bluuebunny/crossref_metadata_2025 huggingface dataset:
A Middle–Upper Miocene fluvial–lacustrine rift sequence in theSong Ba Rift, Vietnam: an analogue to oil-prone, small-scale continental rift basins
Authors: Nielsen L. H. , Petersen H. I. , Thai N. D. , Duc N. A. , Fyhn M. B. W. , Boldreel L. O. , Tuan H. A. , Lindström S. , Hien L. V.
Published: October 2008

The small Neogene Krong Pa graben is situated within the continental Song Ba Rift, which is bounded by strike-slip faults that were reactivated as extensional faults in Middle Miocene time. The 500 m thick graben-fill shows an overall depositional development reflecting the structural evolution, which is very similar to much larger and longer-lived graben. The basal graben-fill consists of thin fluvial sandstones interbedded with well-oxygenated lacustrine siltstones in the basin centre, while very coarse-grained fluvial sandstones and conglomerates dominate at the basin margins. With increased subsidence rate and possibly a higher influx of water from the axial river systems the general water level in the graben rose and deep lakes formed. High organic preservation in the lakes prompted the formation of two excellent oil-prone lacustrine source-rock units. In the late phase of the graben development sedimentation rate outpaced the formation of accommodation space and fluvial activity increased again. During periods when the general sedimentation rate was in balance with the creation of accommodation space the environment changed frequently between lake deposition and intermittent vigorous fluvial activity. It is likely that the resulting interbedding of fluvial sandstones and lacustrine sediments reflects variations in precipitation. In periods of little precipitation the lakes diminished and lake bottoms became exposed. After heavy precipitation, transverse river systems transported sands from the rift shoulders across the exposed lake bottom and fluvial sands were deposited on lake bottom sediments. Subsequently, lake level rose due to increased water supply from the axial river and the sands were drowned and topped by transgressive lacustrine mudstones. These sandstones may function as carrier beds, whereas the braided fluvial sandstones and conglomerates along the graben margins may form reservoirs. The Krong Pa graben thus contains oil-prone lacustrine source rocks, effective conduits for generated hydrocarbons and reservoir sandstones side-sealed by the graben faults toward the footwall granites. In addition to the structural and climatic signals recorded by the graben-fill, sediment partitioning among the partly isolated basins along the rift axis seems to have been important.
Return to rifts – the next wave: fresh insights into the petroleum geology of global rift basins
Authors: Fraser Scot I. , Fraser Alastair J. , Lentini Michael R. , Gawthorpe Robert L.
Published: October 2008

Rift basin exploration has provided the oil and gas industry with almost one third of discovered global hydrocarbon resources. The maturity of prolific passive margin sequence plays has necessitated a shift in technical emphasis to understanding petroleum geology of the deeper precursor rift basin megasequences. Modelling of these petroleum systems relies extensively on theoretical stretching hypotheses for whole-crust evolution and heat flow prediction. Several alternatives have emerged to account for anomalous rift-related thermal stress, asymmetry of structural styles and origin of thick syn-rift ‘sag-basin’ subsidence patterns at passive continental margins. These observations cannot be predicted by the pure shear uniform stretching model first introduced by McKenzie in 1978. Newly acquired, 2D long cable deep seismic records provide empirical evidence that supports more complex, polyphase, depth-dependent stretching origins for rift-basin formation. Heterogeneities are believed to be inherent in the brittle upper crust, in the ductile lower crust and lithospheric mantle and so result in the complex distribution of accommodation space recorded by syn-rift megasequence deposition during episodes of orthogonal or oblique extension. No single stretching model uniquely describes the varied structural response of the anisotropic crust to plate-scale extension. A hybrid of phased simple and pure shear deformation mechanisms separated by regional lateral, and possibly vertical crustal discontinuities, may explain the apparent paradox of along-strike co-existence of uniform versus depth-dependent stretching structural geometries.
Combined effects of structural, stratigraphic and well controls on production variability in faulted shallow-marine reservoirs
Authors: Skorstad A. , Kolbjørnsen O. , Manzocchi T. , Carter J. N. , Howell J. A.
Published: October 2008

Several key parameters that describe a prograding shallow-marine reservoir are investigated for their relative importance on hydrocarbon production variability. Sedimentological parameters are aggradation angle, progradation direction relative to the waterflood, continuity of cemented surfaces and shoreline curvature. Structural parameters are the fault pattern, the density (throw) of the faults and the fault-rock permeability. The last component investigated is the effect of well placements. Having three distinct levels for all sedimentological and structural parameters in addition to a non-faulted case gives a dataset of 2268 reservoir models. Four different sets of well locations produce 9072 production datasets.

The variability of the production data is decomposed into its explanatory factors in order to see the relative importance of the chosen parameters. The production data include the total production, the discounted production and the recovery factor. The sedimentological parameters dominate both the production and the discounted production variability, especially the aggradation angle and progradation direction, whereas the fault pattern is equally significant for the recovery factor. Continuity of sedimentological barriers were found to contribute less than expected to the production variability for these reservoir models, and the well placements also showed a low effect.
Upscaling uncertainty analysis in a shallow-marine environment
Authors: Stephen Karl D. , Yang Canghu , Carter Jonathan N. , Howell John A. , Manzocchi Tom , Skorstad Arne
Published: October 2008

Geological models are often created at a scale finer than is suitable for flow simulation and also ignore the effects of sub-cellular heterogeneities. Upscaling of static and dynamic reservoir properties is an important process that captures the impact of smaller scales, ensuring that both heterogeneity and the flow physics are represented more accurately. A Geopseudo upscaling approach for shallow-marine reservoirs is presented, which captures the essential flow characteristics across a range of scales from laminae to the simulation grid. Starting with a base-case set of minimum assumptions enables generation of one set of pseudo-relative permeability and capillary pressure curves per facies. This is then expanded to investigate the limitations of these assumptions and compare their impact against variations in large-scale geological and structural parameters. For the analysis, two-level full factorial experimental design is used to determine important parameters. A comparison of upscaling effects is also performed.

The most important upscaling and fine-scale parameters identified by the analysis are the shape of the capillary pressure curve, lamina-scale permeability variation and upscaling flow speed. Of similar importance are the sedimentological parameters for shoreline aggradation angle and curvature. Fault direction (perpendicular and parallel to the shoreline) and the fine-scale upscaling method are of moderate to low importance. The shallow-marine parameter for clinoform barrier strength and the direction of flow considered when upscaling are unimportant. Analysis of upscaling effects suggests that the algorithm used at the intermediate scale is not important, while the assumed flow speed is very important, typically resulting in a 10% maximum variation in cumulative recovery. Fine-scale properties and upscaling methods affect recovery mostly due to increased initial water saturations but also because of early breakthrough.
Evaluation of added value in reservoir management by application of flow control with intelligent wells
Authors: Ebadi F. , Davies D. R. , Gardiner A. R. , Corbett P. W. M.
Published: October 2008

Intelligent Well-systems Technology (IWsT) provides the delivery and management of production flexibility thorough downhole measurement and control. This paper uses a new workflow to evaluate the suitability of a wide range of reservoir types for IWsT application. This is achieved by a systematic study of a series of generic reservoir scenarios, based on property distributions derived from real field data and operational oil-field models. These geological scenarios were tested to determine the ‘Added Value’ from IWsT compared with standard well completions. Added value is expected through incremental oil recovery.

Results show that IWsT can control uneven, invading fluid fronts, which develop along the wellbore length due to permeability differences, reservoir compartmentalization, or different strengths of aquifer or gas cap support. The degree of improvement depends on the reservoir type (whether layered, faulted, channelized, etc.) and the distribution of porosity and permeability within it. Guidelines for the optimum placement of Internal Control Valve (ICV) locations in the planned completion zone are discussed. A global methodology was developed for the initial screening of favourable geological scenarios for the implementation of IWsT, and an ‘Application Envelope’ was developed based on the formation's correlation length and variability. The validity of this envelope is illustrated by its application to a real reservoir modelling case.
A methodology for efficiently populating faulted corner point grids with strain
Authors: Cardozo Nestor , Røe Per , Soleng Harald H. , Fredman Niclas , Tveranger Jan , Schueller Sylvie
Published: October 2008

This article describes an algorithm to compute finite strain in faulted corner point grids using the software Havana. The algorithm is based on a simple fault displacement formula, and a volumetric computation of strain in the grid's deformed configuration. The volumetric computation of strain is tested by comparing the finite strain of a 3D trishear model calculated by this method, with that calculated by the tetrahedrons method. The agreement between both methods confirms the validity of the volumetric strain computation. The algorithm is applied to synthetic models of one and three intersecting normal faults, and to a real model with seven faults, the Emerald Field. In all cases the computed finite strain is consistent with the fault network and with the variation of slip along the faults. There is one parameter that affects the computation significantly: the drag radius (
r
d
) or extent of folding across a fault. Low
r
d
models yield high finite strain and strain gradients but limited fault interaction, and vice versa. Using empirical relations between fault throw and damage zone width,
r
d
can be narrowed down and further constrained by evaluating the quality of the grid's restoration. The strain algorithm can be integrated easily into a reservoir modelling workflow and in stochastic modelling. The algorithm provides criteria for conditioning the distribution of deformational features within the reservoir zones affected by faulting, based on the magnitude of finite strain.
Structures and hydrocarbon prospectivity in the northern Davis Strait area, offshore West Greenland
Authors: Gregersen Ulrik , Bidstrup Torben
Published: October 2008

In the northern Davis Strait to southernmost Baffin Bay area, offshore West Greenland, deep basins with Mesozoic and Cenozoic sedimentary successions occur and a number of large structures and closures at likely reservoir levels have been found. Mid-Cretaceous, Upper Cretaceous and Paleocene sand-rich deposits are well known onshore east of the study area and in offshore wells, and equivalent deposits may also be present in the structures. Some of the potential structural leads have thick seals of late Cretaceous–Cenozoic deposits and short distances to deep possible kitchens with mid-Cretaceous and Paleocene source rocks, which mainly came into the oil window during the Neogene. Onshore oil seeps and gas shows, together with amplitude anomalies from seismic data, such as possible bright spots, support a live petroleum system in the region. During Early to mid-Cretaceous time a number of large structures and basins formed as a result of extensional faulting, including the Kangerluk Structure, the Aasiaat Structural Trend, structures in the Aasiaat and Sisimiut basins, and in the Nagssugtôq Sub-basin. A period with less tectonic activity followed in the Late Cretaceous, with deposition of thick, basinal mudstone-dominated successions. In the Late Cretaceous to Early Paleocene renewed tectonic activity caused uplift and faulting of large structures, such as the Davis Strait High and partly the Kangerluk Structure. Late Paleocene to Early Eocene strike-slip movements created thrust faults and compressional structures, mainly in the Ikermiut Fault Zone, associated with formation of the Ikermiut Basin. During the Paleocene and mainly the Early Eocene the >200 km long Ilulissat Graben developed. Paleocene and Eocene basalts occur west of Disko and Nuussuaq and narrow in distribution further south. The basalt cover offshore may be more limited than believed earlier. The area was offered for licensing in two periods from 2006 to early 2008.
An integrated approach to understanding the petroleum system of a frontier deep-water area, offshore Japan
Authors: Okui Akihiko , Kaneko Mitsuyoshi , Nakanishi Satoshi , Monzawa Nobuaki , Yamamoto Hiroshi
Published: October 2008

The Naoetsu Basin is one of several oil- and gas-producing provinces in Japan where thick Neogene strata are deposited, and oil and gas are produced from both onshore and offshore shelf areas. It is believed that the Naoetsu Basin extends into deep-water areas, but exploration activities were limited until 2000, except for regional 2D seismic surveys. After acquisition of a 3D seismic survey in 2001, the first two wells were drilled in 2004 in the deep-water area of the Naoetsu Basin. One well encountered an oil zone.

Multi-dimensional basin modelling was conducted to understand the petroleum system in the deep-water area of the Naoetsu Basin before and after the wells were drilled. The accuracy of basin modelling depends on the accuracy of the input data as well as the calibration process. However, even after the drilling campaign, only two wells were available in the deep-water area of the Naoetsu Basin. Therefore, the integration of various kinds of data, information and different techniques, such as 3D seismic, sedimentological and geochemical data, was carried out in this study. Development of sandstone networks, as well as the presence of major and minor faults, was identified on 3D seismic data. Oil and gas migration were constrained by geochemical data, such as carbon isotope on gases collected at the sea bottom and fluid inclusion chemistry.

Understanding of the petroleum system was increased significantly by this kind of integration, although the deep-water area of the Naoetsu Basin still remains a frontier area for oil and gas exploration. It was found that the petroleum system active in the deep-water area of the Naoetsu Basin is very effective. Even though maturation of the source rock has occurred only since the Pliocene, oil and gas generated and migrated very rapidly, first horizontally along sandstone networks and then vertically through faults reaching a level just below the sea bottom, with the result that the hydrocarbon trap has leaked.
Carbonate production and stratigraphic architecture of shelf-margin wedges (Cretaceous, Vercors): lessons from a stratigraphic modelling approach
Authors: Teles Vanessa , Eschard Rémi , Etienne Gisèle , Lopez Simon , Arnaud-Vanneau Annie
Published: October 2008

This work was presented at the EAGE workshop in Grenoble. Its purpose was to illustrate a stratigraphic modelling approach on a single schematic 2D case and to discuss which sedimentary features are imaged on synthetic seismic sections at different frequencies. The Vercors plateau carbonate sequence, deposited during the Barremian to Early Aptian, was considered. Modelling hypotheses constrained mainly the depositional time length and the geometry of each sequence. In addition, it was assumed that most of the carbonates were produced
in situ
.

The stratigraphic modelling approach and lessons from the simulation results are presented, followed by a discussion of how stratigraphic modelling can be a helpful tool to validate or question the geological model. In order to reproduce the sequence geometries, rates of carbonate production needed to be changed between regressive and transgressive periods. Simulated sea-level changes do not match the geological estimations from field interpretation but they are in agreement with the magnitude of sea-level curve variations, with the exception of the early Barremian sequences. Qualitative and quantitative results from the model simulations help to question or validate the geological model. Stratigraphic modelling provides some insight into the way the carbonate system may have worked.

Secondly, for a smaller 2D geological model, several synthetic seismic sections were computed using wavelets of different dominant frequencies. The seismic sections are compared to underline what is imaged mainly at the different frequencies. The presence of two characteristic facies were also analysed. Results show the importance of some thin beds inside thick sequences and that certain sequence boundaries may not be visible at all.
A game-theoretic model of referential coherence and its empirical verification using large Japanese and English corpora
Authors: Shiramatsu Shun , Komatani Kazunori , Hasida Kôiti , Ogata Tetsuya , Okuno Hiroshi G.
Published: October 2008

Referential coherence represents the smoothness of discourse resulting from topic continuity and pronominalization. Rational individuals prefer a referentially coherent structure of discourse when they select a language expression and its interpretation. This is a preference for cooperation in communication. By what principle do they share coherent expressions and interpretations? Centering theory is the standard theory of referential coherence [Grosz et al. 1995]. Although it is well designed on the bases of first-order inference rules [Joshi and Kuhn 1979], it does not embody a behavioral principle for the cooperation evident in communication. Hasida [1996] proposed a game-theoretic hypothesis in relation to this issue. We aim to empirically verify Hasida's hypothesis by using corpora of multiple languages. We statistically design language-dependent parameters by using a corpus of the target language. This statistical design enables us to objectively absorb language-specific differences and to verify the universality of Hasida's hypothesis by using corpora. We empirically verified our model by using large Japanese and English corpora. The result proves the language universality of the hypothesis.
Analysis of gene expression in pancreatic islets from diet-induced obese mice
Authors: Imai Yumi , Patel Hiral R. , Doliba Nicolai M. , Matschinsky Franz M. , Tobias John W. , Ahima Rexford S.
Published: October 2008

In insulin-resistant status such as obesity, failure of pancreatic islets to increase insulin secretion leads to diabetes. We sought to screen for the islet genes that facilitate islet adaptation to obesity by comparing gene expression profiles between two strains of obesity-prone inbred mice with different propensities for hyperglycemia. C57BL/6J and AKR/J were fed regular rodent chow or high-fat diet, after which islet morphology, secretory function, and gene expression were assessed. AKR/J had lower blood glucose and higher insulin levels compared with C57BL/6J mice on regular rodent chow or high-fat diet. Insulin secretion was 3.2-fold higher in AKR/J than C57BL/6J mice following intraperitoneal glucose injection. Likewise, glucose-stimulated insulin secretion from isolated islets was higher in AKR/J. Additionally, islet mass was 1.4-fold greater in AKR/J compared with C57BL/6J. To elucidate the factors associated with the differences in islet function, we analyzed the gene expression profiles in islets in AKR/J and C57BL/6J mice. Of 14,000 genes examined, 202 were upregulated and 270 were downregulated in islets from diet-induced obese AKR/J mice compared with C57BL/6J mice. Key genes involved in islet signaling and metabolism, e.g., glucagon-like peptide-1 receptor, sterol Co-A desaturase 1 and 2, and fatty acid desaturase 2 were upregulated in obese AKR/J mice. The expression of multiple extracellular matrix proteins was also increased in AKR/J mice, suggesting a role in modulation of islet mass. Functional analyses of differentially regulated genes hold promise for elucidating factors linking obesity to alterations in islet function.
Adapting Content Delivery to Limited Resources and Inferred User Interest
Authors: Plesca Cezar , Charvillat Vincent , Grigoras Romulus
Published: October 2008

This paper discusses adaptation policies for information systems that are subject to dynamic and stochastic contexts such as mobile access to multimedia web sites. In our approach, adaptation agents apply sequential decisional policies under uncertainty. We focus on the modeling of such decisional processes depending on whether the context is fully or partially observable. Our case study is a movie browsing service in a mobile environment that we model by using Markov decision processes (MDPs) and partially observable MDP (POMDP). We derive adaptation policies for this service, that take into account the limited resources such as the network bandwidth. We further refine these policies according to the partially observable users' interest level estimated from implicit feedback. Our theoretical models are validated through numerous simulations.
Some Inequalities Concerning the Weakly Convergent Sequence Coefficient in Banach Spaces
Authors: Jiao Hongwei , Guo Yunrui
Published: October 2008

We establish two inequalities concerning the weakly convergent sequence coefficient and other parameters, which enable us to obtain some sufficient conditions for normal structure.
Presence of Older Thrombus Is an Independent Predictor of Long-Term Mortality in Patients With ST-Elevation Myocardial Infarction Treated With Thrombus Aspiration During Primary Percutaneous Coronary Intervention
Authors: Kramer Miranda C.A. , van der Wal Allard C. , Koch Karel T. , Ploegmakers Johanna P.H.M. , van der Schaaf René J. , Henriques José P.S. , Baan Jan , Rittersma Saskia Z.H. , Vis Marije M. , Piek Jan J. , Tijssen Jan G.P. , de Winter Robbert J.
Published: October 2008

Background—

Routine thrombus aspiration is frequently used during primary percutaneous coronary intervention in patients with ST-elevation myocardial infarction to prevent distal embolization. Recently, evidence of clinical benefit was published. In 50% of the ST-elevation myocardial infarction patients with an onset of symptoms <12 hours before, thrombi were shown to be >1 day old. This observation illustrates that plaque rupture and coronary occlusion are significantly separated in time. In the present study, we correlate the presence of fresh versus older thrombus with long-term mortality.

Methods and Results—

Thrombus aspiration was performed in 1315 patients treated with primary percutaneous coronary intervention with 3 devices (Rescue, Export, and Proxis). Aspirated material was fixed in formalin and processed for histopathology. If possible, thrombus age was classified as either fresh only (<1 day) or older (>1 day). We identified fresh thrombus in 552 patients and older thrombus in 372 patients. The cumulative Kaplan-Meier estimate of all-cause mortality at 4 years was significantly higher in patients with older thrombus (16.0%) compared with patients with fresh thrombus (7.4%), with a hazard ratio of 1.82 (95% confidence interval, 1.17 to 2.85;
P
=0.008). Multivariate analysis identified the presence of older thrombus, in addition to other established predictors, as an independent predictor (hazard ratio, 1.83; 95% confidence interval, 1.14 to 2.93;
P
=0.01) of long-term mortality.

Conclusion—

Our study demonstrates that the presence of older thrombus, in addition to other established predictors, is an independent predictor of long-term mortality in patients with ST-elevation myocardial infarction treated with thrombus aspiration during primary percutaneous coronary intervention.
Long-Term Clinical Outcomes After Drug-Eluting and Bare-Metal Stenting in Massachusetts
Authors: Mauri Laura , Silbaugh Treacy S. , Wolf Robert E. , Zelevinsky Katya , Lovett Ann , Zhou Zheng , Resnic Frederic S. , Normand Sharon-Lise T.
Published: October 2008

Background—

Drug-eluting stents (DES) reduce the need for repeat revascularization, but their long-term safety relative to that of bare-metal stents (BMS) in general use remains uncertain. We sought to compare the clinical outcome of patients treated with DES with that of BMS.

Methods and Results—

All adults undergoing percutaneous coronary intervention with stenting between April 1, 2003, and September 30, 2004, at non–US government hospitals in Massachusetts were identified from a mandatory state database. Patients were classified from the index admission according to stent types used. Clinical and procedural risk factors were collected prospectively. Risk-adjusted mortality, myocardial infarction, and revascularization rate differences (DES−BMS) were estimated through propensity score matching without replacement. A total of 11 556 patients were treated with DES, and 6237 were treated with BMS, with unadjusted 2-year mortality rates of 7.0% and 12.6%, respectively (
P
<0.0001). In 5549 DES patients matched to 5549 BMS patients, 2-year risk-adjusted mortality rates were 9.8% and 12.0%, respectively (
P
=0.0002), whereas the respective rates for myocardial infarction and target-vessel revascularization were 8.3% versus 10.3% (
P
=0.0005) and 11.0% versus 16.8% (
P
<0.0001).

Conclusions—

DES treatment was associated with lower rates of mortality, myocardial infarction, and target-vessel revascularization than BMS treatment in similar patients in a matched population-based study. Comprehensive follow-up in this inclusive population is warranted to identify whether similar safety and efficacy remain beyond 2 years.
Trends in Hypertension Prevalence, Awareness, Treatment, and Control Rates in United States Adults Between 1988–1994 and 1999–2004
Authors: Cutler Jeffrey A. , Sorlie Paul D. , Wolz Michael , Thom Thomas , Fields Larry E. , Roccella Edward J.
Published: October 2008

This study assesses trends in hypertension prevalence, blood pressure distributions and mean levels, and hypertension awareness, treatment, and control among US adults, age ≥18 years, between the third National Health and Nutrition Examination Survey (1988–1994) and the 1999–2004 National Health and Nutrition Examination Survey, a period of ≈10 years. The age-standardized prevalence rate increased from 24.4% to 28.9% (
P
<0.001), with the largest increases among non-Hispanic women. Depending on gender and race/ethnicity, from one fifth to four fifths of the increase could be accounted for by increasing body mass index. Among hypertensive persons, there were modest increases in awareness (
P
=0.04), from 68.5% to 71.8%. The rate for men increased from 61.6% to 69.3% (
P
=0.001), whereas the rate for women did not change significantly. Rates remained higher for women than for men, although the difference narrowed considerably. Improvements in treatment and control rates were larger: 53.1% to 61.4% and 26.1% to 35.1%, respectively (both
P
<0.001). The greatest increases occurred among non-Hispanic white men and non-Hispanic black persons, especially men. Mexican American persons showed improvement in treatment and control rates, but these rates remained the lowest among race/ethnic subgroups (47.4% and 24.3%, respectively). Among all of the race/ethnic groups, women continued to have somewhat better awareness, treatment, and control, except for control rates among non-Hispanic white persons, which became higher in men. Differences between non-Hispanic black and white persons in awareness, treatment, and control were small. These divergent trends may translate into disparate trends in cardiovascular disease morbidity and mortality.
Computing Algebraic Functions with Biochemical Reaction Networks
Authors: Buisman H. J. , ten Eikelder H. M. M. , Hilbers P. A. J. , Liekens A. M. L.
Published: October 2008

In biological organisms, networks of chemical reactions control the processing of information in a cell. A general approach to study the behavior of these networks is to analyze common modules. Instead of this analytical approach to study signaling networks, we construct functional motifs from the bottom up. We formulate conceptual networks of biochemical reactions that implement elementary algebraic operations over the domain and range of positive real numbers. We discuss how the steady state behavior relates to algebraic functions, and study the stability of the networks' fixed points. The primitive networks are then combined in feed-forward networks, allowing us to compute a diverse range of algebraic functions, such as polynomials. With this systematic approach, we explore the range of mathematical functions that can be constructed with these networks.
A Topological Approach to Chemical Organizations
Authors: Benkö Gil , Centler Florian , Dittrich Peter , Flamm Christoph , Stadler Bärbel M. R. , Stadler Peter F.
Published: October 2008

Large chemical reaction networks often exhibit distinctive features that can be interpreted as higher-level structures. Prime examples are metabolic pathways in a biochemical context. We review mathematical approaches that exploit the stoichiometric structure, which can be seen as a particular directed hypergraph, to derive an algebraic picture of chemical organizations. We then give an alternative interpretation in terms of set-valued set functions that encapsulate the production rules of the individual reactions. From the mathematical point of view, these functions define generalized topological spaces on the set of chemical species. We show that organization-theoretic concepts also appear in a natural way in the topological language. This abstract representation in turn suggests the exploration of the chemical meaning of well-established topological concepts. As an example, we consider connectedness in some detail.
Modeling Biochemical Pathways Using an Artificial Chemistry
Authors: Tominaga Kazuto , Suzuki Yoshikazu , Kobayashi Keiji , Watanabe Tooru , Koizumi Kazumasa , Kishi Koji
Published: October 2008

Artificial chemistries are candidates for methodologies that model and design biochemical systems. If artificial chemistries can deal with such systems in beneficial ways, they may facilitate activities in the new area of biomolecular engineering. In order to explore such possibilities, we illustrate four models of biochemical pathways described in our artificial chemistry based on string pattern matching and recombination. The modeled pathways are the replication of DNA, transcription from DNA to mRNA, translation from mRNA to protein, and the oxidation of fatty acids. The descriptions show that the present approach has good modularity and scalability that will be useful for modeling a huge network of pathways. Moreover, we give a procedure to perform reasoning in the artificial chemistry, which checks whether a specified collection of molecules can be generated in a given model, and we demonstrate that it works on a model that describes a natural biochemical pathway.
Anodal Transcranial Direct Current Stimulation of the Prefrontal Cortex Enhances Complex Verbal Associative Thought
Authors: Cerruti Carlo , Schlaug Gottfried
Published: October 2008

The remote associates test (RAT) is a complex verbal task with associations to both creative thought and general intelligence. RAT problems require not only lateral associations and the internal production of many words but a convergent focus on a single answer. Complex problem-solving of this sort may thus require both substantial verbal processing and strong executive function capacities. Previous studies have provided evidence that verbal task performance can be enhanced by noninvasive transcranial direct current stimulation (tDCS). tDCS modulates excitability of neural tissue depending on the polarity of the current. The after-effects of this modulation may have effects on task performance if the task examined draws on the modulated region. Studies of verbal cognition have focused largely on the left dorsolateral prefrontal cortex (F3 of the 10–20 EEG system) as a region of interest. We planned to assess whether modulating excitability at F3 could affect complex verbal abilities. In Experiment 1 (anodal, cathodal, or sham stimulation over F3 with the reference electrode over the contralateral supraorbital region), we found a significant overall effect of stimulation condition on RAT performance. Post hoc tests showed an increase in performance after anodal stimulation (1 mA) compared to sham (p = .025) and to cathodal stimulation (p = .038). In Experiment 2 (either anodal stimulation at F3 or separately at its homologue F4), we replicated the anodal effect of the first study, but also showed that anodal stimulation of F4 had no effect on RAT performance. These data provide evidence that anodal stimulation of the left dorsolateral prefrontal cortex can improve performance on a complex verbal problem-solving task believed to require significant executive function capacity.
Visual Adaptation to Goal-directed Hand Actions
Authors: Barraclough Nick E. , Keith Rebecca H. , Xiao Dengke , Oram Mike W. , Perrett David I.
Published: October 2008

Prolonged exposure to visual stimuli, or adaptation, often results in an adaptation “aftereffect” which can profoundly distort our perception of subsequent visual stimuli. This technique has been commonly used to investigate mechanisms underlying our perception of simple visual stimuli, and more recently, of static faces. We tested whether humans would adapt to movies of hands grasping and placing different weight objects. After adapting to hands grasping light or heavy objects, subsequently perceived objects appeared relatively heavier, or lighter, respectively. The aftereffects increased logarithmically with adaptation action repetition and decayed logarithmically with time. Adaptation aftereffects also indicated that perception of actions relies predominantly on view-dependent mechanisms. Adapting to one action significantly influenced the perception of the opposite action. These aftereffects can only be explained by adaptation of mechanisms that take into account the presence/absence of the object in the hand. We tested if evidence on action processing mechanisms obtained using visual adaptation techniques confirms underlying neural processing. We recorded monkey superior temporal sulcus (STS) single-cell responses to hand actions. Cells sensitive to grasping or placing typically responded well to the opposite action; cells also responded during different phases of the actions. Cell responses were sensitive to the view of the action and were dependent upon the presence of the object in the scene. We show here that action processing mechanisms established using visual adaptation parallel the neural mechanisms revealed during recording from monkey STS. Visual adaptation techniques can thus be usefully employed to investigate brain mechanisms underlying action perception.
The Medial Temporal Lobe and the Left Inferior Prefrontal Cortex Jointly Support Interference Resolution in Verbal Working Memory
Authors: Öztekin Ilke , Curtis Clayton E. , McElree Brian
Published: October 2008

During working memory retrieval, proactive interference (PI) can be induced by semantic similarity and episodic familiarity. Here, we used fMRI to test hypotheses about the role of the left inferior frontal gyrus (LIFG) and the medial temporal lobe (MTL) regions in successful resolution of PI. Participants studied six-word lists and responded to a recognition probe after a short distracter period. We induced semantic PI by using study lists containing words within the same semantic category (e.g., animals). We also measured PI induced by recent study, which should increase episodic familiarity, by comparing recent negative probes (lures studied in previous trial) to distant negative probes (lures that had not been presented within a block). Resolving both types of PI resulted in enhanced activation in LIFG and MTL regions. We propose that the LIFG and the MTL support successful resolution of interference via controlled retrieval processes that serve to recover detailed episodic (e.g., list-specific or source) information: Specifically, the data suggest that BOLD activation in the LIFG reflects the deployment of controlled retrieval operations, regardless of whether the retrieval attempt succeeds in recovering the target information, whereas MTL activation specifically reflects access to relevant episodic information that serves to successfully resolve PI.
Emotion Modulates Early Auditory Response to Speech
Authors: Wang Jade , Nicol Trent , Skoe Erika , Sams Mikko , Kraus Nina
Published: October 2008

In order to understand how emotional state influences the listener's physiological response to speech, subjects looked at emotion-evoking pictures while 32-channel EEG evoked responses (ERPs) to an unchanging auditory stimulus (“danny”) were collected. The pictures were selected from the International Affective Picture System database. They were rated by participants and differed in valence (positive, negative, neutral), but not in dominance and arousal. Effects of viewing negative emotion pictures were seen as early as 20 msec (p = .006). An analysis of the global field power highlighted a time period of interest (30.4–129.0 msec) where the effects of emotion are likely to be the most robust. At the cortical level, the responses differed significantly depending on the valence ratings the subjects provided for the visual stimuli, which divided them into the high valence intensity group and the low valence intensity group. The high valence intensity group exhibited a clear divergent bivalent effect of emotion (ERPs at Cz during viewing neutral pictures subtracted from ERPs during viewing positive or negative pictures) in the time period of interest (r Φ = .534, p < .01). Moreover, group differences emerged in the pattern of global activation during this time period. Although both groups demonstrated a significant effect of emotion (ANOVA, p = .004 and .006, low valence intensity and high valence intensity, respectively), the high valence intensity group exhibited a much larger effect. Whereas the low valence intensity group exhibited its smaller effect predominantly in frontal areas, the larger effect in the high valence intensity group was found globally, especially in the left temporal areas, with the largest divergent bivalent effects (ANOVA, p < .00001) in high valence intensity subjects around the midline. Thus, divergent bivalent effects were observed between 30 and 130 msec, and were dependent on the subject's subjective state, whereas the effects at 20 msec were evident only for negative emotion, independent of the subject's behavioral responses. Taken together, it appears that emotion can affect auditory function early in the sensory processing stream.
Anatomical Segregation of Representations of Personally Familiar and Famous People in the Temporal and Parietal Cortices
Authors: Sugiura Motoaki , Sassa Yuko , Watanabe Jobu , Akitsuki Yuko , Maeda Yasuhiro , Matsue Yoshihiko , Kawashima Ryuta
Published: October 2008

Person recognition has been assumed to entail many types of person-specific cognitive responses, including retrieval of knowledge, episodic recollection, and emotional responses. To demonstrate the cortical correlates of this modular structure of multimodal person representation, we investigated neural responses preferential to personally familiar people and responses dependent on familiarity with famous people in the temporal and parietal cortices. During functional magnetic resonance imaging (fMRI) measurements, normal subjects recognized personally familiar names (personal) or famous names with high or low degrees of familiarity (high or low, respectively). Effects of familiarity with famous people (i.e., high–low) were identified in the bilateral angular gyri, the left supramarginal gyrus, the middle part of the bilateral posterior cingulate cortices, and the left precuneus. Activation preferentially relevant to personally familiar people (i.e., personal–high) was identified in the bilateral temporo-parietal junctions, the right anterolateral temporal cortices, posterior middle temporal gyrus, posterior cingulate cortex (with a peak in the posterodorsal part), and the left precuneus; these activation foci exhibited varying degrees of activation for high and low names. An equivalent extent of activation was observed for all familiar names in the bilateral temporal poles, the left orbito-insular junction, the middle temporal gyrus, and the anterior part of the posterior cingulate cortex. The results demonstrated that distinct cortical areas supported different types of cognitive responses, induced to different degrees during recognition of famous and personally familiar people, providing neuroscientific evidence for the modularity of multimodal person representation.
Lexical Plasticity in Early Bilinguals Does Not Alter Phoneme Categories: II. Experimental Evidence
Authors: Sebastián-Gallés Núria , Vera-Constán Fátima , Larsson Johan P. , Costa Albert , Deco Gustavo
Published: October 2008

When listening to modified speech, either naturally or artificially altered, the human perceptual system rapidly adapts to it. There is some debate about the nature of the mechanisms underlying this adaptation. Although some authors propose that listeners modify their prelexical representations, others assume changes at the lexical level. Recently, Larsson, Vera, Sebastian-Galles, and Deco [Lexical plasticity in early bilinguals does not alter phoneme categories: I. Neurodynamical modelling. Journal of Cognitive Neuroscience, 20, 76–94, 2008] proposed a biologically plausible computational model to account for some existing data, one which successfully modeled how long-term exposure to a dialect triggers the creation of new lexical entries. One specific prediction of the model was that prelexical (phoneme) representations should not be affected by dialectal exposure (as long as the listener is exposed to both standard and dialectal pronunciations). Here we present a series of experiments testing the predictions of the model. Native listeners of Catalan, with extended exposure to Spanish-accented Catalan, were tested on different auditory lexical decision tasks and phoneme discrimination tasks. Behavioral and electrophysiological recordings were obtained. The results supported the predictions of our model. On the one hand, both error rates and N400 measurements indicated the existence of alternative lexical entries for dialectal varieties. On the other hand, no evidence of alterations at the phoneme level, either in the behavioral discrimination task or in the electrophysiological measurement (MMN), could be detected. The results of the present study are compared with those obtained in short-term laboratory exposures in an attempt to provide an integrative account.
Mismatch and Conflict: Neurophysiological and Behavioral Evidence for Conflict Priming
Authors: Mager Ralph , Meuth Sven G. , Kräuchi Kurt , Schmidlin Maria , Müller-Spahn Franz , Falkenstein Michael
Published: October 2008

Conflict-related cognitive processes are critical for adapting to sudden environmental changes that confront the individual with inconsistent or ambiguous information. Thus, these processes play a crucial role to cope with daily life. Generally, conflicts tend to accumulate especially in complex and threatening situations. Therefore, the question arises how conflict-related cognitive processes are modulated by the close succession of conflicts. In the present study, we investigated the effect of interactions between different types of conflict on performance as well as on electrophysiological parameters. A task-irrelevant auditory stimulus and a task-relevant visual stimulus were presented successively. The auditory stimulus consisted of a standard or deviant tone, followed by a congruent or incongruent Stroop stimulus. After standard prestimuli, performance deteriorated for incongruent compared to congruent Stroop stimuli, which were accompanied by a widespread negativity for incongruent versus congruent stimuli in the event-related potentials (ERPs). However, after deviant prestimuli, performance was better for incongruent than for congruent Stroop stimuli and an additional early negativity in the ERP emerged with a fronto-central maximum. Our data show that deviant auditory prestimuli facilitate specifically the processing of stimulus-related conflict, providing evidence for a conflict-priming effect.
Unconscious Learning versus Visual Perception: Dissociable Roles for Gamma Oscillations Revealed in MEG
Authors: Chaumon Maximilien , Schwartz Denis , Tallon-Baudry Catherine
Published: October 2008

Oscillatory synchrony in the gamma band (30–120 Hz) has been involved in various cognitive functions including conscious perception and learning. Explicit memory encoding, in particular, relies on enhanced gamma oscillations. Does this finding extend to unconscious memory encoding? Can we dissociate gamma oscillations related to unconscious learning and to conscious perception? We investigate these issues in a magnetoencephalographic experiment using a modified version of the contextual cueing paradigm. In this visual search task, repeated presentation of search arrays triggers an unconscious spatial learning process that speeds reaction times but leaves conscious perception unaffected. In addition to a high-frequency perceptual gamma activity present throughout the experiment, we reveal the existence of a fronto-occipital network synchronized in the low gamma range specifically engaged in unconscious learning. This network shows up as soon as a display is searched for the second time and disappears as behavior gets affected. We suggest that oscillations in this network shape neural processing to build an efficient neural route for learned displays. Accordingly, in the last part of the experiment, evoked responses dissociate learned images at early latencies, suggesting that a sharpened representation is activated without resort on learning gamma oscillations, whereas perceptual gamma oscillations remain unaffected.
The Media-Art Exhibition TenYearsAfter_v4.0_OuterSpace
Authors: Lee Soo-jin , Wohn Kwang-yun
Published: October 2008

TenYearsAfter is an annual media art exhibition based in Korea, begun in 2003, organized by Kwang-yun Wohn and curator Mira Kim to facilitate collaboration among engineers, scientists, artists and designers. Unlike other major media-art exhibitions, TenYearsAfter has included artworks by mainstream media artists, independent experiments, and products and research results by artists and non-artists alike. The fourth exhibition in this series, TenYearsAfter_v4.0_OuterSpace, organized by the authors, was held in 2006. This article elaborates on the process of organizing this event and contemplates the implications of annual media art events in the Korean media art context.