bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prestimulus Subsequent Memory Effects for Auditory and Visual Events
Authors: Otten Leun J. , Quayle Angela H. , Puvaneswaran Bhamini 
Published: July 2009

Abstract
It has been assumed that the effective encoding of information into memory primarily depends on neural activity elicited when an event is initially encountered. Recently, it has been shown that memory formation also relies on neural activity just before an event. The precise role of such activity in memory is currently unknown. Here, we address whether prestimulus activity affects the encoding of auditory and visual events, is set up on a trial-by-trial basis, and varies as a function of the type of recognition judgment an item later receives. Electrical brain activity was recorded from the scalps of 24 healthy young adults while they made semantic judgments on randomly intermixed series of visual and auditory words. Each word was preceded by a cue signaling the modality of the upcoming word. Auditory words were preceded by auditory cues and visual words by visual cues. A recognition memory test with remember/know judgments followed after a delay of about 45 min. As observed previously, a negative-going, frontally distributed modulation just before visual word onset predicted later recollection of the word. Crucially, the same effect was found for auditory words and observed on stay as well as switch trials. These findings emphasize the flexibility and general role of prestimulus activity in memory formation, and support a functional interpretation of the activity in terms of semantic preparation. At least with an unpredictable trial sequence, the activity is set up anew on each trial.
Temporal Integration in Visual Word Recognition
Authors: Forget Joachim , Buiatti Marco , Dehaene Stanislas 
Published: July 2009

Abstract
When two displays are presented in close temporal succession at the same location, how does the brain assign them to one versus two conscious percepts? We investigate this issue using a novel reading paradigm in which the odd and even letters of a string are presented alternatively at a variable rate. The results reveal a window of temporal integration during reading, with a nonlinear boundary around ∼80 msec of presentation duration. Below this limit, the oscillating stimulus is easily fused into a single percept, with all characteristics of normal reading. Above this limit, reading times are severely slowed and suffer from a word-length effect. ERPs indicate that, even at the fastest frequency, the oscillating stimulus elicits synchronous oscillations in posterior visual cortices, while late ERP components sensitive to lexical status vanish beyond the fusion threshold. Thus, the fusion/segregation dilemma is not resolved by retinal or subcortical filtering, but at cortical level by at most 300 msec. The results argue against theories of visual word recognition and letter binding that rely on temporal synchrony or other fine temporal codes.
Coercion and Compositionality
Authors: Baggio Giosuè , Choma Travis , van Lambalgen Michiel , Hagoort Peter 
Published: July 2009

AbstractResearch in psycholinguistics and in the cognitive neuroscience of language has suggested that semantic and syntactic processing are associated with different neurophysiologic correlates, such as the N400 and the P600 in the ERPs. However, only a handful of studies have investigated the neural basis of the syntax–semantics interface, and even fewer experiments have dealt with the cases in which semantic composition can proceed independently of the syntax. Here we looked into one such case—complement coercion—using ERPs. We compared sentences such as, “The journalist wrote the article” with “The journalist began the article.” The second sentence seems to involve a silent semantic element, which is expressed in the first sentence by the head of the verb phrase (VP) “wrote the article.” The second type of construction may therefore require the reader to infer or recover from memory a richer event sense of the VP “began the article,” such as began writing the article, and to integrate that into a semantic representation of the sentence. This operation is referred to as “complement coercion.” Consistently with earlier reading time, eye tracking, and MEG studies, we found traces of such additional computations in the ERPs: Coercion gives rise to a long-lasting negative shift, which differs at least in duration from a standard N400 effect. Issues regarding the nature of the computation involved are discussed in the light of a neurocognitive model of language processing and a formal semantic analysis of coercion.
Visual Anticipatory Information Modulates Multisensory Interactions of Artificial Audiovisual Stimuli
Authors: Vroomen Jean , Stekelenburg Jeroen J. 
Published: July 2009

Abstract
The neural activity of speech sound processing (the N1 component of the auditory ERP) can be suppressed if a speech sound is accompanied by concordant lip movements. Here we demonstrate that this audiovisual interaction is neither speech specific nor linked to humanlike actions but can be observed with artificial stimuli if their timing is made predictable. In Experiment 1, a pure tone synchronized with a deformation of a rectangle induced a smaller auditory N1 than auditory-only presentations if the temporal occurrence of this audiovisual event was made predictable by two moving disks that touched the rectangle. Local autoregressive average source estimation indicated that this audiovisual interaction may be related to integrative processing in auditory areas. When the moving disks did not precede the audiovisual stimulus—making the onset unpredictable—there was no N1 reduction. In Experiment 2, the predictability of the leading visual signal was manipulated by introducing a temporal asynchrony between the audiovisual event and the collision of moving disks. Audiovisual events occurred either at the moment, before (too “early”), or after (too “late”) the disks collided on the rectangle. When asynchronies varied from trial to trial—rendering the moving disks unreliable temporal predictors of the audiovisual event—the N1 reduction was abolished. These results demonstrate that the N1 suppression is induced by visual information that both precedes and reliably predicts audiovisual onset, without a necessary link to human action-related neural mechanisms.
Semantic Processing in the Anterior Temporal Lobes: A Meta-analysis of the Functional Neuroimaging Literature
Authors: Visser M. , Jefferies E. , Lambon Ralph M. A. 
Published: July 2009

Abstract
The role of the anterior temporal lobes (ATLs) in semantic cognition is not clear from the current literature. Semantic dementia patients show a progressive and a specific semantic impairment, following bilateral atrophy of the ATLs. Neuroimaging studies of healthy participants, however, do not consistently show ATL activation during semantic tasks. Consequently, several influential theories of semantic memory do not ascribe a central role to the ATLs. We conducted a meta-analysis of 164 functional neuroimaging studies of semantic processing to investigate factors that might contribute to the inconsistency in previous results. Four factors influenced the likelihood of finding ATL activation: (1) the use of PET versus fMRI, reflecting the fact that fMRI but not PET is sensitive to distortion artifacts caused by large variations in magnetic susceptibility in the area of the ATL; (2) a field of view (FOV) of more than 15 cm, thereby ensuring whole-brain coverage; (3) the use of a high baseline task to prevent subtraction of otherwise uncontrolled semantic activation; (4) the inclusion of the ATL as an ROI. The type of stimuli or task did not influence the likelihood of ATL activation, consistent with the view that this region underpins an amodal semantic system. Spoken words, written words, and picture stimuli produced overlapping ATL peaks. On average, these were more inferior for picture-based tasks. We suggest that the specific pattern of ATL activation may be influenced by stimulus type due to variations across this region in the degree of connectivity with modality-specific areas in posterior temporal cortex.
The Function of Words: Distinct Neural Correlates for Words Denoting Differently Manipulable Objects
Authors: Rueschemeyer Shirley-Ann , van Rooij Daan , Lindemann Oliver , Willems Roel M. , Bekkering Harold 
Published: July 2009

AbstractRecent research indicates that language processing relies on brain areas dedicated to perception and action. For example, processing words denoting manipulable objects has been shown to activate a fronto-parietal network involved in actual tool use. This is suggested to reflect the knowledge the subject has about how objects are moved and used. However, information about how to use an object may be much more central to the conceptual representation of an object than information about how to move an object. Therefore, there may be much more fine-grained distinctions between objects on the neural level, especially related to the usability of manipulable objects. In the current study, we investigated whether a distinction can be made between words denoting (1) objects that can be picked up to move (e.g., volumetrically manipulable objects: bookend, clock) and (2) objects that must be picked up to use (e.g., functionally manipulable objects: cup, pen). The results show that functionally manipulable words elicit greater levels of activation in the fronto-parietal sensorimotor areas than volumetrically manipulable words. This suggests that indeed a distinction can be made between different types of manipulable objects. Specifically, how an object is used functionally rather than whether an object can be displaced with the hand is reflected in semantic representations in the brain.
Comparative chromosome mapping of repetitive sequences. Implications for genomic evolution in the fish, Hoplias malabaricus
Authors: Cioffi Marcelo B , Martins Cesar , Bertollo Luiz AC 
Published: July 2009

Abstract

Background
Seven karyomorphs of the fish, Hoplias malabaricus (A-G) were previously included in two major groups, Group I (A, B, C, D) and Group II (E, F, G), based on their similar karyotype structure. In this paper, karyomorphs from Group I were analyzed by means of distinct chromosomal markers, including silver-stained nucleolar organizer regions (Ag-NORs) and chromosomal location of repetitive sequences (18S and 5S rDNA, and satellite 5SHind III-DNA), through fluorescence in situ hybridization (FISH), in order to evaluate the evolutionary relationships among them.

Results
The results showed that several chromosomal markers had conserved location in the four karyomorphs. In addition, some other markers were only conserved in corresponding chromosomes of karyomorphs A-B and C-D. These data therefore reinforced and confirmed the proposed grouping of karyomorphs A-D in Group I and highlight a closer relationship between karyomorphs A-B and C-D. Moreover, the mapping pattern of some markers on some autosomes and on the chromosomes of the XY and X1X2Y systems provided new evidence concerning the possible origin of the sex chromosomes.

Conclusion
The in situ investigation of repetitive DNA sequences adds new informative characters useful in comparative genomics at chromosomal level and provides insights into the evolutionary relationships among Hoplias malabaricus karyomorphs.
Whole genome expression analysis within the angiotensin II-apolipoprotein E deficient mouse model of abdominal aortic aneurysm
Authors: Rush Catherine , Nyara Moses , Moxon Joseph V , Trollope Alexandra , Cullen Bradford , Golledge Jonathan 
Published: July 2009

AbstractBackgroundAn animal model commonly used to investigate pathways and potential therapeutic interventions relevant to abdominal aortic aneurysm (AAA) involves subcutaneous infusion of angiotensin II within the apolipoprotein E deficient mouse. The aim of this study was to investigate genes differentially expressed in aneurysms forming within this mouse model in order to assess the relevance of this model to human AAA.ResultsUsing microarrays we identified genes relevant to aneurysm formation within apolipoprotein E deficient mice. Firstly we investigated genes differentially expressed in the aneurysm prone segment of the suprarenal aorta in these mice. Secondly we investigated genes that were differentially expressed in the aortas of mice developing aneurysms relative to those that did not develop aneurysms in response to angiotensin II infusion. Our findings suggest that a host of inflammation and extracellular matrix remodelling pathways are upregulated within the aorta in mice developing aneurysms. Kyoto Encyclopedia of Genes and Genome categories enriched in the aortas of mice with aneurysms included cytokine-cytokine receptor interaction, leukocyte transendothelial migration, natural killer cell mediated cytotoxicity and hematopoietic cell lineage. Genes associated with extracellular matrix remodelling, such as a range of matrix metalloproteinases were also differentially expressed in relation to aneurysm formation.ConclusionThis study is the first report describing whole genome expression arrays in the apolipoprotein E deficient mice in relation to aneurysm formation. The findings suggest that the pathways believed to be critical in human AAA are also relevant to aneurysm formation in this mouse model. The findings therefore support the value of this model to investigate interventions and mechanisms of human AAA.
Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing
Authors: Vega-Arreguín Julio C , Ibarra-Laclette Enrique , Jiménez-Moraila Beatriz , Martínez Octavio , Vielle-Calzada Jean Philippe , Herrera-Estrella Luis , Herrera-Estrella Alfredo 
Published: July 2009

Abstract

Background
In-depth sequencing analysis has not been able to determine the overall complexity of transcriptional activity of a plant organ or tissue sample. In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs), although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure for validating gene prediction and estimating overall gene coverage. This approach could be very valuable for complex plant genomes. In addition, little emphasis has been given to efforts aiming at an estimation of the overall transcriptional universe found in a multicellular organism at a specific developmental stage.

Results
To explore, in depth, the transcriptional diversity in an ancient maize landrace, we developed a protocol to optimize the sequencing of cDNAs and performed 4 consecutive GS20–454 pyrosequencing runs of a cDNA library obtained from 2 week-old Palomero Toluqueño maize plants. The protocol reported here allowed obtaining over 90% of informative sequences. These GS20–454 runs generated over 1.5 Million reads, representing the largest amount of sequences reported from a single plant cDNA library. A collection of 367,391 quality-filtered reads (30.09 Mb) from a single run was sufficient to identify transcripts corresponding to 34% of public maize ESTs databases; total sequences generated after 4 filtered runs increased this coverage to 50%. Comparisons of all 1.5 Million reads to the Maize Assembled Genomic Islands (MAGIs) provided evidence for the transcriptional activity of 11% of MAGIs. We estimate that 5.67% (86,069 sequences) do not align with public ESTs or annotated genes, potentially representing new maize transcripts. Following the assembly of 74.4% of the reads in 65,493 contigs, real-time PCR of selected genes confirmed a predicted correlation between the abundance of GS20–454 sequences and corresponding levels of gene expression.

Conclusion
A protocol was developed that significantly increases the number, length and quality of cDNA reads using massive 454 parallel sequencing. We show that recurrent 454 pyrosequencing of a single cDNA sample is necessary to attain a thorough representation of the transcriptional universe present in maize, that can also be used to estimate transcript abundance of specific genes. This data suggests that the molecular and functional diversity contained in the vast native landraces remains to be explored, and that large-scale transcriptional sequencing of a presumed ancestor of the modern maize varieties represents a valuable approach to characterize the functional diversity of maize for future agricultural and evolutionary studies.
Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens
Authors: Wilkinson Paul , Waterfield Nicholas R , Crossman Lisa , Corton Craig , Sanchez-Contreras Maria , Vlisidou Isabella , Barron Andrew , Bignell Alexandra , Clark Louise , Ormond Douglas , Mayho Matthew , Bason Nathalie , Smith Frances , Simmonds Mark , Churcher Carol , Harris David , Thompson Nicholas R , Quail Michael , Parkhill Julian , ffrench-Constant Richard H 
Published: July 2009

Abstract

Background
The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has been recovered from human infections in both North America and Australia. Recently, Pa has been shown to have a nematode vector that can also infect insects, like its sister species the insect pathogen P. luminescens (Pl). To understand the relationship between pathogenicity to insects and humans in Photorhabdus we have sequenced the complete genome of Pa strain ATCC43949 from North America. This strain (formerly referred to as Xenorhabdus luminescens strain 2) was isolated in 1977 from the blood of an 80 year old female patient with endocarditis, in Maryland, USA. Here we compare the complete genome of Pa ATCC43949 with that of the previously sequenced insect pathogen P. luminescens strain TT01 which was isolated from its entomopathogenic nematode vector collected from soil in Trinidad and Tobago.

Results
We found that the human pathogen Pa had a smaller genome (5,064,808 bp) than that of the insect pathogen Pl (5,688,987 bp) but that each pathogen carries approximately one megabase of DNA that is unique to each strain. The reduced size of the Pa genome is associated with a smaller diversity in insecticidal genes such as those encoding the Toxin complexes (Tc's), Makes caterpillars floppy (Mcf) toxins and the Photorhabdus Virulence Cassettes (PVCs). The Pa genome, however, also shows the addition of a plasmid related to pMT1 from Yersinia pestis and several novel pathogenicity islands including a novel Type Three Secretion System (TTSS) encoding island. Together these data suggest that Pa may show virulence against man via the acquisition of the pMT1-like plasmid and specific effectors, such as SopB, that promote its persistence inside human macrophages. Interestingly the loss of insecticidal genes in Pa is not reflected by a loss of pathogenicity towards insects.

Conclusion
Our results suggest that North American isolates of Pa have acquired virulence against man via the acquisition of a plasmid and specific virulence factors with similarity to those shown to play roles in pathogenicity against humans in other bacteria.
Expressional dynamics of minisatellite 33.15 tagged spermatozoal transcriptome in Bubalus bubalis
Authors: Srivastava Jyoti , Premi Sanjay , Kumar Sudhir , Ali Sher 
Published: July 2009

AbstractBackgroundTranscriptionally quiescent spermatozoa have been established to be a repository of mRNA coding for several functionally essential cellular proteins. This entourage of mRNA is envisaged to be involved in post-fertilization and early embryogenesis. Minisatellites tagged with mRNA transcripts have been implicated with gene organization, regulation and function. However, the organization and expression of the minisatellite tagged transcript diversity, particularly in spermatozoa, remains unclear.ResultsIn the present study, we identified and characterized 12 mRNA transcripts from the spermatozoa of water buffaloBubalus bubalisemploying minisatellite associated sequence amplification (MASA) and a consensus sequence of 33.15 repeat loci. Of these 33.15 tagged transcripts, only one was found to be homologous to Bovine steroid 21-hydroxylase (P-450-c21) gene. Other ten transcripts showed significant similarity with various mRNAs or chromosomal contigs across the species. The remaining one construed to be novel since this was unreported in the database (NCBI GenBank). All these uncharacterized and known transcripts showed highest expression in testis and spermatozoa compared to that in somatic tissues and ovary. Of these 12 mRNA transcripts, 4 showed differential expression in the forebrain and hindbrain of buffalo. Moreover, genes corresponding to all the 33.15 tagged spermatozoal transcripts were found to be conserved across 13 other species analyzed.ConclusionOur results show MASA as an important tool to capture mRNA transcript diversity tagged with minisatellites in the spermatozoa. Comprehensive characterization of these transcripts is envisaged to augment our understanding on the genes involved in testicular functions and sustenance of a viable paternal genome during pre- and post- fertilization events and early stages of development. Prospects of this approach in genome analysis in general and comparative genomics in particular are highlighted.
Comparison of feature selection and classification for MALDI-MS data
Authors: Liu Qingzhong , Sung Andrew H , Qiao Mengyu , Chen Zhongxue , Yang Jack Y , Yang Mary Qu , Huang Xudong , Deng Youping 
Published: July 2009

Abstract

Introduction
In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) data were recently compared; however, the issue of different feature selection methods and different classification models as they relate to classification performance has not been addressed. With the application of intelligent computing, much progress has been made in the development of feature selection methods and learning classifiers for the analysis of high-throughput biological data. The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data.

Results
We compared a well-known method of feature selection, Support Vector Machine Recursive Feature Elimination (SVMRFE), and a recently developed method, Gradient based Leave-one-out Gene Selection (GLGS) that effectively performs microarray data analysis. We also compared several learning classifiers including K-Nearest Neighbor Classifier (KNNC), Naïve Bayes Classifier (NBC), Nearest Mean Scaled Classifier (NMSC), uncorrelated normal based quadratic Bayes Classifier recorded as UDC, Support Vector Machines, and a distance metric learning for Large Margin Nearest Neighbor classifier (LMNN) based on Mahanalobis distance. To compare, we conducted a comprehensive experimental study using three types of MALDI-MS data.

Conclusion
Regarding feature selection, SVMRFE outperformed GLGS in classification. As for the learning classifiers, when classification models derived from the best training were compared, SVMs performed the best with respect to the expected testing accuracy. However, the distance metric learning LMNN outperformed SVMs and other classifiers on evaluating the best testing. In such cases, the optimum classification model based on LMNN is worth investigating for future study.