from SNP genotypes. This study demonstrates that deep learning is appropriate for tackling another genomic problem, i.e., building predictive models to understand genotypes' contribution to gene expression. With the emerging availability of richer genomic data, we anticipate that deep learning models play a bigger role in modeling and interpreting genomics.

  2. An encoding methodology for medical knowledge using SNOMED CT ontology

    Directory of Open Access Journals (Sweden)

    Shaker El-Sappagh

    2016-07-01

    Full Text Available Knowledge-Intensive Case Based Reasoning (KI-CBR systems mainly depend on ontology. Using ontology as domain knowledge supports the implementation of semantically-intelligent case retrieval algorithms. The case-based knowledge must be encoded with the same concepts of the domain ontology. Standard medical ontologies, such as SNOMED CT (SCT, can play the role of domain ontology to enhance case representation and retrieval. This study has three stages. First, we propose an encoding methodology using SCT. Second, this methodology is used to encode the case-based knowledge. Third, all the used SCT concepts are collected in a reference set, and an OWL2 ontology of 550 pre-coordinated concepts is proposed. A diabetes diagnosis is chosen as a case study of our proposed framework. SCT is used to provide a pre-coordination concept coverage of ∼75% for diabetes diagnosis terms. Whereas, the uncovered concepts in SCT are proposed. The resulting OWL2 ontology will be used as domain knowledge representation in diabetes diagnosis CBR systems. The proposed framework is tested by using 60 real cases.

  3. Adult ADHD and working memory: neural evidence of impaired encoding.

    Science.gov (United States)

    Kim, Soyeon; Liu, Zhongxu; Glizer, Daniel; Tannock, Rosemary; Woltering, Steven

    2014-08-01

    To investigate neural and behavioural correlates of visual encoding during a working memory (WM) task in young adults with and without Attention-Deficit/Hyperactivity Disorder (ADHD). A sample of 30 college students currently meeting a diagnosis of ADHD and 25 typically developing students, matched on age and gender, performed a delayed match-to-sample task with low and high memory load conditions. Dense-array electroencephalography was recorded. Specifically, the P3, an event related potential (ERP) associated with WM, was examined because of its relation with attentional allocation during WM. Task performance (accuracy, reaction time) as well as performance on other neuropsychological tasks of WM was analyzed. Neural differences were found between the groups. Specifically, the P3 amplitude was smaller in the ADHD group compared to the comparison group for both load conditions at parietal-occipital sites. Lower scores on behavioural working memory tasks were suggestive of impaired behavioural WM performance in the ADHD group. Findings from this study provide the first evidence of neural differences in the encoding stage of WM in young adults with ADHD, suggesting ineffective allocation of attentional resources involved in encoding of information in WM. These findings, reflecting alternate neural functioning of WM, may explain some of the difficulties related to WM functioning that college students with ADHD report in their every day cognitive functioning. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  4. Chlorella viruses contain genes encoding a complete polyamine biosynthetic pathway

    Science.gov (United States)

    Baumann, Sascha; Sander, Adrianne; Gurnon, James R.; Yanai-Balser, Giane; VanEtten, James L.; Piotrowski, Markus

    2007-01-01

    Two genes encoding the putative polyamine biosynthetic enzymes agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (CPA) were cloned from the chloroviruses PBCV-1, NY-2A and MT325. They were expressed in Escherichia coli to form C-terminal (His)6-tagged proteins and the recombinant proteins were purified by Ni2+- binding affinity chromatography. The biochemical properties of the two enzymes are similar to AIH and CPA enzymes from Arabidopsis thaliana and Pseudomonas aeruginosa. Together with the previously known virus genes encoding ornithine/arginine decarboxlyase (ODC/ADC) and homospermidine synthase, the chloroviruses have genes that encode a complete set of functional enzymes that synthesize the rare polyamine homospermidine from arginine via agmatine, N-carbamoylputrescine and putrescine. The PBCV-1 aih and cpa genes are expressed early during virus infection together with the odc/adc gene, suggesting that biosynthesis of putrescine is important in early stages of viral replication. The aih and cpa genes are widespread in the chlorella viruses. PMID:17101165

  5. ENCODE: A Sourcebook of Epigenomes and Chromatin Language

    Directory of Open Access Journals (Sweden)

    Maryam Yavartanoo

    2013-03-01

    Full Text Available Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI launched an international research consortium called Encyclopedia of DNA Elements (ENCODE to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

  6. Learning from number board games: you learn what you encode.

    Science.gov (United States)

    Laski, Elida V; Siegler, Robert S

    2014-03-01

    We tested the hypothesis that encoding the numerical-spatial relations in a number board game is a key process in promoting learning from playing such games. Experiment 1 used a microgenetic design to examine the effects on learning of the type of counting procedure that children use. As predicted, having kindergartners count-on from their current number on the board while playing a 0-100 number board game facilitated their encoding of the numerical-spatial relations on the game board and improved their number line estimates, numeral identification, and count-on skill. Playing the same game using the standard count-from-1 procedure led to considerably less learning. Experiment 2 demonstrated that comparable improvement in number line estimation does not occur with practice encoding the numerals 1-100 outside of the context of a number board game. The general importance of aligning learning activities and physical materials with desired mental representations is discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  7. QR encoded smart oral dosage forms by inkjet printing.

    Science.gov (United States)

    Edinger, Magnus; Bar-Shalom, Daniel; Sandler, Niklas; Rantanen, Jukka; Genina, Natalja

    2018-01-30

    The use of inkjet printing (IJP) technology enables the flexible manufacturing of personalized medicine with the doses tailored for each patient. In this study we demonstrate, for the first time, the applicability of IJP in the production of edible dosage forms in the pattern of a quick response (QR) code. This printed pattern contains the drug itself and encoded information relevant to the patient and/or healthcare professionals. IJP of the active pharmaceutical ingredient (API)-containing ink in the pattern of QR code was performed onto a newly developed porous and flexible, but mechanically stable substrate with a good absorption capacity. The printing did not affect the mechanical properties of the substrate. The actual drug content of the printed dosage forms was in accordance with the encoded drug content. The QR encoded dosage forms had a good print definition without significant edge bleeding. They were readable by a smartphone even after storage in harsh conditions. This approach of efficient data incorporation and data storage combined with the use of smart devices can lead to safer and more patient-friendly drug products in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Identification of a Novel UTY‐Encoded Minor Histocompatibility Antigen

    DEFF Research Database (Denmark)

    Mortensen, B. K.; Rasmussen, A. H.; Larsen, Malene Erup

    2012-01-01

    Minor histocompatibility antigens (mHags) encoded by the Y‐chromosome (H‐Y‐mHags) are known to play a pivotal role in allogeneic haematopoietic cell transplantation (HCT) involving female donors and male recipients. We present a new H‐Y‐mHag, YYNAFHWAI (UTY139–147), encoded by the UTY gene...... obtained post‐HCT from male recipients of female donor grafts. In one of these recipients, a CD8+ T cell response was observed against a peptide stretch encoded by the UTY gene. Another bioinformatics tool, HLArestrictor, was used to identify the optimal peptide and HLA‐restriction element. Using peptide....../HLA tetramers, the specificity of the CD8+ T cell response was successfully validated as being HLA‐A*24:02‐restricted and directed against the male UTY139–147 peptide. Functional analysis of these T cells demonstrated male UTY139–147 peptide‐specific cytokine secretion (IFNγ, TNFα and MIP‐1β) and cytotoxic...

  9. Copyright Protection of Color Imaging Using Robust-Encoded Watermarking

    Directory of Open Access Journals (Sweden)

    M. Cedillo-Hernandez

    2015-04-01

    Full Text Available In this paper we present a robust-encoded watermarking method applied to color images for copyright protection, which presents robustness against several geometric and signal processing distortions. Trade-off between payload, robustness and imperceptibility is a very important aspect which has to be considered when a watermark algorithm is designed. In our proposed scheme, previously to be embedded into the image, the watermark signal is encoded using a convolutional encoder, which can perform forward error correction achieving better robustness performance. Then, the embedding process is carried out through the discrete cosine transform domain (DCT of an image using the image normalization technique to accomplish robustness against geometric and signal processing distortions. The embedded watermark coded bits are extracted and decoded using the Viterbi algorithm. In order to determine the presence or absence of the watermark into the image we compute the bit error rate (BER between the recovered and the original watermark data sequence. The quality of the watermarked image is measured using the well-known indices: Peak Signal to Noise Ratio (PSNR, Visual Information Fidelity (VIF and Structural Similarity Index (SSIM. The color difference between the watermarked and original images is obtained by using the Normalized Color Difference (NCD measure. The experimental results show that the proposed method provides good performance in terms of imperceptibility and robustness. The comparison among the proposed and previously reported methods based on different techniques is also provided.

  10. Grey-level encoding of openings and closings

    Science.gov (United States)

    Parker, James R.; Horsley, D.

    1993-12-01

    A distance transform will convert a bi-level image into a gray scale image, where the intensity of the object pixels is proportional to their distance from the nearest back-ground pixel. This can be computed in two passes through an image, and has been used to encode all binary erosions and dilations into one `globally eroded' image. It is also possible to encode all possible binary openings and closings as gray levels, allowing any particular opening or closing to be achieved through a simple thresholding operation, or by non-destructive comparisons. We define nodal points in the distance transform as those which have no neighbors having the maximum possible value (For example, 7 for diagonal pixels, and 12 for others using Euclidean distance). At each of these points a digital circle can be drawn, whose values equal that of the significant point. A simple histogram of the thus encoded image yields the roughness spectrum, but the spectrum found using only the significant points may be just as useful.

  11. Binary encoded computer generated holograms for temporal phase shifting.

    Science.gov (United States)

    Amphawan, Angela

    2011-11-07

    The trend towards real-time optical applications predicates the need for real-time interferometry. For real-time interferometric applications, rapid processing of computer generated holograms is crucial as the intractability of rapid phase changes may compromise the input to the system. This paper introduces the design of a set of binary encoded computer generated holograms (CGHs) for real-time five-frame temporal phase shifting interferometry using a binary amplitude spatial light modulator. It is suitable for portable devices with constraints in computational power. The new set of binary encoded CGHs is used for measuring the phase of the generated electric field for a real-time selective launch in multimode fiber. The processing time for the new set of CGHs was reduced by up to 65% relative to the original encoding scheme. The results obtained from the new interferometric technique are in good agreement with the results obtained by phase shifting by means of a piezo-driven flat mirror.

  12. Contribution of stress and sex hormones to memory encoding.

    Science.gov (United States)

    Merz, Christian J

    2017-08-01

    Distinct stages of the menstrual cycle and the intake of oral contraceptives (OC) affect sex hormone levels, stress responses, and memory processes critically involved in the pathogenesis of mental disorders. To characterize the interaction of sex and stress hormones on memory encoding, 30 men, 30 women in the early follicular phase of the menstrual cycle (FO), 30 women in the luteal phase (LU), and 30 OC women were exposed to either a stress (socially evaluated cold-pressor test) or a control condition prior to memory encoding and immediate recall of neutral, positive, and negative words. On the next day, delayed free and cued recall was tested. Sex hormone levels verified distinct estradiol, progesterone, and testosterone levels between groups. Stress increased blood pressure, cortisol concentrations, and ratings of stress appraisal in all four groups as well as cued recall performance of negative words in men. Stress exposure in OC women led to a blunted cortisol response and rather enhanced cued recall of neutral words. Thus, pre-encoding stress facilitated emotional cued recall performance in men only, but not women with different sex hormone statuses pointing to the pivotal role of circulating sex hormones in modulation of learning and memory processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  14. New Complexity Scalable MPEG Encoding Techniques for Mobile Applications

    Directory of Open Access Journals (Sweden)

    Stephan Mietens

    2004-03-01

    Full Text Available Complexity scalability offers the advantage of one-time design of video applications for a large product family, including mobile devices, without the need of redesigning the applications on the algorithmic level to meet the requirements of the different products. In this paper, we present complexity scalable MPEG encoding having core modules with modifications for scalability. The interdependencies of the scalable modules and the system performance are evaluated. Experimental results show scalability giving a smooth change in complexity and corresponding video quality. Scalability is basically achieved by varying the number of computed DCT coefficients and the number of evaluated motion vectors but other modules are designed such they scale with the previous parameters. In the experiments using the “Stefan” sequence, the elapsed execution time of the scalable encoder, reflecting the computational complexity, can be gradually reduced to roughly 50% of its original execution time. The video quality scales between 20 dB and 48 dB PSNR with unity quantizer setting, and between 21.5 dB and 38.5 dB PSNR for different sequences targeting 1500 kbps. The implemented encoder and the scalability techniques can be successfully applied in mobile systems based on MPEG video compression.

  15. Regional Externalities

    NARCIS (Netherlands)

    Heijman, W.J.M.

    2007-01-01

    The book offers practical and theoretical insights in regional externalities. Regional externalities are a specific subset of externalities that can be defined as externalities where space plays a dominant role. This class of externalities can be divided into three categories: (1) externalities

  16. Regional Planning.

    Science.gov (United States)

    Bang, Bryan

    1987-01-01

    Explores ideas about regional planning and provides a framework for developing a secondary level course on regional planning. Claims that such a course can help students understand more about the world around them and improve their attitude toward contributing to the management of change. (BR)

  17. NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOM- PONENT POLYCHLORINATED-BIPHENYL-DEGRADING ENZYME IN PSEUDOMONAS STRAIN LB400

    Science.gov (United States)

    The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. Six open reading frames were identified, four of which are homologous to the components of toluene dioxy...

  18. Cortical networks for encoding near and far space in the non-human primate.

    Science.gov (United States)

    Cléry, Justine; Guipponi, Olivier; Odouard, Soline; Wardak, Claire; Ben Hamed, Suliann

    2018-04-18

    While extra-personal space is often erroneously considered as a unique entity, early neuropsychological studies report a dissociation between near and far space processing both in humans and in monkeys. Here, we use functional MRI in a naturalistic 3D environment to describe the non-human primate near and far space cortical networks. We describe the co-occurrence of two extended functional networks respectively dedicated to near and far space processing. Specifically, far space processing involves occipital, temporal, parietal, posterior cingulate as well as orbitofrontal regions not activated by near space, possibly subserving the processing of the shape and identity of objects. In contrast, near space processing involves temporal, parietal, prefrontal and premotor regions not activated by far space, possibly subserving the preparation of an arm/hand mediated action in this proximal space. Interestingly, this network also involves somatosensory regions, suggesting a cross-modal anticipation of touch by a nearby object. Last, we also describe cortical regions that process both far and near space with a preference for one or the other. This suggests a continuous encoding of relative distance to the body, in the form of a far-to-near gradient. We propose that these cortical gradients in space representation subserve the physically delineable peripersonal spaces described in numerous psychology and psychophysics studies. Copyright © 2018. Published by Elsevier Inc.

  19. DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions

    Directory of Open Access Journals (Sweden)

    Takasugi Masaki

    2010-08-01

    Full Text Available Abstract Background Mitochondria are semi-autonomous, semi-self-replicating organelles harboring their own DNA (mitochondrial DNA, mtDNA, and their dysregulation is involved in the development of various diseases. While mtDNA does not generally undergo epigenetic modifications, almost all mitochondrial proteins are encoded by nuclear DNA. However, the epigenetic regulation of nuclear-encoded mitochondrial genes (nuclear mt genes has not been comprehensively analyzed. Results We analyzed the DNA methylation status of 899 nuclear mt genes in the liver, brain, and heart tissues of mouse, and identified 636 nuclear mt genes carrying tissue-dependent and differentially methylated regions (T-DMRs. These nuclar mt genes are involved in various mitochondrial functions and they also include genes related to human diseases. T-DMRs regulate the expression of nuclear mt genes. Nuclear mt genes with tissue-specific hypomethylated T-DMRs were characterized by enrichment of the target genes of specific transcription factors such as FOXA2 in the liver, and CEBPA and STAT1 in the brain. Conclusions A substantial proportion of nuclear mt genes contained T-DMRs, and the DNA methylation status of numerous T-DMRs should underlie tissue-dependent mitochondrial functions.

  20. Encoding of temporal information by timing, rate, and place in cat auditory cortex.

    Directory of Open Access Journals (Sweden)

    Kazuo Imaizumi

    2010-07-01

    Full Text Available A central goal in auditory neuroscience is to understand the neural coding of species-specific communication and human speech sounds. Low-rate repetitive sounds are elemental features of communication sounds, and core auditory cortical regions have been implicated in processing these information-bearing elements. Repetitive sounds could be encoded by at least three neural response properties: 1 the event-locked spike-timing precision, 2 the mean firing rate, and 3 the interspike interval (ISI. To determine how well these response aspects capture information about the repetition rate stimulus, we measured local group responses of cortical neurons in cat anterior auditory field (AAF to click trains and calculated their mutual information based on these different codes. ISIs of the multiunit responses carried substantially higher information about low repetition rates than either spike-timing precision or firing rate. Combining firing rate and ISI codes was synergistic and captured modestly more repetition information. Spatial distribution analyses showed distinct local clustering properties for each encoding scheme for repetition information indicative of a place code. Diversity in local processing emphasis and distribution of different repetition rate codes across AAF may give rise to concurrent feed-forward processing streams that contribute differently to higher-order sound analysis.

  1. Verbal learning and memory impairments in posttraumatic stress disorder: the role of encoding strategies.

    Science.gov (United States)

    Johnsen, Grethe E; Asbjørnsen, Arve E

    2009-01-30

    The present study examined mechanisms underlying verbal memory impairments in patients with posttraumatic stress disorder (PTSD). Earlier studies have reported that the verbal learning and memory alterations in PTSD are related to impaired encoding, but the use of encoding and organizational strategies in patients with PTSD has not been fully explored. This study examined organizational strategies in 21 refugees/immigrants exposed to war and political violence who fulfilled DSM-IV criteria for chronic PTSD compared with a control sample of 21 refugees/immigrants with similar exposure, but without PTSD. The California Verbal Learning Test was administered to examine differences in organizational strategies and memory. The semantic clustering score was slightly reduced in both groups, but the serial cluster score was significantly impaired in the PTSD group and they also reported more items from the recency region of the list. In addition, intrusive errors were significantly increased in the PTSD group. The data support an assumption of changed memory strategies in patients with PTSD associated with a specific impairment in executive control. However, memory impairment and the use of ineffective learning strategies may not be related to PTSD symptomatology only, but also to self-reported symptoms of depression and general distress.

  2. Dynamic state estimation based on Poisson spike trains—towards a theory of optimal encoding

    International Nuclear Information System (INIS)

    Susemihl, Alex; Opper, Manfred; Meir, Ron

    2013-01-01

    Neurons in the nervous system convey information to higher brain regions by the generation of spike trains. An important question in the field of computational neuroscience is how these sensory neurons encode environmental information in a way which may be simply analyzed by subsequent systems. Many aspects of the form and function of the nervous system have been understood using the concepts of optimal population coding. Most studies, however, have neglected the aspect of temporal coding. Here we address this shortcoming through a filtering theory of inhomogeneous Poisson processes. We derive exact relations for the minimal mean squared error of the optimal Bayesian filter and, by optimizing the encoder, obtain optimal codes for populations of neurons. We also show that a class of non-Markovian, smooth stimuli are amenable to the same treatment, and provide results for the filtering and prediction error which hold for a general class of stochastic processes. This sets a sound mathematical framework for a population coding theory that takes temporal aspects into account. It also formalizes a number of studies which discussed temporal aspects of coding using time-window paradigms, by stating them in terms of correlation times and firing rates. We propose that this kind of analysis allows for a systematic study of temporal coding and will bring further insights into the nature of the neural code. (paper)

  3. Organoids and the genetically encoded self-assembly of embryonic stem cells.

    Science.gov (United States)

    Turner, David A; Baillie-Johnson, Peter; Martinez Arias, Alfonso

    2016-02-01

    Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to self-organization, as often suggested, but rather to a process of genetically encoded self-assembly where genetic programs encode and control the emergence of biological structures. © 2015 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  4. Dynamic state estimation based on Poisson spike trains—towards a theory of optimal encoding

    Science.gov (United States)

    Susemihl, Alex; Meir, Ron; Opper, Manfred

    2013-03-01

    Neurons in the nervous system convey information to higher brain regions by the generation of spike trains. An important question in the field of computational neuroscience is how these sensory neurons encode environmental information in a way which may be simply analyzed by subsequent systems. Many aspects of the form and function of the nervous system have been understood using the concepts of optimal population coding. Most studies, however, have neglected the aspect of temporal coding. Here we address this shortcoming through a filtering theory of inhomogeneous Poisson processes. We derive exact relations for the minimal mean squared error of the optimal Bayesian filter and, by optimizing the encoder, obtain optimal codes for populations of neurons. We also show that a class of non-Markovian, smooth stimuli are amenable to the same treatment, and provide results for the filtering and prediction error which hold for a general class of stochastic processes. This sets a sound mathematical framework for a population coding theory that takes temporal aspects into account. It also formalizes a number of studies which discussed temporal aspects of coding using time-window paradigms, by stating them in terms of correlation times and firing rates. We propose that this kind of analysis allows for a systematic study of temporal coding and will bring further insights into the nature of the neural code.

  5. Dorsal-CA1 Hippocampal Neuronal Ensembles Encode Nicotine-Reward Contextual Associations.

    Science.gov (United States)

    Xia, Li; Nygard, Stephanie K; Sobczak, Gabe G; Hourguettes, Nicholas J; Bruchas, Michael R

    2017-06-06

    Natural and drug rewards increase the motivational valence of stimuli in the environment that, through Pavlovian learning mechanisms, become conditioned stimuli that directly motivate behavior in the absence of the original unconditioned stimulus. While the hippocampus has received extensive attention for its role in learning and memory processes, less is known regarding its role in drug-reward associations. We used in vivo Ca 2+ imaging in freely moving mice during the formation of nicotine preference behavior to examine the role of the dorsal-CA1 region of the hippocampus in encoding contextual reward-seeking behavior. We show the development of specific neuronal ensembles whose activity encodes nicotine-reward contextual memories and that are necessary for the expression of place preference. Our findings increase our understanding of CA1 hippocampal function in general and as it relates to reward processing by identifying a critical role for CA1 neuronal ensembles in nicotine place preference. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Generalized MRI reconstruction including elastic physiological motion and coil sensitivity encoding.

    Science.gov (United States)

    Odille, Freddy; Cîndea, Nicolae; Mandry, Damien; Pasquier, Cédric; Vuissoz, Pierre-André; Felblinger, Jacques

    2008-06-01

    This article describes a general framework for multiple coil MRI reconstruction in the presence of elastic physiological motion. On the assumption that motion is known or can be predicted, it is shown that the reconstruction problem is equivalent to solving an integral equation--known in the literature as a Fredholm equation of the first kind--with a generalized kernel comprising Fourier and coil sensitivity encoding, modified by physiological motion information. Numerical solutions are found using an iterative linear system solver. The different steps in the numerical resolution are discussed, in particular it is shown how over-determination can be used to improve the conditioning of the generalized encoding operator. Practical implementation requires prior knowledge of displacement fields, so a model of patient motion is described which allows elastic displacements to be predicted from various input signals (e.g., respiratory belts, ECG, navigator echoes), after a free-breathing calibration scan. Practical implementation was demonstrated with a moving phantom setup and in two free-breathing healthy subjects, with images from the thoracic-abdominal region. Results show that the method effectively suppresses the motion blurring/ghosting artifacts, and that scan repetitions can be used as a source of over-determination to improve the reconstruction. Copyright (c) 2008 Wiley-Liss, Inc.

  7. Bactofection of sequences encoding a Bax protein peptide chemosensitizes prostate cancer tumor cells.

    Science.gov (United States)

    Hernández-Luna, Marco Antonio; Díaz de León-Ortega, Ricardo; Hernández-Cueto, Daniel Dimitri; Gaxiola-Centeno, Ricardo; Castro-Luna, Raúl; Martínez-Cristóbal, Leonel; Huerta-Yépez, Sara; Luria-Pérez, Rosendo

    Tumor cell resistance to chemotherapy agents is one of the main problems in the eradication of different neoplasias. One of the mechanisms of this process is the overexpression of anti-apoptotic proteins such as Bcl-2 and Bcl- XL ; blocking the activity of these proteins may contribute to the sensitization of tumor cells and allow the adequate effects of chemotherapeutic drugs. This study adressed the transfection of prostate cancer cells (PC3) with a plasmid encoding a recombinant protein with an antagonist peptide from the BH3 region of the Bax protein fused to the GFP reporter protein (BaxGFP). This protein induced apoptosis of these tumor cells; further, selective transport of this plasmid to the tumor cell with Salmonella enterica serovar Typhimurium (strain SL3261), a live-attenuated bacterial vector, can induce sensitization of the tumor cell to the action of drugs such as cisplatin, through a process known as bactofection. These results suggest that Salmonella enterica can be used as a carrier vector of nucleotide sequences encoding heterologous molecules used in antitumor therapy. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  8. The Effects of Age, Memory Performance, and Callosal Integrity on the Neural Correlates of Successful Associative Encoding

    Science.gov (United States)

    Wang, Tracy H.; Minton, Brian; Muftuler, L. Tugan; Rugg, Michael D.

    2011-01-01

    This functional magnetic resonance imaging study investigated the relationship between the neural correlates of associative memory encoding, callosal integrity, and memory performance in older adults. Thirty-six older and 18 young subjects were scanned while making relational judgments on word pairs. Neural correlates of successful encoding (subsequent memory effects) were identified by contrasting the activity elicited by study pairs that were correctly identified as having been studied together with the activity elicited by pairs wrongly judged to have come from different study trials. Subsequent memory effects common to the 2 age groups were identified in several regions, including left inferior frontal gyrus and bilateral hippocampus. Negative effects (greater activity for forgotten than for remembered items) in default network regions in young subjects were reversed in the older group, and the amount of reversal correlated negatively with memory performance. Additionally, older subjects' subsequent memory effects in right frontal cortex correlated positively with anterior callosal integrity and negatively with memory performance. It is suggested that recruitment of right frontal cortex during verbal memory encoding may reflect the engagement of processes that compensate only partially for age-related neural degradation. PMID:21282317

  9. Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243.

    Directory of Open Access Journals (Sweden)

    Andrea J Dowling

    2010-12-01

    Full Text Available Burkholderia pseudomallei is an important human pathogen whose infection biology is still poorly understood. The bacterium is endemic to tropical regions, including South East Asia and Northern Australia, where it causes melioidosis, a serious disease associated with both high mortality and antibiotic resistance. B. pseudomallei is a Gram-negative facultative intracellular pathogen that is able to replicate in macrophages. However despite the critical nature of its interaction with macrophages, few anti-macrophage factors have been characterized to date. Here we perform a genome-wide gain of function screen of B. pseudomallei strain K96243 to identify loci encoding factors with anti-macrophage activity. We identify a total of 113 such loci scattered across both chromosomes, with positive gene clusters encoding transporters and secretion systems, enzymes/toxins, secondary metabolite, biofilm, adhesion and signal response related factors. Further phenotypic analysis of four of these regions shows that the encoded factors cause striking cellular phenotypes relevant to infection biology, including apoptosis, formation of actin 'tails' and multi-nucleation within treated macrophages. The detailed analysis of the remaining host of loci will facilitate genetic dissection of the interaction of this important pathogen with host macrophages and thus further elucidate this critical part of its infection cycle.

  10. Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Group II introns are self-splicing RNAs that act as mobile retroelements in the organelles of plants, fungi and protists. They are also widely distributed in bacteria, and are generally assumed to be the ancestors of nuclear spliceosomal introns. Most bacterial group II introns have a multifunctional intron-encoded protein (IEP ORF within the ribozyme domain IV (DIV. This ORF encodes an N-terminal reverse transcriptase (RT domain, followed by a putative RNA-binding domain with RNA splicing or maturase activity and, in some cases, a C-terminal DNA-binding (D region followed by a DNA endonuclease (En domain. In this study, we focused on bacterial group II intron ORF phylogenetic classes containing only reverse transcriptase/maturase open reading frames, with no recognizable D/En region (classes A, C, D, E, F and unclassified introns. On the basis of phylogenetic analyses of the maturase domain and its C-terminal extension, which appears to be a signature characteristic of ORF phylogenetic class, with support from the phylogeny inferred from the RT domain, we have revised the proposed new class F, defining new intron ORF varieties. Our results increase knowledge of the lineage of group II introns encoding proteins lacking the En-domain.

  11. Global change and biogeochemical cycles: The south Asia region

    Digital Repository Service at National Institute of Oceanography (India)

    Mitra, A.P.; DileepKumar, M.; Kumar, K.R.; Abrol, Y.P.; Kalra, N.; Velayutham, M.; Naqvi, S.W.A.

    stream_size 33 stream_content_type text/plain stream_name Global-Region_Linkage_Earth_Syst_2002_75.pdf.txt stream_source_info Global-Region_Linkage_Earth_Syst_2002_75.pdf.txt Content-Encoding ISO-8859-1 Content-Type text...

  12. Associative polarization-encoded optical shadow casting: gray-level image encoding for serial and parallel operations.

    Science.gov (United States)

    Awwal, A A; Karim, M A

    1989-01-15

    An efficient algorithm for designing a serial and parallel multioutput logic unit using an associative polarization-encoded optical shadow-casting technique is presented. Devices designed as such have a unique contentaddressable associative memory where each of the memory locations has dual addresses. For illustration, the proposed algorithm has been used to design a serial-output and a parallel-output 2-bit gray adder.

  13. Yeast PAH1-encoded phosphatidate phosphatase controls the expression of CHO1-encoded phosphatidylserine synthase for membrane phospholipid synthesis.

    Science.gov (United States)

    Han, Gil-Soo; Carman, George M

    2017-08-11

    The PAH1 -encoded phosphatidate phosphatase (PAP), which catalyzes the committed step for the synthesis of triacylglycerol in Saccharomyces cerevisiae , exerts a negative regulatory effect on the level of phosphatidate used for the de novo synthesis of membrane phospholipids. This raises the question whether PAP thereby affects the expression and activity of enzymes involved in phospholipid synthesis. Here, we examined the PAP-mediated regulation of CHO1 -encoded phosphatidylserine synthase (PSS), which catalyzes the committed step for the synthesis of major phospholipids via the CDP-diacylglycerol pathway. The lack of PAP in the pah1 Δ mutant highly elevated PSS activity, exhibiting a growth-dependent up-regulation from the exponential to the stationary phase of growth. Immunoblot analysis showed that the elevation of PSS activity results from an increase in the level of the enzyme encoded by CHO1 Truncation analysis and site-directed mutagenesis of the CHO1 promoter indicated that Cho1 expression in the pah1 Δ mutant is induced through the inositol-sensitive upstream activation sequence (UAS INO ), a cis -acting element for the phosphatidate-controlled Henry (Ino2-Ino4/Opi1) regulatory circuit. The abrogation of Cho1 induction and PSS activity by a CHO1 UAS INO mutation suppressed pah1 Δ effects on lipid synthesis, nuclear/endoplasmic reticulum membrane morphology, and lipid droplet formation, but not on growth at elevated temperature. Loss of the DGK1 -encoded diacylglycerol kinase, which converts diacylglycerol to phosphatidate, partially suppressed the pah1 Δ-mediated induction of Cho1 and PSS activity. Collectively, these data showed that PAP activity controls the expression of PSS for membrane phospholipid synthesis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. FLOSSWorld Africa regional workshop agenda

    CSIR Research Space (South Africa)

    Tucker, KC

    2006-02-01

    Full Text Available stream_source_info Tucker1_2006.pdf.txt stream_content_type text/plain stream_size 8692 Content-Encoding UTF-8 stream_name Tucker1_2006.pdf.txt Content-Type text/plain; charset=UTF-8 FLOSSWorld Africa Regional Workshop... MIMOS Malaysia: MIMOS Bhd 12 CSIR South Africa: Council for Scientific and Industrial Research 13 UWC South Africa: University of the Western Cape 14 MI2 Croatia: Multimedia Institute MI2 15 CARNET Croatia: Croatian Academic Research Network 16 ITI...

  15. Zea mI, the maize homolog of the allergen-encoding Lol pI gene of rye grass.

    Science.gov (United States)

    Broadwater, A H; Rubinstein, A L; Chay, C H; Klapper, D G; Bedinger, P A

    1993-09-15

    Sequence analysis of a pollen-specific cDNA from maize has identified a homolog (Zea mI) of the gene (Lol pI) encoding the major allergen of rye-grass pollen. The protein encoded by the partial cDNA sequence is 59.3% identical and 72.7% similar to the comparable region of the reported amino acid sequence of Lol pIA. Southern analysis indicates that this cDNA represents a member of a small multigene family in maize. Northern analysis shows expression only in pollen, not in vegetative or female floral tissues. The timing of expression is developmentally regulated, occurring at a low level prior to the first pollen mitosis and at a high level after this postmeiotic division. Western analysis detects a protein in maize pollen lysates using polyclonal antiserum and monoclonal antibodies directed against purified Lolium perenne allergen.

  16. Block-Matching Distortion Correction of Echo-Planar Images With Opposite Phase Encoding Directions.

    Science.gov (United States)

    Hedouin, Renaud; Commowick, Olivier; Bannier, Elise; Scherrer, Benoit; Taquet, Maxime; Warfield, Simon K; Barillot, Christian

    2017-05-01

    By shortening the acquisition time of MRI, Echo Planar Imaging (EPI) enables the acquisition of a large number of images in a short time, compatible with clinical constraints as required for diffusion or functional MRI. However such images are subject to large, local distortions disrupting their correspondence with the underlying anatomy. The correction of those distortions is an open problem, especially in regions where large deformations occur. We propose a new block-matching registration method to perform EPI distortion correction based on the acquisition of two EPI with opposite phase encoding directions (PED). It relies on new transformations between blocks adapted to the EPI distortion model, and on an adapted optimization scheme to ensure an opposite symmetric transformation. We present qualitative and quantitative results of the block-matching correction using different metrics on a phantom dataset and on in-vivo data. We show the ability of the block-matching to robustly correct EPI distortion even in strongly affected areas.

  17. Fabrication of high edge-definition steel-tape gratings for optical encoders

    Science.gov (United States)

    Ye, Guoyong; Liu, Hongzhong; Yan, Jiawei; Ban, Yaowen; Fan, Shanjin; Shi, Yongsheng; Yin, Lei

    2017-10-01

    High edge definition of a scale grating is the basic prerequisite for high measurement accuracy of optical encoders. This paper presents a novel fabrication method of steel tape gratings using graphene oxide nanoparticles as anti-reflective grating strips. Roll-to-roll nanoimprint lithography is adopted to manufacture the steel tape with hydrophobic and hydrophilic pattern arrays. Self-assembly technology is employed to obtain anti-reflective grating strips by depositing the graphene oxide nanoparticles on hydrophobic regions. A thin SiO2 coating is deposited on the grating to protect the grating strips. Experimental results confirm that the proposed fabrication process enables a higher edge definition in making steel-tape gratings, and the new steel tape gratings offer better performance than conventional gratings.

  18. Parietal and early visual cortices encode working memory content across mental transformations.

    Science.gov (United States)

    Christophel, Thomas B; Cichy, Radoslaw M; Hebart, Martin N; Haynes, John-Dylan

    2015-02-01

    Active and flexible manipulations of memory contents "in the mind's eye" are believed to occur in a dedicated neural workspace, frequently referred to as visual working memory. Such a neural workspace should have two important properties: The ability to store sensory information across delay periods and the ability to flexibly transform sensory information. Here we used a combination of functional MRI and multivariate decoding to indentify such neural representations. Subjects were required to memorize a complex artificial pattern for an extended delay, then rotate the mental image as instructed by a cue and memorize this transformed pattern. We found that patterns of brain activity already in early visual areas and posterior parietal cortex encode not only the initially remembered image, but also the transformed contents after mental rotation. Our results thus suggest that the flexible and general neural workspace supporting visual working memory can be realized within posterior brain regions. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.

    Science.gov (United States)

    Lundberg, Scott M; Tu, William B; Raught, Brian; Penn, Linda Z; Hoffman, Michael M; Lee, Su-In

    2016-04-30

    A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.

  20. An Oral DNA Vaccine Encoding Endoglin Eradicates Breast Tumors by Blocking Their Blood Supply

    National Research Council Canada - National Science Library

    Reisfeld, Ralph A

    2006-01-01

    .... We attained our goals for the second fiscal year, first, by constructing unique expression plasmids encoding endoglin and co-expressing IL-15 or encoding IL-7, the latter to be co-expressed with endoglin...