n-Gram-Based Text Compression

PubMed Central

Duong, Hieu N.; Snasel, Vaclav

2016-01-01

We propose an efficient method for compressing Vietnamese text using n-gram dictionaries. It has a significant compression ratio in comparison with those of state-of-the-art methods on the same dataset. Given a text, first, the proposed method splits it into n-grams and then encodes them based on n-gram dictionaries. In the encoding phase, we use a sliding window with a size that ranges from bigram to five grams to obtain the best encoding stream. Each n-gram is encoded by two to four bytes accordingly based on its corresponding n-gram dictionary. We collected 2.5 GB text corpus from some Vietnamese news agencies to build n-gram dictionaries from unigram to five grams and achieve dictionaries with a size of 12 GB in total. In order to evaluate our method, we collected a testing set of 10 different text files with different sizes. The experimental results indicate that our method achieves compression ratio around 90% and outperforms state-of-the-art methods. PMID:27965708

Encoding Standards for Linguistic Corpora.

ERIC Educational Resources Information Center

Ide, Nancy

The demand for extensive reusability of large language text collections for natural languages processing research requires development of standardized encoding formats. Such formats must be capable of representing different kinds of information across the spectrum of text types and languages, capable of representing different levels of…

Cognitive training of self-initiation of semantic encoding strategies in schizophrenia: A pilot study.

PubMed

Guimond, Synthia; Lepage, Martin

2016-01-01

Available cognitive remediation interventions have a significant but relatively small to moderate impact on episodic memory in schizophrenia. The present study aimed to evaluate the efficacy and feasibility of a brief novel episodic memory training targeting the self-initiation of semantic encoding strategies. To select patients with such deficits, 28 participants with schizophrenia performed our Semantic Encoding Memory Task (SEMT) that provides a measure of self-initiated semantic encoding strategies. This task identified a deficit in 13 participants who were then offered two 60-minute training sessions one week apart. After the training, patients performed an alternate version of the SEMT. The CVLT-II (a standardised measure of semantic encoding strategies) and the BVMT-R (a control spatial memory task) were used to quantify memory pre- and post-training. After the training, participants were significantly better at self-initiating semantic encoding strategies in the SEMT (p = .004) and in the CVLT-II (p = .002). No significant differences were found in the BVMT-R. The current study demonstrates that a brief and specific training in memory strategies can help patients to improve a deficient memory process in schizophrenia. Future studies will need to test this intervention further using a randomised controlled trial, and to explore its functional impact.

Self-initiated encoding facilitates object working memory in schizophrenia: implications for the etiology of working memory deficit.

PubMed

Kim, Jejoong; Park, Sohee; Shin, Yong-Wook; Jin Lee, Kyung; Kwon, Jun Soo

2006-02-15

Working memory (WM) deficit is present in a majority of patients with schizophrenia but it is unclear which components of WM are impaired. Past studies suggest that encoding may be compromised. One important determinant of encoding is the deployment of selective attention to the target stimulus. In addition, attention and encoding are modulated by motivational factors. In this study, we investigated the effects of self-initiated encoding (i.e., voluntary attention) on WM. 19 patients with schizophrenia and 19 matched control subjects participated in visual WM and control tasks. Encoding was manipulated by asking subjects to select from two face targets and memorize 1) one of the two identical faces (Non-preference condition), 2) one that is marked (Non-choice condition), and 3) one they prefer (Preference condition). WM accuracy for both location (spatial) and identity (object) was measured. Overall, patients with schizophrenia were less accurate and slower than the control subjects but the deficit was greater for object WM. However, patients were more accurate in object WM when they selected a preferred face as their target during encoding (preference condition) compared with the other two conditions. This effect was not significant for spatial WM. These results suggest that voluntary, self-initiated attention may facilitate object encoding especially if the selection of the target involves affective choice, and that attention may play different roles in encoding 'what' versus 'where' in WM. Since encoding affects all forms of memory, these results may have a more general implication for memory.

Illustrations as Adjuncts to Prose: A Text-Appropriate Processing Approach.

ERIC Educational Resources Information Center

Waddill, Paula J.; And Others

1988-01-01

The effects of pictorial illustrations on memory for text were studied in 144 college students. Two experiments indicated that illustrations serve a supplementary function; adjunct pictures alone, without special processing instructions, do not help learners encode information that is not normally encoded in the first place. (SLD)

Breaking the news on mobile TV: user requirements of a popular mobile content

NASA Astrophysics Data System (ADS)

Knoche, Hendrik O.; Sasse, M. Angela

2006-02-01

This paper presents the results from three lab-based studies that investigated different ways of delivering Mobile TV News by measuring user responses to different encoding bitrates, image resolutions and text quality. All studies were carried out with participants watching News content on mobile devices, with a total of 216 participants rating the acceptability of the viewing experience. Study 1 compared the acceptability of a 15-second video clip at different video and audio encoding bit rates on a 3G phone at a resolution of 176x144 and an iPAQ PDA (240x180). Study 2 measured the acceptability of video quality of full feature news clips of 2.5 minutes which were recorded from broadcast TV, encoded at resolutions ranging from 120x90 to 240x180, and combined with different encoding bit rates and audio qualities presented on an iPAQ. Study 3 improved the legibility of the text included in the video simulating a separate text delivery. The acceptability of News' video quality was greatly reduced at a resolution of 120x90. The legibility of text was a decisive factor in the participants' assessment of the video quality. Resolutions of 168x126 and higher were substantially more acceptable when they were accompanied by optimized high quality text compared to proportionally scaled inline text. When accompanied by high quality text TV news clips were acceptable to the vast majority of participants at resolutions as small as 168x126 for video encoding bitrates of 160kbps and higher. Service designers and operators can apply this knowledge to design a cost-effective mobile TV experience.

The Andes hantavirus NSs protein is expressed from the viral small mRNA by a leaky scanning mechanism.

PubMed

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P; Pino, Karla; Tischler, Nicole D; Ohlmann, Théophile; Darlix, Jean-Luc; López-Lastra, Marcelo

2012-02-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism.

The Andes Hantavirus NSs Protein Is Expressed from the Viral Small mRNA by a Leaky Scanning Mechanism

PubMed Central

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P.; Pino, Karla; Tischler, Nicole D.; Ohlmann, Théophile; Darlix, Jean-Luc

2012-01-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism. PMID:22156529

SOME DIFFERENCES IN ENCODING AND DECODING MESSAGES.

ERIC Educational Resources Information Center

BICKLEY, A. C.; WEAVER, WENDELL W.

LANGUAGE ENCODING AND DECODING PROCESSES WERE EXAMINED BY DETERMINING THE ABILITY OF SUBJECTS TO PREDICT OMISSIONS FROM A NATURAL LANGUAGE TEXT WHICH THEY HAD PREVIOUSLY PRODUCED THEMSELVES, AND BY COMPARING THIS PERFORMANCE WITH THAT OF OTHER SUBJECTS TO PREDICT OMISSIONS FROM THESE SAME TEXTS WHICH THE SECOND GROUP READ AT THE TIME OF…

A general natural-language text processor for clinical radiology.

PubMed Central

Friedman, C; Alderson, P O; Austin, J H; Cimino, J J; Johnson, S B

1994-01-01

OBJECTIVE: Development of a general natural-language processor that identifies clinical information in narrative reports and maps that information into a structured representation containing clinical terms. DESIGN: The natural-language processor provides three phases of processing, all of which are driven by different knowledge sources. The first phase performs the parsing. It identifies the structure of the text through use of a grammar that defines semantic patterns and a target form. The second phase, regularization, standardizes the terms in the initial target structure via a compositional mapping of multi-word phrases. The third phase, encoding, maps the terms to a controlled vocabulary. Radiology is the test domain for the processor and the target structure is a formal model for representing clinical information in that domain. MEASUREMENTS: The impression sections of 230 radiology reports were encoded by the processor. Results of an automated query of the resultant database for the occurrences of four diseases were compared with the analysis of a panel of three physicians to determine recall and precision. RESULTS: Without training specific to the four diseases, recall and precision of the system (combined effect of the processor and query generator) were 70% and 87%. Training of the query component increased recall to 85% without changing precision. PMID:7719797

Learning and memory performance in breast cancer survivors 2 to 6 years post-treatment: the role of encoding versus forgetting.

PubMed

Root, James C; Andreotti, Charissa; Tsu, Loretta; Ellmore, Timothy M; Ahles, Tim A

2016-06-01

Our previous retrospective analysis of clinically referred breast cancer survivors' performance on learning and memory measures found a primary weakness in initial encoding of information into working memory with intact retention and recall of this same information at a delay. This suggests that survivors may misinterpret cognitive lapses as being due to forgetting when, in actuality, they were not able to properly encode this information at the time of initial exposure. Our objective in this study was to replicate and extend this pattern of performance to a research sample to increase the generalizability of this finding in a sample in which subjects were not clinically referred for cognitive issues. We contrasted learning and memory performance between breast cancer survivors on endocrine therapy 2 to 6 years post-treatment with age- and education-matched healthy controls. We then stratified lower- and higher-performing breast cancer survivors to examine specific patterns of learning and memory performance. Contrasts were generated for four aggregate visual and verbal memory variables from the California Verbal Learning Test-2 (CVLT-2) and the Brown Location Test (BLT): Single-trial Learning: Trial 1 performance, Multiple-trial Learning: Trial 5 performance, Delayed Recall: Long-delay Recall performance, and Memory Errors: False-positive errors. As predicted, breast cancer survivors' performance as a whole was significantly lower on Single-trial Learning than the healthy control group but exhibited no significant difference in Delayed Recall. In the secondary analysis contrasting lower- and higher-performing survivors on cognitive measures, the same pattern of lower Single-trial Learning performance was exhibited in both groups, with the additional finding of significantly weaker Multiple-trial Learning performance in the lower-performing breast cancer group and intact Delayed Recall performance in both groups. As with our earlier finding of weaker initial encoding with intact recall in a cohort of clinically referred breast cancer survivors, our results indicate this same profile in a research sample of breast cancer survivors. Further, when the breast cancer group was stratified by lower and higher performance, both groups exhibited significantly lower performance on initial encoding, with more pronounced encoding weakness in the lower-performing group. As in our previous research, survivors did not lose successfully encoded information over longer delays, either in the lower- or higher-performing group, again arguing against memory decay in survivors. The finding of weaker initial encoding of information together with intact delayed recall in survivors points to specific treatment interventions in rehabilitation of cognitive dysfunction. The finding of weaker initial encoding of information together with intact delayed recall in survivors points to specific treatment interventions in rehabilitation of cognitive dysfunction and is discussed.

Hiding Techniques for Dynamic Encryption Text based on Corner Point

NASA Astrophysics Data System (ADS)

Abdullatif, Firas A.; Abdullatif, Alaa A.; al-Saffar, Amna

2018-05-01

Hiding technique for dynamic encryption text using encoding table and symmetric encryption method (AES algorithm) is presented in this paper. The encoding table is generated dynamically from MSB of the cover image points that used as the first phase of encryption. The Harris corner point algorithm is applied on cover image to generate the corner points which are used to generate dynamic AES key to second phase of text encryption. The embedded process in the LSB for the image pixels except the Harris corner points for more robust. Experimental results have demonstrated that the proposed scheme have embedding quality, error-free text recovery, and high value in PSNR.

Beyond Initial Encoding: Measures of the Post-Encoding Status of Memory Traces Predict Long-Term Recall during Infancy

ERIC Educational Resources Information Center

Pathman, Thanujeni; Bauer, Patricia J.

2013-01-01

The first years of life are witness to rapid changes in long-term recall ability. In the current research we contributed to an explanation of the changes by testing the absolute and relative contributions to long-term recall of encoding and post-encoding processes. Using elicited imitation, we sampled the status of 16-, 20-, and 24-month-old…

Negative base encoding in optical linear algebra processors

NASA Technical Reports Server (NTRS)

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.

Thought probes during prospective memory encoding: Evidence for perfunctory processes

PubMed Central

McDaniel, Mark A.; Dasse, Michelle N.; Lee, Ji hae; Kurinec, Courtney A.; Tami, Claudina; Krueger, Madison L.

2018-01-01

For nearly 50 years, psychologists have studied prospective memory, or the ability to execute delayed intentions. Yet, there remains a gap in understanding as to whether initial encoding of the intention must be elaborative and strategic, or whether some components of successful encoding can occur in a perfunctory, transient manner. In eight studies (N = 680), we instructed participants to remember to press the Q key if they saw words representing fruits (cue) during an ongoing lexical decision task. They then typed what they were thinking and responded whether they encoded fruits as a general category, as specific exemplars, or hardly thought about it at all. Consistent with the perfunctory view, participants often reported mind wandering (42.9%) and hardly thinking about the prospective memory task (22.5%). Even though participants were given a general category cue, many participants generated specific category exemplars (34.5%). Bayesian analyses of encoding durations indicated that specific exemplars came to mind in a perfunctory manner rather than via strategic, elaborative mechanisms. Few participants correctly guessed the research hypotheses and changing from fruit category cues to initial-letter cues eliminated reports of specific exemplar generation, thereby arguing against demand characteristics in the thought probe procedure. In a final experiment, encoding duration was unrelated to prospective memory performance; however, specific-exemplar encoders outperformed general-category encoders with no ongoing task monitoring costs. Our findings reveal substantial variability in intention encoding, and demonstrate that some components of prospective memory encoding can be done “in passing.” PMID:29874277

Thought probes during prospective memory encoding: Evidence for perfunctory processes.

PubMed

Scullin, Michael K; McDaniel, Mark A; Dasse, Michelle N; Lee, Ji Hae; Kurinec, Courtney A; Tami, Claudina; Krueger, Madison L

2018-01-01

For nearly 50 years, psychologists have studied prospective memory, or the ability to execute delayed intentions. Yet, there remains a gap in understanding as to whether initial encoding of the intention must be elaborative and strategic, or whether some components of successful encoding can occur in a perfunctory, transient manner. In eight studies (N = 680), we instructed participants to remember to press the Q key if they saw words representing fruits (cue) during an ongoing lexical decision task. They then typed what they were thinking and responded whether they encoded fruits as a general category, as specific exemplars, or hardly thought about it at all. Consistent with the perfunctory view, participants often reported mind wandering (42.9%) and hardly thinking about the prospective memory task (22.5%). Even though participants were given a general category cue, many participants generated specific category exemplars (34.5%). Bayesian analyses of encoding durations indicated that specific exemplars came to mind in a perfunctory manner rather than via strategic, elaborative mechanisms. Few participants correctly guessed the research hypotheses and changing from fruit category cues to initial-letter cues eliminated reports of specific exemplar generation, thereby arguing against demand characteristics in the thought probe procedure. In a final experiment, encoding duration was unrelated to prospective memory performance; however, specific-exemplar encoders outperformed general-category encoders with no ongoing task monitoring costs. Our findings reveal substantial variability in intention encoding, and demonstrate that some components of prospective memory encoding can be done "in passing."

If at First You Don't Remember, Try, Try Again: The Role of Initial Encoding in Children's False Reports

ERIC Educational Resources Information Center

Principe, Gabrielle F.

2004-01-01

To examine the extent to which differences in the initial encoding of information affect preschoolers' vulnerability to suggestion, 4 groups of 4-year-olds (N = 54) individually participated in a simulated shopping event in which they were asked to purchase 6 items from a specially constructed grocery store. Half the children had only 1…

What–where–when memory and encoding strategies in healthy aging

PubMed Central

2016-01-01

Older adults exhibit disproportionate impairments in memory for item-associations. These impairments may stem from an inability to self-initiate deep encoding strategies. The present study investigates this using the “treasure-hunt task”; a what–where–when style episodic memory test that requires individuals to “hide” items around complex scenes. This task separately assesses memory for item, location, and temporal order, as well as bound what–where–when information. The results suggest that older adults are able to ameliorate integration memory deficits by using self-initiated encoding strategies when these are externally located and therefore place reduced demands on working memory and attentional resources. PMID:26884230

Lexical stress encoding in single word production estimated by event-related brain potentials.

PubMed

Schiller, Niels O

2006-09-27

An event-related brain potentials (ERPs) experiment was carried out to investigate the time course of lexical stress encoding in language production. Native speakers of Dutch viewed a series of pictures corresponding to bisyllabic names which were either stressed on the first or on the second syllable and made go/no-go decisions on the lexical stress location of those picture names. Behavioral results replicated a pattern that was observed earlier, i.e. faster button-press latencies to initial as compared to final stress targets. The electrophysiological results indicated that participants could make a lexical stress decision significantly earlier when picture names had initial than when they had final stress. Moreover, the present data suggest the time course of lexical stress encoding during single word form formation in language production. When word length is corrected for, the temporal interval for lexical stress encoding specified by the current ERP results falls into the time window previously identified for phonological encoding in language production.

Neural Correlates of Encoding Predict Infants' Memory in the Paired-Comparison Procedure

ERIC Educational Resources Information Center

Snyder, Kelly A.

2010-01-01

The present study used event-related potentials (ERPs) to monitor infant brain activity during the initial encoding of a previously novel visual stimulus, and examined whether ERP measures of encoding predicted infants' subsequent performance on a visual memory task (i.e., the paired-comparison task). A late slow wave component of the ERP measured…

Sleep can reduce the testing effect: it enhances recall of restudied items but can leave recall of retrieved items unaffected.

PubMed

Bäuml, Karl-Heinz T; Holterman, Christoph; Abel, Magdalena

2014-11-01

The testing effect refers to the finding that retrieval practice in comparison to restudy of previously encoded contents can improve memory performance and reduce time-dependent forgetting. Naturally, long retention intervals include both wake and sleep delay, which can influence memory contents differently. In fact, sleep immediately after encoding can induce a mnemonic benefit, stabilizing and strengthening the encoded contents. We investigated in a series of 5 experiments whether sleep influences the testing effect. After initial study of categorized item material (Experiments 1, 2, and 4A), paired associates (Experiment 3), or educational text material (Experiment 4B), subjects were asked to restudy encoded contents or engage in active retrieval practice. A final recall test was conducted after a 12-hr delay that included diurnal wakefulness or nocturnal sleep. The results consistently showed typical testing effects after the wake delay. However, these testing effects were reduced or even eliminated after sleep, because sleep benefited recall of restudied items but left recall of retrieved items unaffected. The findings are consistent with the bifurcation model of the testing effect (Kornell, Bjork, & Garcia, 2011), according to which the distribution of memory strengths across items is shifted differentially by retrieving and restudying, with retrieval strengthening items to a much higher degree than restudy does. On the basis of this model, most of the retrieved items already fall above recall threshold in the absence of sleep, so additional sleep-induced strengthening may not improve recall of retrieved items any further. PsycINFO Database Record (c) 2014 APA, all rights reserved.

The first does the work, but the third time's the charm: the effects of massed repetition on episodic encoding of multimodal face-name associations.

PubMed

Mangels, Jennifer A; Manzi, Alberto; Summerfield, Christopher

2010-03-01

In social interactions, it is often necessary to rapidly encode the association between visually presented faces and auditorily presented names. The present study used event-related potentials to examine the neural correlates of associative encoding for multimodal face-name pairs. We assessed study-phase processes leading to high-confidence recognition of correct pairs (and consistent rejection of recombined foils) as compared to lower-confidence recognition of correct pairs (with inconsistent rejection of recombined foils) and recognition failures (misses). Both high- and low-confidence retrieval of face-name pairs were associated with study-phase activity suggestive of item-specific processing of the face (posterior inferior temporal negativity) and name (fronto-central negativity). However, only those pairs later retrieved with high confidence recruited a sustained centro-parietal positivity that an ancillary localizer task suggested may index an association-unique process. Additionally, we examined how these processes were influenced by massed repetition, a mnemonic strategy commonly employed in everyday situations to improve face-name memory. Differences in subsequent memory effects across repetitions suggested that associative encoding was strongest at the initial presentation, and thus, that the initial presentation has the greatest impact on memory formation. Yet, exploratory analyses suggested that the third presentation may have benefited later memory by providing an opportunity for extended processing of the name. Thus, although encoding of the initial presentation was critical for establishing a strong association, the extent to which processing was sustained across subsequent immediate (massed) presentations may provide additional encoding support that serves to differentiate face-name pairs from similar (recombined) pairs by providing additional encoding opportunities for the less dominant stimulus dimension (i.e., name).

Burkholderia Mallei tssM Encodes a Secreted Deubiquitinase that is Expressed Inside Infected RAW 264.7 Murine Macrophages

DTIC Science & Technology

2008-10-13

Furthermore, the encoded protein of this gene is only 30 kDa. A potential GTG start codon at position 625 also encodes a protein that is too small...horizontal bar and putative alternate translation initiation sites (ATG, GTG , and TTG) are indicated. The sizes and locations of the proteins encoded... gray line with rounded rectangles showing sequence features and motifs, including the Ala- and Pro-rich N-terminal region and the C-terminal Cys and

Explaining Variance in Long-Term Recall in 3- and 4-Year-Old Children: The Importance of Post-Encoding Processes

ERIC Educational Resources Information Center

Bauer, Patricia J.; Larkina, Marina; Doydum, Ayzit O.

2012-01-01

Long-term recall is influenced by what originally was encoded as well as by the efficacy of retrieval processes. The possible explanatory role of post-encoding processes by which initially labile memory traces are stabilized and integrated into long-term memory (i.e., consolidated) has received relatively less research attention. In the current…

Validation of an optical encoder during free weight resistance movements and analysis of bench press sticking point power during fatigue.

PubMed

Drinkwater, Eric J; Galna, Brook; McKenna, Michael J; Hunt, Patrick H; Pyne, David B

2007-05-01

During the concentric movement of the bench press, there is an initial high-power push after chest contact, immediately followed by a characteristic area of low power, the so-called "sticking region." During high-intensity lifting, a decline in power can result in a failed lift attempt. The purpose of this study was to determine the validity of an optical encoder to measure power and then employ this device to determine power changes during the initial acceleration and sticking region during fatiguing repeated bench press training. Twelve subjects performed a free weight bench press, a Smith Machine back squat, and a Smith Machine 40-kg bench press throw for power validation measures. All barbell movements were simultaneously monitored using cinematography and an optical encoder. Eccentric and concentric mean and peak power were calculated using time and position data derived from each method. Validity of power measures between the video (criterion) and optical encoder scores were evaluated by standard error of the estimate (SEE) and coefficient of variation (CV). Seven subjects then performed 4 sets of 6 free weight bench press repetitions progressively increasing from 85 to 95% of their 6 repetition maximum, with each repetition continually monitored by an optical encoder. The SEE for power ranged from 3.6 to 14.4 W (CV, 1.0-3.0%; correlation, 0.97-1.00). During the free weight bench press training, peak power declined by approximately 55% (p < 0.01) during the initial acceleration phase of the final 2 repetitions of the final set. Although decreases in power of the sticking point were significant (p < 0.01), as early as repetition 5 (-40%) they reached critically low levels in the final 2 repetitions (>-95%). In conclusion, the optical encoder provided valid measures of kinetics during free weight resistance training movements. The decline in power during the initial acceleration phase appears a factor in a failed lift attempt at the sticking point.

Programmable Pulse-Position-Modulation Encoder

NASA Technical Reports Server (NTRS)

Zhu, David; Farr, William

2006-01-01

A programmable pulse-position-modulation (PPM) encoder has been designed for use in testing an optical communication link. The encoder includes a programmable state machine and an electronic code book that can be updated to accommodate different PPM coding schemes. The encoder includes a field-programmable gate array (FPGA) that is programmed to step through the stored state machine and code book and that drives a custom high-speed serializer circuit board that is capable of generating subnanosecond pulses. The stored state machine and code book can be updated by means of a simple text interface through the serial port of a personal computer.

The RAS Initiative

Cancer.gov

NCI established the RAS Initiative to explore innovative approaches for attacking the proteins encoded by mutant forms of RAS genes and to ultimately create effective, new therapies for RAS-related cancers.

Goal-directed mechanisms that constrain retrieval predict subsequent memory for new "foil" information.

PubMed

Vogelsang, David A; Bonnici, Heidi M; Bergström, Zara M; Ranganath, Charan; Simons, Jon S

2016-08-01

To remember a previous event, it is often helpful to use goal-directed control processes to constrain what comes to mind during retrieval. Behavioral studies have demonstrated that incidental learning of new "foil" words in a recognition test is superior if the participant is trying to remember studied items that were semantically encoded compared to items that were non-semantically encoded. Here, we applied subsequent memory analysis to fMRI data to understand the neural mechanisms underlying the "foil effect". Participants encoded information during deep semantic and shallow non-semantic tasks and were tested in a subsequent blocked memory task to examine how orienting retrieval towards different types of information influences the incidental encoding of new words presented as foils during the memory test phase. To assess memory for foils, participants performed a further surprise old/new recognition test involving foil words that were encountered during the previous memory test blocks as well as completely new words. Subsequent memory effects, distinguishing successful versus unsuccessful incidental encoding of foils, were observed in regions that included the left inferior frontal gyrus and posterior parietal cortex. The left inferior frontal gyrus exhibited disproportionately larger subsequent memory effects for semantic than non-semantic foils, and significant overlap in activity during semantic, but not non-semantic, initial encoding and foil encoding. The results suggest that orienting retrieval towards different types of foils involves re-implementing the neurocognitive processes that were involved during initial encoding. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

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

Mir-Sanchis, Ignacio; Roman, Christina A.; Misiura, Agnieszka

2016-08-29

Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA–binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-familymore » replicative helicases, belongs to the pre–sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.« less

Different Words for the Same Concept: Learning Collaboratively from Multiple Documents

ERIC Educational Resources Information Center

Jucks, Regina; Paus, Elisabeth

2013-01-01

This study investigated how varying the lexical encodings of technical terms in multiple texts influences learners' dyadic processing of scientific-related information. Fifty-seven pairs of college students read journalistic texts on depression. Each partner in a dyad received one text; for half of the dyads the partner's text contained different…

The Diffusion of Electronic Text among University Students and Faculty: A Strategy for Laboratory Research. Monograph Number One of the Electronic Text Monograph Series.

ERIC Educational Resources Information Center

Dozier, David M.

This monograph defines and describes research in the study of adoption of electronic text services in higher education institutions. Electronic text here includes text and graphic information encoded and transmitted via broadcast, signal, or cable, under user control. It places the diffusion of electronic text in higher education within the…

Remembering operations.

PubMed

Kolers, P A

1973-09-01

Two commonplace assumptions about encoding are that sentences are encoded and recognized on the basis of their semantic features primarily and that information regarding form features such as typography is typically ignored or discarded. These assumptions were tested m the present experiment where, within a signal-detection paradigm, S sorted sentences according to whether he had seen them before or not (old vs new) and, if they were old, whether their reappearance was in the same typography as on the first occurrence or a different one. Of the two typographies, one was familiar and the other unfamiliar. Results show that a considerable amount of information regarding surface features is stored for many minutes and that ease of initial encoding is inversely related to likelihood of subsequent recognition: sentences in the unfamiliar typography were remembered better. The results are probably not due to time spent encoding; control tests suggest that time spent encoding a difficult typography does not by itself increase recognition of the semantic content embodied in the typography. Other control tests show that pictorial features or images of the sentences play no significant role in their subsequent recognition. One interpretation of the results is that the analytic activities or cognitive operations that characterize initial acquisition play a significant role in subsequent recognition.

Phonological Planning during Sentence Production: Beyond the Verb.

PubMed

Schnur, Tatiana T

2011-01-01

The current study addresses the extent of phonological planning during spontaneous sentence production. Previous work shows that at articulation, phonological encoding occurs for entire phrases, but encoding beyond the initial phrase may be due to the syntactic relevance of the verb in planning the utterance. I conducted three experiments to investigate whether phonological planning crosses multiple grammatical phrase boundaries (as defined by the number of lexical heads of phrase) within a single phonological phrase. Using the picture-word interference paradigm, I found in two separate experiments a significant phonological facilitation effect to both the verb and noun of sentences like "He opens the gate." I also altered the frequency of the direct object and found longer utterance initiation times for sentences ending with a low-frequency vs. high-frequency object offering further support that the direct object was phonologically encoded at the time of utterance initiation. That phonological information for post-verbal elements was activated suggests that the grammatical importance of the verb does not restrict the extent of phonological planning. These results suggest that the phonological phrase is unit of planning, where all elements within a phonological phrase are encoded before articulation. Thus, consistent with other action sequencing behavior, there is significant phonological planning ahead in sentence production.

Narrative organisation at encoding facilitated children's long-term episodic memory.

PubMed

Wang, Qi; Bui, Van-Kim; Song, Qingfang

2015-01-01

This study examined the effect of narrative organisation at encoding on long-term episodic memory in a sample of five- to seven-year-old children (N = 113). At an initial interview, children were asked to narrate a story from a picture book. Six months later, they were interviewed again and asked to recall the story and answer a series of direct questions about the story. Children who initially encoded more information in narrative and produced more complete, complex, cohesive and coherent narratives remembered the story in greater detail and accuracy following the six-month interval, independent of age and verbal skills. The relation between narrative organisation and memory was consistent across culture and gender. These findings provide new insight into the critical role of narrative in episodic memory.

Trichome-Related Mutants Provide a New Perspective on Multicellular Trichome Initiation and Development in Cucumber (Cucumis sativus L)

PubMed Central

Liu, Xingwang; Bartholomew, Ezra; Cai, Yanling; Ren, Huazhong

2016-01-01

Trichomes are specialized epidermal cells located in aerial parts of plants that function in plant defense against biotic and abiotic stresses. The simple unicellular trichomes of Arabidopsis serve as an excellent model to study the molecular mechanism of cell differentiation and pattern formation in plants. Loss-of-function mutations in Arabidopsis thaliana have suggested that the core genes GL1 (which encodes a MYB transcription factor) and TTG1 (which encodes a WD40 repeat-containing protein) are important for the initiation and spacing of leaf trichomes, while for normal trichome initiation, the genes GL3, and EGL3 (which encode a bHLH protein) are needed. However, the positive regulatory genes involved in multicellular trichrome development in cucumber remain unclear. This review focuses on the phenotype of mutants (csgl3, tril, tbh, mict, and csgl1) with disturbed trichomes in cucumber and then infers which gene(s) play key roles in trichome initiation and development in those mutants. Evidence indicates that MICT, TBH, and CsGL1 are allelic with alternative splicing. CsGL3 and TRIL are allelic and override the effect of TBH, MICT, and CsGL1 on the regulation of multicellular trichome development; and affect trichome initiation. CsGL3, TRIL, MICT, TBH, and CsGL1 encode HD-Zip proteins with different subfamilies. Genetic and molecular analyses have revealed that CsGL3, TRIL, MICT, TBH, and CsGL1 are responsible for the differentiation of epidermal cells and the development of trichomes. Based on current knowledge, a positive regulator pathway model for trichome development in cucumber was proposed and compared to a model in Arabidopsis. These data suggest that trichome development in cucumber may differ from that in Arabidopsis. PMID:27559338

The Nature of Phonological Encoding During Spoken Word Retrieval.

ERIC Educational Resources Information Center

Sullivan, Michael P.; Riffel, Brian

1999-01-01

Examined whether phonological selection occurs sequentially or in parallel. College students named picture primes and targets, with varied response stimulus intervals between primes and targets. Results were consistent with Dell's (1988) two-stage sequential model of encoding, which shows an initial parallel activation within a lexical network…

What-Where-When Memory and Encoding Strategies in Healthy Aging

ERIC Educational Resources Information Center

Cheke, Lucy G.

2016-01-01

Older adults exhibit disproportionate impairments in memory for item-associations. These impairments may stem from an inability to self-initiate deep encoding strategies. The present study investigates this using the "treasure-hunt task"; a what-where-when style episodic memory test that requires individuals to "hide" items…

Exploring Encoding and Retrieval Effects of Background Information on Text Memory

ERIC Educational Resources Information Center

Rawson, Katherine A.; Kintsch, Walter

2004-01-01

Two experiments were conducted (a) to evaluate how providing background information at test may benefit retrieval and (b) to further examine how providing background information prior to study influences encoding. Half of the participants read background information prior to study, and the other half did not. In each group, half were presented…

Page layout analysis and classification for complex scanned documents

NASA Astrophysics Data System (ADS)

Erkilinc, M. Sezer; Jaber, Mustafa; Saber, Eli; Bauer, Peter; Depalov, Dejan

2011-09-01

A framework for region/zone classification in color and gray-scale scanned documents is proposed in this paper. The algorithm includes modules for extracting text, photo, and strong edge/line regions. Firstly, a text detection module which is based on wavelet analysis and Run Length Encoding (RLE) technique is employed. Local and global energy maps in high frequency bands of the wavelet domain are generated and used as initial text maps. Further analysis using RLE yields a final text map. The second module is developed to detect image/photo and pictorial regions in the input document. A block-based classifier using basis vector projections is employed to identify photo candidate regions. Then, a final photo map is obtained by applying probabilistic model based on Markov random field (MRF) based maximum a posteriori (MAP) optimization with iterated conditional mode (ICM). The final module detects lines and strong edges using Hough transform and edge-linkages analysis, respectively. The text, photo, and strong edge/line maps are combined to generate a page layout classification of the scanned target document. Experimental results and objective evaluation show that the proposed technique has a very effective performance on variety of simple and complex scanned document types obtained from MediaTeam Oulu document database. The proposed page layout classifier can be used in systems for efficient document storage, content based document retrieval, optical character recognition, mobile phone imagery, and augmented reality.

Fast and memory efficient text image compression with JBIG2.

PubMed

Ye, Yan; Cosman, Pamela

2003-01-01

In this paper, we investigate ways to reduce encoding time, memory consumption and substitution errors for text image compression with JBIG2. We first look at page striping where the encoder splits the input image into horizontal stripes and processes one stripe at a time. We propose dynamic dictionary updating procedures for page striping to reduce the bit rate penalty it incurs. Experiments show that splitting the image into two stripes can save 30% of encoding time and 40% of physical memory with a small coding loss of about 1.5%. Using more stripes brings further savings in time and memory but the return diminishes. We also propose an adaptive way to update the dictionary only when it has become out-of-date. The adaptive updating scheme can resolve the time versus bit rate tradeoff and the memory versus bit rate tradeoff well simultaneously. We then propose three speedup techniques for pattern matching, the most time-consuming encoding activity in JBIG2. When combined together, these speedup techniques can save up to 75% of the total encoding time with at most 1.7% of bit rate penalty. Finally, we look at improving reconstructed image quality for lossy compression. We propose enhanced prescreening and feature monitored shape unifying to significantly reduce substitution errors in the reconstructed images.

Semantic encoding and retrieval in the left inferior prefrontal cortex: a functional MRI study of task difficulty and process specificity.

PubMed

Demb, J B; Desmond, J E; Wagner, A D; Vaidya, C J; Glover, G H; Gabrieli, J D

1995-09-01

Prefrontal cortical function was examined during semantic encoding and repetition priming using functional magnetic resonance imaging (fMRI), a noninvasive technique for localizing regional changes in blood oxygenation, a correlate of neural activity. Words studied in a semantic (deep) encoding condition were better remembered than words studied in both easier and more difficult nonsemantic (shallow) encoding conditions, with difficulty indexed by response time. The left inferior prefrontal cortex (LIPC) (Brodmann's areas 45, 46, 47) showed increased activation during semantic encoding relative to nonsemantic encoding regardless of the relative difficulty of the nonsemantic encoding task. Therefore, LIPC activation appears to be related to semantic encoding and not task difficulty. Semantic encoding decisions are performed faster the second time words are presented. This represents semantic repetition priming, a facilitation in semantic processing for previously encoded words that is not dependent on intentional recollection. The same LIPC area activated during semantic encoding showed decreased activation during repeated semantic encoding relative to initial semantic encoding of the same words. This decrease in activation during repeated encoding was process specific; it occurred when words were semantically reprocessed but not when words were nonsemantically reprocessed. The results were apparent in both individual and averaged functional maps. These findings suggest that the LIPC is part of a semantic executive system that contributes to the on-line retrieval of semantic information.

Does Spatial or Visual Information in Maps Facilitate Text Recall?: Reconsidering the Conjoint Retention Hypothesis

ERIC Educational Resources Information Center

Griffin, Marlynn M.; Robinson, Daniel H.; Sarama, Julie

2005-01-01

The conjoint retention hypothesis (CRH) claims that students recall more text information when they study geographic maps in addition to text than when they study text alone, because the maps are encoded spatially (Kulhavy, Lee, & Caterino, 1985). This claim was recently challenged by Griffin and Robinson (2000), who found no advantage for maps…

Level of Processing Modulates the Neural Correlates of Emotional Memory Formation

ERIC Educational Resources Information Center

Ritchey, Maureen; LaBar, Kevin S.; Cabeza, Roberto

2011-01-01

Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study used a levels-of-processing manipulation to characterize the impact of emotion on…

Two-layer contractive encodings for learning stable nonlinear features.

PubMed

Schulz, Hannes; Cho, Kyunghyun; Raiko, Tapani; Behnke, Sven

2015-04-01

Unsupervised learning of feature hierarchies is often a good strategy to initialize deep architectures for supervised learning. Most existing deep learning methods build these feature hierarchies layer by layer in a greedy fashion using either auto-encoders or restricted Boltzmann machines. Both yield encoders which compute linear projections of input followed by a smooth thresholding function. In this work, we demonstrate that these encoders fail to find stable features when the required computation is in the exclusive-or class. To overcome this limitation, we propose a two-layer encoder which is less restricted in the type of features it can learn. The proposed encoder is regularized by an extension of previous work on contractive regularization. This proposed two-layer contractive encoder potentially poses a more difficult optimization problem, and we further propose to linearly transform hidden neurons of the encoder to make learning easier. We demonstrate the advantages of the two-layer encoders qualitatively on artificially constructed datasets as well as commonly used benchmark datasets. We also conduct experiments on a semi-supervised learning task and show the benefits of the proposed two-layer encoders trained with the linear transformation of perceptrons. Copyright © 2014 Elsevier Ltd. All rights reserved.

Eighth Grade Students' Reading Responses to Encoded Inflectional, Syntactic, Grammatical and Semantic Errors.

ERIC Educational Resources Information Center

Williamson, Leon E.; And Others

A study investigated the reading responses of 60 eighth grade students to encoded inflectional, syntactic, grammatical, and semantic errors. The students were equally divided into three categories based on grade level reading competency and given three Aesopian fables to read. The text of the fables contained the following errors: (1) words to…

Syllabic encoding during overt speech production in Cantonese: Evidence from temporal brain responses.

PubMed

Wong, Andus Wing-Kuen; Wang, Jie; Ng, Tin-Yan; Chen, Hsuan-Chih

2016-10-01

The time course of phonological encoding in overt Cantonese disyllabic word production was investigated using a picture-word interference task with concurrent recording of the event-related brain potentials (ERPs). Participants were asked to name aloud individually presented pictures and ignore a distracting Chinese character. Participants' naming responses were faster, relative to an unrelated control, when the distractor overlapped with the target's word-initial or word-final syllables. Furthermore, ERP waves in the syllable-related conditions were more positive-going than those in the unrelated control conditions from 500ms to 650ms post target onset (i.e., a late positivity). The mean and peak amplitudes of this late positivity correlated with the size of phonological facilitation. More importantly, the onset of the late positivity associated with word-initial syllable priming was 44ms earlier than that associated with word-final syllable priming, suggesting that phonological encoding in overt speech runs incrementally and the encoding duration for one syllable unit is approximately 44ms. Although the size of effective phonological units might vary across languages, as suggested by previous speech production studies, the present data indicate that the incremental nature of phonological encoding is a universal mechanism. Copyright © 2016 Elsevier B.V. All rights reserved.

Nocturnal Mnemonics: Sleep and Hippocampal Memory Processing

PubMed Central

Saletin, Jared M.; Walker, Matthew P.

2012-01-01

As critical as waking brain function is to learning and memory, an established literature now describes an equally important yet complementary role for sleep in information processing. This overview examines the specific contribution of sleep to human hippocampal memory processing; both the detriments caused by a lack of sleep, and conversely, the proactive benefits that develop following the presence of sleep. First, a role for sleep before learning is discussed, preparing the hippocampus for initial memory encoding. Second, a role for sleep after learning is considered, modulating the post-encoding consolidation of hippocampal-dependent memory. Third, a model is outlined in which these encoding and consolidation operations are symbiotically accomplished, associated with specific NREM sleep physiological oscillations. As a result, the optimal network outcome is achieved: increasing hippocampal independence and hence overnight consolidation, while restoring next-day sparse hippocampal encoding capacity for renewed learning ability upon awakening. Finally, emerging evidence is considered suggesting that, unlike previous conceptions, sleep does not universally consolidate all information. Instead, and based on explicit as well as saliency cues during initial encoding, sleep executes the discriminatory offline consolidation only of select information. Consequently, sleep promotes the targeted strengthening of some memories while actively forgetting others; a proposal with significant theoretical and clinical ramifications. PMID:22557988

Pattern-Directed Processing of Knowledge from Texts.

ERIC Educational Resources Information Center

Thorndyke, Perry W.

A framework for viewing human text comprehension, memory, and recall is presented that assumes patterns of abstract conceptual relations are used to guide processing. These patterns consist of clusters of knowledge that encode prototypical co-occurrences of situations and events in narrative texts. The patterns are assumed to be a part of a…

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

PubMed

Glass, Jennifer B; Kretz, Cecilia B; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L; Buck, Kristen N; Landing, William M; Morton, Peter L; Moffett, James W; Giovannoni, Stephen J; Vergin, Kevin L; Stewart, Frank J

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Potential digitization/compression techniques for Shuttle video

NASA Technical Reports Server (NTRS)

Habibi, A.; Batson, B. H.

1978-01-01

The Space Shuttle initially will be using a field-sequential color television system but it is possible that an NTSC color TV system may be used for future missions. In addition to downlink color TV transmission via analog FM links, the Shuttle will use a high resolution slow-scan monochrome system for uplink transmission of text and graphics information. This paper discusses the characteristics of the Shuttle video systems, and evaluates digitization and/or bandwidth compression techniques for the various links. The more attractive techniques for the downlink video are based on a two-dimensional DPCM encoder that utilizes temporal and spectral as well as the spatial correlation of the color TV imagery. An appropriate technique for distortion-free coding of the uplink system utilizes two-dimensional HCK codes.

A method for encoding clinical datasets with SNOMED CT.

PubMed

Lee, Dennis H; Lau, Francis Y; Quan, Hue

2010-09-17

Over the past decade there has been a growing body of literature on how the Systematised Nomenclature of Medicine Clinical Terms (SNOMED CT) can be implemented and used in different clinical settings. Yet, for those charged with incorporating SNOMED CT into their organisation's clinical applications and vocabulary systems, there are few detailed encoding instructions and examples available to show how this can be done and the issues involved. This paper describes a heuristic method that can be used to encode clinical terms in SNOMED CT and an illustration of how it was applied to encode an existing palliative care dataset. The encoding process involves: identifying input data items; cleaning the data items; encoding the cleaned data items; and exporting the encoded terms as output term sets. Four outputs are produced: the SNOMED CT reference set; interface terminology set; SNOMED CT extension set and unencodeable term set. The original palliative care database contained 211 data elements, 145 coded values and 37,248 free text values. We were able to encode ~84% of the terms, another ~8% require further encoding and verification while terms that had a frequency of fewer than five were not encoded (~7%). From the pilot, it would seem our SNOMED CT encoding method has the potential to become a general purpose terminology encoding approach that can be used in different clinical systems.

Secure multiparty computation of a comparison problem.

PubMed

Liu, Xin; Li, Shundong; Liu, Jian; Chen, Xiubo; Xu, Gang

2016-01-01

Private comparison is fundamental to secure multiparty computation. In this study, we propose novel protocols to privately determine [Formula: see text], or [Formula: see text] in one execution. First, a 0-1-vector encoding method is introduced to encode a number into a vector, and the Goldwasser-Micali encryption scheme is used to compare integers privately. Then, we propose a protocol by using a geometric method to compare rational numbers privately, and the protocol is information-theoretical secure. Using the simulation paradigm, we prove the privacy-preserving property of our protocols in the semi-honest model. The complexity analysis shows that our protocols are more efficient than previous solutions.

Self-initiated object-location memory in young and older adults.

PubMed

Berger-Mandelbaum, Anat; Magen, Hagit

2017-11-20

The present study explored self-initiated object-location memory in ecological contexts, as aspect of memory that is largely absent from the research literature. Young and older adults memorized objects-location associations they selected themselves or object-location associations provided to them, and elaborated on the strategy they used when selecting the locations themselves. Retrieval took place 30 min and 1 month after encoding. The results showed an age-related decline in self-initiated and provided object-location memory. Older adults benefited from self-initiation more than young adults when tested after 30 min, while the benefit was equal when tested after 1 month. Furthermore, elaboration enhanced memory only in older adults, and only after 30 min. Both age groups used deep encoding strategies on the majority of the trials, but their percentage was lower in older adults. Overall, the study demonstrated the processes involved in self-initiated object-location memory, which is an essential part of everyday functioning.

The Role of Manual Encoding in Learning by the Prelingually Deaf: An Initial Investigation.

ERIC Educational Resources Information Center

Stall, C. Harmon; Marshall, Philip H.

1984-01-01

A study tested the hypothesis that manual encoding aids learning in the prelingually deaf. Twenty-four adults who used fingerspelling as their primary means of communication participated in two groups of a paired-associate learning paradigm, using eight study-test trial sequences. Those using fingerspelling showed more recall and a faster learning…

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

PubMed

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.

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

PubMed Central

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. PMID:28403240

Inter-subject variability modulates phonological advance planning in the production of adjective-noun phrases.

PubMed

Michel Lange, Violaine; Laganaro, Marina

2014-01-01

The literature on advance phonological planning in adjective-noun phrases (NPs) presents diverging results: while many experimental studies suggest that the entire NP is encoded before articulation, other results favor a span of encoding limited to the first word. Although cross-linguistic differences in the structure of adjective-NPs may account for some of these contrasting results, divergences have been reported even among similar languages and syntactic structures. Here we examined whether inter-individual differences account for variability in the span of phonological planning in the production of French NPs, where previous results indicated encoding limited to the first word. The span of phonological encoding is tested with the picture-word interference (PWI) paradigm using phonological distractors related to the noun or to the adjective of the NPs. In Experiment 1, phonological priming effects were limited to the first word in adjective NPs whichever the position of the adjective (pre-nominal or post-nominal). Crucially, phonological priming effects on the second word interacted with speakers' production speed suggesting different encoding strategies for participants. In Experiment 2, we tested this hypothesis further with a larger group of participants. Results clearly showed that slow and fast initializing participants presented different phonological priming patterns on the last element of adjective-NPs: while the first word was primed by a distractor for all speakers, only the slow speaker group presented a priming effect on the second element of the NP. These results show that the span of phonological encoding is modulated by inter-individual strategies: in experimental paradigms some speakers plan word by word whereas others encode beyond the initial word. We suggest that the diverging results reported in the literature on advance phonological planning may partly be reconciled in light of the present results.

Method for non-referential defect characterization using fractal encoding and active contours

DOEpatents

Gleason, Shaun S [Knoxville, TN; Sari-Sarraf, Hamed [Lubbock, TX

2007-05-15

A method for identification of anomalous structures, such as defects, includes the steps of providing a digital image and applying fractal encoding to identify a location of at least one anomalous portion of the image. The method does not require a reference image to identify the location of the anomalous portion. The method can further include the step of initializing an active contour based on the location information obtained from the fractal encoding step and deforming an active contour to enhance the boundary delineation of the anomalous portion.

On the Suitability of Suffix Arrays for Lempel-Ziv Data Compression

NASA Astrophysics Data System (ADS)

Ferreira, Artur J.; Oliveira, Arlindo L.; Figueiredo, Mário A. T.

Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding. In order to speed up the encoding process, efficient data structures, like suffix trees, have been used. In this paper, we explore the use of suffix arrays to hold the dictionary of the LZ encoder, and propose an algorithm to search over it. We show that the resulting encoder attains roughly the same compression ratios as those based on suffix trees. However, the amount of memory required by the suffix array is fixed, and much lower than the variable amount of memory used by encoders based on suffix trees (which depends on the text to encode). We conclude that suffix arrays, when compared to suffix trees in terms of the trade-off among time, memory, and compression ratio, may be preferable in scenarios (e.g., embedded systems) where memory is at a premium and high speed is not critical.

What Can Pictures Tell Us About Web Pages? Improving Document Search Using Images.

PubMed

Rodriguez-Vaamonde, Sergio; Torresani, Lorenzo; Fitzgibbon, Andrew W

2015-06-01

Traditional Web search engines do not use the images in the HTML pages to find relevant documents for a given query. Instead, they typically operate by computing a measure of agreement between the keywords provided by the user and only the text portion of each page. In this paper we study whether the content of the pictures appearing in a Web page can be used to enrich the semantic description of an HTML document and consequently boost the performance of a keyword-based search engine. We present a Web-scalable system that exploits a pure text-based search engine to find an initial set of candidate documents for a given query. Then, the candidate set is reranked using visual information extracted from the images contained in the pages. The resulting system retains the computational efficiency of traditional text-based search engines with only a small additional storage cost needed to encode the visual information. We test our approach on one of the TREC Million Query Track benchmarks where we show that the exploitation of visual content yields improvement in accuracies for two distinct text-based search engines, including the system with the best reported performance on this benchmark. We further validate our approach by collecting document relevance judgements on our search results using Amazon Mechanical Turk. The results of this experiment confirm the improvement in accuracy produced by our image-based reranker over a pure text-based system.

Combination Base64 Algorithm and EOF Technique for Steganography

NASA Astrophysics Data System (ADS)

Rahim, Robbi; Nurdiyanto, Heri; Hidayat, Rahmat; Saleh Ahmar, Ansari; Siregar, Dodi; Putera Utama Siahaan, Andysah; Faisal, Ilham; Rahman, Sayuti; Suita, Diana; Zamsuri, Ahmad; Abdullah, Dahlan; Napitupulu, Darmawan; Ikhsan Setiawan, Muhammad; Sriadhi, S.

2018-04-01

The steganography process combines mathematics and computer science. Steganography consists of a set of methods and techniques to embed the data into another media so that the contents are unreadable to anyone who does not have the authority to read these data. The main objective of the use of base64 method is to convert any file in order to achieve privacy. This paper discusses a steganography and encoding method using base64, which is a set of encoding schemes that convert the same binary data to the form of a series of ASCII code. Also, the EoF technique is used to embed encoding text performed by Base64. As an example, for the mechanisms a file is used to represent the texts, and by using the two methods together will increase the security level for protecting the data, this research aims to secure many types of files in a particular media with a good security and not to damage the stored files and coverage media that used.

Reading between the Lines: A Distinctly Pragmatic Approach to 1 Thess 4:13-5:11 and 2 Thess 2:1-12

ERIC Educational Resources Information Center

Schulze, Robert J.

2010-01-01

This dissertation investigates the viability of utilizing linguistic pragmatics to interpret the biblical text and to determine its hermeneutical significance. As a complementary aid to historical and literary readings of a text, linguistic pragmatics utilizes certain tools to discover and/or describe the implicit meaning encoded into a text. A…

Beyond initial encoding: measures of the post-encoding status of memory traces predict long-term recall during infancy.

PubMed

Pathman, Thanujeni; Bauer, Patricia J

2013-02-01

The first years of life are witness to rapid changes in long-term recall ability. In the current research we contributed to an explanation of the changes by testing the absolute and relative contributions to long-term recall of encoding and post-encoding processes. Using elicited imitation, we sampled the status of 16-, 20-, and 24-month-old infants' memory representations at various time points after experience of events. In Experiment 1, infants were tested immediately, 1 week after encoding, and again after 1 month. The measure of 1-week trace status was a unique predictor of 1-month delayed recall. In Experiment 2, infants were tested immediately, 15 min, 48 h, and 2 weeks after encoding and again 1 month later. The measures of 15-min and 48-h trace strength contributed unique variance in 1-month delayed recall. The findings highlight the need to consider post-encoding processes in explanations of variability in long-term memory during infancy. Copyright © 2012 Elsevier Inc. All rights reserved.

You can go your own way: Effectiveness of participant-driven versus experimenter-driven processing strategies in memory training and transfer

PubMed Central

Flegal, Kristin E.; Lustig, Cindy

2016-01-01

Cognitive training programs that instruct specific strategies frequently show limited transfer. Open-ended approaches can achieve greater transfer, but may fail to benefit many older adults due to age deficits in self-initiated processing. We examined whether a compromise that encourages effort at encoding without an experimenter-prescribed strategy might yield better results. Older adults completed memory training under conditions that either 1) mandated a specific strategy to increase deep, associative encoding, 2) attempted to suppress such encoding by mandating rote rehearsal, or 3) encouraged time and effort towards encoding but allowed for strategy choice. The experimenter-enforced associative encoding strategy succeeded in creating integrated representations of studied items, but training-task progress was related to pre-existing ability. Independent of condition assignment, self-reported deep encoding was associated with positive training and transfer effects, suggesting that the most beneficial outcomes occur when environmental support guiding effort is provided but participants generate their own strategies. PMID:26549616

The effects of divided attention on encoding processes under incidental and intentional learning instructions: underlying mechanisms?

PubMed

Naveh-Benjamin, Moshe; Guez, Jonathan; Hara, Yoko; Brubaker, Matthew S; Lowenschuss-Erlich, Iris

2014-01-01

Divided attention (DA) at encoding has been shown to significantly disrupt later memory for the studied information. However, what type of processing gets disrupted during DA remains unresolved. In this study, we assessed the degree to which strategic effortful processes are affected under DA by comparing the effects of DA at encoding under intentional and pure incidental learning instructions. In three experiments, participants studied list of words or word pairs under either full or divided attention. Results of three experiments, which used different methodologies, converged to show that the effects of DA at encoding reduce memory performance to the same degree under incidental and intentional learning. Secondary task performance indicated that encoding under intentional learning instructions was more effortful than under incidental learning instructions. In addition, the results indicated enhanced attention to the initial appearance of the words under both types of learning instructions. Results are interpreted to imply that other processes, rather than only strategic effortful ones, might be affected by DA at encoding.

You can go your own way: effectiveness of participant-driven versus experimenter-driven processing strategies in memory training and transfer.

PubMed

Flegal, Kristin E; Lustig, Cindy

2016-07-01

Cognitive training programs that instruct specific strategies frequently show limited transfer. Open-ended approaches can achieve greater transfer, but may fail to benefit many older adults due to age deficits in self-initiated processing. We examined whether a compromise that encourages effort at encoding without an experimenter-prescribed strategy might yield better results. Older adults completed memory training under conditions that either (1) mandated a specific strategy to increase deep, associative encoding, (2) attempted to suppress such encoding by mandating rote rehearsal, or (3) encouraged time and effort toward encoding but allowed for strategy choice. The experimenter-enforced associative encoding strategy succeeded in creating integrated representations of studied items, but training-task progress was related to pre-existing ability. Independent of condition assignment, self-reported deep encoding was associated with positive training and transfer effects, suggesting that the most beneficial outcomes occur when environmental support guiding effort is provided but participants generate their own strategies.

Encoding methods for B1+ mapping in parallel transmit systems at ultra high field

NASA Astrophysics Data System (ADS)

Tse, Desmond H. Y.; Poole, Michael S.; Magill, Arthur W.; Felder, Jörg; Brenner, Daniel; Jon Shah, N.

2014-08-01

Parallel radiofrequency (RF) transmission, either in the form of RF shimming or pulse design, has been proposed as a solution to the B1+ inhomogeneity problem in ultra high field magnetic resonance imaging. As a prerequisite, accurate B1+ maps from each of the available transmit channels are required. In this work, four different encoding methods for B1+ mapping, namely 1-channel-on, all-channels-on-except-1, all-channels-on-1-inverted and Fourier phase encoding, were evaluated using dual refocusing acquisition mode (DREAM) at 9.4 T. Fourier phase encoding was demonstrated in both phantom and in vivo to be the least susceptible to artefacts caused by destructive RF interference at 9.4 T. Unlike the other two interferometric encoding schemes, Fourier phase encoding showed negligible dependency on the initial RF phase setting and therefore no prior B1+ knowledge is required. Fourier phase encoding also provides a flexible way to increase the number of measurements to increase SNR, and to allow further reduction of artefacts by weighted decoding. These advantages of Fourier phase encoding suggest that it is a good choice for B1+ mapping in parallel transmit systems at ultra high field.

DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information.

PubMed

Neri, Dario; Lerner, Richard A

2018-06-20

The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.

Laying the Groundwork for Enterprise-Wide Medical Language Processing Services: Architecture and Process

PubMed Central

Chen, Elizabeth S.; Maloney, Francine L.; Shilmayster, Eugene; Goldberg, Howard S.

2009-01-01

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs. PMID:20351830

Laying the groundwork for enterprise-wide medical language processing services: architecture and process.

PubMed

Chen, Elizabeth S; Maloney, Francine L; Shilmayster, Eugene; Goldberg, Howard S

2009-11-14

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs.

Pictures as Prose-Learning Devices.

ERIC Educational Resources Information Center

Levin, Joel R.

Most popular strategies, including illustrations, for improving prose processing consist of procedures that force attention either to the text's macrostructure or to the organization and interconnections of its propositions. These strategies are assumed to enhance students' comprehension of the text as encoded, as well as to afford students an…

SGML-Based Markup for Literary Texts: Two Problems and Some Solutions.

ERIC Educational Resources Information Center

Barnard, David; And Others

1988-01-01

Identifies the Standard Generalized Markup Language (SGML) as the best basis for a markup standard for encoding literary texts. Outlines solutions to problems using SGML and discusses the problem of maintaining multiple views of a document. Examines several ways of reducing the burden of markups. (GEA)

Graph State-Based Quantum Secret Sharing with the Chinese Remainder Theorem

NASA Astrophysics Data System (ADS)

Guo, Ying; Luo, Peng; Wang, Yijun

2016-11-01

Quantum secret sharing (QSS) is a significant quantum cryptography technology in the literature. Dividing an initial secret into several sub-secrets which are then transferred to other legal participants so that it can be securely recovered in a collaboration fashion. In this paper, we develop a quantum route selection based on the encoded quantum graph state, thus enabling the practical QSS scheme in the small-scale complex quantum network. Legal participants are conveniently designated with the quantum route selection using the entanglement of the encoded graph states. Each participant holds a vertex of the graph state so that legal participants are selected through performing operations on specific vertices. The Chinese remainder theorem (CRT) strengthens the security of the recovering process of the initial secret among the legal participants. The security is ensured by the entanglement of the encoded graph states that are cooperatively prepared and shared by legal users beforehand with the sub-secrets embedded in the CRT over finite fields.

fMRI differences in encoding and retrieval of pictures due to encoding strategy in the elderly.

PubMed

Mandzia, Jennifer L; Black, Sandra E; McAndrews, Mary Pat; Grady, Cheryl; Graham, Simon

2004-01-01

Functional MRI (fMRI) was used to examine the neural correlates of depth of processing during encoding and retrieval of photographs in older normal volunteers (n = 12). Separate scans were run during deep (natural vs. man-made decision) and shallow (color vs. black-and-white decision) encoding and during old/new recognition of pictures initially presented in one of the two encoding conditions. A baseline condition consisting of a scrambled, color photograph was used as a contrast in each scan. Recognition accuracy was greater for the pictures on which semantic decisions were made at encoding, consistent with the expected levels of processing effect. A mixed-effects model was used to compare fMRI differences between conditions (deep-baseline vs. shallow-baseline) in both encoding and retrieval. For encoding, this contrast revealed greater activation associated with deep encoding in several areas, including the left parahippocampal gyrus (PHG), left middle temporal gyrus, and left anterior thalamus. Increased left hippocampal, right dorsolateral, and inferior frontal activations were found for recognition of items that had been presented in the deep relative to the shallow encoding condition. We speculate that the modulation of activity in these regions by the depth of processing manipulation shows that these regions support effective encoding and successful retrieval. A direct comparison between encoding and retrieval revealed greater activation during retrieval in the medial temporal (right hippocampus and bilateral PHG), anterior cingulate, and bilateral prefrontal (inferior and dorsolateral). Most notably, greater right posterior PHG was found during encoding compared to recognition. Focusing on the medial temporal lobe (MTL) region, our results suggest a greater involvement of both anterior MTL and prefrontal regions in retrieval compared to encoding. Copyright 2003 Wiley-Liss, Inc.

SEMG signal compression based on two-dimensional techniques.

PubMed

de Melo, Wheidima Carneiro; de Lima Filho, Eddie Batista; da Silva Júnior, Waldir Sabino

2016-04-18

Recently, two-dimensional techniques have been successfully employed for compressing surface electromyographic (SEMG) records as images, through the use of image and video encoders. Such schemes usually provide specific compressors, which are tuned for SEMG data, or employ preprocessing techniques, before the two-dimensional encoding procedure, in order to provide a suitable data organization, whose correlations can be better exploited by off-the-shelf encoders. Besides preprocessing input matrices, one may also depart from those approaches and employ an adaptive framework, which is able to directly tackle SEMG signals reassembled as images. This paper proposes a new two-dimensional approach for SEMG signal compression, which is based on a recurrent pattern matching algorithm called multidimensional multiscale parser (MMP). The mentioned encoder was modified, in order to efficiently work with SEMG signals and exploit their inherent redundancies. Moreover, a new preprocessing technique, named as segmentation by similarity (SbS), which has the potential to enhance the exploitation of intra- and intersegment correlations, is introduced, the percentage difference sorting (PDS) algorithm is employed, with different image compressors, and results with the high efficiency video coding (HEVC), H.264/AVC, and JPEG2000 encoders are presented. Experiments were carried out with real isometric and dynamic records, acquired in laboratory. Dynamic signals compressed with H.264/AVC and HEVC, when combined with preprocessing techniques, resulted in good percent root-mean-square difference [Formula: see text] compression factor figures, for low and high compression factors, respectively. Besides, regarding isometric signals, the modified two-dimensional MMP algorithm outperformed state-of-the-art schemes, for low compression factors, the combination between SbS and HEVC proved to be competitive, for high compression factors, and JPEG2000, combined with PDS, provided good performance allied to low computational complexity, all in terms of percent root-mean-square difference [Formula: see text] compression factor. The proposed schemes are effective and, specifically, the modified MMP algorithm can be considered as an interesting alternative for isometric signals, regarding traditional SEMG encoders. Besides, the approach based on off-the-shelf image encoders has the potential of fast implementation and dissemination, given that many embedded systems may already have such encoders available, in the underlying hardware/software architecture.

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms.

PubMed

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding.

Working Memory Replay Prioritizes Weakly Attended Events.

PubMed

Jafarpour, Anna; Penny, Will; Barnes, Gareth; Knight, Robert T; Duzel, Emrah

2017-01-01

One view of working memory posits that maintaining a series of events requires their sequential and equal mnemonic replay. Another view is that the content of working memory maintenance is prioritized by attention. We decoded the dynamics for retaining a sequence of items using magnetoencephalography, wherein participants encoded sequences of three stimuli depicting a face, a manufactured object, or a natural item and maintained them in working memory for 5000 ms. Memory for sequence position and stimulus details were probed at the end of the maintenance period. Decoding of brain activity revealed that one of the three stimuli dominated maintenance independent of its sequence position or category; and memory was enhanced for the selectively replayed stimulus. Analysis of event-related responses during the encoding of the sequence showed that the selectively replayed stimuli were determined by the degree of attention at encoding. The selectively replayed stimuli had the weakest initial encoding indexed by weaker visual attention signals at encoding. These findings do not rule out sequential mnemonic replay but reveal that attention influences the content of working memory maintenance by prioritizing replay of weakly encoded events. We propose that the prioritization of weakly encoded stimuli protects them from interference during the maintenance period, whereas the more strongly encoded stimuli can be retrieved from long-term memory at the end of the delay period.

Continuous in vitro evolution of bacteriophage RNA polymerase promoters

NASA Technical Reports Server (NTRS)

Breaker, R. R.; Banerji, A.; Joyce, G. F.

1994-01-01

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.

Contextuality and Cultural Texts: A Case Study of Workplace Learning in Call Centres

ERIC Educational Resources Information Center

Crouch, Margaret

2006-01-01

Purpose: The paper seeks to show the contextualisation of call centres as a work-specific ethnographically and culturally based community, which, in turn, influences pedagogical practices through the encoding and decoding of cultural texts in relation to two logics: cost-efficiency and customer-orientation. Design/methodology/approach: The paper…

Adverse Event extraction from Structured Product Labels using the Event-based Text-mining of Health Electronic Records (ETHER)system.

PubMed

Pandey, Abhishek; Kreimeyer, Kory; Foster, Matthew; Botsis, Taxiarchis; Dang, Oanh; Ly, Thomas; Wang, Wei; Forshee, Richard

2018-01-01

Structured Product Labels follow an XML-based document markup standard approved by the Health Level Seven organization and adopted by the US Food and Drug Administration as a mechanism for exchanging medical products information. Their current organization makes their secondary use rather challenging. We used the Side Effect Resource database and DailyMed to generate a comparison dataset of 1159 Structured Product Labels. We processed the Adverse Reaction section of these Structured Product Labels with the Event-based Text-mining of Health Electronic Records system and evaluated its ability to extract and encode Adverse Event terms to Medical Dictionary for Regulatory Activities Preferred Terms. A small sample of 100 labels was then selected for further analysis. Of the 100 labels, Event-based Text-mining of Health Electronic Records achieved a precision and recall of 81 percent and 92 percent, respectively. This study demonstrated Event-based Text-mining of Health Electronic Record's ability to extract and encode Adverse Event terms from Structured Product Labels which may potentially support multiple pharmacoepidemiological tasks.

Levels-Of-Processing Effect on Word Recognition in Schizophrenia

PubMed Central

Ragland, J. Daniel; Moelter, Stephen T.; McGrath, Claire; Hill, S. Kristian; Gur, Raquel E.; Bilker, Warren B.; Siegel, Steven J.; Gur, Ruben C.

2015-01-01

Background Individuals with schizophrenia have difficulty organizing words semantically to facilitate encoding. This is commonly attributed to organizational rather than semantic processing limitations. By requiring participants to classify and encode words on either a shallow (e.g., uppercase/lowercase) or deep level (e.g., concrete/abstract), the levels-of-processing paradigm eliminates the need to generate organizational strategies. Methods This paradigm was administered to 30 patients with schizophrenia and 30 healthy comparison subjects to test whether providing a strategy would improve patient performance. Results Word classification during shallow and deep encoding was slower and less accurate in patients. Patients also responded slowly during recognition testing and maintained a more conservative response bias following deep encoding; however, both groups showed a robust levels-of-processing effect on recognition accuracy, with unimpaired patient performance following both shallow and deep encoding. Conclusions This normal levels-of-processing effect in the patient sample suggests that semantic processing is sufficiently intact for patients to benefit from organizational cues. Memory remediation efforts may therefore be most successful if they focus on teaching patients to form organizational strategies during initial encoding. PMID:14643082

Levels-of-processing effect on word recognition in schizophrenia.

PubMed

Ragland, J Daniel; Moelter, Stephen T; McGrath, Claire; Hill, S Kristian; Gur, Raquel E; Bilker, Warren B; Siegel, Steven J; Gur, Ruben C

2003-12-01

Individuals with schizophrenia have difficulty organizing words semantically to facilitate encoding. This is commonly attributed to organizational rather than semantic processing limitations. By requiring participants to classify and encode words on either a shallow (e.g., uppercase/lowercase) or deep level (e.g., concrete/abstract), the levels-of-processing paradigm eliminates the need to generate organizational strategies. This paradigm was administered to 30 patients with schizophrenia and 30 healthy comparison subjects to test whether providing a strategy would improve patient performance. Word classification during shallow and deep encoding was slower and less accurate in patients. Patients also responded slowly during recognition testing and maintained a more conservative response bias following deep encoding; however, both groups showed a robust levels-of-processing effect on recognition accuracy, with unimpaired patient performance following both shallow and deep encoding. This normal levels-of-processing effect in the patient sample suggests that semantic processing is sufficiently intact for patients to benefit from organizational cues. Memory remediation efforts may therefore be most successful if they focus on teaching patients to form organizational strategies during initial encoding.

Role of sleep for encoding of emotional memory.

PubMed

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.

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms

PubMed Central

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding. PMID:28334002

Memory Reactivation Predicts Resistance to Retroactive Interference: Evidence from Multivariate Classification and Pattern Similarity Analyses

PubMed Central

Rugg, Michael D.

2016-01-01

Memory reactivation—the reinstatement of processes and representations engaged when an event is initially experienced—is believed to play an important role in strengthening and updating episodic memory. The present study examines how memory reactivation during a potentially interfering event influences memory for a previously experienced event. Participants underwent fMRI during the encoding phase of an AB/AC interference task in which some words were presented twice in association with two different encoding tasks (AB and AC trials) and other words were presented once (DE trials). The later memory test required retrieval of the encoding tasks associated with each of the study words. Retroactive interference was evident for the AB encoding task and was particularly strong when the AC encoding task was remembered rather than forgotten. We used multivariate classification and pattern similarity analysis (PSA) to measure reactivation of the AB encoding task during AC trials. The results demonstrated that reactivation of generic task information measured with multivariate classification predicted subsequent memory for the AB encoding task regardless of whether interference was strong and weak (trials for which the AC encoding task was remembered or forgotten, respectively). In contrast, reactivation of neural patterns idiosyncratic to a given AB trial measured with PSA only predicted memory when the strength of interference was low. These results suggest that reactivation of features of an initial experience shared across numerous events in the same category, but not features idiosyncratic to a particular event, are important in resisting retroactive interference caused by new learning. SIGNIFICANCE STATEMENT Reactivating a previously encoded memory is believed to provide an opportunity to strengthen the memory, but also to return the memory to a labile state, making it susceptible to interference. However, there is debate as to how memory reactivation elicited by a potentially interfering event influences subsequent retrieval of the memory. The findings of the current study indicate that reactivating features idiosyncratic to a particular experience during interference only influences subsequent memory when interference is relatively weak. Critically, reactivation of generic contextual information predicts subsequent source memory when retroactive interference is either strong and weak. The results indicate that reactivation of generic information about a prior episode mitigates forgetting due to retroactive interference. PMID:27076433

The importance of situation-specific encodings: analysis of a simple connectionist model of letter transposition effects

NASA Astrophysics Data System (ADS)

Fang, Shin-Yi; Smith, Garrett; Tabor, Whitney

2018-04-01

This paper analyses a three-layer connectionist network that solves a translation-invariance problem, offering a novel explanation for transposed letter effects in word reading. Analysis of the hidden unit encodings provides insight into two central issues in cognitive science: (1) What is the novelty of claims of "modality-specific" encodings? and (2) How can a learning system establish a complex internal structure needed to solve a problem? Although these topics (embodied cognition and learnability) are often treated separately, we find a close relationship between them: modality-specific features help the network discover an abstract encoding by causing it to break the initial symmetries of the hidden units in an effective way. While this neural model is extremely simple compared to the human brain, our results suggest that neural networks need not be black boxes and that carefully examining their encoding behaviours may reveal how they differ from classical ideas about the mind-world relationship.

Audiovisual semantic congruency during encoding enhances memory performance.

PubMed

Heikkilä, Jenni; Alho, Kimmo; Hyvönen, Heidi; Tiippana, Kaisa

2015-01-01

Studies of memory and learning have usually focused on a single sensory modality, although human perception is multisensory in nature. In the present study, we investigated the effects of audiovisual encoding on later unisensory recognition memory performance. The participants were to memorize auditory or visual stimuli (sounds, pictures, spoken words, or written words), each of which co-occurred with either a semantically congruent stimulus, incongruent stimulus, or a neutral (non-semantic noise) stimulus in the other modality during encoding. Subsequent memory performance was overall better when the stimulus to be memorized was initially accompanied by a semantically congruent stimulus in the other modality than when it was accompanied by a neutral stimulus. These results suggest that semantically congruent multisensory experiences enhance encoding of both nonverbal and verbal materials, resulting in an improvement in their later recognition memory.

Memory strength and specificity revealed by pupillometry

PubMed Central

Papesh, Megan H.; Goldinger, Stephen D.; Hout, Michael C.

2011-01-01

Voice-specificity effects in recognition memory were investigated using both behavioral data and pupillometry. Volunteers initially heard spoken words and nonwords in two voices; they later provided confidence-based old/new classifications to items presented in their original voices, changed (but familiar) voices, or entirely new voices. Recognition was more accurate for old-voice items, replicating prior research. Pupillometry was used to gauge cognitive demand during both encoding and testing: Enlarged pupils revealed that participants devoted greater effort to encoding items that were subsequently recognized. Further, pupil responses were sensitive to the cue match between encoding and retrieval voices, as well as memory strength. Strong memories, and those with the closest encoding-retrieval voice matches, resulted in the highest peak pupil diameters. The results are discussed with respect to episodic memory models and Whittlesea’s (1997) SCAPE framework for recognition memory. PMID:22019480

The National Geographic Names Data Base: Phase II instructions

USGS Publications Warehouse

Orth, Donald J.; Payne, Roger L.

1987-01-01

not recorded on topographic maps be added. The systematic collection of names from other sources, including maps, charts, and texts, is termed Phase II. In addition, specific types of features not compiled during Phase I are encoded and added to the data base. Other names of importance to researchers and users, such as historical and variant names, are also included. The rules and procedures for Phase II research, compilation, and encoding are contained in this publication.

Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor.

PubMed

McKinley, Brian; Rooney, William; Wilkerson, Curtis; Mullet, John

2016-11-01

Biomass accumulated preferentially in leaves of the sweet sorghum Della until floral initiation, then stems until anthesis, followed by panicles until grain maturity, and apical tillers. Sorghum stem RNA-seq transcriptome profiles and composition data were collected for approximately 100 days of development beginning at floral initiation. The analysis identified >200 differentially expressed genes involved in stem growth, cell wall biology, and sucrose accumulation. Genes encoding expansins and xyloglucan endotransglucosylase/hydrolases were differentially expressed in growing stem internodes. Genes encoding enzymes involved in the synthesis of cellulose, lignin, and glucuronoarabinoxylan were expressed at elevated levels in stems until approximately 7 days before anthesis and then down-regulated. CESA genes involved in primary and secondary cell wall synthesis showed different temporal patterns of expression. Following floral initiation, the level of sucrose and other non-structural carbohydrates increased to approximately 50% of the stem's dry weight. Stem sucrose accumulation was inversely correlated with >100-fold down-regulation of SbVIN1, a gene encoding a vacuolar invertase. Accumulation of stem sucrose was also correlated with cessation of leaf and stem growth at anthesis, decreased expression of genes involved in stem cell wall synthesis, and approximately 10-fold lower expression of SbSUS4, a gene encoding sucrose synthase that generates UDP-glucose from sucrose for cell wall biosynthesis. Genes for mixed linkage glucan synthesis (CSLF) and turnover were expressed at high levels in stems throughout development. Overall, the stem transcription profile resource and the genes and regulatory dynamics identified in this study will be useful for engineering sorghum stem composition for improved conversion to biofuels and bio-products. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Highlighting Text as a Study Strategy: Beyond Attentional Focusing.

ERIC Educational Resources Information Center

Lindner, Reinhard W.; And Others

Two experiments were conducted to investigate whether the strategy of differentiating main and supporting ideas with different colored highlighter pens resulted in greater use of schema building and increased recall of information by students and whether the benefits of text marking come at the time of encoding or at the time of review. Sixty-six…

Lessons Learned from Professional Development Workshops on Using GIS to Teach Geography and History in the K-12 Classroom

ERIC Educational Resources Information Center

Tabor, Lisa K.; Harrington, John A., Jr.

2014-01-01

The brain perceives, recognizes, interprets, comprehends, appreciates, and remembers experiences that are both text and non-text or verbal and nonverbal. This article discusses Dual- encoding as a proven method of teaching that increases student learning retention and incorporates multiple learning styles. Students learn both subjects better when…

Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes

PubMed Central

Delwart, Eric; Li, Linlin

2011-01-01

The genomes of numerous circoviruses and distantly related circular DNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, and plants (geminivirus and nanovirus), human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting their past host range. An ancient origin for viruses with rep-encoding single stranded small circular genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular viral genomes. PMID:22155583

Working Memory Replay Prioritizes Weakly Attended Events

PubMed Central

Penny, Will; Knight, Robert T.; Duzel, Emrah

2017-01-01

Abstract One view of working memory posits that maintaining a series of events requires their sequential and equal mnemonic replay. Another view is that the content of working memory maintenance is prioritized by attention. We decoded the dynamics for retaining a sequence of items using magnetoencephalography, wherein participants encoded sequences of three stimuli depicting a face, a manufactured object, or a natural item and maintained them in working memory for 5000 ms. Memory for sequence position and stimulus details were probed at the end of the maintenance period. Decoding of brain activity revealed that one of the three stimuli dominated maintenance independent of its sequence position or category; and memory was enhanced for the selectively replayed stimulus. Analysis of event-related responses during the encoding of the sequence showed that the selectively replayed stimuli were determined by the degree of attention at encoding. The selectively replayed stimuli had the weakest initial encoding indexed by weaker visual attention signals at encoding. These findings do not rule out sequential mnemonic replay but reveal that attention influences the content of working memory maintenance by prioritizing replay of weakly encoded events. We propose that the prioritization of weakly encoded stimuli protects them from interference during the maintenance period, whereas the more strongly encoded stimuli can be retrieved from long-term memory at the end of the delay period. PMID:28824955

The Cortex Transform as an image preprocessor for sparse distributed memory: An initial study

NASA Technical Reports Server (NTRS)

Olshausen, Bruno; Watson, Andrew

1990-01-01

An experiment is described which was designed to evaluate the use of the Cortex Transform as an image processor for Sparse Distributed Memory (SDM). In the experiment, a set of images were injected with Gaussian noise, preprocessed with the Cortex Transform, and then encoded into bit patterns. The various spatial frequency bands of the Cortex Transform were encoded separately so that they could be evaluated based on their ability to properly cluster patterns belonging to the same class. The results of this study indicate that by simply encoding the low pass band of the Cortex Transform, a very suitable input representation for the SDM can be achieved.

High-resolution absolute position detection using a multiple grating

NASA Astrophysics Data System (ADS)

Schilling, Ulrich; Drabarek, Pawel; Kuehnle, Goetz; Tiziani, Hans J.

1996-08-01

To control electro-mechanical engines, high-resolution linear and rotary encoders are needed. Interferometric methods (grating interferometers) promise a resolution of a few nanometers, but have an ambiguity range of some microns. Incremental encoders increase the absolute measurement range by counting the signal periods starting from a defined initial point. In many applications, however, it is not possible to move to this initial point, so that absolute encoders have to be used. Absolute encoders generally have a scale with two or more tracks placed next to each other. Therefore, they use a two-dimensional grating structure to measure a one-dimensional position. We present a new method, which uses a one-dimensional structure to determine the position in one dimension. It is based on a grating with a large grating period up to some millimeters, having the same diffraction efficiency in several predefined diffraction orders (multiple grating). By combining the phase signals of the different diffraction orders, it is possible to establish the position in an absolute range of the grating period with a resolution like incremental grating interferometers. The principal functionality was demonstrated by applying the multiple grating in a heterodyne grating interferometer. The heterodyne frequency was generated by a frequency modulated laser in an unbalanced interferometer. In experimental measurements an absolute range of 8 mm was obtained while achieving a resolution of 10 nm.

Changes in Striatal Dopamine Release Associated with Human Motor-Skill Acquisition

PubMed Central

Kawashima, Shoji; Ueki, Yoshino; Kato, Takashi; Matsukawa, Noriyuki; Mima, Tatsuya; Hallett, Mark; Ito, Kengo; Ojika, Kosei

2012-01-01

The acquisition of new motor skills is essential throughout daily life and involves the processes of learning new motor sequence and encoding elementary aspects of new movement. Although previous animal studies have suggested a functional importance for striatal dopamine release in the learning of new motor sequence, its role in encoding elementary aspects of new movement has not yet been investigated. To elucidate this, we investigated changes in striatal dopamine levels during initial skill-training (Day 1) compared with acquired conditions (Day 2) using 11C-raclopride positron-emission tomography. Ten volunteers learned to perform brisk contractions using their non-dominant left thumbs with the aid of visual feedback. On Day 1, the mean acceleration of each session was improved through repeated training sessions until performance neared asymptotic levels, while improved motor performance was retained from the beginning on Day 2. The 11C-raclopride binding potential (BP) in the right putamen was reduced during initial skill-training compared with under acquired conditions. Moreover, voxel-wise analysis revealed that 11C-raclopride BP was particularly reduced in the right antero-dorsal to the lateral part of the putamen. Based on findings from previous fMRI studies that show a gradual shift of activation within the striatum during the initial processing of motor learning, striatal dopamine may play a role in the dynamic cortico-striatal activation during encoding of new motor memory in skill acquisition. PMID:22355391

Emotional Encoding Context Leads to Memory Bias in Individuals with High Anxiety

PubMed Central

Fernandes, Myra A.

2017-01-01

We investigated whether anxious individuals, who adopt an inherently negative mindset, demonstrate a particularly salient memory bias for words tainted by negative contexts. To this end, sequentially presented target words, overlayed onto negative or neutral pictures, were studied in separate blocks (within-subjects) using a deep or shallow encoding instruction (between-subjects). Following study, in Test 1, participants completed separate recognition test blocks for the words overlayed onto the negative and the neutral contexts. Following this, in Test 2, participants completed a recognition test for the foils from each Test 1 block. We found a significant three-way interaction on Test 2, such that individuals with high anxiety who initially studied target words using a shallow encoding instruction, demonstrated significantly elevated memory for foils that were contained within the negative Test 1 block. Results show that during retrieval (Test 1), participants re-entered the mode of processing (negative or neutral) engaged at encoding, tainting the encoding of foils with that same mode of processing. The findings suggest that individuals with high relative to low anxiety, adopt a particularly salient negative retrieval mode, and this creates a downstream bias in encoding and subsequent retrieval of otherwise neutral information. PMID:29280957

Emotional Encoding Context Leads to Memory Bias in Individuals with High Anxiety.

PubMed

Lee, Christopher; Fernandes, Myra A

2017-12-27

We investigated whether anxious individuals, who adopt an inherently negative mindset, demonstrate a particularly salient memory bias for words tainted by negative contexts. To this end, sequentially presented target words, overlayed onto negative or neutral pictures, were studied in separate blocks (within-subjects) using a deep or shallow encoding instruction (between-subjects). Following study, in Test 1, participants completed separate recognition test blocks for the words overlayed onto the negative and the neutral contexts. Following this, in Test 2, participants completed a recognition test for the foils from each Test 1 block. We found a significant three-way interaction on Test 2, such that individuals with high anxiety who initially studied target words using a shallow encoding instruction, demonstrated significantly elevated memory for foils that were contained within the negative Test 1 block. Results show that during retrieval (Test 1), participants re-entered the mode of processing (negative or neutral) engaged at encoding, tainting the encoding of foils with that same mode of processing. The findings suggest that individuals with high relative to low anxiety, adopt a particularly salient negative retrieval mode, and this creates a downstream bias in encoding and subsequent retrieval of otherwise neutral information.

Orienting in virtual environments: How are surface features and environmental geometry weighted in an orientation task?

PubMed

Kelly, Debbie M; Bischof, Walter F

2008-10-01

We investigated how human adults orient in enclosed virtual environments, when discrete landmark information is not available and participants have to rely on geometric and featural information on the environmental surfaces. In contrast to earlier studies, where, for women, the featural information from discrete landmarks overshadowed the encoding of the geometric information, Experiment 1 showed that when featural information is conjoined with the environmental surfaces, men and women encoded both types of information. Experiment 2 showed that, although both types of information are encoded, performance in locating a goal position is better if it is close to a geometrically or featurally distinct location. Furthermore, although features are relied upon more strongly than geometry, initial experience with an environment influences the relative weighting of featural and geometric cues. Taken together, these results show that human adults use a flexible strategy for encoding spatial information.

School-aged children can benefit from audiovisual semantic congruency during memory encoding.

PubMed

Heikkilä, Jenni; Tiippana, Kaisa

2016-05-01

Although we live in a multisensory world, children's memory has been usually studied concentrating on only one sensory modality at a time. In this study, we investigated how audiovisual encoding affects recognition memory. Children (n = 114) from three age groups (8, 10 and 12 years) memorized auditory or visual stimuli presented with a semantically congruent, incongruent or non-semantic stimulus in the other modality during encoding. Subsequent recognition memory performance was better for auditory or visual stimuli initially presented together with a semantically congruent stimulus in the other modality than for stimuli accompanied by a non-semantic stimulus in the other modality. This congruency effect was observed for pictures presented with sounds, for sounds presented with pictures, for spoken words presented with pictures and for written words presented with spoken words. The present results show that semantically congruent multisensory experiences during encoding can improve memory performance in school-aged children.

Evidence of an Intelligent Tutoring System as a Mindtool to Promote Strategic Memory of Expository Texts and Comprehension with Children in Grades 4 and 5

ERIC Educational Resources Information Center

Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Puiwa; Cheng, Weiyi; Ji, Xuejun; Joshi, R. M.

2017-01-01

Reading and comprehending content area texts require learners to effectively select and encode with hierarchically strategic memory structures in order to combine new information with prior knowledge. Unfortunately, evidence from state and national tests shows that children fail to successfully navigate the reading comprehension challenges they…

Social gating of sensory information during ongoing communication.

PubMed

Anders, Silke; Heussen, Yana; Sprenger, Andreas; Haynes, John-Dylan; Ethofer, Thomas

2015-01-01

Social context plays an important role in human communication. Depending on the nature of the source, the same communication signal might be processed in fundamentally different ways. However, the selective modulation (or "gating") of the flow of neural information during communication is not fully understood. Here, we use multivoxel pattern analysis (MVPA) and multivoxel connectivity analysis (MVCA), a novel technique that allows to analyse context-dependent changes of the strength interregional coupling between ensembles of voxels, to examine how the human brain differentially gates content-specific sensory information during ongoing perception of communication signals. In a simulated electronic communication experiment, participants received two alternative text messages during fMRI ("happy" or "sad") which they believed had been sent either by their real-life friend outside the scanner or by a computer. A region in the dorsal medial prefrontal cortex (dmPFC) selectively increased its functional coupling with sensory-content encoding regions in the visual cortex when a text message was perceived as being sent by the participant's friend, and decreased its functional coupling with these regions when a text message was perceived as being sent by the computer. Furthermore, the strength of neural encoding of content-specific information of text messages in the dmPFC was modulated by the social tie between the participant and her friend: the more of her spare time a participant reported to spend with her friend the stronger was the neural encoding. This suggests that the human brain selectively gates sensory information into the relevant network for processing the mental states of others, depending on the source of the communication signal. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1.

PubMed

Mauffrey, Florian; Cucaita, Alexandra; Constant, Philippe; Villemur, Richard

2017-01-01

Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N 2 O) reductase, suggesting that NO and N 2 O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Series of oxic and anoxic cultures of strain JAM1 were performed with N 2 O, [Formula: see text] or sodium nitroprusside, and growth and N 2 O, [Formula: see text], [Formula: see text] and N 2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N 2 O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N 2 O was performed in 15 NH 4 + -amended cultures. Cultures with the JAM1Δ narG1narG2 double mutant were performed to assess the involvement of the Nar systems on N 2 O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc -type nitric oxide reductase ( cnorB1 and cnorB2 ) and nitrous oxide reductase ( nosZ ), and also nnrS and norR that encode NO-sensitive regulators. Strain JAM1 can reduce NO to N 2 O and N 2 O to N 2 and can sustain growth under anoxic conditions by reducing N 2 O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N 2 O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of c norB1 , cnorB2, nnrS and norR during the growth and the N 2 O accumulation phases suggests NO production in strain JAM1 cultures. By showing that all the three denitrification reductases are active, this demonstrates that M. nitratireducenticrescens JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such an incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of the denitrification reactor from which it originates. The production of N 2 O in strain JAM1 did not involve Nar, contrary to what was demonstrated in Escherichia coli . M. nitratireducenticrescens JAM1 is the only reported Methylophaga species that has the capacity to grow under anoxic conditions by using [Formula: see text] and N 2 O as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities.

[On-line processing mechanisms in text comprehension: a theoretical review on constructing situation models].

PubMed

Iseki, Ryuta

2004-12-01

This article reviewed research on construction of situation models during reading. To position variety of research in overall process appropriately, an unitary framework was devised in terms of three theories for on-line processing: resonance process, event-indexing model, and constructionist theory. Resonance process was treated as a basic activation mechanism in the framework. Event-indexing model was regarded as a screening system which selected and encoded activated information in situation models along with situational dimensions. Constructionist theory was considered to have a supervisory role based on coherence and explanation. From a view of the unitary framework, some problems concerning each theory were examined and possible interpretations were given. Finally, it was pointed out that there were little theoretical arguments on associative processing at global level and encoding text- and inference-information into long-term memory.

A Comparison of Declarative and Hybrid Declarative-Procedural Models for Rover Operations

NASA Technical Reports Server (NTRS)

Knight, Russell; Rabideau, Gregg; Lenda, Matthew; Maldague, Pierre

2012-01-01

The MAPGEN [2] (Mixed-initiative Activity Plan GENerator) planning system is a great example of a hybrid procedural/declarative system where the advantages of each are leveraged to produce an effective planner/scheduler for Mars Exploration Rover tactical planning. We explore the adaptation of the same domain to an entirely declarative planning system (ASPEN [4] Activity Scheduling and Planning ENvironment), and demonstrate that, with some translation, much of the procedural knowledge encoding is amenable to a declarative knowledge encoding.

Draft Map of Human Proteome Published | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a recently published article in the journal Nature, researchers have developed a draft map of the human proteome.  Striving for the protein equivalent of the Human Genome Project, an international team of researchers has created an initial catalog of the human proteome. In total, using 30 different human tissues, the researchers identified proteins encoded by 17,294 genes, which is approximately 84 percent of all of the genes in the human genome predicted to encode proteins.

A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

PubMed

Moraes, Fernanda; Góes, Andréa

2016-05-06

The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Neural correlates of encoding processes predicting subsequent cued recall and source memory.

PubMed

Angel, Lucie; Isingrini, Michel; Bouazzaoui, Badiâa; Fay, Séverine

2013-03-06

In this experiment, event-related potentials were used to examine whether the neural correlates of encoding processes predicting subsequent successful recall differed from those predicting successful source memory retrieval. During encoding, participants studied lists of words and were instructed to memorize each word and the list in which it occurred. At test, they had to complete stems (the first four letters) with a studied word and then make a judgment of the initial temporal context (i.e. list). Event-related potentials recorded during encoding were segregated according to subsequent memory performance to examine subsequent memory effects (SMEs) reflecting successful cued recall (cued recall SME) and successful source retrieval (source memory SME). Data showed a cued recall SME on parietal electrode sites from 400 to 1200 ms and a late inversed cued recall SME on frontal sites in the 1200-1400 ms period. Moreover, a source memory SME was reported from 400 to 1400 ms on frontal areas. These findings indicate that patterns of encoding-related activity predicting successful recall and source memory are clearly dissociated.

Ultrashort Phenomena in Biochemistry and Biological Signaling

NASA Astrophysics Data System (ADS)

Splinter, Robert

2014-11-01

In biological phenomena there are indications that within the long pulse-length of the action potential on millisecond scale, there is additional ultrashort perturbation encoding that provides the brain with detailed information about the origin (location) and physiological characteristics. The objective is to identify the mechanism-of-action providing the potential for encoding in biological signal propagation. The actual molecular processes involved in the initiation of the action potential have been identified to be in the femtosecond and pico-second scale. The depolarization process of the cellular membrane itself, leading to the onset of the actionpotential that is transmitted to the brain, however is in the millisecond timeframe. One example of the femtosecond chemical interaction is the photoresponse of bacteriorhodopsin. No clear indication for the spatial encoding has so far been verified. Further research will be required on a cellular signal analysis level to confirm or deny the spatial and physiological encoding in the signal wave-trains of intercellular communications and sensory stimuli. The pathological encoding process for cardiac depolarization is however very pronounced and validated, however this electro-chemical process is in the millisecond amplitude and frequency modulation spectrum.

Deficits in Cross-Race Face Learning: Insights From Eye Movements and Pupillometry

PubMed Central

Goldinger, Stephen D.; He, Yi; Papesh, Megan H.

2010-01-01

The own-race bias (ORB) is a well-known finding wherein people are better able to recognize and discriminate own-race faces, relative to cross-race faces. In 2 experiments, participants viewed Asian and Caucasian faces, in preparation for recognition memory tests, while their eye movements and pupil diameters were continuously monitored. In Experiment 1 (with Caucasian participants), systematic differences emerged in both measures as a function of depicted race: While encoding cross-race faces, participants made fewer (and longer) fixations, they preferentially attended to different sets of features, and their pupils were more dilated, all relative to own-race faces. Also, in both measures, a pattern emerged wherein some participants reduced their apparent encoding effort to cross-race faces over trials. In Experiment 2 (with Asian participants), the authors observed the same patterns, although the ORB favored the opposite set of faces. Taken together, the results suggest that the ORB appears during initial perceptual encoding. Relative to own-race face encoding, cross-race encoding requires greater effort, which may reduce vigilance in some participants. PMID:19686008

Encoding of Reward and Space During a Working Memory Task in the Orbitofrontal Cortex and Anterior Cingulate Sulcus

PubMed Central

Kennerley, Steven W.

2009-01-01

Several lines of research indicate that emotional and motivational information may be useful in guiding the allocation of attentional resources. Two areas of the frontal lobe that are particularly implicated in the encoding of motivational information are the orbital prefrontal cortex (PFo) and the dorsomedial region of prefrontal cortex, specifically the anterior cingulate sulcus (PFcs). However, it remains unclear whether these areas use this information to influence spatial attention. We used single-unit neurophysiology to examine whether, at the level of individual neurons, there was evidence for integration between reward information and spatial attention. We trained two subjects to perform a task that required them to attend to a spatial location across a delay under different expectancies of reward for correct performance. We balanced the order of presentation of spatial and reward information so we could assess the neuronal encoding of the two pieces of information independently and conjointly. We found little evidence for encoding of the spatial location in either PFo or PFcs. In contrast, both areas encoded the expected reward. Furthermore, PFo consistently encoded reward more quickly than PFcs, although reward encoding was subsequently more prevalent and stronger in PFcs. These results suggest a differential contribution of PFo and PFcs to reward encoding, with PFo potentially more important for initially determining the value of rewards predicted by sensory stimuli. They also suggest that neither PFo nor PFcs play a direct role in the control of spatial attention. PMID:19776363

Mollusk genes encoding lysine tRNA (UUU) contain introns.

PubMed

Matsuo, M; Abe, Y; Saruta, Y; Okada, N

1995-11-20

New intron-containing genes encoding tRNAs were discovered when genomic DNA isolated from various animal species was amplified by the polymerase chain reaction (PCR) with primers based on sequences of rabbit tRNA(Lys). From sequencing analysis of the products of PCR, we found that introns are present in several genes encoding tRNA(Lys) in mollusks, such as Loligo bleekeri (squid) and Octopus vulgaris (octopus). These introns were specific to genes encoding tRNA(Lys)(CUU) and were not present in genes encoding tRNA(Lys)(CUU). In addition, the sequences of the introns were different from one another. To confirm the results of our initial experiments, we isolated and sequenced genes encoding tRNA(Lys)(CUU) and tRNA(Lys)(UUU). The gene for tRNA(Lys)(UUU) from squid contained an intron, whose sequence was the same as that identified by PCR, and the gene formed a cluster with a corresponding pseudogene. Several DNA regions of 2.1 kb containing this cluster appeared to be tandemly arrayed in the squid genome. By contrast, the gene encoding tRNA(Lys)(CUU) did not contain an intron, as shown also by PCR. The tRNA(Lys)(UUU) that corresponded to the analyzed gene was isolated and characterized. The present study provides the first example of an intron-containing gene encoding a tRNA in mollusks and suggests the universality of introns in such genes in higher eukaryotes.

Choice by value encoding and value construction: processes of loss aversion.

PubMed

Willemsen, Martijn C; Böckenholt, Ulf; Johnson, Eric J

2011-08-01

Loss aversion and reference dependence are 2 keystones of behavioral theories of choice, but little is known about their underlying cognitive processes. We suggest an additional account for loss aversion that supplements the current account of the value encoding of attributes as gains or losses relative to a reference point, introducing a value construction account. Value construction suggests that loss aversion results from biased evaluations during information search and comparison processes. We develop hypotheses that identify the influence of both accounts and examine process-tracing data for evidence. Our data suggest that loss aversion is the result of the initial direct encoding of losses that leads to the subsequent process of directional comparisons distorting attribute valuations and the final choice.

Visual short-term memory: activity supporting encoding and maintenance in retinotopic visual cortex.

PubMed

Sneve, Markus H; Alnæs, Dag; Endestad, Tor; Greenlee, Mark W; Magnussen, Svein

2012-10-15

Recent studies have demonstrated that retinotopic cortex maintains information about visual stimuli during retention intervals. However, the process by which transient stimulus-evoked sensory responses are transformed into enduring memory representations is unknown. Here, using fMRI and short-term visual memory tasks optimized for univariate and multivariate analysis approaches, we report differential involvement of human retinotopic areas during memory encoding of the low-level visual feature orientation. All visual areas show weaker responses when memory encoding processes are interrupted, possibly due to effects in orientation-sensitive primary visual cortex (V1) propagating across extrastriate areas. Furthermore, intermediate areas in both dorsal (V3a/b) and ventral (LO1/2) streams are significantly more active during memory encoding compared with non-memory (active and passive) processing of the same stimulus material. These effects in intermediate visual cortex are also observed during memory encoding of a different stimulus feature (spatial frequency), suggesting that these areas are involved in encoding processes on a higher level of representation. Using pattern-classification techniques to probe the representational content in visual cortex during delay periods, we further demonstrate that simply initiating memory encoding is not sufficient to produce long-lasting memory traces. Rather, active maintenance appears to underlie the observed memory-specific patterns of information in retinotopic cortex. Copyright © 2012 Elsevier Inc. All rights reserved.

A Knowledge-Based Approach to Language Production

DTIC Science & Technology

1985-08-01

representation -- the internal structures which the system is generating from. and (3) the choice problem -- how the intricate relationship between the...texts from several different internal representations. One example of the output produced by MUMBLE is the following text, produced from a...brackets. This notation is used to illustrate some templates which are encoded in Ace. The internal representation of these templates is achieved using

Phylogeny of replication initiator protein TrfA reveals a highly divergent clade of incompatibility group P1 plasmids

USDA-ARS?s Scientific Manuscript database

Incompatibility group P-1 (incP-1) includes broad host range plasmids of Gram negative bacteria and are classified into five subgroups (alpha, beta, gamma, delta, and epsilon). The incP-1 replication module consists of the trfA gene, encoding the replication initiator protein TrfA, and the origin o...

Primary phonological planning units in spoken word production are language-specific: Evidence from an ERP study.

PubMed

Wang, Jie; Wong, Andus Wing-Kuen; Wang, Suiping; Chen, Hsuan-Chih

2017-07-19

It is widely acknowledged in Germanic languages that segments are the primary planning units at the phonological encoding stage of spoken word production. Mixed results, however, have been found in Chinese, and it is still unclear what roles syllables and segments play in planning Chinese spoken word production. In the current study, participants were asked to first prepare and later produce disyllabic Mandarin words upon picture prompts and a response cue while electroencephalogram (EEG) signals were recorded. Each two consecutive pictures implicitly formed a pair of prime and target, whose names shared the same word-initial atonal syllable or the same word-initial segments, or were unrelated in the control conditions. Only syllable repetition induced significant effects on event-related brain potentials (ERPs) after target onset: a widely distributed positivity in the 200- to 400-ms interval and an anterior positivity in the 400- to 600-ms interval. We interpret these to reflect syllable-size representations at the phonological encoding and phonetic encoding stages. Our results provide the first electrophysiological evidence for the distinct role of syllables in producing Mandarin spoken words, supporting a language specificity hypothesis about the primary phonological units in spoken word production.

Transcription Factors Expressed in Lateral Organ Boundaries: Identification of Downstream Targets

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

Springer, Patricia S

2010-07-12

The processes of lateral organ initiation and patterning are central to the generation of mature plant form. Characterization of the molecular mechanisms underlying these processes is essential to our understanding of plant development. Communication between the shoot apical meristem and initiating organ primordia is important both for functioning of the meristem and for proper organ patterning, and very little is known about this process. In particular, the boundary between meristem and leaf is emerging as a critical region that is important for SAM maintenance and regulation of organogenesis. The goal of this project was to characterize three boundary-expressed genes thatmore » encode predicted transcription factors. Specifically, we have studied LATERAL ORGAN BOUNDARIES (LOB), LATERAL ORGAN FUSION1 (LOF1), and LATERAL ORGAN FUSION2 (LOF2). LOB encodes the founding member of the LOB-DOMAIN (LBD) plant-specific DNA binding transcription factor family and LOF1 and LOF2 encode paralogous MYB-domain transcription factors. We characterized the genetic relationship between these three genes and other boundary and meristem genes. We also used an ectopic inducible expression system to identify direct targets of LOB.« less

Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes.

PubMed

Delwart, Eric; Li, Linlin

2012-03-01

The genomes of numerous circoviruses and distantly related circular ssDNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, plants (geminivirus and nanovirus), in human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also recently identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting the very wide past host range of rep bearing viruses. An ancient origin for viruses with Rep-encoding small circular ssDNA genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular ssDNA genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular ssDNA viral genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

Distinctiveness and encoding effects in online sentence comprehension

PubMed Central

Hofmeister, Philip; Vasishth, Shravan

2014-01-01

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. PMID:25566105

SfDronc, an initiator caspase involved in apoptosis in the fall armyworm Spodoptera frugiperda

PubMed Central

Huang, Ning; Civciristov, Srgjan; Hawkins, Christine J.; Clem, Rollie J.

2013-01-01

Initiator caspases are the first caspases that are activated following an apoptotic stimulus, and are responsible for cleaving and activating downstream effector caspases, which directly cause apoptosis. We have cloned a cDNA encoding an ortholog of the initiator caspase Dronc in the lepidopteran insect Spodoptera frugiperda. The SfDronc cDNA encodes a predicted protein of 447 amino acids with a molecular weight of 51 kDa. Overexpression of SfDronc induced apoptosis in Sf9 cells, while partial silencing of SfDronc expression in Sf9 cells reduced apoptosis induced by baculovirus infection or by treatment with UV or actinomycin D. Recombinant SfDronc exhibited several expected biochemical characteristics of an apoptotic initiator caspase: 1) SfDronc efficiently cleaved synthetic initiator caspase substrates, but had very little activity against effector caspase substrates; 2) mutation of a predicted cleavage site at position D340 blocked autoprocessing of recombinant SfDronc and reduced enzyme activity by approximately 10-fold; 3) SfDronc cleaved the effector caspase Sf-caspase-1 at the expected cleavage site, resulting in Sf-caspase-1 activation; and 4) SfDronc was strongly inhibited by the baculovirus caspase inhibitor SpliP49, but not by the related protein AcP35. These results indicate that SfDronc is an initiator caspase involved in caspase-dependent apoptosis in S. frugiperda, and as such is likely to be responsible for the initiator caspase activity in S. frugiperda cells known as Sf-caspase-X. PMID:23474489

Representing spatial structure through maps and language: Lord of the Rings encodes the spatial structure of middle Earth.

PubMed

Louwerse, Max M; Benesh, Nick

2012-01-01

Spatial mental representations can be derived from linguistic and non-linguistic sources of information. This study tested whether these representations could be formed from statistical linguistic frequencies of city names, and to what extent participants differed in their performance when they estimated spatial locations from language or maps. In a computational linguistic study, we demonstrated that co-occurrences of cities in Tolkien's Lord of the Rings trilogy and The Hobbit predicted the authentic longitude and latitude of those cities in Middle Earth. In a human study, we showed that human spatial estimates of the location of cities were very similar regardless of whether participants read Tolkien's texts or memorized a map of Middle Earth. However, text-based location estimates obtained from statistical linguistic frequencies better predicted the human text-based estimates than the human map-based estimates. These findings suggest that language encodes spatial structure of cities, and that human cognitive map representations can come from implicit statistical linguistic patterns, from explicit non-linguistic perceptual information, or from both. Copyright © 2012 Cognitive Science Society, Inc.

NREL and Partners Support Hawaii Clean Energy Initiative - Text Version |

Science.gov Websites

NREL NREL and Partners Support Hawaii Clean Energy Initiative - Text Version NREL and Partners Support Hawaii Clean Energy Initiative - Text Version Below is the text version for the video NREL and

Neural Mechanisms Underlying Paradoxical Performance for Monetary Incentives Are Driven by Loss Aversion

PubMed Central

Chib, Vikram S.; De Martino, Benedetto; Shimojo, Shinsuke; O'Doherty, John P.

2012-01-01

Summary Employers often make payment contingent on performance in order to motivate workers. We used fMRI with a novel incentivized skill task to examine the neural processes underlying behavioral responses to performance-based pay. We found that individuals' performance increased with increasing incentives; however, very high incentive levels led to the paradoxical consequence of worse performance. Between initial incentive presentation and task execution, striatal activity rapidly switched between activation and deactivation in response to increasing incentives. Critically, decrements in performance and striatal deactivations were directly predicted by an independent measure of behavioral loss aversion. These results suggest that incentives associated with successful task performance are initially encoded as a potential gain; however, when actually performing a task, individuals encode the potential loss that would arise from failure. PMID:22578508

Generation of Recombinant Ebola Viruses Using Reverse Genetics.

PubMed

Groseth, Allison

2017-01-01

Reverse genetics systems encompass a wide array of tools aimed at recapitulating some or all of the virus life cycle. In their most complete form, full-length clone systems allow us to use plasmid-encoded versions of the ribonucleoprotein (RNP) components to initiate the transcription and replication of a plasmid-encoded version of the complete viral genome, thereby initiating the complete virus life cycle and resulting in infectious virus. As such this approach is ideal for the generation of tailor-made recombinant filoviruses, which can be used to study virus biology. In addition, the generation of tagged and particularly fluorescent or luminescent viruses can be applied as tools for both diagnostic applications and for screening to identify novel countermeasures. Here we describe the generation and basic characterization of recombinant Ebola viruses rescued from cloned cDNA using a T7-driven system.

First-spike latency in Hodgkin's three classes of neurons.

PubMed

Wang, Hengtong; Chen, Yueling; Chen, Yong

2013-07-07

We study the first-spike latency (FSL) in Hodgkin's three classes of neurons with the Morris-Lecar neuron model. It is found that all the three classes of neurons can encode an external stimulus into FSLs. With DC inputs, the FSLs of all of the neurons decrease with input intensity. With input current decreased to the threshold, class 1 neurons show an arbitrary long FSL whereas class 2 and 3 neurons exhibit the short-limit FSLs. When the input current is sinusoidal, the amplitude, frequency and initial phase can be encoded by all the three classes of neurons. The FSLs of all of the neurons decrease with the input amplitude and frequency. When the input frequency is too high, all of the neurons respond with infinite FSLs. When the initial phase increases, the FSL decreases and then jumps to a maximal value and finally decreases linearly. With changes in the input parameters, the FSLs of the class 1 and 2 neurons exhibit similar properties. However, the FSL of the class 3 neurons became slightly longer and only produces responses for a narrow range of initial phase if input frequencies are low. Moreover, our results also show that the FSL and firing rate responses are mutually independent processes and that neurons can encode an external stimulus into different FSLs and firing rates simultaneously. This finding is consistent with the current theory of dual or multiple complementary coding mechanisms. Copyright © 2013 Elsevier Ltd. All rights reserved.

Perceived freedom of choice is associated with neural encoding of option availability.

PubMed

Rens, Natalie; Bode, Stefan; Cunnington, Ross

2018-05-03

Freedom of choice has been defined as the opportunity to choose alternative plans of action. In this fMRI study, we investigated how the perceived freedom of choice and the underlying neural correlates are influenced by the availability of options. Participants made an initial free choice between left or right doors before beginning a virtual walk along a corridor. At the mid-point of the corridor, lock cues appeared to reveal whether one or both doors remained available, requiring participants either to select a particular door or allowing them to freely choose to stay or switch their choice. We found that participants rated trials as free when they were able to carry out their initial choice, but even more so when both doors remained available. Multi-voxel pattern analysis showed that upcoming choices could initially be decoded from visual cortices before the appearance of the lock cues, and additionally from the motor cortex after the lock cues had confirmed which doors were open. When participants were able to maintain the same choice that they originally selected, the availability of alternative options was represented in fine-grained patterns of activity in the dorsolateral prefrontal cortex. Further, decoding accuracy in this region correlated with the subjective level of freedom that participants reported. These results suggest that there is neural encoding of the availability of alternative options in the dorsolateral prefrontal cortex, and the degree of this encoding predicts an individual's perceived freedom of choice. Copyright © 2018 Elsevier Inc. All rights reserved.

Memory and comprehension deficits in spatial descriptions of children with non-verbal and reading disabilities.

PubMed

Mammarella, Irene C; Meneghetti, Chiara; Pazzaglia, Francesca; Cornoldi, Cesare

2014-01-01

The present study investigated the difficulties encountered by children with non-verbal learning disability (NLD) and reading disability (RD) when processing spatial information derived from descriptions, based on the assumption that both groups should find it more difficult than matched controls, but for different reasons, i.e., due to a memory encoding difficulty in cases of RD and to spatial information comprehension problems in cases of NLD. Spatial descriptions from both survey and route perspectives were presented to 9-12-year-old children divided into three groups: NLD (N = 12); RD (N = 12), and typically developing controls (TD; N = 15); then participants completed a sentence verification task and a memory for locations task. The sentence verification task was presented in two conditions: in one the children could refer to the text while answering the questions (i.e., text present condition), and in the other the text was withdrawn (i.e., text absent condition). Results showed that the RD group benefited from the text present condition, but was impaired to the same extent as the NLD group in the text absent condition, suggesting that the NLD children's difficulty is due mainly to their poor comprehension of spatial descriptions, while the RD children's difficulty is due more to a memory encoding problem. These results are discussed in terms of their implications in the neuropsychological profiles of children with NLD or RD, and the processes involved in spatial descriptions.

Pupil size reflects successful encoding and recall of memory in humans.

PubMed

Kucewicz, Michal T; Dolezal, Jaromir; Kremen, Vaclav; Berry, Brent M; Miller, Laura R; Magee, Abigail L; Fabian, Vratislav; Worrell, Gregory A

2018-03-21

Pupil responses are known to indicate brain processes involved in perception, attention and decision-making. They can provide an accessible biomarker of human memory performance and cognitive states in general. Here we investigated changes in the pupil size during encoding and recall of word lists. Consistent patterns in the pupil response were found across and within distinct phases of the free recall task. The pupil was most constricted in the initial fixation phase and was gradually more dilated through the subsequent encoding, distractor and recall phases of the task, as the word items were maintained in memory. Within the final recall phase, retrieving memory for individual words was associated with pupil dilation in absence of visual stimulation. Words that were successfully recalled showed significant differences in pupil response during their encoding compared to those that were forgotten - the pupil was more constricted before and more dilated after the onset of word presentation. Our results suggest pupil size as a potential biomarker for probing and modulation of memory processing.

Two Closely Related Genes of Arabidopsis Encode Plastidial Cytidinediphosphate Diacylglycerol Synthases Essential for Photoautotrophic Growth1[C

PubMed Central

Haselier, André; Akbari, Hana; Weth, Agnes; Baumgartner, Werner; Frentzen, Margrit

2010-01-01

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth. PMID:20442275

Consolidation in older adults depends upon competition between resting-state networks

PubMed Central

Jacobs, Heidi I. L.; Dillen, Kim N. H.; Risius, Okka; Göreci, Yasemin; Onur, Oezguer A.; Fink, Gereon R.; Kukolja, Juraj

2015-01-01

Memory encoding and retrieval problems are inherent to aging. To date, however, the effect of aging upon the neural correlates of forming memory traces remains poorly understood. Resting-state fMRI connectivity can be used to investigate initial consolidation. We compared within and between network connectivity differences between healthy young and older participants before encoding, after encoding and before retrieval by means of resting-state fMRI. Alterations over time in the between-network connectivity analyses correlated with retrieval performance, whereas within-network connectivity did not: a higher level of negative coupling or competition between the default mode and the executive networks during the after encoding condition was associated with increased retrieval performance in the older adults, but not in the young group. Data suggest that the effective formation of memory traces depends on an age-dependent, dynamic reorganization of the interaction between multiple, large-scale functional networks. Our findings demonstrate that a cross-network based approach can further the understanding of the neural underpinnings of aging-associated memory decline. PMID:25620930

The Many Facets and Applications of Text Structure in Supporting Educational Trajectories of Elementary and Middle Grade Children in Content Area Reading Comprehension and Writing

ERIC Educational Resources Information Center

Albro, Elizabeth; Williams, Joanna P.; Wijekumar, Kausalai; Meyer, Bonnie J. F.; Harris, Karen R.

2015-01-01

Content area reading comprehension and writing have been a challenge for children in the U.S. schools for many years as evidenced by state and national assessments. One promising solution to the problem is text structure based instruction that promotes strategic selection, encoding, retrieval, and use of information for myriads of activities…

An fMRI study of semantic processing in men with schizophrenia

PubMed Central

Kubicki, M.; McCarley, R.W.; Nestor, P.G.; Huh, T.; Kikinis, R.; Shenton, M.E.; Wible, C.G.

2009-01-01

As a means toward understanding the neural bases of schizophrenic thought disturbance, we examined brain activation patterns in response to semantically and superficially encoded words in patients with schizophrenia. Nine male schizophrenic and 9 male control subjects were tested in a visual levels of processing (LOP) task first outside the magnet and then during the fMRI scanning procedures (using a different set of words). During the experiments visual words were presented under two conditions. Under the deep, semantic encoding condition, subjects made semantic judgments as to whether the words were abstract or concrete. Under the shallow, nonsemantic encoding condition, subjects made perceptual judgments of the font size (uppercase/lowercase) of the presented words. After performance of the behavioral task, a recognition test was used to assess the depth of processing effect, defined as better performance for semantically encoded words than for perceptually encoded words. For the scanned version only, the words for both conditions were repeated in order to assess repetition-priming effects. Reaction times were assessed in both testing scenarios. Both groups showed the expected depth of processing effect for recognition, and control subjects showed the expected increased activation of the left inferior prefrontal cortex (LIPC) under semantic encoding relative to perceptual encoding conditions as well as repetition priming for semantic conditions only. In contrast, schizophrenics showed similar patterns of fMRI activation regardless of condition. Most striking in relation to controls, patients showed decreased LIFC activation concurrent with increased left superior temporal gyrus activation for semantic encoding versus shallow encoding. Furthermore, schizophrenia subjects did not show the repetition priming effect, either behaviorally or as a decrease in LIPC activity. In patients with schizophrenia, LIFC underactivation and left superior temporal gyrus overactivation for semantically encoded words may reflect a disease-related disruption of a distributed frontal temporal network that is engaged in the representation and processing of meaning of words, text, and discourse and which may underlie schizophrenic thought disturbance. PMID:14683698

An fMRI study of semantic processing in men with schizophrenia.

PubMed

Kubicki, M; McCarley, R W; Nestor, P G; Huh, T; Kikinis, R; Shenton, M E; Wible, C G

2003-12-01

As a means toward understanding the neural bases of schizophrenic thought disturbance, we examined brain activation patterns in response to semantically and superficially encoded words in patients with schizophrenia. Nine male schizophrenic and 9 male control subjects were tested in a visual levels of processing (LOP) task first outside the magnet and then during the fMRI scanning procedures (using a different set of words). During the experiments visual words were presented under two conditions. Under the deep, semantic encoding condition, subjects made semantic judgments as to whether the words were abstract or concrete. Under the shallow, nonsemantic encoding condition, subjects made perceptual judgments of the font size (uppercase/lowercase) of the presented words. After performance of the behavioral task, a recognition test was used to assess the depth of processing effect, defined as better performance for semantically encoded words than for perceptually encoded words. For the scanned version only, the words for both conditions were repeated in order to assess repetition-priming effects. Reaction times were assessed in both testing scenarios. Both groups showed the expected depth of processing effect for recognition, and control subjects showed the expected increased activation of the left inferior prefrontal cortex (LIPC) under semantic encoding relative to perceptual encoding conditions as well as repetition priming for semantic conditions only. In contrast, schizophrenics showed similar patterns of fMRI activation regardless of condition. Most striking in relation to controls, patients showed decreased LIFC activation concurrent with increased left superior temporal gyrus activation for semantic encoding versus shallow encoding. Furthermore, schizophrenia subjects did not show the repetition priming effect, either behaviorally or as a decrease in LIPC activity. In patients with schizophrenia, LIFC underactivation and left superior temporal gyrus overactivation for semantically encoded words may reflect a disease-related disruption of a distributed frontal temporal network that is engaged in the representation and processing of meaning of words, text, and discourse and which may underlie schizophrenic thought disturbance.

NLP-based Identification of Pneumonia Cases from Free-Text Radiological Reports

PubMed Central

Elkin, Peter L.; Froehling, David; Wahner-Roedler, Dietlind; Trusko, Brett; Welsh, Gail; Ma, Haobo; Asatryan, Armen X.; Tokars, Jerome I.; Rosenbloom, S. Trent; Brown, Steven H.

2008-01-01

Radiological reports are a rich source of clinical data which can be mined to assist with biosurveillance of emerging infectious diseases. In addition to biosurveillance, radiological reports are an important source of clinical data for health service research. Pneumonias and other radiological findings on chest xray or chest computed tomography (CT) are one type of relevant finding to both biosurveillance and health services research. In this study we examined the ability of a Natural Language Processing system to accurately identify pneumonias and other lesions from within free-text radiological reports. The system encoded the reports in the SNOMED CT Ontology and then a set of SNOMED CT based rules were created in our Health Archetype Language aimed at the identification of these radiological findings and diagnoses. The encoded rule was executed against the SNOMED CT encodings of the radiological reports. The accuracy of the reports was compared with a Clinician review of the Radiological Reports. The accuracy of the system in the identification of pneumonias was high with a Sensitivity (recall) of 100%, a specificity of 98%, and a positive predictive value (precision) of 97%. We conclude that SNOMED CT based computable rules are accurate enough for the automated biosurveillance of pneumonias from radiological reports. PMID:18998791

[The ENCODE project and functional genomics studies].

PubMed

Ding, Nan; Qu, Hongzhu; Fang, Xiangdong

2014-03-01

Upon the completion of the Human Genome Project, scientists have been trying to interpret the underlying genomic code for human biology. Since 2003, National Human Genome Research Institute (NHGRI) has invested nearly $0.3 billion and gathered over 440 scientists from more than 32 institutions in the United States, China, United Kingdom, Japan, Spain and Singapore to initiate the Encyclopedia of DNA Elements (ENCODE) project, aiming to identify and analyze all regulatory elements in the human genome. Taking advantage of the development of next-generation sequencing technologies and continuous improvement of experimental methods, ENCODE had made remarkable achievements: identified methylation and histone modification of DNA sequences and their regulatory effects on gene expression through altering chromatin structures, categorized binding sites of various transcription factors and constructed their regulatory networks, further revised and updated database for pseudogenes and non-coding RNA, and identified SNPs in regulatory sequences associated with diseases. These findings help to comprehensively understand information embedded in gene and genome sequences, the function of regulatory elements as well as the molecular mechanism underlying the transcriptional regulation by noncoding regions, and provide extensive data resource for life sciences, particularly for translational medicine. We re-viewed the contributions of high-throughput sequencing platform development and bioinformatical technology improve-ment to the ENCODE project, the association between epigenetics studies and the ENCODE project, and the major achievement of the ENCODE project. We also provided our prospective on the role of the ENCODE project in promoting the development of basic and clinical medicine.

Alpha Oscillations during Incidental Encoding Predict Subsequent Memory for New "Foil" Information.

PubMed

Vogelsang, David A; Gruber, Matthias; Bergström, Zara M; Ranganath, Charan; Simons, Jon S

2018-05-01

People can employ adaptive strategies to increase the likelihood that previously encoded information will be successfully retrieved. One such strategy is to constrain retrieval toward relevant information by reimplementing the neurocognitive processes that were engaged during encoding. Using EEG, we examined the temporal dynamics with which constraining retrieval toward semantic versus nonsemantic information affects the processing of new "foil" information encountered during a memory test. Time-frequency analysis of EEG data acquired during an initial study phase revealed that semantic compared with nonsemantic processing was associated with alpha decreases in a left frontal electrode cluster from around 600 msec after stimulus onset. Successful encoding of semantic versus nonsemantic foils during a subsequent memory test was related to decreases in alpha oscillatory activity in the same left frontal electrode cluster, which emerged relatively late in the trial at around 1000-1600 msec after stimulus onset. Across participants, left frontal alpha power elicited by semantic processing during the study phase correlated significantly with left frontal alpha power associated with semantic foil encoding during the memory test. Furthermore, larger left frontal alpha power decreases elicited by semantic foil encoding during the memory test predicted better subsequent semantic foil recognition in an additional surprise foil memory test, although this effect did not reach significance. These findings indicate that constraining retrieval toward semantic information involves reimplementing semantic encoding operations that are mediated by alpha oscillations and that such reimplementation occurs at a late stage of memory retrieval, perhaps reflecting additional monitoring processes.

Associative learning in baboons (Papio papio) and humans (Homo sapiens): species differences in learned attention to visual features.

PubMed

Fagot, J; Kruschke, J K; Dépy, D; Vauclair, J

1998-10-01

We examined attention shifting in baboons and humans during the learning of visual categories. Within a conditional matching-to-sample task, participants of the two species sequentially learned two two-feature categories which shared a common feature. Results showed that humans encoded both features of the initially learned category, but predominantly only the distinctive feature of the subsequently learned category. Although baboons initially encoded both features of the first category, they ultimately retained only the distinctive features of each category. Empirical data from the two species were analyzed with the 1996 ADIT connectionist model of Kruschke. ADIT fits the baboon data when the attentional shift rate is zero, and the human data when the attentional shift rate is not zero. These empirical and modeling results suggest species differences in learned attention to visual features.

Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

NASA Astrophysics Data System (ADS)

Machutta, Carl A.; Kollmann, Christopher S.; Lind, Kenneth E.; Bai, Xiaopeng; Chan, Pan F.; Huang, Jianzhong; Ballell, Lluis; Belyanskaya, Svetlana; Besra, Gurdyal S.; Barros-Aguirre, David; Bates, Robert H.; Centrella, Paolo A.; Chang, Sandy S.; Chai, Jing; Choudhry, Anthony E.; Coffin, Aaron; Davie, Christopher P.; Deng, Hongfeng; Deng, Jianghe; Ding, Yun; Dodson, Jason W.; Fosbenner, David T.; Gao, Enoch N.; Graham, Taylor L.; Graybill, Todd L.; Ingraham, Karen; Johnson, Walter P.; King, Bryan W.; Kwiatkowski, Christopher R.; Lelièvre, Joël; Li, Yue; Liu, Xiaorong; Lu, Quinn; Lehr, Ruth; Mendoza-Losana, Alfonso; Martin, John; McCloskey, Lynn; McCormick, Patti; O'Keefe, Heather P.; O'Keeffe, Thomas; Pao, Christina; Phelps, Christopher B.; Qi, Hongwei; Rafferty, Keith; Scavello, Genaro S.; Steiginga, Matt S.; Sundersingh, Flora S.; Sweitzer, Sharon M.; Szewczuk, Lawrence M.; Taylor, Amy; Toh, May Fern; Wang, Juan; Wang, Minghui; Wilkins, Devan J.; Xia, Bing; Yao, Gang; Zhang, Jean; Zhou, Jingye; Donahue, Christine P.; Messer, Jeffrey A.; Holmes, David; Arico-Muendel, Christopher C.; Pope, Andrew J.; Gross, Jeffrey W.; Evindar, Ghotas

2017-07-01

The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery.

Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers.

PubMed

Zhu, Bin; Wang, Longfei; Mitsunobu, Hitoshi; Lu, Xueling; Hernandez, Alfredo J; Yoshida-Takashima, Yukari; Nunoura, Takuro; Tabor, Stanley; Richardson, Charles C

2017-03-21

A DNA polymerase is encoded by the deep-sea vent phage NrS-1. NrS-1 has a unique genome organization containing genes that are predicted to encode a helicase and a single-stranded DNA (ssDNA)-binding protein. The gene for an unknown protein shares weak homology with the bifunctional primase-polymerases (prim-pols) from archaeal plasmids but is missing the zinc-binding domain typically found in primases. We show that this gene product has efficient DNA polymerase activity and is processive in DNA synthesis in the presence of the NrS-1 helicase and ssDNA-binding protein. Remarkably, this NrS-1 DNA polymerase initiates DNA synthesis from a specific template DNA sequence in the absence of any primer. The de novo DNA polymerase activity resides in the N-terminal domain of the protein, whereas the C-terminal domain enhances DNA binding.

Creating buzz: the neural correlates of effective message propagation.

PubMed

Falk, Emily B; Morelli, Sylvia A; Welborn, B Locke; Dambacher, Karl; Lieberman, Matthew D

2013-07-01

Social interaction promotes the spread of values, attitudes, and behaviors. Here, we report on neural responses to ideas that are destined to spread. We scanned message communicators using functional MRI during their initial exposure to the to-be-communicated ideas. These message communicators then had the opportunity to spread the messages and their corresponding subjective evaluations to message recipients outside the scanner. Successful ideas were associated with neural responses in the communicators' mentalizing systems and reward systems when they first heard the messages, prior to spreading them. Similarly, individuals more able to spread their own views to others produced greater mentalizing-system activity during initial encoding. Unlike prior social-influence studies that focused on the individuals being influenced, this investigation focused on the brains of influencers. Successful social influence is reliably associated with an influencer-to-be's state of mind when first encoding ideas.

Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

USGS Publications Warehouse

Chen, C.; Xia, J.; Liu, J.; Feng, G.

2006-01-01

Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant result is that final solution is determined by the average model derived from multiple trials instead of one computation due to the randomness in a genetic algorithm procedure. These advantages were demonstrated by synthetic and real-world examples of inversion of potential-field data. ?? 2005 Elsevier Ltd. All rights reserved.

Discovering Recurring Anomalies in Text Reports Regarding Complex Space Systems

NASA Technical Reports Server (NTRS)

Zane-Ulman, Brett; Srivastava, Ashok N.

2005-01-01

Many existing complex space systems have a significant amount of historical maintenance and problem data bases that are stored in unstructured text forms. For some platforms, these reports may be encoded as scanned images rather than even searchable text. The problem that we address in this paper is the discovery of recurring anomalies and relationships between different problem reports that may indicate larger systemic problems. We will illustrate our techniques on data from discrepancy reports regarding software anomalies in the Space Shuttle. These free text reports are written by a number of different penp!e, thus the emphasis and wording varies considerably.

SfDronc, an initiator caspase involved in apoptosis in the fall armyworm Spodoptera frugiperda.

PubMed

Huang, Ning; Civciristov, Srgjan; Hawkins, Christine J; Clem, Rollie J

2013-05-01

Initiator caspases are the first caspases that are activated following an apoptotic stimulus, and are responsible for cleaving and activating downstream effector caspases, which directly cause apoptosis. We have cloned a cDNA encoding an ortholog of the initiator caspase Dronc in the lepidopteran insect Spodoptera frugiperda. The SfDronc cDNA encodes a predicted protein of 447 amino acids with a molecular weight of 51 kDa. Overexpression of SfDronc induced apoptosis in Sf9 cells, while partial silencing of SfDronc expression in Sf9 cells reduced apoptosis induced by baculovirus infection or by treatment with UV or actinomycin D. Recombinant SfDronc exhibited several expected biochemical characteristics of an apoptotic initiator caspase: 1) SfDronc efficiently cleaved synthetic initiator caspase substrates, but had very little activity against effector caspase substrates; 2) mutation of a predicted cleavage site at position D340 blocked autoprocessing of recombinant SfDronc and reduced enzyme activity by approximately 10-fold; 3) SfDronc cleaved the effector caspase Sf-caspase-1 at the expected cleavage site, resulting in Sf-caspase-1 activation; and 4) SfDronc was strongly inhibited by the baculovirus caspase inhibitor SpliP49, but not by the related protein AcP35. These results indicate that SfDronc is an initiator caspase involved in caspase-dependent apoptosis in S. frugiperda, and as such is likely to be responsible for the initiator caspase activity in S. frugiperda cells known as Sf-caspase-X. Copyright © 2013 Elsevier Ltd. All rights reserved.

Geoparsing text for characterizing urban operational environments through machine learning techniques

NASA Astrophysics Data System (ADS)

Garfinkle, Noah W.; Selig, Lucas; Perkins, Timothy K.; Calfas, George W.

2017-05-01

Increasing worldwide internet connectivity and access to sources of print and open social media has increased near realtime availability of textual information. Capabilities to structure and integrate textual data streams can contribute to more meaningful representations of operational environment factors (i.e., Political, Military, Economic, Social, Infrastructure, Information, Physical Environment, and Time [PMESII-PT]) and tactical civil considerations (i.e., Areas, Structures, Capabilities, Organizations, People and Events [ASCOPE]). However, relying upon human analysts to encode this information as it arrives quickly proves intractable. While human analysts possess an ability to comprehend context in unstructured text far beyond that of computers, automated geoparsing (the extraction of locations from unstructured text) can empower analysts to automate sifting through datasets for areas of interest. This research evaluates existing approaches to geoprocessing as well as initiating the research and development of locally-improved methods of tagging parts of text as possible locations, resolving possible locations into coordinates, and interfacing such results with human analysts. The objective of this ongoing research is to develop a more contextually-complete picture of an area of interest (AOI) including human-geographic context for events. In particular, our research is working to make improvements to geoparsing (i.e., the extraction of spatial context from documents), which requires development, integration, and validation of named-entity recognition (NER) tools, gazetteers, and entity-attribution. This paper provides an overview of NER models and methodologies as applied to geoparsing, explores several challenges encountered, presents preliminary results from the creation of a flexible geoparsing research pipeline, and introduces ongoing and future work with the intention of contributing to the efficient geocoding of information containing valuable insights into human activities in space.

Roles of ON Cone Bipolar Cell Subtypes in Temporal Coding in the Mouse Retina

PubMed Central

Fyk-Kolodziej, Bozena; Cohn, Jesse

2014-01-01

In the visual system, diverse image processing starts with bipolar cells, which are the second-order neurons of the retina. Thirteen subtypes of bipolar cells have been identified, which are thought to encode different features of image signaling and to initiate distinct signal-processing streams. Although morphologically identified, the functional roles of each bipolar cell subtype in visual signal encoding are not fully understood. Here, we investigated how ON cone bipolar cells of the mouse retina encode diverse temporal image signaling. We recorded bipolar cell voltage changes in response to two different input functions: sinusoidal light and step light stimuli. Temporal tuning in ON cone bipolar cells was diverse and occurred in a subtype-dependent manner. Subtypes 5s and 8 exhibited low-pass filtering property in response to a sinusoidal light stimulus, and responded with sustained fashion to step-light stimulation. Conversely, subtypes 5f, 6, 7, and XBC exhibited bandpass filtering property in response to sinusoidal light stimuli, and responded transiently to step-light stimuli. In particular, subtypes 7 and XBC were high-temporal tuning cells. We recorded responses in different ways to further examine the underlying mechanisms of temporal tuning. Current injection evoked low-pass filtering, whereas light responses in voltage-clamp mode produced bandpass filtering in all ON bipolar cells. These findings suggest that cone photoreceptor inputs shape bandpass filtering in bipolar cells, whereas intrinsic properties of bipolar cells shape low-pass filtering. Together, our results demonstrate that ON bipolar cells encode diverse temporal image signaling in a subtype-dependent manner to initiate temporal visual information-processing pathways. PMID:24966376

The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases.

PubMed

Ruiz-Romero, Cristina; Calamia, Valentina; Albar, Juan Pablo; Casal, José Ignacio; Corrales, Fernando J; Fernández-Puente, Patricia; Gil, Concha; Mateos, Jesús; Vivanco, Fernando; Blanco, Francisco J

2015-09-08

The Spanish Chromosome 16 consortium is integrated in the global initiative Human Proteome Project, which aims to develop an entire map of the proteins encoded following a gene-centric strategy (C-HPP) in order to make progress in the understanding of human biology in health and disease (B/D-HPP). Chromosome 16 contains many genes encoding proteins involved in the development of a broad range of diseases, which have a significant impact on the health care system. The Spanish HPP consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. Proteomics strategies have enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. In this manuscript we describe how the Spanish HPP-16 consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. We show how the Proteomic strategy has enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

Predicting the integration of overlapping memories by decoding mnemonic processing states during learning

PubMed Central

Richter, Franziska R.; Chanales, Avi J. H.; Kuhl, Brice A.

2015-01-01

The hippocampal memory system is thought to alternate between two opposing processing states: encoding and retrieval. When present experience overlaps with past experience, this creates a potential tradeoff between encoding the present and retrieving the past. This tradeoff may be resolved by memory integration—that is, by forming a mnemonic representation that links present experience with overlapping past experience. Here, we used fMRI decoding analyses to predict when—and establish how—past and present experiences become integrated in memory. In an initial experiment, we alternately instructed subjects to adopt encoding, retrieval or integration states during overlapping learning. We then trained across-subject pattern classifiers to ‘read out’ the instructed processing states from fMRI activity patterns. We show that an integration state was clearly dissociable from encoding or retrieval states. Moreover, trial-by-trial fluctuations in decoded evidence for an integration state during learning reliably predicted behavioral expressions of successful memory integration. Strikingly, the decoding algorithm also successfully predicted specific instances of spontaneous memory integration in an entirely independent sample of subjects for whom processing state instructions were not administered. Finally, we show that medial prefrontal cortex and hippocampus differentially contribute to encoding, retrieval, and integration states: whereas hippocampus signals the tradeoff between encoding vs. retrieval states, medial prefrontal cortex actively represents past experience in relation to new learning. PMID:26327243

Early remodeling of the neocortex upon episodic memory encoding

PubMed Central

Bero, Adam W.; Meng, Jia; Cho, Sukhee; Shen, Abra H.; Canter, Rebecca G.; Ericsson, Maria; Tsai, Li-Huei

2014-01-01

Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, whereas reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural, and functional remodeling of the neocortex. Parallel studies using genome-wide RNA sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal–hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states. PMID:25071187

Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters

PubMed Central

WANG, JIACHEN; DASGUPTA, INDRANI; FOX, GEORGE E.

2009-01-01

The genomic associations of the archaeal ribosomal proteins, (r-proteins), were examined in detail. The archaeal versions of the universal r-protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r-protein genes examined, the gene encoding L18e was found to be associated with the conserved L13 cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of the spc operon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such. PMID:19478915

Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400.

PubMed Central

Seeger, M; Timmis, K N; Hofer, B

1995-01-01

Metabolism of 21 chlorobiphenyls by the enzymes of the upper biphenyl catabolic pathway encoded by the bph locus of Pseudomonas sp. strain LB400 was investigated by using recombinant strains harboring gene cassettes containing bphABC or bphABCD. The enzymes of the upper pathway were generally able to metabolize mono- and dichlorinated biphenyls but only partially transform most trichlorinated congeners investigated: 14 of 15 mono- and dichlorinated and 2 of 6 trichlorinated congeners were converted into benzoates. All mono- and at least 8 of 12 dichlorinated congeners were attacked by the bphA-encoded biphenyl dioxygenase virtually exclusively at ortho and meta carbons. This enzyme exhibited a high degree of selectivity for the aromatic ring to be attacked, with the order of ring preference being non- > ortho- > meta- > para-substituted for mono- and dichlorinated congeners. The influence of the chlorine substitution pattern of the metabolized ring on benzoate formation resembled its influence on the reactivity of initial dioxygenation, suggesting that the rate of benzoate formation may frequently be determined by the rate of initial attack. The absorption spectra of phenylhexadienoates formed correlated with the presence or absence of a chlorine substituent at an ortho position. PMID:7618878

Pareto-optimal multi-objective dimensionality reduction deep auto-encoder for mammography classification.

PubMed

Taghanaki, Saeid Asgari; Kawahara, Jeremy; Miles, Brandon; Hamarneh, Ghassan

2017-07-01

Feature reduction is an essential stage in computer aided breast cancer diagnosis systems. Multilayer neural networks can be trained to extract relevant features by encoding high-dimensional data into low-dimensional codes. Optimizing traditional auto-encoders works well only if the initial weights are close to a proper solution. They are also trained to only reduce the mean squared reconstruction error (MRE) between the encoder inputs and the decoder outputs, but do not address the classification error. The goal of the current work is to test the hypothesis that extending traditional auto-encoders (which only minimize reconstruction error) to multi-objective optimization for finding Pareto-optimal solutions provides more discriminative features that will improve classification performance when compared to single-objective and other multi-objective approaches (i.e. scalarized and sequential). In this paper, we introduce a novel multi-objective optimization of deep auto-encoder networks, in which the auto-encoder optimizes two objectives: MRE and mean classification error (MCE) for Pareto-optimal solutions, rather than just MRE. These two objectives are optimized simultaneously by a non-dominated sorting genetic algorithm. We tested our method on 949 X-ray mammograms categorized into 12 classes. The results show that the features identified by the proposed algorithm allow a classification accuracy of up to 98.45%, demonstrating favourable accuracy over the results of state-of-the-art methods reported in the literature. We conclude that adding the classification objective to the traditional auto-encoder objective and optimizing for finding Pareto-optimal solutions, using evolutionary multi-objective optimization, results in producing more discriminative features. Copyright © 2017 Elsevier B.V. All rights reserved.

Learning to generate combinatorial action sequences utilizing the initial sensitivity of deterministic dynamical systems.

PubMed

Nishimoto, Ryu; Tani, Jun

2004-09-01

This study shows how sensory-action sequences of imitating finite state machines (FSMs) can be learned by utilizing the deterministic dynamics of recurrent neural networks (RNNs). Our experiments indicated that each possible combinatorial sequence can be recalled by specifying its respective initial state value and also that fractal structures appear in this initial state mapping after the learning converges. We also observed that the sequences of mimicking FSMs are encoded utilizing the transient regions rather than the invariant sets of the evolved dynamical systems of the RNNs.

Total teleportation of a single-photon state

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

Humble, Travis S; Bennink, Ryan S; Grice, Warren P

2008-01-01

Recent demonstrations of teleportation have transferred quantum information encoded into either polarization or field-quadrature degrees of freedom (DOFs), but an outstanding question is how to simultaneously teleport quantum information encoded into multiple DOFs. We describe how the transverse-spatial, spectral and polarization states of a single photon can be simultaneously teleported using a pair of multimode, polarization-entangled photons derived from spontaneous parametric down-conversion. Furthermore, when the initial photon pair is maximally entangled in the spatial, spectral, and polarization DOFs then the photon s full quantum state can be reliably teleported using a Bell-state measurement based on sum-frequency generation.

Neuronal encoding of subjective value in dorsal and ventral anterior cingulate cortex

PubMed Central

Cai, Xinying; Padoa-Schioppa, Camillo

2012-01-01

We examined the activity of individual cells in the primate anterior cingulate cortex during an economic choice task. In the experiments, monkeys chose between different juices offered in variables amounts and subjective values were inferred from the animals’ choices. We analyzed neuronal firing rates in relation to a large number of behaviorally relevant variables. We report three main results. First, there were robust differences between the dorsal bank (ACCd) and the ventral bank (ACCv) of the cingulate sulcus. Specifically, neurons in ACCd but not in ACCv were modulated by the movement direction. Furthermore, neurons in ACCd were most active prior to movement initiation whereas neurons in ACCv were most active after juice delivery. Second, neurons in both areas encoded the identity and the subjective value of the juice chosen by the animal. In contrast, neither region encoded the value of individual offers. Third, the population of value-encoding neurons in both ACCd and ACCv underwent range adaptation. With respect to economic choice, it is interesting to compare these areas with the orbitofrontal cortex (OFC), previously examined. While neurons in OFC encoded both pre-decision and post-decision variables, neurons in ACCd and ACCv only encoded post-decision variables. Moreover, the encoding of chosen value in ACCd and ACCv trailed that found in OFC. These observations indicate that economic decisions (value comparisons) take place upstream of ACCd and ACCv. The coexistence of choice outcome and movement signals in ACCd suggests that this area constitutes a getaway through which the choice system informs motor systems. PMID:22423100

Efficient processing of MPEG-21 metadata in the binary domain

NASA Astrophysics Data System (ADS)

Timmerer, Christian; Frank, Thomas; Hellwagner, Hermann; Heuer, Jörg; Hutter, Andreas

2005-10-01

XML-based metadata is widely adopted across the different communities and plenty of commercial and open source tools for processing and transforming are available on the market. However, all of these tools have one thing in common: they operate on plain text encoded metadata which may become a burden in constrained and streaming environments, i.e., when metadata needs to be processed together with multimedia content on the fly. In this paper we present an efficient approach for transforming such kind of metadata which are encoded using MPEG's Binary Format for Metadata (BiM) without additional en-/decoding overheads, i.e., within the binary domain. Therefore, we have developed an event-based push parser for BiM encoded metadata which transforms the metadata by a limited set of processing instructions - based on traditional XML transformation techniques - operating on bit patterns instead of cost-intensive string comparisons.

VRX-496(VIRxSYS).

PubMed

Morris, Kevin V

2005-02-01

VIRxSYS is developing VRX-496, a lentiviral HIV-based vector encoding anti-HIV antisense envelope sequences, as a potential gene therapy for HIV infection. In July 2003, VIRxSYS undertook the initial dosing of an HIV-positive patient in a phase I/IIa trial.

Rest-related consolidation protects the fine detail of new memories.

PubMed

Craig, Michael; Dewar, Michaela

2018-05-01

Newly encoded memories are labile and consolidate over time. The importance of sleep in memory consolidation has been well known for almost a decade. However, recent research has shown that awake quiescence, too, can support consolidation: people remember more new memories if they quietly rest after encoding than if they engage in a task. It is not yet known how exactly this rest-related consolidation benefits new memories, and whether it affects the fine detail of new memories. Using a sensitive picture recognition task, we show that awake quiescence aids the fine detail of new memories. Young adults were significantly better at discriminating recently encoded target pictures from similar lure pictures when the initial encoding of target pictures had been followed immediately by 10 minutes of awake quiescence than an unrelated perceptual task. This novel finding indicates that, in addition to influencing how much we remember, our behavioural state during wakeful consolidation determines, at least in part, the level of fine detail of our new memories. Thus, our results suggest that rest-related consolidation protects the fine detail of new memories, allowing us to retain detailed memories.

Text analysis devices, articles of manufacture, and text analysis methods

DOEpatents

Turner, Alan E; Hetzler, Elizabeth G; Nakamura, Grant C

2013-05-28

Text analysis devices, articles of manufacture, and text analysis methods are described according to some aspects. In one aspect, a text analysis device includes processing circuitry configured to analyze initial text to generate a measurement basis usable in analysis of subsequent text, wherein the measurement basis comprises a plurality of measurement features from the initial text, a plurality of dimension anchors from the initial text and a plurality of associations of the measurement features with the dimension anchors, and wherein the processing circuitry is configured to access a viewpoint indicative of a perspective of interest of a user with respect to the analysis of the subsequent text, and wherein the processing circuitry is configured to use the viewpoint to generate the measurement basis.

Level of processing modulates the neural correlates of emotional memory formation

PubMed Central

Ritchey, Maureen; LaBar, Kevin S.; Cabeza, Roberto

2010-01-01

Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study employed a levels-of-processing manipulation to characterize the impact of emotion on encoding with and without the influence of elaborative processes. Participants viewed emotionally negative, neutral, and positive scenes under two conditions: a shallow condition focused on the perceptual features of the scenes and a deep condition that queried their semantic meaning. Recognition memory was tested 2 days later. Results showed that emotional memory enhancements were greatest in the shallow condition. FMRI analyses revealed that the right amygdala predicted subsequent emotional memory in the shallow more than deep condition, whereas the right ventrolateral prefrontal cortex demonstrated the reverse pattern. Furthermore, the association of these regions with the hippocampus was modulated by valence: the amygdala-hippocampal link was strongest for negative stimuli, whereas the prefrontal-hippocampal link was strongest for positive stimuli. Taken together, these results suggest two distinct activation patterns underlying emotional memory formation: an amygdala component that promotes memory during shallow encoding, especially for negative information, and a prefrontal component that provides extra benefits during deep encoding, especially for positive information. PMID:20350176

Level of processing modulates the neural correlates of emotional memory formation.

PubMed

Ritchey, Maureen; LaBar, Kevin S; Cabeza, Roberto

2011-04-01

Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study used a levels-of-processing manipulation to characterize the impact of emotion on encoding with and without the influence of elaborative processes. Participants viewed emotionally negative, neutral, and positive scenes under two conditions: a shallow condition focused on the perceptual features of the scenes and a deep condition that queried their semantic meaning. Recognition memory was tested 2 days later. Results showed that emotional memory enhancements were greatest in the shallow condition. fMRI analyses revealed that the right amygdala predicted subsequent emotional memory in the shallow more than deep condition, whereas the right ventrolateral PFC demonstrated the reverse pattern. Furthermore, the association of these regions with the hippocampus was modulated by valence: the amygdala-hippocampal link was strongest for negative stimuli, whereas the prefrontal-hippocampal link was strongest for positive stimuli. Taken together, these results suggest two distinct activation patterns underlying emotional memory formation: an amygdala component that promotes memory during shallow encoding, especially for negative information, and a prefrontal component that provides extra benefits during deep encoding, especially for positive information.

GeNemo: a search engine for web-based functional genomic data.

PubMed

Zhang, Yongqing; Cao, Xiaoyi; Zhong, Sheng

2016-07-08

A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of the initiation site of poliovirus polyprotein synthesis

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

Dorner, A.J.; Dorner, L.F.; Larsen, G.R.

1982-06-01

The complete nucleotide sequence of poliovirus RNA has a long open reading frame capable of encoding the precursor polyprotein NCVPOO. The first AUG codon in this reading frame is located 743 nucleotides from the 5' end of the RNA and is preceded by eight AUG codons in all three reading frames. Because all proteins that map at the amino terminus of the polyprotein (P1-1a, VPO, and VP4) are blocked at their amino termini and previous studies of ribosome binding have been inconclusive, direct identification of the initiation site of protein synthesis was difficult. We separated and identified all of themore » tryptic peptides of capsid protein VP4 and correlated these peptides with the amino acid sequence predicted to follow the AUG codon at nucleotide 743. Our data indicate that VP4 begins with a blocked glycine that is encoded immediately after the AUG codon at nucleotide 743. An S1 nuclease analysis of poliovirus mRNA failed to reveal a splice in the 5' region. We concluded that synthesis of poliovirus polyprotein is initiated at nucleotide 743, the first AUG codon in the long open reading frame.« less

MobileASL: intelligibility of sign language video over mobile phones.

PubMed

Cavender, Anna; Vanam, Rahul; Barney, Dane K; Ladner, Richard E; Riskin, Eve A

2008-01-01

For Deaf people, access to the mobile telephone network in the United States is currently limited to text messaging, forcing communication in English as opposed to American Sign Language (ASL), the preferred language. Because ASL is a visual language, mobile video phones have the potential to give Deaf people access to real-time mobile communication in their preferred language. However, even today's best video compression techniques can not yield intelligible ASL at limited cell phone network bandwidths. Motivated by this constraint, we conducted one focus group and two user studies with members of the Deaf Community to determine the intelligibility effects of video compression techniques that exploit the visual nature of sign language. Inspired by eye tracking results that show high resolution foveal vision is maintained around the face, we studied region-of-interest encodings (where the face is encoded at higher quality) as well as reduced frame rates (where fewer, better quality, frames are displayed every second). At all bit rates studied here, participants preferred moderate quality increases in the face region, sacrificing quality in other regions. They also preferred slightly lower frame rates because they yield better quality frames for a fixed bit rate. The limited processing power of cell phones is a serious concern because a real-time video encoder and decoder will be needed. Choosing less complex settings for the encoder can reduce encoding time, but will affect video quality. We studied the intelligibility effects of this tradeoff and found that we can significantly speed up encoding time without severely affecting intelligibility. These results show promise for real-time access to the current low-bandwidth cell phone network through sign-language-specific encoding techniques.

Translating working memory into action: behavioral and neural evidence for using motor representations in encoding visuo-spatial sequences.

PubMed

Langner, Robert; Sternkopf, Melanie A; Kellermann, Tanja S; Grefkes, Christian; Kurth, Florian; Schneider, Frank; Zilles, Karl; Eickhoff, Simon B

2014-07-01

The neurobiological organization of action-oriented working memory is not well understood. To elucidate the neural correlates of translating visuo-spatial stimulus sequences into delayed (memory-guided) sequential actions, we measured brain activity using functional magnetic resonance imaging while participants encoded sequences of four to seven dots appearing on fingers of a left or right schematic hand. After variable delays, sequences were to be reproduced with the corresponding fingers. Recall became less accurate with longer sequences and was initiated faster after long delays. Across both hands, encoding and recall activated bilateral prefrontal, premotor, superior and inferior parietal regions as well as the basal ganglia, whereas hand-specific activity was found (albeit to a lesser degree during encoding) in contralateral premotor, sensorimotor, and superior parietal cortex. Activation differences after long versus short delays were restricted to motor-related regions, indicating that rehearsal during long delays might have facilitated the conversion of the memorandum into concrete motor programs at recall. Furthermore, basal ganglia activity during encoding selectively predicted correct recall. Taken together, the results suggest that to-be-reproduced visuo-spatial sequences are encoded as prospective action representations (motor intentions), possibly in addition to retrospective sensory codes. Overall, our study supports and extends multi-component models of working memory, highlighting the notion that sensory input can be coded in multiple ways depending on what the memorandum is to be used for. Copyright © 2013 Wiley Periodicals, Inc.

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

PubMed

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

2018-06-01

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.

Multi-modulus algorithm based on global artificial fish swarm intelligent optimization of DNA encoding sequences.

PubMed

Guo, Y C; Wang, H; Wu, H P; Zhang, M Q

2015-12-21

Aimed to address the defects of the large mean square error (MSE), and the slow convergence speed in equalizing the multi-modulus signals of the constant modulus algorithm (CMA), a multi-modulus algorithm (MMA) based on global artificial fish swarm (GAFS) intelligent optimization of DNA encoding sequences (GAFS-DNA-MMA) was proposed. To improve the convergence rate and reduce the MSE, this proposed algorithm adopted an encoding method based on DNA nucleotide chains to provide a possible solution to the problem. Furthermore, the GAFS algorithm, with its fast convergence and global search ability, was used to find the best sequence. The real and imaginary parts of the initial optimal weight vector of MMA were obtained through DNA coding of the best sequence. The simulation results show that the proposed algorithm has a faster convergence speed and smaller MSE in comparison with the CMA, the MMA, and the AFS-DNA-MMA.

A PRESTO-SENSE sequence with alternating partial-Fourier encoding for rapid susceptibility-weighted 3D MRI time series.

PubMed

Klarhöfer, Markus; Dilharreguy, Bixente; van Gelderen, Peter; Moonen, Chrit T W

2003-10-01

A 3D sequence for dynamic susceptibility imaging is proposed which combines echo-shifting principles (such as PRESTO), sensitivity encoding (SENSE), and partial-Fourier acquisition. The method uses a moderate SENSE factor of 2 and takes advantage of an alternating partial k-space acquisition in the "slow" phase encode direction allowing an iterative reconstruction using high-resolution phase estimates. Offering an isotropic spatial resolution of 4 x 4 x 4 mm(3), the novel sequence covers the whole brain including parts of the cerebellum in 0.5 sec. Its temporal signal stability is comparable to that of a full-Fourier, full-FOV EPI sequence having the same dynamic scan time but much less brain coverage. Initial functional MRI experiments showed consistent activation in the motor cortex with an average signal change slightly less than that of EPI. Copyright 2003 Wiley-Liss, Inc.

Divided attention in younger and older adults: effects of strategy and relatedness on memory performance and secondary task costs.

PubMed

Naveh-Benjamin, Moshe; Craik, Fergus I M; Guez, Jonathan; Kreuger, Sharyn

2005-05-01

Divided attention at encoding leads to a significant decline in memory performance, whereas divided attention during retrieval has relatively little effect; nevertheless, retrieval carries significant secondary task costs, especially for older adults. The authors further investigated the effects of divided attention in younger and older adults by using a cued-recall task and by measuring retrieval accuracy, retrieval latency, and the temporal distribution of attentional costs at encoding and retrieval. An age-related memory deficit was reduced by pair relatedness, whereas strategy instructions benefited both age groups equally. Attentional costs were greater for retrieval than for encoding, especially for older adults. These findings are interpreted in light of notions of an age-related associative deficit (M. Naveh-Benjamin, 2000) and age-related differences in the use of self-initiated activities and environmental support (F. I. M. Craik, 1983, 1986).

Temporal distribution of favourite books, movies, and records: differential encoding and re-sampling.

PubMed

Janssen, Steve M J; Chessa, Antonio G; Murre, Jaap M J

2007-10-01

The reminiscence bump is the effect that people recall more personal events from early adulthood than from childhood or adulthood. The bump has been examined extensively. However, the question of whether the bump is caused by differential encoding or re-sampling is still unanswered. To examine this issue, participants were asked to name their three favourite books, movies, and records. Furthermore,they were asked when they first encountered them. We compared the temporal distributions and found that they all showed recency effects and reminiscence bumps. The distribution of favourite books had the largest recency effect and the distribution of favourite records had the largest reminiscence bump. We can explain these results by the difference in rehearsal. Books are read two or three times, movies are watched more frequently, whereas records are listened to numerous times. The results suggest that differential encoding initially causes the reminiscence bump and that re-sampling increases the bump further.

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 ▿ †

PubMed Central

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

Achievement and Retention of Spanish Presented Via Videodisc in Linear, Segmented and Interactive Modes.

DTIC Science & Technology

1987-01-01

with non-emotional mate- rial . . . . P5. Students who are able to choose from a ’ menu ’ of topics to provide the general con- text of the exercise...smaller version of the videodisc encoded digitally and capable of storing vast numbers of still frames and text files, presents yet another opportunity for...37. En el restaurante , Ramiro pide . a. chorizo y tinto. b. sardinas y vino. c. tortilla y vino. 38. Cuando es t comiendo en el restaurante , Ramiro

The role of rehearsal on the output order of immediate free recall of short and long lists.

PubMed

Grenfell-Essam, Rachel; Ward, Geoff; Tan, Lydia

2013-03-01

Participants tend to initiate immediate free recall (IFR) of short lists of words with the very first word on the list. Three experiments examined whether rehearsal is necessary for this recent finding. In Experiment 1, participants were presented with lists of between 2 and 12 words for IFR at a fast, medium, or slow rate, with and without articulatory suppression (AS). The tendency to initiate output with the first item for short lists (a) did not change greatly when presentation rate was increased from a medium to a fast rate under normal conditions, (b) was reduced but not eliminated by AS, and (c) was maintained at slower rates when rehearsal was allowed but decreased at slower rates when rehearsal was prevented. In Experiment 2, the overt rehearsal methodology was used, and the tendency to initiate output with the first item for short lists was present even in the absence of overt rehearsal. Experiment 3 re-examined IFR under normal encoding conditions and replicated the main findings from the normal encoding conditions of Experiment 1 while using the presentation rates and list lengths of Experiment 2. We argue that rehearsal is not strictly necessary for the tendency to initiate recall with the first item under normal conditions, but rehearsal nevertheless contributes to this effect at slower rates. (c) 2013 APA, all rights reserved.

Effect of adiponectin-encoding gene ADIPOQ single nucleotide polymorphisms +45 and +276 on serum lipid levels after antiretroviral therapy in Japanese patients with HIV-1-infection.

PubMed

Kato, Hideaki; Ohata, Aya; Samukawa, Sei; Ueda, Atsuhisa; Ishigatsubo, Yoshiaki

2016-04-01

To investigate the association between single nucleotide polymorphisms (SNPs) in the adiponectin-encoding gene ADIPOQ and changes in serum lipid levels in HIV-1-infected patients after antiretroviral therapy (ART). ART-naïve HIV-1-infected patients were recruited to this prospective analysis. SNP +45 and SNP +276 genotype was determined by direct sequencing. Multivariate linear regression analysis was performed to analyse the effects of genotype, and predisposing conditions on serum total cholesterol and triglyceride in the 4 months before and after ART initiation. The study enrolled 78 patients with HIV-1-infection (73 male, five female; age range 22-67 years). HIV-1 viral load ≥5 log10 copies/ml, baseline total cholesterol ≥160 mg/dl, and CD4(+) lymphocyte count <200/µl were associated with increased serum total cholesterol levels after ART initiation. Protease inhibitor treatment and body mass index ≥25 kg/m(2) were associated with increased triglyceride levels after ART initiation. There were no significant associations between SNP +45 or SNP +276 genotype and serum total cholesterol or triglyceride levels. SNP +45 and SNP +276 genotype is not associated with changes in serum total cholesterol or triglyceride levels after ART initiation. © The Author(s) 2016.

Stress priming in picture naming: an SOA study.

PubMed

Schiller, Niels O; Fikkert, Paula; Levelt, Clara C

2004-01-01

This study investigates whether or not the representation of lexical stress information can be primed during speech production. In four experiments, we attempted to prime the stress position of bisyllabic target nouns (picture names) having initial and final stress with auditory prime words having either the same or different stress as the target (e.g., WORtel-MOtor vs. koSTUUM-MOtor; capital letters indicate stressed syllables in prime-target pairs). Furthermore, half of the prime words were semantically related, the other half unrelated. Overall, picture names were not produced faster when the prime word had the same stress as the target than when the prime had different stress, i.e., there was no stress-priming effect in any experiment. This result would not be expected if stress were stored in the lexicon. However, targets with initial stress were responded to faster than final-stress targets. The reason for this effect was neither the quality of the pictures nor frequency of occurrence or voice-key characteristics. We hypothesize here that this stress effect is a genuine encoding effect, i.e., words with stress on the second syllable take longer to be encoded because their stress pattern is irregular with respect to the lexical distribution of bisyllabic stress patterns, even though it can be regular with respect to metrical stress rules in Dutch. The results of the experiments are discussed in the framework of models of phonological encoding.

Requirement of carbon dioxide for initial growth of facultative methylotroph, Acidomonas methanolica MB58.

PubMed

Mitsui, Ryoji; Katayama, Hiroko; Tanaka, Mitsuo

2015-07-01

The facultative methylotrophic bacterium Acidomonas methanolica MB58 can utilize C1 compounds via the ribulose monophosphate pathway. A large gene cluster comprising three components related to C1 metabolism was found in the genome. From upstream, the first was an mxa cluster encoding proteins for oxidation of methanol to formaldehyde; the second was the rmp cluster encoding enzymes for formaldehyde fixation; and the third was the cbb gene cluster encoding proteins for carbon dioxide (CO2) fixation. Examination of CO2 requirements for growth of A. methanolica MB58 cells demonstrated that it did not grow on any carbon source under CO2-free conditions. Measurement of ribulose-1,5-bisphosphate carboxylase activity and RT-PCR analysis demonstrated enzymatic activity was detected in A. methanolica MB58 at growth phase, regardless of carbon sources. However, methanol dehydrogenase and 3-hexlose-6-phosphate synthase expression was regulated by methanol or formaldehyde; it were detected during growth and apparently differed from ribulose-1,5-bisphosphate carboxylase expression. These results suggested that A. methanolica MB58 may be initially dependent on autotrophic growth and that carbon assimilation was subsequently coupled with the ribulose monophosphate pathway at early- to mid-log phases during methylotrophic growth. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Distinct Calcium Signaling Pathways Regulate Calmodulin Gene Expression in Tobacco1

PubMed Central

van der Luit, Arnold H.; Olivari, Claudio; Haley, Ann; Knight, Marc R.; Trewavas, Anthony J.

1999-01-01

Cold shock and wind stimuli initiate Ca2+ transients in transgenic tobacco (Nicotiana plumbaginifolia) seedlings (named MAQ 2.4) containing cytoplasmic aequorin. To investigate whether these stimuli initiate Ca2+ pathways that are spatially distinct, stress-induced nuclear and cytoplasmic Ca2+ transients and the expression of a stress-induced calmodulin gene were compared. Tobacco seedlings were transformed with a construct that encodes a fusion protein between nucleoplasmin (a major oocyte nuclear protein) and aequorin. Immunocytochemical evidence indicated targeting of the fusion protein to the nucleus in these plants, which were named MAQ 7.11. Comparison between MAQ 7.11 and MAQ 2.4 seedlings confirmed that wind stimuli and cold shock invoke separate Ca2+ signaling pathways. Partial cDNAs encoding two tobacco calmodulin genes, NpCaM-1 and NpCaM-2, were identified and shown to have distinct nucleotide sequences that encode identical polypeptides. Expression of NpCaM-1, but not NpCaM-2, responded to wind and cold shock stimulation. Comparison of the Ca2+ dynamics with NpCaM-1 expression after stimulation suggested that wind-induced NpCaM-1 expression is regulated by a Ca2+ signaling pathway operational predominantly in the nucleus. In contrast, expression of NpCaM-1 in response to cold shock is regulated by a pathway operational predominantly in the cytoplasm. PMID:10557218

A novel chaotic image encryption scheme using DNA sequence operations

NASA Astrophysics Data System (ADS)

Wang, Xing-Yuan; Zhang, Ying-Qian; Bao, Xue-Mei

2015-10-01

In this paper, we propose a novel image encryption scheme based on DNA (Deoxyribonucleic acid) sequence operations and chaotic system. Firstly, we perform bitwise exclusive OR operation on the pixels of the plain image using the pseudorandom sequences produced by the spatiotemporal chaos system, i.e., CML (coupled map lattice). Secondly, a DNA matrix is obtained by encoding the confused image using a kind of DNA encoding rule. Then we generate the new initial conditions of the CML according to this DNA matrix and the previous initial conditions, which can make the encryption result closely depend on every pixel of the plain image. Thirdly, the rows and columns of the DNA matrix are permuted. Then, the permuted DNA matrix is confused once again. At last, after decoding the confused DNA matrix using a kind of DNA decoding rule, we obtain the ciphered image. Experimental results and theoretical analysis show that the scheme is able to resist various attacks, so it has extraordinarily high security.

[The DRG responsible physician in trauma and orthopedic surgery. Surgeon, encoder, and link to medical controlling].

PubMed

Ruffing, T; Huchzermeier, P; Muhm, M; Winkler, H

2014-05-01

Precise coding is an essential requirement in order to generate a valid DRG. The aim of our study was to evaluate the quality of the initial coding of surgical procedures, as well as to introduce our "hybrid model" of a surgical specialist supervising medical coding and a nonphysician for case auditing. The department's DRG responsible physician as a surgical specialist has profound knowledge both in surgery and in DRG coding. At a Level 1 hospital, 1000 coded cases of surgical procedures were checked. In our department, the DRG responsible physician who is both a surgeon and encoder has proven itself for many years. The initial surgical DRG coding had to be corrected by the DRG responsible physician in 42.2% of cases. On average, one hour per working day was necessary. The implementation of a DRG responsible physician is a simple, effective way to connect medical and business expertise without interface problems. Permanent feedback promotes both medical and economic sensitivity for the improvement of coding quality.

Function and horizontal transfer of the small terminase subunit of the tailed bacteriophage Sf6 DNA packaging nanomotor

PubMed Central

Leavitt, Justin C.; Gilcrease, Eddie B.; Wilson, Kassandra; Casjens, Sherwood R.

2013-01-01

Bacteriophage Sf6 DNA packaging series initiate at many locations across a 2 kbp region. Our in vivo studies that show that Sf6 small terminase subunit (TerS) protein recognizes a specific packaging (pac) site near the center of this region, that this site lies within the portion of the Sf6 gene that encodes the DNA-binding domain of TerS protein, that this domain of the TerS protein is responsible for the imprecision in Sf6 packaging initiation, and that the DNA-binding domain of TerS must be covalently attached to the domain that interacts with the rest of the packaging motor. The TerS DNA-binding domain is self-contained in that it apparently does not interact closely with the rest of the motor and it binds to a recognition site that lies within the DNA that encodes the domain. This arrangement has allowed the horizontal exchange of terS genes among phages to be very successful. PMID:23562538

Effects of Severe Bothersome Tinnitus on Cognitive Function Measured with Standardized Tests

PubMed Central

Pierce, Katherine J.; Kallogjeri, Dorina; Piccirillo, Jay F.; Garcia, Keith S.; Nicklaus, Joyce E.; Burton, Harold

2012-01-01

Neurocognitive tests compared abilities in people with bothersome tinnitus against an age, gender, and education matched normative population. Participants between 18 and 60 years had subjective, unilateral or bilateral, non-pulsatile tinnitus for >6 months, and a Tinnitus Handicap Inventory score of ≥38. Results from a first testing session showed deficits in learning, learning rates, immediate recall of heard words, and use of a serial order encoding strategy. Initial reliance on serial order encoding and later, increased intrusion of incorrect words towards normal levels might indicate a less demanding strategy to compensate for weakness in associative memory for semantic categories. PMID:22168528

Modulation of TCRβ surface expression during TCR revision.

PubMed

Simmons, Kalynn B; Wubeshet, Maramawit; Ames, Kristina T; McMahan, Catherine J; Hale, J Scott; Fink, Pamela J

2012-01-01

TCR revision is a tolerance mechanism by which self-reactive TCRs expressed by mature CD4(+) peripheral T cells are replaced by receptors encoded by genes generated by post-thymic DNA rearrangement. The downmodulation of surface TCR expression initiates TCR revision, and serves as a likely trigger for the induction of the recombinase machinery. We show here in a Vβ5 transgenic mouse model system that downregulation of the self-reactive transgene-encoded TCR is not maintained by transgene loss or diminished transcription or translation. The downregulation of surface TCR expression likely occurs in two stages, only one of which requires tolerogen expression. Copyright © 2011 Elsevier Inc. All rights reserved.

Active listening impairs visual perception and selectivity: an ERP study of auditory dual-task costs on visual attention.

PubMed

Gherri, Elena; Eimer, Martin

2011-04-01

The ability to drive safely is disrupted by cell phone conversations, and this has been attributed to a diversion of attention from the visual environment. We employed behavioral and ERP measures to study whether the attentive processing of spoken messages is, in itself, sufficient to produce visual-attentional deficits. Participants searched for visual targets defined by a unique feature (Experiment 1) or feature conjunction (Experiment 2), and simultaneously listened to narrated text passages that had to be recalled later (encoding condition), or heard backward-played speech sounds that could be ignored (control condition). Responses to targets were slower in the encoding condition, and ERPs revealed that the visual processing of search arrays and the attentional selection of target stimuli were less efficient in the encoding relative to the control condition. Results demonstrate that the attentional processing of visual information is impaired when concurrent spoken messages are encoded and maintained, in line with cross-modal links in selective attention, but inconsistent with the view that attentional resources are modality-specific. The distraction of visual attention by active listening could contribute to the adverse effects of cell phone use on driving performance.

Is music a memory booster in normal aging? The influence of emotion.

PubMed

Ratovohery, Stéphie; Baudouin, Alexia; Gachet, Aude; Palisson, Juliette; Narme, Pauline

2018-05-17

Age-related differences in episodic memory have been explained by a decrement in strategic encoding implementation. It has been shown in clinical populations that music can be used during the encoding stage as a mnemonic strategy to learn verbal information. The effectiveness of this strategy remains equivocal in older adults (OA). Furthermore, the impact of the emotional valence of the music used has never been investigated in this context. Thirty OA and 24 young adults (YA) learned texts that were either set to music that was positively or negatively valenced, or spoken only. Immediate and delayed recalls were measured. Results showed that: (i) OA perform worse than YA in immediate and delayed recall; (ii) sung lyrics are better remembered than spoken ones in OA, but only when the associated music is positively-valenced; (iii) this pattern is observed regardless the retention delay. These findings support the benefit of a musical encoding on verbal learning in healthy OA and are consistent with the positivity effect classically reported in normal aging. Added to the potential applications in daily life, the results are discussed with respect to the theoretical hypotheses of the mechanisms underlying the advantage of musical encoding.

Honors Students as Philosophers and Detectives

ERIC Educational Resources Information Center

Briggs, Kaitlin A.

2013-01-01

This article explores the multiple educational uses of the question, "what do you mean by_____?" as an interlocutor's conversational gesture during classroom discussion, as a text-based prompt for both encoding/writing and decoding/reading, and as a rhetorical device for an effective oral presentation. Kaitlin Briggs explains that the…

Spatial Updating of Environments Described in Texts

ERIC Educational Resources Information Center

Avraamides, Marios N.

2003-01-01

People update egocentric spatial relations in an effortless and on-line manner when they move in the environment, but not when they only imagine themselves moving. In contrast to previous studies, the present experiments examined egocentric updating with spatial scenes that were encoded linguistically instead of perceived directly. Experiment 1…

Large-Scale Modeling of Wordform Learning and Representation

ERIC Educational Resources Information Center

Sibley, Daragh E.; Kello, Christopher T.; Plaut, David C.; Elman, Jeffrey L.

2008-01-01

The forms of words as they appear in text and speech are central to theories and models of lexical processing. Nonetheless, current methods for simulating their learning and representation fail to approach the scale and heterogeneity of real wordform lexicons. A connectionist architecture termed the "sequence encoder" is used to learn…

The Interplay between Automatic and Control Processes in Reading.

ERIC Educational Resources Information Center

Walczyk, Jeffrey J.

2000-01-01

Reviews prominent reading theories in light of their accounts of how automatic and control processes combine to produce successful text comprehension, and the trade-offs between the two. Presents the Compensatory-Encoding Model of reading, which explicates how, when, and why automatic and control processes interact. Notes important educational…

Processing Determinants of Reading Speed.

ERIC Educational Resources Information Center

Jackson, Mark D.; McClelland, James L.

1979-01-01

Two groups of undergraduates differing in reading ability were tested on a number of reaction-time tasks designed to determine the speed of encoding visual information at several different levels, tests of sensory functions, verbal and quantitative reasoning ability, short-term auditory memory span, and ability to comprehend spoken text.…

Do EBV Encoded Small RNAs Interfere with Tumor Suppressor APC in EBV Associated Breast Cancers

DTIC Science & Technology

2006-08-01

acute infectious mononucleosis but ultimately establishes persistent lifetime latent infection. In all latently infected cells EBVexpresses two small non...human initially causes acute infectious mononucleosis and later establishes persistent lifetime latent infection. In all latently EBV-infected cells, only

Reflections of Distraction in Memory: Transfer of Previous Distraction Improves Recall in Younger and Older Adults

PubMed Central

Thomas, Ruthann C.; Hasher, Lynn

2012-01-01

Three studies explored whether younger and older adults’ free recall performance can benefit from prior exposure to distraction that becomes relevant in a memory task. Participants initially read stories that included distracting text. Later, they studied a list of words for free recall, with half of the list consisting of previously distracting words. When the memory task was indirect in its use of distraction (Study 1), only older adults showed transfer, with better recall of previously distracting compared with new words, which increased their recall to match that of younger adults. However, younger adults showed transfer when cued about the relevance of previous distraction both before studying the words (Study 2) and before recalling the words (Study 3) in the memory test. Results suggest that both younger and older adults encode distraction, but younger adults require explicit cueing to use their knowledge of distraction. In contrast, older adults transfer knowledge of distraction in both explicitly cued and indirect memory tasks. Results are discussed in terms of age differences in inhibition and source-constrained retrieval. PMID:21843024

Reflections of distraction in memory: transfer of previous distraction improves recall in younger and older adults.

PubMed

Thomas, Ruthann C; Hasher, Lynn

2012-01-01

Three studies explored whether younger and older adults' free recall performance can benefit from prior exposure to distraction that becomes relevant in a memory task. Participants initially read stories that included distracting text. Later, they studied a list of words for free recall, with half of the list consisting of previously distracting words. When the memory task was indirect in its use of distraction (Study 1), only older adults showed transfer, with better recall of previously distracting compared with new words, which increased their recall to match that of younger adults. However, younger adults showed transfer when cued about the relevance of previous distraction both before studying the words (Study 2) and before recalling the words (Study 3) in the memory test. Results suggest that both younger and older adults encode distraction, but younger adults require explicit cueing to use their knowledge of distraction. In contrast, older adults transfer knowledge of distraction in both explicitly cued and indirect memory tasks. Results are discussed in terms of age differences in inhibition and source-constrained retrieval.

Neuromodulation: acetylcholine and memory consolidation.

PubMed

Hasselmo

1999-09-01

Clinical and experimental evidence suggests that hippocampal damage causes more severe disruption of episodic memories if those memories were encoded in the recent rather than the more distant past. This decrease in sensitivity to damage over time might reflect the formation of multiple traces within the hippocampus itself, or the formation of additional associative links in entorhinal and association cortices. Physiological evidence also supports a two-stage model of the encoding process in which the initial encoding occurs during active waking and deeper consolidation occurs via the formation of additional memory traces during quiet waking or slow-wave sleep. In this article I will describe the changes in cholinergic tone within the hippocampus in different stages of the sleep-wake cycle and will propose that these changes modulate different stages of memory formation. In particular, I will suggest that the high levels of acetylcholine that are present during active waking might set the appropriate dynamics for encoding new information in the hippocampus, by partially suppressing excitatory feedback connections and so facilitating encoding without interference from previously stored information. By contrast, the lower levels of acetylcholine that are present during quiet waking and slow-wave sleep might release this suppression and thereby allow a stronger spread of activity within the hippocampus itself and from the hippocampus to the entorhinal cortex, thus facilitating the process of consolidation of separate memory traces.

Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags

PubMed Central

Litovchick, Alexander; Clark, Matthew A; Keefe, Anthony D

2014-01-01

The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writing) for such libraries and two different cDNA-generation methods as examples of information retrieval processes (reading) from such libraries. The example writing methods include uncatalyzed and Cu(I)-catalyzed alkyne-azide cycloadditions and a novel photochemical thymidine-psoralen cycloaddition. The first reading method “relay primer-dependent bypass” utilizes a relay primer that hybridizes across a chemical ligation junction embedded in a fixed-sequence and is extended at its 3′-terminus prior to ligation to adjacent oligonucleotides. The second reading method “repeat-dependent bypass” utilizes chemical ligation junctions that are flanked by repeated sequences. The upstream repeat is copied prior to a rearrangement event during which the 3′-terminus of the cDNA hybridizes to the downstream repeat and polymerization continues. In principle these reading methods may be used with any ligation chemistry and offer universal strategies for the encoding (writing) and interpretation (reading) of DNA-encoded chemical libraries. PMID:25483841

Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames

PubMed Central

1996-01-01

An increasing amount of evidence has shown that epitopes restricted to MHC class I molecules and recognized by CTL need not be encoded in a primary open reading frame (ORF). Such epitopes have been demonstrated after stop codons, in alternative reading frames (RF) and within introns. We have used a series of frameshifts (FS) introduced into the Influenza A/PR/8 /34 nucleoprotein (NP) gene to confirm the previous in vitro observations of cryptic epitope expression, and show that they are sufficiently expressed to prime immune responses in vivo. This presentation is not due to sub-dominant epitopes, transcription from cryptic promoters beyond the point of the FS, or internal initiation of translation. By introducing additional mutations to the construct exhibiting the most potent presentation, we have identified initiation codon readthrough (termed scanthrough here, where the scanning ribosome bypasses the conventional initiation codon, initiating translation further downstream) as the likely mechanism of epitope production. Further mutational analysis demonstrated that, while it should operate during the expression of wild-type (WT) protein, scanthrough does not provide a major source of processing substrate in our system. These findings suggest (i) that the full array of self- and pathogen-derived epitopes available during thymic selection and infection has not been fully appreciated and (ii) that cryptic epitope expression should be considered when the specificity of a CTL response cannot be identified or in therapeutic situations when conventional CTL targets are limited, as may be the case with latent viral infections and transformed cells. Finally, initiation codon readthrough provides a plausible explanation for the presentation of exocytic proteins by MHC class I molecules. PMID:8879204

Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number.

PubMed

Lyons, Jonathan J; Yu, Xiaomin; Hughes, Jason D; Le, Quang T; Jamil, Ali; Bai, Yun; Ho, Nancy; Zhao, Ming; Liu, Yihui; O'Connell, Michael P; Trivedi, Neil N; Nelson, Celeste; DiMaggio, Thomas; Jones, Nina; Matthews, Helen; Lewis, Katie L; Oler, Andrew J; Carlson, Ryan J; Arkwright, Peter D; Hong, Celine; Agama, Sherene; Wilson, Todd M; Tucker, Sofie; Zhang, Yu; McElwee, Joshua J; Pao, Maryland; Glover, Sarah C; Rothenberg, Marc E; Hohman, Robert J; Stone, Kelly D; Caughey, George H; Heller, Theo; Metcalfe, Dean D; Biesecker, Leslie G; Schwartz, Lawrence B; Milner, Joshua D

2016-12-01

Elevated basal serum tryptase levels are present in 4-6% of the general population, but the cause and relevance of such increases are unknown. Previously, we described subjects with dominantly inherited elevated basal serum tryptase levels associated with multisystem complaints including cutaneous flushing and pruritus, dysautonomia, functional gastrointestinal symptoms, chronic pain, and connective tissue abnormalities, including joint hypermobility. Here we report the identification of germline duplications and triplications in the TPSAB1 gene encoding α-tryptase that segregate with inherited increases in basal serum tryptase levels in 35 families presenting with associated multisystem complaints. Individuals harboring alleles encoding three copies of α-tryptase had higher basal serum levels of tryptase and were more symptomatic than those with alleles encoding two copies, suggesting a gene-dose effect. Further, we found in two additional cohorts (172 individuals) that elevated basal serum tryptase levels were exclusively associated with duplication of α-tryptase-encoding sequence in TPSAB1, and affected individuals reported symptom complexes seen in our initial familial cohort. Thus, our findings link duplications in TPSAB1 with irritable bowel syndrome, cutaneous complaints, connective tissue abnormalities, and dysautonomia.

Gene ercA, encoding a putative iron-containing alcohol dehydrogenase, is involved in regulation of ethanol utilization in Pseudomonas aeruginosa.

PubMed

Hempel, Niels; Görisch, Helmut; Mern, Demissew S

2013-09-01

Several two-component regulatory systems are known to be involved in the signal transduction pathway of the ethanol oxidation system in Pseudomonas aeruginosa ATCC 17933. These sensor kinases and response regulators are organized in a hierarchical manner. In addition, a cytoplasmic putative iron-containing alcohol dehydrogenase (Fe-ADH) encoded by ercA (PA1991) has been identified to play an essential role in this regulatory network. The gene ercA (PA1991) is located next to ercS, which encodes a sensor kinase. Inactivation of ercA (PA1991) by insertion of a kanamycin resistance cassette created mutant NH1. NH1 showed poor growth on various alcohols. On ethanol, NH1 grew only with an extremely extended lag phase. During the induction period on ethanol, transcription of structural genes exa and pqqABCDEH, encoding components of initial ethanol oxidation in P. aeruginosa, was drastically reduced in NH1, which indicates the regulatory function of ercA (PA1991). However, transcription in the extremely delayed logarithmic growth phase was comparable to that in the wild type. To date, the involvement of an Fe-ADH in signal transduction processes has not been reported.

Gene ercA, Encoding a Putative Iron-Containing Alcohol Dehydrogenase, Is Involved in Regulation of Ethanol Utilization in Pseudomonas aeruginosa

PubMed Central

Hempel, Niels; Görisch, Helmut

2013-01-01

Several two-component regulatory systems are known to be involved in the signal transduction pathway of the ethanol oxidation system in Pseudomonas aeruginosa ATCC 17933. These sensor kinases and response regulators are organized in a hierarchical manner. In addition, a cytoplasmic putative iron-containing alcohol dehydrogenase (Fe-ADH) encoded by ercA (PA1991) has been identified to play an essential role in this regulatory network. The gene ercA (PA1991) is located next to ercS, which encodes a sensor kinase. Inactivation of ercA (PA1991) by insertion of a kanamycin resistance cassette created mutant NH1. NH1 showed poor growth on various alcohols. On ethanol, NH1 grew only with an extremely extended lag phase. During the induction period on ethanol, transcription of structural genes exa and pqqABCDEH, encoding components of initial ethanol oxidation in P. aeruginosa, was drastically reduced in NH1, which indicates the regulatory function of ercA (PA1991). However, transcription in the extremely delayed logarithmic growth phase was comparable to that in the wild type. To date, the involvement of an Fe-ADH in signal transduction processes has not been reported. PMID:23813731

Telemedicine. Final report/project accomplishments summary CRADA number 95-KCP-1014

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

VanDeusen, A.L.

1997-04-01

This project was initiated to fill existing voids in the telemedicine equipment market. Currently, when a medical facility adds telemedicine capability to their video conference system, they must purchase expensive and bulky encoders and decoders in order to send information over the available data channel. Even with this expensive equipment, only one data type (stethoscope or ECG) can be sent at a time. In addition, since existing encoders and decoders are not designed specifically for telemedicine, special cables must be built to connect with this equipment. This project resulted in the design and construction of an encoder/decoder system that resolvedmore » these issues. The unit (referred to as the Telecoder) is designed specifically for the telemedicine market. The Telecoder is compact, handles two types of data (stethoscope and ECG) simultaneously, integrates with existing medical equipment, and is less expensive. In addition to the Telecoder module, a prototype was built that adds all the necessary logic and interfaces necessary to integrate the basic encoder design into additional Cardionics products. Although a complete integration into other Cardionics products was not in the scope of this CRADA, all the basic design work has been done to allow Cardionics to complete the work.« less

Flexibility of Event Boundaries in Autobiographical Memory

PubMed Central

Hohman, Timothy J.; Peynircioğlu, Zehra F.; Beason-Held, Lori L.

2014-01-01

Events have clear and consistent boundaries that are defined during perception in a manner that influences memory performance. The natural process of event segmentation shapes event definitions during perception, and appears to play a critical role in defining distinct episodic memories at encoding. However, the role of retrieval processes in modifying event definitions is not clear. We explored how such processes changed event boundary definitions at recall. In Experiment 1 we showed that distance from encoding is related to boundary flexibility. Participants were more likely to move self-reported event boundaries to include information reported beyond those boundaries when recalling more distant events compared to more recent events. In Experiment 2, we showed that age also influenced boundary flexibility. Older Age adults were more likely to move event boundaries than College Age adults, and the relationship between distance from encoding and boundary flexibility seen in Experiment 1 was present only in College Age and Middle Age adults. These results suggest that factors at retrieval have a direct impact on event definitions in memory and that, although episodic memories may be initially defined at encoding, these definitions are not necessarily maintained in long-term memory. PMID:22989194

Hippocampal-medial prefrontal circuit supports memory updating during learning and post-encoding rest

PubMed Central

Schlichting, Margaret L.; Preston, Alison R.

2015-01-01

Learning occurs in the context of existing memories. Encountering new information that relates to prior knowledge may trigger integration, whereby established memories are updated to incorporate new content. Here, we provide a critical test of recent theories suggesting hippocampal (HPC) and medial prefrontal (MPFC) involvement in integration, both during and immediately following encoding. Human participants with established memories for a set of initial (AB) associations underwent fMRI scanning during passive rest and encoding of new related (BC) and unrelated (XY) pairs. We show that HPC-MPFC functional coupling during learning was more predictive of trial-by-trial memory for associations related to prior knowledge relative to unrelated associations. Moreover, the degree to which HPC-MPFC functional coupling was enhanced following overlapping encoding was related to memory integration behavior across participants. We observed a dissociation between anterior and posterior MPFC, with integration signatures during post-encoding rest specifically in the posterior subregion. These results highlight the persistence of integration signatures into post-encoding periods, indicating continued processing of interrelated memories during rest. We also interrogated the coherence of white matter tracts to assess the hypothesis that integration behavior would be related to the integrity of the underlying anatomical pathways. Consistent with our predictions, more coherent HPC-MPFC white matter structure was associated with better performance across participants. This HPC-MPFC circuit also interacted with content-sensitive visual cortex during learning and rest, consistent with reinstatement of prior knowledge to enable updating. These results show that the HPC-MPFC circuit supports on- and offline integration of new content into memory. PMID:26608407

Rated Measures of Narrative Structure for Written Smoking-Cessation Texts

PubMed Central

Sanders-Jackson, Ashley

2014-01-01

This article describes the effect of a series of rated measures of narrative structure on recognition memory, agreement on story-relevant beliefs, and intention to engage in a health-related behavior—in this case smoking cessation. Using short smoking-cessation stories as stimuli, data were collected in a nationally representative sample of adult smokers (n = 1,312). Results suggested that messages rated as more sequential improved encoding and messages rated as containing more context decreased encoding. Messages rated high in transportation were associated with increased recognition, agreement with story-relevant beliefs, and intention to quit. Both positive and negative emotion were positively associated with intention to quit, but were negatively associated with recognition memory. PMID:24447036

Information hiding based on double random-phase encoding and public-key cryptography.

PubMed

Sheng, Yuan; Xin, Zhou; Alam, Mohammed S; Xi, Lu; Xiao-Feng, Li

2009-03-02

A novel information hiding method based on double random-phase encoding (DRPE) and Rivest-Shamir-Adleman (RSA) public-key cryptosystem is proposed. In the proposed technique, the inherent diffusion property of DRPE is cleverly utilized to make up the diffusion insufficiency of RSA public-key cryptography, while the RSA cryptosystem is utilized for simultaneous transmission of the cipher text and the two phase-masks, which is not possible under the DRPE technique. This technique combines the complementary advantages of the DPRE and RSA encryption techniques and brings security and convenience for efficient information transmission. Extensive numerical simulation results are presented to verify the performance of the proposed technique.

Adaptive Communication: Languages with More Non-Native Speakers Tend to Have Fewer Word Forms

PubMed Central

Bentz, Christian; Verkerk, Annemarie; Kiela, Douwe; Hill, Felix; Buttery, Paula

2015-01-01

Explaining the diversity of languages across the world is one of the central aims of typological, historical, and evolutionary linguistics. We consider the effect of language contact-the number of non-native speakers a language has-on the way languages change and evolve. By analysing hundreds of languages within and across language families, regions, and text types, we show that languages with greater levels of contact typically employ fewer word forms to encode the same information content (a property we refer to as lexical diversity). Based on three types of statistical analyses, we demonstrate that this variance can in part be explained by the impact of non-native speakers on information encoding strategies. Finally, we argue that languages are information encoding systems shaped by the varying needs of their speakers. Language evolution and change should be modeled as the co-evolution of multiple intertwined adaptive systems: On one hand, the structure of human societies and human learning capabilities, and on the other, the structure of language. PMID:26083380

An Evaluation of a Natural Language Processing Tool for Identifying and Encoding Allergy Information in Emergency Department Clinical Notes

PubMed Central

Goss, Foster R.; Plasek, Joseph M.; Lau, Jason J.; Seger, Diane L.; Chang, Frank Y.; Zhou, Li

2014-01-01

Emergency department (ED) visits due to allergic reactions are common. Allergy information is often recorded in free-text provider notes; however, this domain has not yet been widely studied by the natural language processing (NLP) community. We developed an allergy module built on the MTERMS NLP system to identify and encode food, drug, and environmental allergies and allergic reactions. The module included updates to our lexicon using standard terminologies, and novel disambiguation algorithms. We developed an annotation schema and annotated 400 ED notes that served as a gold standard for comparison to MTERMS output. MTERMS achieved an F-measure of 87.6% for the detection of allergen names and no known allergies, 90% for identifying true reactions in each allergy statement where true allergens were also identified, and 69% for linking reactions to their allergen. These preliminary results demonstrate the feasibility using NLP to extract and encode allergy information from clinical notes. PMID:25954363

Stability of Recent and Remote Contextual Fear Memory

ERIC Educational Resources Information Center

Frankland, Paul W.; Ding, Hoi-Ki; Takahashi, Eiki; Suzuki, Akinobu; Kida, Satoshi; Silva, Alcino J.

2006-01-01

Following initial encoding, memories undergo a prolonged period of reorganization. While such reorganization may occur in many different memory systems, its purpose is not clear. Previously, we have shown that recall of recent contextual fear memories engages the dorsal hippocampus (dHPC). In contrast, recall of remote contextual fear memories…

12 CFR Supplement I to Part 1005 - Official Interpretations

Code of Federal Regulations, 2013 CFR

2013-01-01

... used to capture the Magnetic Ink Character Recognition (MICR) encoding to initiate a one-time automated clearinghouse (ACH) debit. For example, if a consumer authorizes a one-time ACH debit from the consumer's... involved at the time of the transaction, if the consumer's asset account is subsequently debited for the...

12 CFR Supplement I to Part 1005 - Official Interpretations

Code of Federal Regulations, 2012 CFR

2012-01-01

... used to capture the Magnetic Ink Character Recognition (MICR) encoding to initiate a one-time automated clearinghouse (ACH) debit. For example, if a consumer authorizes a one-time ACH debit from the consumer's... involved at the time of the transaction, if the consumer's asset account is subsequently debited for the...

Initial Morphological Learning in Preverbal Infants

ERIC Educational Resources Information Center

Marquis, Alexandra; Shi, Rushen

2012-01-01

How do children learn the internal structure of inflected words? We hypothesized that bound functional morphemes begin to be encoded at the preverbal stage, driven by their frequent occurrence with highly variable roots, and that infants in turn use these morphemes to interpret other words with the same inflections. Using a preferential looking…

Young Children's Understanding of Conflicting Mental Representation Predicts Suggestibility.

ERIC Educational Resources Information Center

Welch-Ross, Melissa K.; And Others

1997-01-01

Examined the relation between developmental suggestibility effects and preschoolers' emerging ability to reason about conflicting mental representations. Subjects were 42 three- to five-year-olds. Found in the children significant initial encoding and ability to retrieve event details. Also found an integration between children's theory of mind…

Wheat streak mosaic virus-encoded NIa-Pro and coat protein are involved in virus superinfection exclusion

USDA-ARS?s Scientific Manuscript database

Cross protection or superinfection exclusion (SE) is defined as the phenomenon whereby initial infection by one virus prevents subsequent infection by closely related viruses. The mechanisms of SE are just beginning to be understood. Wheat streak mosaic virus (WSMV; genus: Tritimovirus; family: Poty...

ISIM3D: AN ANSI-C THREE-DIMENSIONAL MULTIPLE INDICATOR CONDITIONAL SIMULATION PROGRAM

EPA Science Inventory

The indicator conditional simulation technique provides stochastic simulations of a variable that (i) honor the initial data and (ii) can feature a richer family of spatial structures not limited by Gaussianity. he data are encoded into a series of indicators which then are used ...

12 CFR 205.3 - Coverage.

Code of Federal Regulations, 2014 CFR

2014-01-01

... to initiate a one-time electronic fund transfer from a consumer's account. The consumer must...-time electronic fund transfer (in providing a check to a merchant or other payee for the MICR encoding... information for the transfer shall also provide a notice to the consumer at the same time it provides the...

12 CFR 205.3 - Coverage.

Code of Federal Regulations, 2011 CFR

2011-01-01

... to initiate a one-time electronic fund transfer from a consumer's account. The consumer must...-time electronic fund transfer (in providing a check to a merchant or other payee for the MICR encoding... information for the transfer shall also provide a notice to the consumer at the same time it provides the...

12 CFR 205.3 - Coverage.

Code of Federal Regulations, 2013 CFR

2013-01-01

... to initiate a one-time electronic fund transfer from a consumer's account. The consumer must...-time electronic fund transfer (in providing a check to a merchant or other payee for the MICR encoding... information for the transfer shall also provide a notice to the consumer at the same time it provides the...

A Molecular Basis of Cancer.

ERIC Educational Resources Information Center

Weinberg, Robert A.

1983-01-01

Discusses the molecular basis of cancer, focusing on genetics of the disease. Indicates that human cancers are initiated by oncogenes (altered versions of normal genes) and that in one case the critical alteration is a single point mutation that changes one amino acid in the protein encoded by the gene. (JN)

[Design of standard voice sample text for subjective auditory perceptual evaluation of voice disorders].

PubMed

Li, Jin-rang; Sun, Yan-yan; Xu, Wen

2010-09-01

To design a speech voice sample text with all phonemes in Mandarin for subjective auditory perceptual evaluation of voice disorders. The principles for design of a speech voice sample text are: The short text should include the 21 initials and 39 finals, this may cover all the phonemes in Mandarin. Also, the short text should have some meanings. A short text was made out. It had 155 Chinese words, and included 21 initials and 38 finals (the final, ê, was not included because it was rarely used in Mandarin). Also, the text covered 17 light tones and one "Erhua". The constituent ratios of the initials and finals presented in this short text were statistically similar as those in Mandarin according to the method of similarity of the sample and population (r = 0.742, P < 0.001 and r = 0.844, P < 0.001, respectively). The constituent ratios of the tones presented in this short text were statistically not similar as those in Mandarin (r = 0.731, P > 0.05). A speech voice sample text with all phonemes in Mandarin was made out. The constituent ratios of the initials and finals presented in this short text are similar as those in Mandarin. Its value for subjective auditory perceptual evaluation of voice disorders need further study.

Optical noise-free image encryption based on quick response code and high dimension chaotic system in gyrator transform domain

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Xu, Minjie; Tian, Ailing

2017-04-01

A novel optical image encryption scheme is proposed based on quick response code and high dimension chaotic system, where only the intensity distribution of encoded information is recorded as ciphertext. Initially, the quick response code is engendered from the plain image and placed in the input plane of the double random phase encoding architecture. Then, the code is encrypted to the ciphertext with noise-like distribution by using two cascaded gyrator transforms. In the process of encryption, the parameters such as rotation angles and random phase masks are generated as interim variables and functions based on Chen system. A new phase retrieval algorithm is designed to reconstruct the initial quick response code in the process of decryption, in which a priori information such as three position detection patterns is used as the support constraint. The original image can be obtained without any energy loss by scanning the decrypted code with mobile devices. The ciphertext image is the real-valued function which is more convenient for storing and transmitting. Meanwhile, the security of the proposed scheme is enhanced greatly due to high sensitivity of initial values of Chen system. Extensive cryptanalysis and simulation have performed to demonstrate the feasibility and effectiveness of the proposed scheme.

Breaking cover: neural responses to slow and fast camouflage-breaking motion.

PubMed

Yin, Jiapeng; Gong, Hongliang; An, Xu; Chen, Zheyuan; Lu, Yiliang; Andolina, Ian M; McLoughlin, Niall; Wang, Wei

2015-08-22

Primates need to detect and recognize camouflaged animals in natural environments. Camouflage-breaking movements are often the only visual cue available to accomplish this. Specifically, sudden movements are often detected before full recognition of the camouflaged animal is made, suggesting that initial processing of motion precedes the recognition of motion-defined contours or shapes. What are the neuronal mechanisms underlying this initial processing of camouflaged motion in the primate visual brain? We investigated this question using intrinsic-signal optical imaging of macaque V1, V2 and V4, along with computer simulations of the neural population responses. We found that camouflaged motion at low speed was processed as a direction signal by both direction- and orientation-selective neurons, whereas at high-speed camouflaged motion was encoded as a motion-streak signal primarily by orientation-selective neurons. No population responses were found to be invariant to the camouflage contours. These results suggest that the initial processing of camouflaged motion at low and high speeds is encoded as direction and motion-streak signals in primate early visual cortices. These processes are consistent with a spatio-temporal filter mechanism that provides for fast processing of motion signals, prior to full recognition of camouflage-breaking animals. © 2015 The Authors.

Breaking cover: neural responses to slow and fast camouflage-breaking motion

PubMed Central

Yin, Jiapeng; Gong, Hongliang; An, Xu; Chen, Zheyuan; Lu, Yiliang; Andolina, Ian M.; McLoughlin, Niall; Wang, Wei

2015-01-01

Primates need to detect and recognize camouflaged animals in natural environments. Camouflage-breaking movements are often the only visual cue available to accomplish this. Specifically, sudden movements are often detected before full recognition of the camouflaged animal is made, suggesting that initial processing of motion precedes the recognition of motion-defined contours or shapes. What are the neuronal mechanisms underlying this initial processing of camouflaged motion in the primate visual brain? We investigated this question using intrinsic-signal optical imaging of macaque V1, V2 and V4, along with computer simulations of the neural population responses. We found that camouflaged motion at low speed was processed as a direction signal by both direction- and orientation-selective neurons, whereas at high-speed camouflaged motion was encoded as a motion-streak signal primarily by orientation-selective neurons. No population responses were found to be invariant to the camouflage contours. These results suggest that the initial processing of camouflaged motion at low and high speeds is encoded as direction and motion-streak signals in primate early visual cortices. These processes are consistent with a spatio-temporal filter mechanism that provides for fast processing of motion signals, prior to full recognition of camouflage-breaking animals. PMID:26269500

Rules of Engagement: Incomplete and Complete Pronoun Resolution

ERIC Educational Resources Information Center

Love, Jessica; McKoon, Gail

2011-01-01

Research on shallow processing suggests that readers sometimes encode only a superficial representation of a text and fail to make use of all available information. Greene, McKoon, and Ratcliff (1992) extended this work to pronouns, finding evidence that readers sometimes fail to automatically identify referents even when these are unambiguous. In…

How Can You Translate If You Can't Express Yourself in Writing?

ERIC Educational Resources Information Center

Zucker, George K.

Good translation requires writing skills in each of its three stages: decoding the original text; transferring its cultural and linguistic element into the context of the target language; and encoding the information in that context. During decoding, the translator must be conscious of speech level, word usage, cultural references, syntactic…

HyperText MARCup: A Conceptualization for Encoding, De-Constructing, Searching, Retrieving, and Using Traditional Knowledge Tools.

ERIC Educational Resources Information Center

Wall, C. Edward; And Others

1995-01-01

Discusses the integration of Standard General Markup Language, Hypertext Markup Language, and MARC format to parse classified analytical bibliographies. Use of the resulting electronic knowledge constructs in local library systems as maps of a specified subset of resources is discussed, and an example is included. (LRW)

Optimal Weight Assignment for a Chinese Signature File.

ERIC Educational Resources Information Center

Liang, Tyne; And Others

1996-01-01

Investigates the performance of a character-based Chinese text retrieval scheme in which monogram keys and bigram keys are encoded into document signatures. Tests and verifies the theoretical predictions of the optimal weight assignments and the minimal false hit rate in experiments using a real Chinese corpus for disyllabic queries of different…

Memory reactivation during rest supports upcoming learning of related content.

PubMed

Schlichting, Margaret L; Preston, Alison R

2014-11-04

Although a number of studies have highlighted the importance of offline processes for memory, how these mechanisms influence future learning remains unknown. Participants with established memories for a set of initial face-object associations were scanned during passive rest and during encoding of new related and unrelated pairs of objects. Spontaneous reactivation of established memories and enhanced hippocampal-neocortical functional connectivity during rest was related to better subsequent learning, specifically of related content. Moreover, the degree of functional coupling during rest was predictive of neural engagement during the new learning experience itself. These results suggest that through rest-phase reactivation and hippocampal-neocortical interactions, existing memories may come to facilitate encoding during subsequent related episodes.

Memory reactivation during rest supports upcoming learning of related content

PubMed Central

Schlichting, Margaret L.; Preston, Alison R.

2014-01-01

Although a number of studies have highlighted the importance of offline processes for memory, how these mechanisms influence future learning remains unknown. Participants with established memories for a set of initial face–object associations were scanned during passive rest and during encoding of new related and unrelated pairs of objects. Spontaneous reactivation of established memories and enhanced hippocampal–neocortical functional connectivity during rest was related to better subsequent learning, specifically of related content. Moreover, the degree of functional coupling during rest was predictive of neural engagement during the new learning experience itself. These results suggest that through rest-phase reactivation and hippocampal–neocortical interactions, existing memories may come to facilitate encoding during subsequent related episodes. PMID:25331890

Overproduction, purification, and biochemical characterization of the dual specificity H1 protein phosphatase encoded by variola major virus.

PubMed

Tropea, Joseph E; Phan, Jason; Waugh, David S

2006-11-01

Smallpox, a highly contagious infectious disease caused by the variola major virus, has an overall mortality rate of about 30%. Because there currently is no specific treatment for smallpox, and the only prevention is vaccination, there is an urgent need for the development of effective antiviral drugs. The dual specificity protein phosphatase encoded by the smallpox virus (H1) is essential for the production of infectious viral particles, making it a promising molecular target for antiviral therapeutics. Here, we report the molecular cloning, overproduction, purification, and initial biochemical characterization of H1 phosphatase, thereby paving the way for the discovery of small molecule inhibitors.

Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer.

PubMed

Bowring, Janine; Neamah, Maan M; Donderis, Jorge; Mir-Sanchis, Ignacio; Alite, Christian; Ciges-Tomas, J Rafael; Maiques, Elisa; Medmedov, Iltyar; Marina, Alberto; Penadés, José R

2017-08-08

Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature's most fascinating subcellular parasites.

Distinct Developmental Origins Manifest in the Specialized Encoding of Movement by Adult Neurons of the External Globus Pallidus

PubMed Central

Dodson, Paul D.; Larvin, Joseph T.; Duffell, James M.; Garas, Farid N.; Doig, Natalie M.; Kessaris, Nicoletta; Duguid, Ian C.; Bogacz, Rafal; Butt, Simon J.B.; Magill, Peter J.

2015-01-01

Summary Transcriptional codes initiated during brain development are ultimately realized in adulthood as distinct cell types performing specialized roles in behavior. Focusing on the mouse external globus pallidus (GPe), we demonstrate that the potential contributions of two GABAergic GPe cell types to voluntary action are fated from early life to be distinct. Prototypic GPe neurons derive from the medial ganglionic eminence of the embryonic subpallium and express the transcription factor Nkx2-1. These neurons fire at high rates during alert rest, and encode movements through heterogeneous firing rate changes, with many neurons decreasing their activity. In contrast, arkypallidal GPe neurons originate from lateral/caudal ganglionic eminences, express the transcription factor FoxP2, fire at low rates during rest, and encode movements with robust increases in firing. We conclude that developmental diversity positions prototypic and arkypallidal neurons to fulfil distinct roles in behavior via their disparate regulation of GABA release onto different basal ganglia targets. PMID:25843402

Nucleotide sequence of RNA2 of Lettuce big-vein virus and evidence for a possible transcription termination/initiation strategy similar to that of rhabdoviruses.

PubMed

Sasaya, Takahide; Kusaba, Shinnosuke; Ishikawa, Koichi; Koganezawa, Hiroki

2004-09-01

Lettuce big-vein virus (LBVV) is the type species of the genus Varicosavirus and is a two-segmented negative-sense single-stranded RNA virus. The larger LBVV genome segment (RNA1) consists of 6797 nt and encodes an L polymerase that resembles that of rhabdoviruses. Here, the nucleotide sequence of the second LBVV genome segment (RNA2) is reported. LBVV RNA2 consisted of 6081 nt and contained antisense information for five major ORFs: ORF1 (nt 210-1403 on the viral RNA), ORF2 (nt 1493-2494), ORF3 (nt 2617-3489), ORF4 (nt 3843-4337) and ORF5 (nt 4530-5636), which had coding capacities of 44, 36, 32, 19 and 41 kDa, respectively. The gene at the 3' end of the viral RNA encoded a coat protein, while the other four genes encoded proteins of unknown functions. The 3'-terminal 11 nt of LBVV RNA2 were identical to those of LBVV RNA1, and the 5'-terminal regions of LBVV RNA1 and RNA2 contained a long common nucleotide stretch of about 100 nt. Northern blot analysis using probes specific to the individual ORFs revealed that LBVV transcribes monocistronic RNAs. Analysis of the terminal sequences, and primer extension and RNase H digestion analysis of LBVV mRNAs, suggested that LBVV utilizes a transcription termination/initiation strategy comparable with that of rhabdoviruses.

Prefrontal neurons encode context-based response execution and inhibition in reward seeking and extinction

PubMed Central

Moorman, David E.; Aston-Jones, Gary

2015-01-01

The prefrontal cortex (PFC) guides execution and inhibition of behavior based on contextual demands. In rodents, the dorsal/prelimbic (PL) medial PFC (mPFC) is frequently considered essential for execution of goal-directed behavior (“go”) whereas ventral/infralimbic (IL) mPFC is thought to control behavioral suppression (“stop”). This dichotomy is commonly seen for fear-related behaviors, and for some behaviors related to cocaine seeking. Overall, however, data for reward-directed behaviors are ambiguous, and few recordings of PL/IL activity have been performed to demonstrate single-neuron correlates. We recorded neuronal activity in PL and IL during discriminative stimulus driven sucrose seeking followed by multiple days of extinction of the reward-predicting stimulus. Contrary to a generalized PL-go/IL-stop hypothesis, we found cue-evoked activity in PL and IL during reward seeking and extinction. Upon analyzing this activity based on resultant behavior (lever press or withhold), we found that neurons in both areas encoded contextually appropriate behavioral initiation (during reward seeking) and withholding (during extinction), where context was dictated by response–outcome contingencies. Our results demonstrate that PL and IL signal contextual information for regulation of behavior, irrespective of whether that involves initiation or suppression of behavioral responses, rather than topographically encoding go vs. stop behaviors. The use of context to optimize behavior likely plays an important role in maximizing utility-promoting exertion of activity when behaviors are rewarded and conservation of energy when not. PMID:26170333

Ensemble codes involving hippocampal neurons are at risk during delayed performance tests.

PubMed

Hampson, R E; Deadwyler, S A

1996-11-26

Multielectrode recording techniques were used to record ensemble activity from 10 to 16 simultaneously active CA1 and CA3 neurons in the rat hippocampus during performance of a spatial delayed-nonmatch-to-sample task. Extracted sources of variance were used to assess the nature of two different types of errors that accounted for 30% of total trials. The two types of errors included ensemble "miscodes" of sample phase information and errors associated with delay-dependent corruption or disappearance of sample information at the time of the nonmatch response. Statistical assessment of trial sequences and associated "strength" of hippocampal ensemble codes revealed that miscoded error trials always followed delay-dependent error trials in which encoding was "weak," indicating that the two types of errors were "linked." It was determined that the occurrence of weakly encoded, delay-dependent error trials initiated an ensemble encoding "strategy" that increased the chances of being correct on the next trial and avoided the occurrence of further delay-dependent errors. Unexpectedly, the strategy involved "strongly" encoding response position information from the prior (delay-dependent) error trial and carrying it forward to the sample phase of the next trial. This produced a miscode type error on trials in which the "carried over" information obliterated encoding of the sample phase response on the next trial. Application of this strategy, irrespective of outcome, was sufficient to reorient the animal to the proper between trial sequence of response contingencies (nonmatch-to-sample) and boost performance to 73% correct on subsequent trials. The capacity for ensemble analyses of strength of information encoding combined with statistical assessment of trial sequences therefore provided unique insight into the "dynamic" nature of the role hippocampus plays in delay type memory tasks.

Movement Interferes with Visuospatial Working Memory during the Encoding: An ERP Study

PubMed Central

Gunduz Can, Rumeysa; Schack, Thomas; Koester, Dirk

2017-01-01

The present study focuses on the functional interactions of cognition and manual action control. Particularly, we investigated the neurophysiological correlates of the dual-task costs of a manual-motor task (requiring grasping an object, holding it, and subsequently placing it on a target) for working memory (WM) domains (verbal and visuospatial) and processes (encoding and retrieval). Thirty participants were tested in a cognitive-motor dual-task paradigm, in which a single block (a verbal or visuospatial WM task) was compared with a dual block (concurrent performance of a WM task and a motor task). Event-related potentials (ERPs) were analyzed separately for the encoding and retrieval processes of verbal and visuospatial WM domains both in single and dual blocks. The behavioral analyses show that the motor task interfered with WM and decreased the memory performance. The performance decrease was larger for the visuospatial task compared with the verbal task, i.e., domain-specific memory costs were obtained. The ERP analyses show the domain-specific interference also at the neurophysiological level, which is further process-specific to encoding. That is, comparing the patterns of WM-related ERPs in the single block and dual block, we showed that visuospatial ERPs changed only for the encoding process when a motor task was performed at the same time. Generally, the present study provides evidence for domain- and process-specific interactions of a prepared manual-motor movement with WM (visuospatial domain during the encoding process). This study, therefore, provides an initial neurophysiological characterization of functional interactions of WM and manual actions in a cognitive-motor dual-task setting, and contributes to a better understanding of the neuro-cognitive mechanisms of motor action control. PMID:28611714

Interference from retrieval cues in Parkinson's disease.

PubMed

Crescentini, Cristiano; Marin, Dario; Del Missier, Fabio; Biasutti, Emanuele; Shallice, Tim

2011-11-01

Existing studies on memory interference in Parkinson's disease (PD) patients have provided mixed results and it is unknown whether PD patients have problems in overcoming interference from retrieval cues. We investigated this issue by using a part-list cuing paradigm. In this paradigm, after the study of a list of items, the presentation of some of these items as retrieval cues hinders the recall of the remaining ones. We tested PD patients' (n = 19) and control participants' (n = 16) episodic memory in the presence and absence of part-list cues, using initial-letter probes, and following either weak or strong serial associative encoding of list items. Both PD patients and control participants showed a comparable and significant part-list cuing effect after weak associative encoding (13% vs. 12% decrease in retrieval in part-list cuing vs. no part-list cuing -control- conditions in PD patients and control participants, respectively), denoting a similar effect of cue-driven interference in the two populations when a serial retrieval strategy is hard to develop. However, only PD patients showed a significant part-list cuing effect after strong associative encoding (20% vs. 5% decrease in retrieval in patients and controls, respectively). When encoding promotes the development of an effective serial retrieval strategy, the presentation of part-list cues has a specifically disruptive effect in PD patients. This indicates problems in strategic retrieval, probably related to PD patients' increased tendency to rely on external cues. Findings in control conditions suggest that less effective encoding may have contributed to PD patients' memory performance.

Gene Cluster Encoding Cholate Catabolism in Rhodococcus spp.

PubMed Central

Wilbrink, Maarten H.; Casabon, Israël; Stewart, Gordon R.; Liu, Jie; van der Geize, Robert; Eltis, Lindsay D.

2012-01-01

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. PMID:23024343

Enhancing Free-Recall Rates of Individuals with Mental Retardation.

ERIC Educational Resources Information Center

Carlin, Michael T.; Soraci, Sal A.; Dennis, Nancy A.; Chechile, Nicholas A.; Loiselle, Raquel C.

2001-01-01

This study with 16 adolescents with mental retardation compared free-recall rates under two encoding conditions: (1) fade-in, initially presenting pictures out of focus then slowly fading them into focus; and (2) fade-out, slowly blurring originally clear pictures. Results indicated that free-recall rates were greater for the fade-in items for…

Context Affects Feeling-of-Knowing Accuracy in Younger and Older Adults

ERIC Educational Resources Information Center

Thomas, Ayanna K.; Bulevich, John B.; Dubois, Stacey J.

2011-01-01

In feeling of knowing (FOK) studies, participants predict subsequent recognition memory performance on items that were initially encoded but that cannot presently be recalled. Research suggests that FOK judgment magnitude may be influenced by the total amount, or quantity, of contextual information retrieved related to the unrecalled target (e.g.,…

Encoding Strategy Changes and Spacing Effects in the Free Recall of Unmixed Lists

ERIC Educational Resources Information Center

Delaney, P.F.; Knowles, M.E.

2005-01-01

Memory for repeated items often improves when repetitions are separated by other items-a phenomenon called the spacing effect. In two experiments, we explored the complex interaction between study strategies, serial position, and spacing effects. When people studied several unmixed lists, they initially used mainly rote rehearsal, but some people…

Skill Acquisition: Compilation of Weak-Method Problem Solutions.

ERIC Educational Resources Information Center

Anderson, John R.

According to the ACT theory of skill acquisition, cognitive skills are encoded by a set of productions, which are organized according to a hierarchical goal structure. People solve problems in new domains by applying weak problem-solving procedures to declarative knowledge they have about this domain. From these initial problem solutions,…

Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa

USDA-ARS?s Scientific Manuscript database

Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, a major regulator of biofilm formation, and antibiotic-resistance traits, a...

RPO41-independent maintenance of [rho-] mitochondrial DNA in Saccharomyces cerevisiae.

PubMed

Fangman, W L; Henly, J W; Brewer, B J

1990-01-01

A subset of promoters in the mitochondrial DNA (mtDNA) of the yeast Saccharomyces cerevisiae has been proposed to participate in replication initiation, giving rise to a primer through site-specific cleavage of an RNA transcript. To test whether transcription is essential for mtDNA maintenance, we examined two simple mtDNA deletion ([rho-]) genomes in yeast cells. One genome (HS3324) contains a consensus promoter (ATATAAGTA) for the mitochondrial RNA polymerase encoded by the nuclear gene RPO41, and the other genome (4a) does not. As anticipated, in RPO41 cells transcripts from the HS3324 genome were more abundant than were transcripts from the 4a genome. When the RPO41 gene was disrupted, both [rho-] genomes were efficiently maintained. The level of transcripts from HS3324 mtDNA was decreased greater than 400-fold in cells carrying the RPO41 disrupted gene; however, the low-level transcripts from 4a mtDNA were undiminished. These results indicate that replication of [rho-] genomes can be initiated in the absence of wild-type levels of the RPO41-encoded RNA polymerase.

Emotional memory can be persistently weakened by suppressing cortisol during retrieval.

PubMed

Rimmele, Ulrike; Besedovsky, Luciana; Lange, Tanja; Born, Jan

2015-03-01

Cortisol's effects on memory follow an inverted U-shaped function such that memory retrieval is impaired with very low concentrations, presumably due to insufficient activation of high-affine mineralocorticoid receptors (MR), or with very high concentrations, due to predominant low-affine glucocorticoid receptor (GR) activation. Through corresponding changes in re-encoding, the retrieval effect of cortisol might translate into a persistent change of the retrieved memory. We tested whether partial suppression of morning cortisol synthesis by metyrapone, leading to intermediate, circadian nadir-like levels with presumed predominant MR activation, improves retrieval, particularly of emotional memory, and persistently changes the memory. In a randomized, placebo-controlled, double-blind, within-subject cross-over design, 18 men were orally administered metyrapone (1g) vs. placebo at 4:00 AM to suppress the morning cortisol rise. Retrieval of emotional and neutral texts and pictures (learned 3 days earlier) was assessed 4h after substance administration and a second time one week later. Metyrapone suppressed endogenous cortisol release to circadian nadir-equivalent levels at the time of retrieval testing. Contrary to our expectations, metyrapone significantly impaired free recall of emotional texts (p<.05), whereas retrieval of neutral texts or pictures remained unaffected. One week later, participants still showed lower memory for emotional texts in the metyrapone than placebo condition (p<.05). Our finding that suppressing morning cortisol to nadir-like concentrations not only impairs acute retrieval, but also persistently weakens emotional memories corroborates the concept that retrieval effects of cortisol produce persistent memory changes, possibly by affecting re-encoding. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study.

PubMed

Li, Li; Chase, Herbert S; Patel, Chintan O; Friedman, Carol; Weng, Chunhua

2008-11-06

The prevalence of electronic medical record (EMR) systems has made mass-screening for clinical trials viable through secondary uses of clinical data, which often exist in both structured and free text formats. The tradeoffs of using information in either data format for clinical trials screening are understudied. This paper compares the results of clinical trial eligibility queries over ICD9-encoded diagnoses and NLP-processed textual discharge summaries. The strengths and weaknesses of both data sources are summarized along the following dimensions: information completeness, expressiveness, code granularity, and accuracy of temporal information. We conclude that NLP-processed patient reports supplement important information for eligibility screening and should be used in combination with structured data.

An Investigation of the Effects of Reader Characteristics on Reading Comprehension Of a General Chemistry Text

NASA Astrophysics Data System (ADS)

Neiles, Kelly Y.

There is great concern in the scientific community that students in the United States, when compared with other countries, are falling behind in their scientific achievement. Increasing students' reading comprehension of scientific text may be one of the components involved in students' science achievement. To investigate students' reading comprehension this quantitative study examined the effects of different reader characteristics, namely, students' logical reasoning ability, factual chemistry knowledge, working memory capacity, and schema of the chemistry concepts, on reading comprehension of a chemistry text. Students' reading comprehension was measured through their ability to encode the text, access the meanings of words (lexical access), make bridging and elaborative inferences, and integrate the text with their existing schemas to make a lasting mental representation of the text (situational model). Students completed a series of tasks that measured the reader characteristic and reading comprehension variables. Some of the variables were measured using new technologies and software to investigate different cognitive processes. These technologies and software included eye tracking to investigate students' lexical accessing and a Pathfinder program to investigate students' schema of the chemistry concepts. The results from this study were analyzed using canonical correlation and regression analysis. The canonical correlation analysis allows for the ten variables described previously to be included in one multivariate analysis. Results indicate that the relationship between the reader characteristic variables and the reading comprehension variables is significant. The resulting canonical function accounts for a greater amount of variance in students' responses then any individual variable. Regression analysis was used to further investigate which reader characteristic variables accounted for the differences in students' responses for each reading comprehension variable. The results from this regression analysis indicated that the two schema measures (measured by the Pathfinder program) accounted for the greatest amount of variance in four of the reading comprehension variables (encoding the text, bridging and elaborative inferences, and delayed recall of a general summary). This research suggest that providing students with background information on chemistry concepts prior to having them read the text may result in better understanding and more effective incorporation of the chemistry concepts into their schema.

Reduced prefrontal activation in pediatric patients with obsessive-compulsive disorder during verbal episodic memory encoding.

PubMed

Batistuzzo, Marcelo Camargo; Balardin, Joana Bisol; Martin, Maria da Graça Morais; Hoexter, Marcelo Queiroz; Bernardes, Elisa Teixeira; Borcato, Sonia; Souza, Marina de Marco E; Querido, Cicero Nardini; Morais, Rosa Magaly; de Alvarenga, Pedro Gomes; Lopes, Antonio Carlos; Shavitt, Roseli Gedanke; Savage, Cary R; Amaro, Edson; Miguel, Euripedes C; Polanczyk, Guilherme V; Miotto, Eliane C

2015-10-01

Patients with obsessive-compulsive disorder (OCD) often present with deficits in episodic memory, and there is evidence that these difficulties may be secondary to executive dysfunction, that is, impaired selection and/or application of memory-encoding strategies (mediation hypothesis). Semantic clustering is an effective strategy to enhance encoding of verbal episodic memory (VEM) when word lists are semantically related. Self-initiated mobilization of this strategy has been associated with increased activity in the prefrontal cortex, particularly the orbitofrontal cortex, a key region in the pathophysiology of OCD. We therefore studied children and adolescents with OCD during uncued semantic clustering strategy application in a VEM functional magnetic resonance imaging (fMRI)-encoding paradigm. A total of 25 pediatric patients with OCD (aged 8.1-17.5 years) and 25 healthy controls (HC, aged 8.1-16.9) matched for age, gender, handedness, and IQ were evaluated using a block design VEM paradigm that manipulated semantically related and unrelated words. The semantic clustering strategy score (SCS) predicted VEM performance in HC (p < .001, R(2) = 0.635), but not in patients (p = .099). Children with OCD also presented hypoactivation in the dorsomedial prefrontal cortex (cluster-corrected p < .001). Within-group analysis revealed a negative correlation between Yale-Brown Obsessive Compulsive Scale scores and activation of orbitofrontal cortex in the group with OCD. Finally, a positive correlation between age and SCS was found in HC (p = .001, r = 0.635), but not in patients with OCD (p = .936, r = 0.017). Children with OCD presented altered brain activation during the VEM paradigm and absence of expected correlation between SCS and age, and between SCS and total words recalled. These results suggest that different neural mechanisms underlie self-initiated semantic clustering in OCD. Copyright © 2015 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins.

PubMed

Nydam, Marie L; Netuschil, Nikolai; Sanders, Erin; Langenbacher, Adam; Lewis, Daniel D; Taketa, Daryl A; Marimuthu, Arumugapradeep; Gracey, Andrew Y; De Tomaso, Anthony W

2013-01-01

The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid-secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains. While northern blotting revealed only these two mRNAs, both PCR and mRNA-seq detect a single capped and polyadenylated transcript that encodes processed forms of both genes linked by the intergenic region, as well as other transcripts in which exons of the two genes are spliced together. These results might suggest that the two genes are expressed as an operon, during which both genes are co-transcribed and then trans-spliced into two separate messages. This type of transcriptional regulation has been described in tunicates previously; however, the membrane-bound gene does not encode a typical Splice Leader (SL) sequence at the 5' terminus that usually accompanies trans-splicing. Thus, the presence of stable transcripts encoding both genes may suggest a novel mechanism of regulation, or conversely may be rare but stable transcripts in which the two mRNAs are linked due to a small amount of read-through by RNA polymerase. Both genes are highly polymorphic and co-expressed on tissues involved in histocompatibility. In addition, polymorphisms on both genes correlate with outcome, although we have found a case in which it appears that the secreted form may be major allorecognition determinant.

X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre.

PubMed

de Hoon, B; Splinter, Erik; Eussen, B; Douben, J C W; Rentmeester, E; van de Heijning, M; Laven, J S E; de Klein, J E M M; Liebelt, J; Gribnau, J

2017-11-05

X chromosome inactivation (XCI) is a mechanism specifically initiated in female cells to silence one X chromosome, thereby equalizing the dose of X-linked gene products between male and female cells. XCI is regulated by a locus on the X chromosome termed the X-inactivation centre (XIC). Located within the XIC is XIST , which acts as a master regulator of XCI. During XCI, XIST is upregulated on the inactive X chromosome and chromosome-wide cis spreading of XIST leads to inactivation. In mouse, the Xic comprises Xist and all cis -regulatory elements and genes involved in Xist regulation. The activity of the XIC is regulated by trans -acting factors located elsewhere in the genome: X-encoded XCI activators positively regulating XCI, and autosomally encoded XCI inhibitors providing the threshold for XCI initiation. Whether human XCI is regulated through a similar mechanism, involving trans -regulatory factors acting on the XIC has remained elusive so far. Here, we describe a female individual with ovarian dysgenesis and a small X chromosomal deletion of the XIC. SNP-array and targeted locus amplification (TLA) analysis defined the deletion to a 1.28 megabase region, including XIST and all elements and genes that perform cis -regulatory functions in mouse XCI. Cells carrying this deletion still initiate XCI on the unaffected X chromosome, indicating that XCI can be initiated in the presence of only one XIC. Our results indicate that the trans -acting factors required for XCI initiation are located outside the deletion, providing evidence that the regulatory mechanisms of XCI are conserved between mouse and human.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'. © 2017 The Authors.

Reading and Language Learning: Crosslinguistic Constraints on Second Language Reading Development

ERIC Educational Resources Information Center

Koda, Keiko

2007-01-01

The ultimate goal of reading is to construct text meaning based on visually encoded information. Essentially, it entails converting print into language and then to the message intended by the author. It is hardly accidental, therefore, that, in all languages, reading builds on oral language competence and that learning to read uniformly requires…

Using Art Media during Prewriting: Helping Students with Dysgraphia Manage Idea Generation before Encoding Text

ERIC Educational Resources Information Center

Dunn, Michael

2013-01-01

Many students struggle with writing skills. This study focuses on three students (second and fourth grades) who were classified with a learning disability by their school. These children had writing goals and objectives (i.e., characteristics of having dysgraphia) included in their Individual Education Plan. In a single case design format, each…

Ellipsis and the Structure of Expectation. San Jose State Occasional Papers in Linguistics, Vol. 1, November, 1975.

ERIC Educational Resources Information Center

Ross, Robert N.

This paper discusses one way of exploring how we perceive and understand the connections between some parts of texts, or between one sentence and the whole discourse. Understanding ellipsis involves non-syntactic understanding; the semantic structure is responsible for our understanding of elliptical sentences and encoding the knowledge contained…

What Makes a Word Difficult? Insights into the Mental Representation of Technical Terms

ERIC Educational Resources Information Center

Jucks, Regina; Paus, Elisabeth

2012-01-01

Learning from texts requires reflection on how far one has mastered the material. Learners use such metacognitive processes to decide whether to engage in deeper learning activities or not. This article examines how the lexical surface of specialist concepts influences their mental representation. Lexical encodings that are the concise wordings of…

Cumulative Repetition Effects across Multiple Readings of a Word: Evidence from Eye Movements

ERIC Educational Resources Information Center

Kamienkowski, Juan E.; Carbajal, M. Julia; Bianchi, Bruno; Sigman, Mariano; Shalom, Diego E.

2018-01-01

When a word is read more than once, reading time generally decreases in the successive occurrences. This Repetition Effect has been used to study word encoding and memory processes in a variety of experimental measures. We studied naturally occurring repetitions of words within normal texts (stories of around 3,000 words). Using linear mixed…

Parietal cortex integrates contextual and saliency signals during the encoding of natural scenes in working memory.

PubMed

Santangelo, Valerio; Di Francesco, Simona Arianna; Mastroberardino, Serena; Macaluso, Emiliano

2015-12-01

The Brief presentation of a complex scene entails that only a few objects can be selected, processed indepth, and stored in memory. Both low-level sensory salience and high-level context-related factors (e.g., the conceptual match/mismatch between objects and scene context) contribute to this selection process, but how the interplay between these factors affects memory encoding is largely unexplored. Here, during fMRI we presented participants with pictures of everyday scenes. After a short retention interval, participants judged the position of a target object extracted from the initial scene. The target object could be either congruent or incongruent with the context of the scene, and could be located in a region of the image with maximal or minimal salience. Behaviourally, we found a reduced impact of saliency on visuospatial working memory performance when the target was out-of-context. Encoding-related fMRI results showed that context-congruent targets activated dorsoparietal regions, while context-incongruent targets de-activated the ventroparietal cortex. Saliency modulated activity both in dorsal and ventral regions, with larger context-related effects for salient targets. These findings demonstrate the joint contribution of knowledge-based and saliency-driven attention for memory encoding, highlighting a dissociation between dorsal and ventral parietal regions. © 2015 Wiley Periodicals, Inc.

Face and object encoding under perceptual load: ERP evidence.

PubMed

Neumann, Markus F; Mohamed, Tarik N; Schweinberger, Stefan R

2011-02-14

According to the perceptual load theory, processing of a task-irrelevant distractor is abolished when attentional resources are fully consumed by task-relevant material. As an exception, however, famous faces have been shown to elicit repetition modulations in event-related potentials - an N250r - despite high load at initial presentation, suggesting preserved face-encoding. Here, we recorded N250r repetition modulations by unfamiliar faces, hands, and houses, and tested face specificity of preserved encoding under high load. In an immediate (S1-S2) repetition priming paradigm, participants performed a letter identification task on S1 by indicating whether an "X" vs. "N" was among 6 different (high load condition) or 6 identical (low load condition) letters. Letter strings were superimposed on distractor faces, hands, or houses. Subsequent S2 probes were either identical repetitions of S1 distractors, non-repeated exemplars from the same category, or infrequent butterflies, to which participants responded. Independent of attentional load at S1, an occipito-temporal N250r was found for unfamiliar faces. In contrast, no repetition-related neural modulation emerged for houses or hands. This strongly suggests that a putative face-selective attention module supports encoding under high load, and that similar mechanisms are unavailable for other natural or artificial objects. Copyright © 2010 Elsevier Inc. All rights reserved.

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

PubMed

Fozo, Elizabeth M; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S; Jones, Kristi L; Ocampo, Alejandro; Rudd, Kenneth E; Storz, Gisela

2008-12-01

The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, although the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five-sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18- to 19-amino-acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by coexpression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell.

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

PubMed Central

Fozo, Elizabeth M.; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S.; Jones, Kristi L.; Ocampo, Alejandro; Rudd, Kenneth E.; Storz, Gisela

2008-01-01

Summary The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, though the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18–19 amino acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by co-expression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell. PMID:18710431

Effect of text message follow-up on patient's self-reported level of pain and anxiety.

PubMed

Keith, Daniel J; Rinchuse, Daniel J; Kennedy, Meghan; Zullo, Thomas

2013-07-01

To determine whether a text message reduces the severity of patient self-reported levels of pain and anxiety following initial placement of orthodontic appliances. Thirty-nine orthodontic patients were randomly assigned to one of two groups and matched for age, gender, and bracket type (self-ligating vs conventional). The subjects completed baseline questionnaires to ascertain their levels of pain and anxiety before initiating orthodontic treatment. Following the initial appointment, subjects completed the pain questionnaire and anxiety inventory at the same time daily for 1 week. One group received a structured text message showing concern and reassurance, while the second group served as a control and received no postprocedural communication. There was a statistically significant difference in pain in relation to time between the text message group and the control group as it was demonstrated that demonstrated that compared with the text message group, mean pain intensity increased and selfreported discomfort was longer in the control group. Anxiety was determined to be at its peak the day following initial orthodontic appliance placement and gradually tapered off from that time point. No intergroup difference was noted when analyzing anxiety. This study demonstrated that a text message sent from an orthodontic office following initial appliance placement resulted in a lower level of patient's self-reported pain. Additionally, patient anxiety is at its peak the day following the initial appointment and decreases from that point forward.

Perceiving speech in context: Compensation for contextual variability during acoustic cue encoding and categorization

NASA Astrophysics Data System (ADS)

Toscano, Joseph Christopher

Several fundamental questions about speech perception concern how listeners understand spoken language despite considerable variability in speech sounds across different contexts (the problem of lack of invariance in speech). This contextual variability is caused by several factors, including differences between individual talkers' voices, variation in speaking rate, and effects of coarticulatory context. A number of models have been proposed to describe how the speech system handles differences across contexts. Critically, these models make different predictions about (1) whether contextual variability is handled at the level of acoustic cue encoding or categorization, (2) whether it is driven by feedback from category-level processes or interactions between cues, and (3) whether listeners discard fine-grained acoustic information to compensate for contextual variability. Separating the effects of cue- and category-level processing has been difficult because behavioral measures tap processes that occur well after initial cue encoding and are influenced by task demands and linguistic information. Recently, we have used the event-related brain potential (ERP) technique to examine cue encoding and online categorization. Specifically, we have looked at differences in the auditory N1 as a measure of acoustic cue encoding and the P3 as a measure of categorization. This allows us to examine multiple levels of processing during speech perception and can provide a useful tool for studying effects of contextual variability. Here, I apply this approach to determine the point in processing at which context has an effect on speech perception and to examine whether acoustic cues are encoded continuously. Several types of contextual variability (talker gender, speaking rate, and coarticulation), as well as several acoustic cues (voice onset time, formant frequencies, and bandwidths), are examined in a series of experiments. The results suggest that (1) at early stages of speech processing, listeners encode continuous differences in acoustic cues, independent of phonological categories; (2) at post-perceptual stages, fine-grained acoustic information is preserved; and (3) there is preliminary evidence that listeners encode cues relative to context via feedback from categories. These results are discussed in relation to proposed models of speech perception and sources of contextual variability.

UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text.

PubMed

Demner-Fushman, Dina; Mork, James G; Shooshan, Sonya E; Aronson, Alan R

2010-08-01

Identification of medical terms in free text is a first step in such Natural Language Processing (NLP) tasks as automatic indexing of biomedical literature and extraction of patients' problem lists from the text of clinical notes. Many tools developed to perform these tasks use biomedical knowledge encoded in the Unified Medical Language System (UMLS) Metathesaurus. We continue our exploration of automatic approaches to creation of subsets (UMLS content views) which can support NLP processing of either the biomedical literature or clinical text. We found that suppression of highly ambiguous terms in the conservative AutoFilter content view can partially replace manual filtering for literature applications, and suppression of two character mappings in the same content view achieves 89.5% precision at 78.6% recall for clinical applications. Published by Elsevier Inc.

Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to Process Medication Information in Outpatient Clinical Notes

PubMed Central

Zhou, Li; Plasek, Joseph M; Mahoney, Lisa M; Karipineni, Neelima; Chang, Frank; Yan, Xuemin; Chang, Fenny; Dimaggio, Dana; Goldman, Debora S.; Rocha, Roberto A.

2011-01-01

Clinical information is often coded using different terminologies, and therefore is not interoperable. Our goal is to develop a general natural language processing (NLP) system, called Medical Text Extraction, Reasoning and Mapping System (MTERMS), which encodes clinical text using different terminologies and simultaneously establishes dynamic mappings between them. MTERMS applies a modular, pipeline approach flowing from a preprocessor, semantic tagger, terminology mapper, context analyzer, and parser to structure inputted clinical notes. Evaluators manually reviewed 30 free-text and 10 structured outpatient clinical notes compared to MTERMS output. MTERMS achieved an overall F-measure of 90.6 and 94.0 for free-text and structured notes respectively for medication and temporal information. The local medication terminology had 83.0% coverage compared to RxNorm’s 98.0% coverage for free-text notes. 61.6% of mappings between the terminologies are exact match. Capture of duration was significantly improved (91.7% vs. 52.5%) from systems in the third i2b2 challenge. PMID:22195230

Error suppression for Hamiltonian quantum computing in Markovian environments

NASA Astrophysics Data System (ADS)

Marvian, Milad; Lidar, Daniel A.

2017-03-01

Hamiltonian quantum computing, such as the adiabatic and holonomic models, can be protected against decoherence using an encoding into stabilizer subspace codes for error detection and the addition of energy penalty terms. This method has been widely studied since it was first introduced by Jordan, Farhi, and Shor (JFS) in the context of adiabatic quantum computing. Here, we extend the original result to general Markovian environments, not necessarily in Lindblad form. We show that the main conclusion of the original JFS study holds under these general circumstances: Assuming a physically reasonable bath model, it is possible to suppress the initial decay out of the encoded ground state with an energy penalty strength that grows only logarithmically in the system size, at a fixed temperature.

Cloning and sequence analysis of the invertase gene INV 1 from the yeast Pichia anomala.

PubMed

Pérez, J A; Rodríguez, J; Rodríguez, L; Ruiz, T

1996-02-01

A genomic library from the yeast Pichia anomala has been constructed and employed to clone the gene encoding the sucrose-hydrolysing enzyme invertase by complementation of a sucrose non-fermenting mutant of Saccharomyces cerevisiae. The cloned gene, INV1, was sequenced and found to encode a polypeptide of 550 amino acids which contained a 22 amino-acid signal sequence and ten potential glycosylation sites. The amino-acid sequence shows significant identity with other yeast invertases and also with Kluyveromyces marxianus inulinase, a yeast beta-fructofuranosidase which has a different substrate specificity. The nucleotide sequences of the 5' and 3' non-coding regions were found to contain several consensus motifs probably involved in the initiation and termination of gene transcription.

Deciding Full Branching Time Logic by Program Transformation

NASA Astrophysics Data System (ADS)

Pettorossi, Alberto; Proietti, Maurizio; Senni, Valerio

We present a method based on logic program transformation, for verifying Computation Tree Logic (CTL*) properties of finite state reactive systems. The finite state systems and the CTL* properties we want to verify, are encoded as logic programs on infinite lists. Our verification method consists of two steps. In the first step we transform the logic program that encodes the given system and the given property, into a monadic ω -program, that is, a stratified program defining nullary or unary predicates on infinite lists. This transformation is performed by applying unfold/fold rules that preserve the perfect model of the initial program. In the second step we verify the property of interest by using a proof method for monadic ω-programs.

Cloning and characterization of the human 5,10-methenyltetrahydrofolate synthetase-encoding cDNA.

PubMed

Dayan, A; Bertrand, R; Beauchemin, M; Chahla, D; Mamo, A; Filion, M; Skup, D; Massie, B; Jolivet, J

1995-11-20

Methenyltetrahydrofolate synthetase (MTHFS) catalyses the obligatory initial metabolic step in the intracellular conversion of 5-formyltetrahydrofolate to other reduced folates. We have isolated and sequenced a human MTHFS cDNA which is 872-bp long and codes for a 203-amino-acid protein of 23,229 Da. Escherichia coli BL21(DE3), transfected with pET11c plasmids containing an open reading frame encoding MTHFS, showed a 100-fold increase in MTHFS activity in bacterial extracts after IPTG induction. Northern blot studies of human tissues determined that the MTHFS mRNA was expressed preferentially in the liver and Southern blot analysis of human genomic DNA suggested the presence of a single-copy gene.

Memory processes during sleep: beyond the standard consolidation theory.

PubMed

Axmacher, Nikolai; Draguhn, Andreas; Elger, Christian E; Fell, Juergen

2009-07-01

Two-step theories of memory formation suggest that an initial encoding stage, during which transient neural assemblies are formed in the hippocampus, is followed by a second step called consolidation, which involves re-processing of activity patterns and is associated with an increasing involvement of the neocortex. Several studies in human subjects as well as in animals suggest that memory consolidation occurs predominantly during sleep (standard consolidation model). Alternatively, it has been suggested that consolidation may occur during waking state as well and that the role of sleep is rather to restore encoding capabilities of synaptic connections (synaptic downscaling theory). Here, we review the experimental evidence favoring and challenging these two views and suggest an integrative model of memory consolidation.

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages.

PubMed

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia.

Cranial nerve clock. Part II: functional MR imaging of brain activation during a declarative memory task.

PubMed

Weiss, K L; Welsh, R C; Eldevik, P; Bieliauskas, L A; Steinberg, B A

2001-12-01

The authors performed this study to assess brain activation during encoding and successful recall with a declarative memory paradigm that has previously been demonstrated to be effective for teaching students about the cranial nerves. Twenty-four students underwent functional magnetic resonance (MR) imaging during encoding and recall of the name, number, and function of the 12 cranial nerves. The students viewed mnemonic graphic and text slides related to individual nerves, as well as their respective control slides. For the recall paradigm, students were prompted with the numbers 1-12 (test condition) intermixed with the number 14 (control condition). Subjects were tested about their knowledge of cranial nerves outside the MR unit before and after functional MR imaging. Students learned about the cranial nerves while undergoing functional MR imaging (mean post- vs preparadigm score, 8.1 +/- 3.4 [of a possible 12] vs 0.75 +/- 0.94, bilateral prefrontal cortex, left greater than right; P < 2.0 x 10(-12)) and maintained this knowledge at I week. The encoding and recall paradigms elicited distributed networks of brain activation. Encoding revealed statistically significant activation in the bilateral prefrontal cortex, left greater than right [corrected]; bilateral occipital and parietal associative cortices, parahippocampus region, fusiform gyri, and cerebellum. Successful recall activated the left much more than the right prefrontal, parietal associative, and anterior cingulate cortices; bilateral precuneus and cerebellum; and right more than the left posterior cingulate. A predictable pattern of brain activation at functional MR imaging accompanies the encoding and successful recall of the cranial nerves with this declarative memory paradigm.

Still at the choice-point: action selection and initiation in instrumental conditioning.

PubMed

Balleine, Bernard W; Ostlund, Sean B

2007-05-01

Contrary to classic stimulus-response (S-R) theory, recent evidence suggests that, in instrumental conditioning, rats encode the relationship between their actions and the specific consequences that these actions produce. It has remained unclear, however, how encoding this relationship acts to control instrumental performance. Although S-R theories were able to give a clear account of how learning translates into performance, the argument that instrumental learning constitutes the acquisition of information of the form "response R leads to outcome O" does not directly imply a particular performance rule or policy; this information can be used both to perform R and to avoid performing R. Recognition of this problem has forced the development of accounts that allow the O and stimuli that predict the O (i.e., S-O) to play a role in the initiation of specific Rs. In recent experiments, we have used a variety of behavioral procedures in an attempt to isolate the processes that contribute to instrumental performance, including outcome devaluation, reinstatement, and Pavlovian-instrumental transfer. Our results, particularly from experiments assessing outcome-selective reinstatement, suggest that both "feed-forward" (O-R) and "feed-back" (R-O) associations are critical and that although the former appear to be important to response selection, the latter-together with processes that determine outcome value-mediate response initiation. We discuss a conceptual model that integrates these processes and its neural implementation.

Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization.

PubMed

Menanteau-Ledouble, Simon; Lawrence, Mark L

2013-03-23

Initial invasion of the host is the first and vital part of any infection process. We have demonstrated that Edwardsiella ictaluri is capable of colonizing and penetrating catfish skin. Therefore, a mutant library was constructed by random insertion of the Mar2xT7 transposon into the chromosome of E. ictaluri harboring the bioluminescence plasmid pAKgfplux1. This library was then screened through a series of three consecutive challenges for mutants showing a decreased ability to colonize the catfish epithelium. Eighteen mutants were identified that have decreased adhesion and virulence. Mutated genes encoded one sensor protein, two transport proteins, five enzymes, two regulatory proteins, and five hypothetical proteins. Among the mutated genes, the first one identified was a gene encoding for RstA/B, which is known to play a role in regulating the expression of invasion genes in Salmonella enterica Typhimurium. Another mutant was lacking a putative ribonuclease similar to a Shigella protein that regulates the expression of adhesin. A third mutant was defective in a protein similar to a Brucella protein that was initially identified as a transporter, but actually is a member of a newly discovered adhesin family. Results from this study could enable development of a new strategy for blocking E. ictaluri invasion at the initial adherence stage. Copyright © 2012 Elsevier B.V. All rights reserved.

Self-Explanations: How Students Study and Use Examples in Learning To Solve Problems. Technical Report No. 9.

ERIC Educational Resources Information Center

Chi, Michelene T. H.; And Others

A study examined in detail the initial encoding of worked-out examples of mechanics problems by "good" and "poor" students, and their subsequent reliance on examples during problem solving. The subjects, three males and five females, were selected from responses to a university campus advertisement. Six of them were working…

GLABROUS (CmGL) encodes a HD-ZIP IV transcription factor playing roles in multicellular trichome initiation in melon

USDA-ARS?s Scientific Manuscript database

Trichomes are small hairs covering the above-ground parts of plants that serve multiple functions in plant life such as protection against insects and pathogens. Little is known about the genetic control and regulation of trichome development in melon. In this study, we identified a melon mutant, cm...

Aflatoxin biosynthesis is a novel source of reactive oxygen species—a potential redox signal to initiate resistance to oxidative stress?

USDA-ARS?s Scientific Manuscript database

Aflatoxin biosynthesis in the filamentous fungus Aspergillus parasiticus involves a minimum of 21 enzymes, encoded by genes located in a 70 kb gene cluster. For aflatoxin biosynthesis to be completed, the required enzymes must be transported to specialized early and late endosomes called aflatoxisom...

12 CFR Supplement I to Part 205 - Official Staff Interpretations

Code of Federal Regulations, 2013 CFR

2013-01-01

...) encoding to initiate a one-time ACH debit. For example, if a consumer authorizes a one-time ACH debit from... electronic terminal is involved at the time of the transaction, if the consumer's asset account is... receive a notice that the transaction will be processed as an EFT for each transaction at POS or each time...

12 CFR Supplement I to Part 205 - Official Staff Interpretations

Code of Federal Regulations, 2014 CFR

2014-01-01

...) encoding to initiate a one-time ACH debit. For example, if a consumer authorizes a one-time ACH debit from... electronic terminal is involved at the time of the transaction, if the consumer's asset account is... receive a notice that the transaction will be processed as an EFT for each transaction at POS or each time...

Expression of almond KNOTTED1 homologue (PdKn1) anticipates adventitious shoot initiation

USDA-ARS?s Scientific Manuscript database

Background and Aims: The transcription factor encoded by the gene Knotted1 is a nuclear homeodomain protein, regulating meristematic cells at the shoot apical meristem. It has been proven that Knotted1 (KN1) has a role in the switch from an indeterminate to determinate cell fate and as such this gen...

Word Learning in 6-Month-Olds: Fast Encoding-Weak Retention

ERIC Educational Resources Information Center

Friedrich, Manuela; Friederici, Angela D.

2011-01-01

There has been general consensus that initial word learning during early infancy is a slow and time-consuming process that requires very frequent exposure, whereas later in development, infants are able to quickly learn a novel word for a novel meaning. From the perspective of memory maturation, this shift in behavioral development might represent…

DARPA ADAMS Project

DTIC Science & Technology

2015-05-11

it means that Mary distrusts John. We showed that it is possible to analyze such trust- distrust relationships within signed social networks in... relationship problems) − Professional Problems (negative changes at workplace, interpersonal conflicts) Furthermore, we encode in 2nd degree variables...a social media forum data. • Processed initial set of Vegas metrics data (clustering coefficient, # similar users, # skip levels) through time

An Advantage for Perceptual Edges in Young Infants' Memory for Speech

ERIC Educational Resources Information Center

Hochmann, Jean-Rémy; Langus, Alan; Mehler, Jacques

2016-01-01

Models of language acquisition are constrained by the information that learners can extract from their input. Experiment 1 investigated whether 3-month-old infants are able to encode a repeated, unsegmented sequence of five syllables. Event-related-potentials showed that infants reacted to a change of the initial or the final syllable, but not to…

The Selectivity of Aversive Memory Reconsolidation and Extinction Processes Depends on the Initial Encoding of the Pavlovian Association

ERIC Educational Resources Information Center

Debiec, Jacek; Diaz-Mataix, Lorenzo; Bush, David E. A.; Doyère, Valérie; LeDoux, Joseph E.

2013-01-01

In reconsolidation studies, memories are typically retrieved by an exposure to a single conditioned stimulus (CS). We have previously demonstrated that reconsolidation processes are CS-selective, suggesting that memories retrieved by the CS exposure are discrete and reconsolidate separately. Here, using a compound stimulus in which two distinct…

When Practice Doesn't Lead to Retrieval: An Analysis of Children's Errors with Simple Addition

ERIC Educational Resources Information Center

de Villiers, Celéste; Hopkins, Sarah

2013-01-01

Counting strategies initially used by young children to perform simple addition are often replaced by more efficient counting strategies, decomposition strategies and rule-based strategies until most answers are encoded in memory and can be directly retrieved. Practice is thought to be the key to developing fluent retrieval of addition facts. This…

USGIN ISO metadata profile

NASA Astrophysics Data System (ADS)

Richard, S. M.

2011-12-01

The USGIN project has drafted and is using a specification for use of ISO 19115/19/39 metadata, recommendations for simple metadata content, and a proposal for a URI scheme to identify resources using resolvable http URI's(see http://lab.usgin.org/usgin-profiles). The principal target use case is a catalog in which resources can be registered and described by data providers for discovery by users. We are currently using the ESRI Geoportal (Open Source), with configuration files for the USGIN profile. The metadata offered by the catalog must provide sufficient content to guide search engines to locate requested resources, to describe the resource content, provenance, and quality so users can determine if the resource will serve for intended usage, and finally to enable human users and sofware clients to obtain or access the resource. In order to achieve an operational federated catalog system, provisions in the ISO specification must be restricted and usage clarified to reduce the heterogeneity of 'standard' metadata and service implementations such that a single client can search against different catalogs, and the metadata returned by catalogs can be parsed reliably to locate required information. Usage of the complex ISO 19139 XML schema allows for a great deal of structured metadata content, but the heterogenity in approaches to content encoding has hampered development of sophisticated client software that can take advantage of the rich metadata; the lack of such clients in turn reduces motivation for metadata producers to produce content-rich metadata. If the only significant use of the detailed, structured metadata is to format into text for people to read, then the detailed information could be put in free text elements and be just as useful. In order for complex metadata encoding and content to be useful, there must be clear and unambiguous conventions on the encoding that are utilized by the community that wishes to take advantage of advanced metadata content. The use cases for the detailed content must be well understood, and the degree of metadata complexity should be determined by requirements for those use cases. The ISO standard provides sufficient flexibility that relatively simple metadata records can be created that will serve for text-indexed search/discovery, resource evaluation by a user reading text content from the metadata, and access to the resource via http, ftp, or well-known service protocols (e.g. Thredds; OGC WMS, WFS, WCS).

Aging and Predicting Inferences: A Diffusion Model Analysis

ERIC Educational Resources Information Center

McKoon, Gail; Ratcliff, Roger

2013-01-01

In the domain of discourse processing, it has been claimed that older adults (60-0-year-olds) are less likely to encode and remember some kinds of information from texts than young adults. The experiment described here shows that they do make a particular kind of inference to the same extent that college-age adults do. The inferences examined were…

User's Manual for the Database of Sources of Environmental Releases of Dioxin-Like Compounds in the U.S.: Reference Years 1987 and 1995

EPA Science Inventory

ERIC Educational Resources Information Center

Cartier, Sylvie

2002-01-01

Examined strategies reported by students during reading to develop knowledge in their area of professional training. Discovered the reading, encoding, self-regulation, and resource management strategies used most often by students, which were not sufficient to attain effective learning. Less frequently used strategies added nuances to the…