bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explicit versus Implicit Processing of Representational Space in Neglect: Dissociations in Accessing the Mental Number Line
Authors: Priftis Konstantinos , Zorzi Marco , Meneghello Francesca , Marenzi Roberto , Umiltà Carlo 
Published: May 2006

Abstract
The present study investigated the effects of left hemispatial neglect on two tasks activating the mental number line (MNL). Six patients with left neglect performed a mental number bisection task and a modified version of the Spatial Numerical Association of Response Codes (SNARC) task. Effects of left neglect were observed in the number bisection task, but not in the SNARC task. We argue that the dissociation between number bisection and SNARC resembles, in the representational space of the MNL, previously reported dissociations on neglect between explicit knowledge (assessed by direct tasks) and implicit knowledge (assessed by indirect tasks).
Orienting Attention to Points in Time Improves Stimulus Processing Both within and across Modalities
Authors: Lange Kathrin , Röder Brigitte 
Published: May 2006

Abstract
Spatial attention affects the processing of stimuli of both a task-relevant and a task-irrelevant modality. The present study investigated if similar cross-modal effects exist when attention is oriented to a point in time. Short (600 msec) and long (1200 msec) empty intervals, marked by a tactile onset and an auditory or a tactile offset marker, were presented. In each block, the participants had to attend one interval and one modality. Event-related potentials (ERPs) to auditory and tactile offset markers of attended as compared to unattended intervals were characterized by an enhancement of early negative deflections of the auditory and somatosensory ERPs (audition, 100–140 msec; touch, 130–180 msec) when audition or touch was task relevant, respectively. Similar effects were found for auditory stimuli when touch was task relevant. An additional reaction time experiment revealed faster responses to both auditory and tactile stimuli at the attended as compared to the unattended point in time, irrespective of which modality was primary. Both behavioral and ERP data show that attention can be focused on a point in time, which results in a more efficient processing of auditory and tactile stimuli. The ERP data further suggest that a relative enhancement at perceptual processing stages contributes to the processing advantage for temporally attended stimuli. The existence of cross-modal effects of temporal attention underlines the importance of time as a feature for binding input across different modalities.
Neural Activity in Monkey Prefrontal Cortex Is Modulated by Task Context and Behavioral Instruction during Delayed-match-to-sample and Conditional Prosaccade—Antisaccade Tasks
Authors: Johnston Kevin , Everling Stefan 
Published: May 2006

Abstract
Complex behavior often requires the formation of associations between environmental stimuli and motor responses appropriate to those stimuli. Moreover, the appropriate response to a given stimulus may vary depending on environmental context. Stimulus-response associations that are adaptive in one situation may not be in another. The prefrontal cortex (PFC) has been shown to be critical for stimulus-response mapping and the implementation of task context. To investigate the neural representation of sensory-motor associations and task context in the PFC, we recorded the activity of prefrontal neurons in two monkeys while they performed two tasks. The first task was a delayed-match-to-sample task in which monkeys were presented with a sample picture and rewarded for making a saccade to the test picture that matched the sample picture following a delay period. The second task was a conditional visuomotor task in which identical sample pictures were presented. In this task, animals were rewarded for performing either prosaccades or antisaccades following the delay period depending on sample picture identity. PFC neurons showed task selectivity, object selectivity, and combinations of task and object selectivity. These modulations of activity took the form of a reduction in stimulus and delay-related activity, and a pro/anti instruction-based grouping of delay activity in the conditional visuomotor task. These data show that activity in PFC neurons is modulated by experimental context, and that this activity represents the formal demands of the task currently being performed.
Singularities in Primate Orientation Maps
Authors: Obermayer K. , Blasdel G. G. 
Published: May 2006

We report the results of an analysis of orientation maps in primate striate cortex with focus on singularities and their distribution. Data were obtained from squirrel monkeys and macaque monkeys of different ages. We find that approximately 80% of singularities that are nearest neighbors have the opposite sign and that the spatial distribution of singularities differs significantly from a random distribution of points. We do not find evidence for consistent geometric patterns that singularities may form across the cortex. Except for a different overall alignment of orientation bands and different periods of repetition, maps obtained from different animals and different ages are found similar with respect to the measures used. Orientation maps are then compared with two different pattern models that are currently discussed in the literature: bandpass-filtered white noise, which accounts very well for the overall map structure, and the field analogy model, which specifies the orientation map by the location of singularities and their properties. The bandpass-filtered noise approach to orientation patterns correctly predicts the sign correlations between singularities and accounts for the deviations in the spatial distribution of singularities away from a random dot pattern. The field analogy model can account for the structure of certain local patches of the orientation map but not for the whole map. Neither of the models is completely satisfactory, and the structure of the orientation map remains to be fully explained.
Multiunit Normalized Cross Correlation Differs from the Average Single-Unit Normalized Correlation
Authors: Bedenbaugh Purvis , Gerstein George L. 
Published: May 2006

As the technology for simultaneously recording from many brain locations becomes more available, more and more laboratories are measuring the cross-correlation between single-neuron spike trains, and between composite spike trains derived from several undiscriminated cells recorded on a single electrode (multiunit clusters). The relationship between single-unit correlations and multiunit cluster correlations has not yet been fully explored. We calculated the normalized cross-correlation (NCC) between single unit spike trains and between small clusters of units recorded in the rat somatosensory cortex. The NCC between small clusters of units was larger than the NCC between single units. To understand this result, we investigated the scaling of the NCC with the number of units in a cluster. Multiunit cross-correlation can be a more sensitive detector of neuronal relationship than single-unit cross-correlation. However, changes in multiunit cross-correlation are difficult to interpret uniquely because they depend on the number of cells recorded on each electrode and because they can arise from changes in the correlation between cells recorded on a single electrode or from changes in the correlation between cells recorded on two electrodes.
Workplace Interactions that Facilitate or Impede Reflective Practice
Authors: Heel David , Sparrow John , Ashford Robert 
Published: May 2006

This article highlights a study undertaken in the workplace that observed the features of a National Health Service (NHS) general manager's job that determined ‘reflective space’ at work. The study was initiated following the suggestion that the workplace might conspire to limit reflective practice amongst NHS general managers who would ordinarily espouse the value of such an approach. Assessing this inference would, arguably, illuminate the relative productivity of meetings and workplace events and assist in future application amongst NHS employees. The study did not attempt to question whether NHS general managers were armed with the competencies of reflection but whether they were able to apply it having developed the skills and what might constrain them. In doing so there would then be opportunities to challenge convention through the application of a reflective tool. The study involved the classification of work events where reflection was notably high or low. An analysis of data indicated five major characteristics of the reflective practitioner's workplace that can inhibit or facilitate reflective practice. This has enabled the development of a reflective tool to assist NHS general managers. The tool might therefore be added to the personal management development ‘toolkit’ that each general manager might wish to access.
The molecular classification of multiple myeloma
Authors: Zhan Fenghuang , Huang Yongsheng , Colla Simona , Stewart James P. , Hanamura Ichiro , Gupta Sushil , Epstein Joshua , Yaccoby Shmuel , Sawyer Jeffrey , Burington Bart , Anaissie Elias , Hollmig Klaus , Pineda-Roman Mauricio , Tricot Guido , van Rhee Frits , Walker Ronald , Zangari Maurizio , Crowley John , Barlogie Bart , Shaughnessy John D. 
Published: May 2006

AbstractTo better define the molecular basis of multiple myeloma (MM), we performed unsupervised hierarchic clustering of mRNA expression profiles in CD138-enriched plasma cells from 414 newly diagnosed patients who went on to receive high-dose therapy and tandem stem cell transplants. Seven disease subtypes were validated that were strongly influenced by known genetic lesions, such as c-MAF– and MAFB-, CCND1- and CCND3-, and MMSET-activating translocations and hyperdiploidy. Indicative of the deregulation of common pathways by gene orthologs, common gene signatures were observed in cases with c-MAF and MAFB activation and CCND1 and CCND3 activation, the latter consisting of 2 subgroups, one characterized by expression of the early B-cell markers CD20 and PAX5. A low incidence of focal bone disease distinguished one and increased expression of proliferation-associated genes of another novel subgroup. Comprising varying fractions of each of the other 6 subgroups, the proliferation subgroup dominated at relapse, suggesting that this signature is linked to disease progression. Proliferation and MMSET-spike groups were characterized by significant overexpression of genes mapping to chromosome 1q, and both exhibited a poor prognosis relative to the other groups. A subset of cases with a predominating myeloid gene expression signature, excluded from the profiling analyses, had more favorable baseline characteristics and superior prognosis to those lacking this signature.
An integrated approach to the prediction of domain-domain interactions
Authors: Lee Hyunju , Deng Minghua , Sun Fengzhu , Chen Ting 
Published: May 2006

Abstract

Background
The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain interactions, it is crucial to understand protein interactions at the level of the domains. The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets.

Results
We combine protein interaction data sets from multiple species, molecular sequences, and gene ontology to construct a set of high-confidence domain-domain interactions. First, we propose a new measure, the expected number of interactions for each pair of domains, to score domain interactions based on protein interaction data in one species and show that it has similar performance as the E-value defined by Riley et al. [1]. Our new measure is applied to the protein interaction data sets from yeast, worm, fruitfly and humans. Second, information on pairs of domains that coexist in known proteins and on pairs of domains with the same gene ontology function annotations are incorporated to construct a high-confidence set of domain-domain interactions using a Bayesian approach. Finally, we evaluate the set of domain-domain interactions by comparing predicted domain interactions with those defined in iPfam database [2, 3] that were derived based on protein structures. The accuracy of predicted domain interactions are also confirmed by comparing with experimentally obtained domain interactions from H. pylori [4]. As a result, a total of 2,391 high-confidence domain interactions are obtained and these domain interactions are used to unravel detailed protein and domain interactions in several protein complexes.

Conclusion
Our study shows that integration of multiple biological data sets based on the Bayesian approach provides a reliable framework to predict domain interactions. By integrating multiple data sources, the coverage and accuracy of predicted domain interactions can be significantly increased.
Cytogenetic characterization and H-ras associated transformation of immortalized human mammary epithelial cells
Authors: Rao Krishna , Alper Özge , Opheim Kent E , Bonnet George , Wolfe Kristine , Bryant Eileen , Larivee Siobhan O'Hara , Porter Peggy , McDougall James K 
Published: May 2006

Abstract

Introduction
Immortalization is a key step in malignant transformation, but immortalization alone is insufficient for transformation. Human mammary epithelial cell (HMEC) transformation is a complex process that requires additional genetic changes beyond immortalization and can be accomplished in vitro by accumulation of genetic changes and expression of H-ras.

Methods
HMEC were immortalized by serial passaging and transduction with the catalytic subunit of the human telomerase gene (hTERT). The immortalized cells were passaged in vitro and studied by a combination of G- banding and Spectral Karyotyping (SKY). H-ras transduced, hTERT immortalized cells were cloned in soft agar and injected into nude mice. Extensive analysis was performed on the tumors that developed in nude mice, including immunohistochemistry and western blotting.

Results
Immortal HMEC alone were not tumorigenic in γ-irradiated nude mice and could not grow in soft agar. Late passage hTERT immortalized HMEC from a donor transduced with a retroviral vector containing the mutant, autoactive, human H-ras 61L gene acquired anchorage independent growth properties and the capacity for tumorigenic growth in vivo. The tumors that developed in the nude mice were poorly differentiated epithelial carcinomas that continued to overexpress ras. These cells were resistant to doxorubicin mediated G1/S phase arrest but were sensitive to treatment with a farnesyltransferase inhibitor.

Conclusion
Some of the cytogenetic changes are similar to what is observed in premalignant and malignant breast lesions. Despite these changes, late passage immortal HMEC are not tumorigenic and could only be transformed with overexpression of a mutant H-ras oncogene.
Expression and processing of the Hepatitis E virus ORF1 nonstructural polyprotein
Authors: Sehgal Deepak , Thomas Saijo , Chakraborty Mahua , Jameel Shahid 
Published: May 2006

Abstract

Background
The ORF1 of hepatitis E virus (HEV) encodes a nonstructural polyprotein of ~186 kDa that has putative domains for four enzymes: a methyltransferase, a papain-like cysteine protease, a RNA helicase and a RNA dependent RNA polymerase. In the absence of a culture system for HEV, the ORF1 expressed using bacterial and mammalian expression systems has shown an ~186 kDa protein, but no processing of the polyprotein has been observed. Based on these observations, it was proposed that the ORF1 polyprotein does not undergo processing into functional units. We have studied ORF1 polyprotein expression and processing through a baculovirus expression vector system because of the high level expression and post-translational modification abilities of this system.

Results
The baculovirus expressed ORF1 polyprotein was processed into smaller fragments that could be detected using antibodies directed against tags engineered at both ends. Processing of this ~192 kDa tagged ORF1 polyprotein and accumulation of lower molecular weight species took place in a time-dependent manner. This processing was inhibited by E-64d, a cell-permeable cysteine protease inhibitor. MALDI-TOF analysis of a 35 kDa processed fragment revealed 9 peptide sequences that matched the HEV methyltransferase (MeT), the first putative domain of the ORF1 polyprotein. Antibodies to the MeT region also revealed an ORF1 processing pattern identical to that observed for the N-terminal tag.

Conclusion
When expressed through baculovirus, the ORF1 polyprotein of HEV was processed into smaller proteins that correlated with their proposed functional domains. Though the involvement of non-cysteine protease(s) could not be be ruled out, this processing mainly depended upon a cysteine protease.
Comparative plasticity of brain synapses in inbred mouse strains
Authors: Nguyen P. V. 
Published: May 2006

SUMMARYOne niche of experimental biology that has experienced considerable progress is the neurobiology of learning and memory. A key contributor to such progress has been the widespread use of transgenic and `knockout' mice to elucidate the mechanisms of identifiable phenotypes of learning and memory. Inbred mouse strains are needed to generate genetically modified mice. However, genetic variations between inbred strains can confound the interpretation of cellular neurophysiological phenotypes of mutant mice. It is known that altered physiological strength of synaptic transmission (`synaptic plasticity') can modify and regulate learning and memory. Characterization of the synaptic phenotypes of inbred mouse strains is needed to identify the most appropriate strains to use for generating mutant mouse models of memory function. More importantly, comparative electrophysiological analyses of inbred mice per se can also shed light on which forms of synaptic plasticity underlie particular types of learning and memory. Many such analyses have focused on synaptic plasticity in the hippocampus because of the critical roles of this brain structure in the formation and consolidation of long-term memories. Comparative electrophysiological data obtained from several inbred mouse strains are reviewed here to highlight the following key notions: (1) synaptic plasticity is influenced by the genetic backgrounds of inbred mice; (2) the plasticity of hippocampal synapses in inbred mice is`tuned' to particular temporal patterns of activity; (3) long-term potentiation, but not long-term depression, is a cellular correlate of behavioural memory performance in some strains; (4) synaptic phenotyping of inbred mouse strains can identify cellular models of memory impairment that can be used to elucidate mechanisms that may cause specific memory deficits.
Phenotypic plasticity of adult myocardium: molecular mechanisms
Authors: Swynghedauw Bernard 
Published: May 2006

SUMMARYCardiac phenotypic plasticity (so-called cardiac remodelling, CR) is characterized by changes in myocardial structure that happen in response to either mechanical overload or a loss of substance such as that occurring after myocardial infarction.Mechanosensation is a widespread biological process and is inextricably mixed with other transduction systems from hormones and vasopeptides, which ultimately produce post-translational modifications of transcription factors. The expression of the four main transcription factors during cardiogenesis is also enhanced as a link to foetal reprogramming.CR results from re-expression of the foetal programme, which is mostly adaptive, but also from several other phenotypic modifications that are not usually adaptive, such as fibrosis. (i) The initial determinant is mechanical,and re-expression of the foetal programme includes a global increase in genetic expression with cardiac hypertrophy, re-expression of genes that are normally not expressed in the adult ventricles, repression of genes not expressed during the foetal life, and activation of pre-exisiting stem cells. Microarray technology has revealed a coordinated change in expression of genes pertaining to signal transduction, metabolic function, structure and motility,and cell organism defence. The physiological consequence is a better adapted muscle. (ii) During clinical conditions, the effects of mechanics are modified by several interfering determinants that modify CR, including senescence,obesity, diabetes, ischemia and the neurohormonal reaction. Each of these factors can alter myocardial gene expression and modify molecular remodelling of mechanical origin.Finally, as compared to evolutionary phenotypic plasticity described in plants and insects in response to variations in environmental conditions, in CR, the environmental factor is internal, plasticity is primarily adaptive,and it involves coordinated changes in over 1400 genes. Study of reaction norms showed that the genotypes from different animal species are similarly plastic, but there are transgenic models in which adaptation to mechanics is not caused by hypertrophy but by qualitative changes in gene expression.
Neuronal networks and synaptic plasticity: understanding complex system dynamics by interfacing neurons with silicon technologies
Authors: Colicos Michael A. , Syed Naweed I. 
Published: May 2006

SUMMARY
Information processing in the central nervous system is primarily mediated through synaptic connections between neurons. This connectivity in turn defines how large ensembles of neurons may coordinate network output to execute complex sensory and motor functions including learning and memory. The synaptic connectivity between any given pair of neurons is not hard-wired;rather it exhibits a high degree of plasticity, which in turn forms the basis for learning and memory. While there has been extensive research to define the cellular and molecular basis of synaptic plasticity, at the level of either pairs of neurons or smaller networks, analysis of larger neuronal ensembles has proved technically challenging. The ability to monitor the activities of larger neuronal networks simultaneously and non-invasively is a necessary prerequisite to understanding how neuronal networks function at the systems level. Here we describe recent breakthroughs in the area of various bionic hybrids whereby neuronal networks have been successfully interfaced with silicon devices to monitor the output of synaptically connected neurons. These technologies hold tremendous potential for future research not only in the area of synaptic plasticity but also for the development of strategies that will enable implantation of electronic devices in live animals during various memory tasks.