bluuebunny/crossref_metadata_2025_split huggingface dataset:
When Heuristics Clash with Parsing Routines: ERP Evidence for Conflict Monitoring in Sentence Perception
Authors: van Herten Marieke , Chwilla Dorothee J. , Kolk Herman H. J. 
Published: July 2006

Abstract
Monitoring refers to a process of quality control designed to optimize behavioral outcome. Monitoring for action errors manifests itself in an error-related negativity in event-related potential (ERP) studies and in an increase in activity of the anterior cingulate in functional magnetic resonance imaging studies. Here we report evidence for a monitoring process in perception, in particular, language perception, manifesting itself in a late positivity in the ERP. This late positivity, the P600, appears to be triggered by a conflict between two interpretations, one delivered by the standard syntactic algorithm and one by a plausibility heuristic which combines individual word meanings in the most plausible way. To resolve this conflict, we propose that the brain reanalyzes the memory trace of the perceptual input to check for the possibility of a processing error. Thus, as in Experiment 1, when the reader is presented with semantically anomalous sentences such as, “The fox that shot the poacher…,” full syntactic analysis indicates a semantic anomaly, whereas the word-based heuristic leads to a plausible interpretation, that of a poacher shooting a fox. That readers actually pursue such a word-based analysis is indicated by the fact that the usual ERP index of semantic anomaly, the so-called N400 effect, was absent in this case. A P600 effect appeared instead. In Experiment 2, we found that even when the word-based heuristic indicated that only part of the sentence was plausible (e.g., “…that the elephants pruned the trees”), a P600 effect was observed and the N400 effect of semantic anomaly was absent. It thus seems that the plausibility of part of the sentence (e.g., that of pruning trees) was sufficient to create a conflict with the implausible meaning of the sentence as a whole, giving rise to a monitoring response.
On Framing Effects in Decision Making: Linking Lateral versus Medial Orbitofrontal Cortex Activation to Choice Outcome Processing
Authors: Windmann Sabine , Kirsch Peter , Mier Daniela , Stark Rudolf , Walter Bertram , Güntürkün Onur , Vaitl Dieter 
Published: July 2006

AbstractTwo correlates of outcome processing in the orbitofrontal cortex (OFC) have been proposed in the literature: One hypothesis suggests that the lateral/medial division relates to representation of outcome valence (negative vs. positive), and the other suggests that the medial OFC maintains steady stimulus-outcome associations, whereas the lateral OFC represents changing (unsteady) outcomes to prepare for response shifts. These two hypotheses were contrasted by comparing the original with the inverted version of the Iowa Gambling Task in an event-related functional magnetic resonance imaging experiment. Results showed (1) that (caudo) lateral OFC was indeed sensitive to the steadiness of the outcomes and not merely to outcome valence and (2) that the original and the inverted tasks, although both designed to measure sensitivity for future outcomes, were not equivalent as they enacted different behaviors and brain activation patterns. Results are interpreted in terms of Kahneman and Tversky's prospect theory suggesting that cognitions and decisions are biased differentially when probabilistic future rewards are weighed against consistent punishments relative to the opposite scenario [Kahneman, D., & Tversky, A. Choices, values, and frames. American Psychologist, 39, 341–350, 1984]. Specialized processing of unsteady rewards (involving caudolateral OFC) may have developed during evolution in support of goal-related thinking, prospective planning, and problem solving.
Cognitive Rehabilitation Interventions for Executive Function: Moving from Bench to Bedside in Patients with Traumatic Brain Injury
Authors: Cicerone Keith , Levin Harvey , Malec James , Stuss Donald , Whyte John 
Published: July 2006

Abstract
Executive function mediated by prefrontally driven distributed networks is frequently impaired by traumatic brain injury (TBI) as a result of diffuse axonal injury and focal lesions. In addition to executive cognitive functions such as planning and working memory, the effects of TBI impact social cognition and motivation processes. To encourage application of cognitive neuroscience methods to studying recovery from TBI, associated reorganization of function, and development of interventions, this article reviews the pathophysiology of TBI, critiques currently employed methods of assessing executive function, and evaluates promising interventions that reflect advances in cognitive neuroscience. Brain imaging to identify neural mechanisms mediating executive dysfunction and response to interventions following TBI is also discussed.
Cognitive Rehabilitation Interventions for Neglect and Related Disorders: Moving from Bench to Bedside in Stroke Patients
Authors: Barrett Anna M. , Buxbaum Laurel J. , Coslett H. Branch , Edwards Emmeline , Heilman Kenneth M. , Hillis Argye E. , Milberg William P. , Robertson Ian H. 
Published: July 2006

AbstractThe spatial neglect syndrome, defined by asymmetric attention and action not attributed to primary motor or sensory dysfunction and accompanied by functional disability, is a major cause of post-stroke morbidity. In this review, we consider the challenges and obstacles facing scientific researches wishing to evaluate the mechanisms and effectiveness of rehabilitation interventions. Spatial neglect is a heterogeneous disorder, for which consensus research definitions are not currently available, and it is unclear which of the deficits associated with the syndrome causes subsequent disability. We review current opinion about methods of assessment, suggest a rational approach to selecting therapies which requires further study, and make systems-level and theoretical recommendations for building theory. We lastly review some creative questions for consideration in future research.
Do bronchial biopsies represent mast cell density in airways? A stereological study
Authors: Carroll M. L. , Carroll N. G. , James A. L. 
Published: July 2006

Endobronchial biopsy specimens may not adequately represent inflammatory cell counts throughout the airway wall. The present study aimed to compare mast cell density in biopsies and airway sections using both stereological and nonstereological methods.Post mortembiopsies and adjacent transverse sections were obtained from a mean of five proximal airways per case in 10 subjects who had died of nonrespiratory causes. Tryptase-positive mast cells were measured stereologically in 30-μm sections and nonstereologically in 5-μm sections using an optical disector (cells·mm-3) and cell profiles (cells·mm-2), respectively. Reference areas included the inner and total airway wall and to 100 μm below the basement membrane.Case means, based on four or more biopsy sites, significantly correlated with those on transverse sections for counts over the inner airway wall only, using both stereological and nonstereological methods. Cells·mm-3and cells·mm-2were significantly correlated within all reference areas.When endobronchial biopsies are obtained from at least four proximal airways per case, inter-subject comparisons of mean mast cell density in the inner airway wall are as well represented by counts on biopsies as they are on transverse sections. This is the case using either three-dimensional, stereological or two-dimensional, nonstereological methods.
Interstitial lung diseases associated with amyopathic dermatomyositis
Authors: Suda T. , Fujisawa T. , Enomoto N. , Nakamura Y. , Inui N. , Naito T. , Hashimoto D. , Sato J. , Toyoshima M. , Hashizume H. , Chida K. 
Published: July 2006

The aim of the present study was to clarify the clinical characteristics and prognosis of patients with interstitial lung disease (ILD) associated with amyopathic dermatomyositis (ILD-ADM).The study consisted of 14 consecutive patients with ILD-ADM. Patients were classified into two categories, acute/subacute and chronic forms, according to the clinical presentation of ILD. The clinical features, responsiveness to therapy, and prognosis between the two forms were compared.Nine ILD-ADM patients were categorised as the acute/subacute form, and five as the chronic form. Arterial oxygen tension was significantly lower in the acute/subacute ILD than chronic ILD patients. On high-resolution computed tomography, ground-glass opacities were frequently found in the two forms, but consolidation was more common in acute/subacute ILD than chronic ILD. Bronchoalveolar lavage analysis showed higher numbers of total cells and lymphocytes in acute/subacute ILD than chronic ILD. Histologically, the most common finding was nonspecific interstitial pneumonia in the two forms, while diffuse alveolar damage was only found in acute/subacute ILD. Acute/subacute ILD was generally resistant to therapy, while chronic ILD responded well. Notably, the mortality of acute/subacute ILD was much higher than that of chronic ILD (67versus0%, respectively).In conclusion, interstitial lung disease associated with amyopathic dermatomyositis includes two different forms, the acute/subacute and chronic forms, with distinct prognoses.
Thalidomide reduces IL-18, IL-8 and TNF-α release from alveolar macrophages in interstitial lung disease
Authors: Ye Q. , Chen B. , Tong Z. , Nakamura S. , Sarria R. , Costabel U. , Guzman J. 
Published: July 2006

Thalidomide exhibits diverse actions of anti-inflammation, immunomodulation and anti-angiogenesis. The efficacy of thalidomide treatment in sarcoidosis with lupus pernio is thought to be due to inhibition of tumour necrosis factor (TNF)-α. The mechanisms that underlie the properties of thalidomide are still unclear in interstitial lung disease.The current authors investigated the potential inhibitory effects of thalidomide at concentrations of 0.1, 0.01 and 0.001 mM on the production of transforming growth factor-β, TNF-α, interleukin (IL)-1β, IL-6, IL-8, IL-10, IL-12p70, IL-12p40 and IL-18 by alveolar macrophages from bronchoalveolar lavage in patients with sarcoidosis (n = 8), hypersensitivity pneumonitis (HP; n = 8) and idiopathic pulmonary fibrosis (IPF; n = 12).In sarcoidosis and HP patients, thalidomide induced a dose-dependent, partial suppression of lipopolysacchride (LPS)-stimulated TNF-α, IL-12p40 and IL-18 release. At the highest thalidomide concentration (0.1 mM), LPS-stimulated IL-8 production was also suppressed. In IPF patients, although spontaneous production of TNF-α, IL-12p40, IL-18 and IL-8 was lower than in sarcoidosis and HP patients, with LPS stimulation the cytokines were significantly elevated and also partially inhibited by thalidomide.In conclusion, thalidomide has the potential to improve the therapeutic regimens for sarcoidosis, hypersensitivity pneumonitis and idiopathic pulmonary fibrosis by reducing tumour necrosis factor-α, interleukin-12p40, interleukin-18 and interleukin-8 production.
Genetic linkage analysis of pulmonary fibrotic response to silica in mice
Authors: Ohtsuka Y. , Wang X-T. , Saito J. , Ishida T. , Munakata M. 
Published: July 2006

Inter-individual variations in the development of silicosis, even within the same environments, have been reported, which suggest the contribution of genetic factors in silicosis aetiology. The aim of the present study was to determine whether there is any significant genetic influence on the development of silicosis. Furthermore, which genetic loci are responsible for the pulmonary response to silica exposure?Eight strains of inbred mice were used to examine the genetic influence on the lung fibrotic response to silica exposure. After intercross-breeding between the most susceptible and most resistant strains, a genome-wide linkage analysis of quantitative trait loci (QTL) was performed. Hydroxyproline was applied as an index, and genotypes of 167 marker genes were analysed by fragment analysis using a capillary-type sequencer.There was significant inter-strain difference in the mean concentration of hydroxyproline contents among the eight strains of mice. Breeding studies were conducted between the most susceptible, C57BL/6J, and the most resistant strain, CBA/J. A genome-wide linkage analysis of silica-exposed intercrossed cohorts identified significant QTL on chromosome 4 and suggestive QTL on chromosomes 3 and 18.The present study demonstrates that genetic factors may play a significant role in fibrotic-lung responses to silica; one significant and two suggestive quantitative trait loci were identified.
Mechanical ventilation affects alveolar fibrinolysis in LPS-induced lung injury
Authors: Dahlem P. , Bos A. P. , Haitsma J. J. , Schultz M. J. , Wolthuis E. K. , Meijers J. C. M. , Lachmann B. 
Published: July 2006

The aim of the present study was to determine the effects of mechanical ventilation on alveolar fibrin turnover in lipopolysaccharide (LPS)-induced lung injury.In a randomised controlled trial, Sprague–Dawley rats (n = 61) were allocated to three ventilation groups after intratracheal LPS (Salmonella enteritidis) instillations. Group I animals were subjected to 16 cmH2O positive inspiratory pressure (PIP) and 5 cmH2O positive end-expiratory pressure (PEEP); group II animals to 26 cmH2O PIP and 5 cmH2O PEEP; and group III animals to 35 cmH2O PIP and 5 cmH2O PEEP. Control rats (not mechanically ventilated) received LPS. Healthy rats served as a reference group. Levels of thrombin–antithrombin complex (TATc),D-dimer, plasminogen activator inhibitor (PAI) activity and PAI-1 antigen in bronchoalveolar lavage fluid were measured.LPS-induced lung injury increased TATc,D-dimer and PAI activity and PAI-1 antigen levelsversushealthy animals. High pressure-amplitude ventilation increased TATc concentrations.D-dimer concentrations were not significantly raised. Instead, PAI activity increased with the amplitude of the pressure, from 0.7 U·mL-1in group I to 3.4 U·mL-1in group II and 5.0 U·mL-1in group III. There was no change in PAI-1 antigen levels.In conclusion, mechanical ventilation creates an alveolar/pulmonary anti-fibrinolytic milieu in endotoxin-induced lung injury which, at least in part, might be due to an increase in plasminogen activator inhibitor activity.
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
Authors: Hu Jianjun , Yang Yifeng D , Kihara Daisuke 
Published: July 2006

Abstract

Background
Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.

Results
We proposed a novel clustering-based ensemble algorithm named EMD for de novo motif discovery by combining multiple predictions from multiple runs of one or more base component algorithms. The ensemble approach is applied to the motif discovery problem for the first time. The algorithm is tested on a benchmark dataset generated from E. coli RegulonDB. The EMD algorithm has achieved 22.4% improvement in terms of the nucleotide level prediction accuracy over the best stand-alone component algorithm. The advantage of the EMD algorithm is more significant for shorter input sequences, but most importantly, it always outperforms or at least stays at the same performance level of the stand-alone component algorithms even for longer sequences.

Conclusion
We proposed an ensemble approach for the motif discovery problem by taking advantage of the availability of a large number of motif discovery programs. We have shown that the ensemble approach is an effective strategy for improving both sensitivity and specificity, thus the accuracy of the prediction. The advantage of the EMD algorithm is its flexibility in the sense that a new powerful algorithm can be easily added to the system.
Bcl-2 protein expression is associated with p27 and p53 protein expressions and MIB-1 counts in breast cancer
Authors: Tsutsui Shinichi , Yasuda Kazuhiro , Suzuki Kosuke , Takeuchi Hideya , Nishizaki Takashi , Higashi Hidefumi , Era Shoichi 
Published: July 2006

Abstract

Background
Recent experimental studies have shown that Bcl-2, which has been established as a key player in the control of apoptosis, plays a role in regulating the cell cycle and proliferation. The aim of this study was to investigate the relationship between Bcl-2 and p27 protein expression, p53 protein expression and the proliferation activity as defined by the MIB-1 counts. The prognostic implication of Bcl-2 protein expression in relation to p27 and p53 protein expressions and MIB-1 counts for breast cancer was also evaluated.

Methods
The immunohistochemical expression of Bcl-2 protein was evaluated in a series of 249 invasive ductal carcinomas of the breast, in which p27 and p53 protein expressions and MIB-1 counts had been determined previously.

Results
The Bcl-2 protein expression was found to be decreased in 105 (42%) cases. A decreased Bcl-2 protein expression was significantly correlated with a nuclear grade of III, a negative estrogen receptor, a decreased p27 protein expression, a positive p53 protein expression, positive MIB-1 counts and a positive HER2 protein expression. The incidence of a nuclear grade of III and positive MIB-1 counts increased as the number of abnormal findings of Bcl-2, p27 and p53 protein expressions increased. A univariate analysis indicated a decreased Bcl-2 protein expression to be significantly (p = 0.0089) associated with a worse disease free survival (DFS), while a multivariate analysis indicated the lymph node status and MIB-1 counts to be independently significant prognostic factors for the DFS.

Conclusion
The Bcl-2 protein expression has a close correlation with p27 and p53 protein expressions and the proliferation activity determined by MIB-1 counts in invasive ductal carcinoma of the breast. The prognostic value of Bcl-2 as well as p27 and p53 protein expressions was dependent on the proliferation activity in breast cancer.
Endostatin inhibits VEGF-A induced osteoclastic bone resorption in vitro
Authors: Sipola Annina , Nelo Katri , Hautala Timo , Ilvesaro Joanna , Tuukkanen Juha 
Published: July 2006

Abstract

Background
Endostatin is a C-terminal fragment of collagen XVIII which is a component of basement membranes with the structural properties of both collagens and proteoglycans. Endostatin has a major role in angiogenesis which is intimately associated with bone development and remodeling. Signaling between the endothelial cells and the bone cells, for example, may have a role in recruitment of osteoclastic precursor cells. Our study aims at exploring a possibility that endostatin, either as a part of basement membrane or as a soluble molecule, may control osteoclastogenesis and osteoclastic bone resorption in vitro.

Methods
Rat pit formation assay was employed in order to examine the effect of endostatin alone or in combination with vascular endothelial growth factor-A (VEGF-A) on bone resorption in vitro. Effect of these agents on osteoclast differentiation in vitro was also tested. Osteoclastogenesis and the number of osteoclasts were followed by tartrate resistant acid phosphatase (TRACP) staining and resorption was evaluated by measuring the area of excavated pits.

Results
Endostatin inhibited the VEGF-A stimulated osteoclastic bone resorption, whereas endostatin alone had no effect on the basal resorption level in the absence of VEGF-A. In addition, endostatin could inhibit osteoclast differentiation in vitro independent of VEGF-A.

Conclusion
Our in vitro data indicate that collagen XVIII/endostatin can suppress VEGF-A induced osteoclastic bone resorption to the basal level. Osteoclastogenesis is also inhibited by endostatin. The regulatory effect of endostatin, however, is not critical since endostatin alone does not modify the basal bone resorption.
Structured data entry for narrative data in a broad specialty: patient history and physical examination in pediatrics
Authors: Bleeker Sacha E , Derksen-Lubsen Gerarda , van Ginneken Astrid M , van der Lei Johan , Moll Henriëtte A 
Published: July 2006

Abstract

Background
Whereas an electronic medical record (EMR) system can partly address the limitations, of paper-based documentation, such as fragmentation of patient data, physical paper records missing and poor legibility, structured data entry (SDE, i.e. data entry based on selection of predefined medical concepts) is essential for uniformity of data, easier reporting, decision support, quality assessment, and patient-oriented clinical research. The aim of this project was to explore whether a previously developed generic (i.e. content independent) SDE application to support the structured documentation of narrative data (called OpenSDE) can be used to model data obtained at history taking and physical examination of a broad specialty.

Methods
OpenSDE was customized for the broad domain of general pediatrics: medical concepts and its descriptors from history taking and physical examination were modeled into a tree structure.

Results
An EMR system allowing structured recording (OpenSDE) of pediatric narrative data was developed. Patient history is described by 20 main concepts and physical examination by 11. In total, the thesaurus consists of about 1800 items, used in 8648 nodes in the tree with a maximum depth of 9 levels. Patient history contained 6312 nodes, and physical examination 2336. User-defined entry forms can be composed according to individual needs, without affecting the underlying data representation. The content of the tree can be adjusted easily and sharing records among different disciplines is possible. Data that are relevant in more than one context can be accessed from multiple branches of the tree without duplication or ambiguity of data entry via "shortcuts".

Conclusion
An expandable EMR system with structured data entry (OpenSDE) for pediatrics was developed, allowing structured documentation of patient history and physical examination. For further evaluation in other environments, the tree structure for general pediatrics is available at the Erasmus MC Web site (in Dutch, translation into English in progress) [1]. The generic OpenSDE application is available at the OpenSDE Web site [2].
The Impact of Petrosal Vein Preservation on Postoperative Auditory Function in Surgery of Petrous Apex Meningiomas
Authors: Gharabaghi Alireza , Koerbel Andrei , Hubert Löwenheim , Kaminsky Jan , Samii Madjid , Tatagiba Marcos 
Published: July 2006

Abstract

OBJECTIVE:
The importance of preserving the superior petrosal vein has received increasing attention in the surgical treatment of pathologies involving the petrous apex. Recent reports have associated postoperative auditory nerve dysfunction with petrosal vein sacrifice. However, there is no systematic clinical study available thus far focusing on the postoperative auditory function after petrosal vein obliteration.

METHODS:
In 55 patients with meningiomas involving the petrous apex, pre- and intraoperative findings including petrosal vein sectioning were analyzed retrospectively concerning their impact on postoperative auditory function.

RESULTS:
The petrosal vein was preserved in 26 (47%) cases. In 27 (49%) cases, this vein was not preserved. Hearing loss occurred in 11% of all cases. In the preserved-vein group, postoperative hearing loss occurred in 3 of 26 (11%) cases and in the sacrificed-vein group in 3 of 27 (11%) cases.

CONCLUSION:
Sacrifice of the petrosal vein during surgery of petrous apex meningiomas seems not to have an impact on postoperative auditory function.