bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land subsidence in drained peat areas of the Province of Friesland, The Netherlands
Authors: Nieuwenhuis H. S. , Schokking F. 
Published: November 2007

Abstract
The Holocene peat areas in the Province of Friesland consisting of peat and clay deposits are used extensively for agriculture and are drained by maintaining a low surface water level in polder ditches. Considerable rates of land subsidence (1 to 12mrrdyear) result from processes such as soil shrinkage, consolidation and peat oxidation, the last named being the major contributor.
In the Province of Friesland studies of the future effects of continuous long-term land subsidence have been made as part of the hydrological masterplan. For these studies the Geological Survey of The Netherlands (RGD) has compiled maps showing the estimated subsidence over a 50-year period for three scenarios of freeboard (difference in elevation between surface water level and the ground surface). Data sources consist of recent ground surface levels measured for the construction of utility lines, to be used for the transport of water, gas or sewage, earlier topographical maps, historical surface water level records and soil profiles.
Maximum estimates for rates of subsidence for peat with and without clay cover have been established by evaluation of the data with subsequent subsidence process analysis for various situations of drainage, duration of drainage, soil and hydrological conditions. Three maps showing the estimated land subsidence over a 50-year period for freeboards of 0.4, 0.8 and 1.2 m have been compiled using a two-dimensional Geographical Information System (2D-GIS), coupled with the RGD database, and have been presented in 1 km2 grids. A comprehensive map of estimated land subsidence is being compiled by the Province, taking into account the actual freeboards at each location. The presented study forms a new approach to the estimation of future land subsidence in peat areas on a regional scale.
The Chalk as a karstified aquifer: closed circuit television images of macrobiota
Authors: Waters A. , Banks D. 
Published: November 2007

Abstract
The use of closed circuit television (CCTV) imaging in the Chalk aquifer of the Thames catchment of southern England, has shed much light on the aquifer's flow mechanisms. CCTV images indicate that flow to a Chalk abstraction borehole is typically via a limited number of highly transmissive solutionenhanced fracture features. These bear some similarities to conduits found in true karstic aquifer systems, and have implications for the modelling of mass transport in the Chalk aquifer. Another feature, typical of karst aquifers, noted during CCTV surveys is the occasional presence of macroscopic biota, arthropods and annelids, apparently inhabiting the Chalk aquifer system.
Aquifers as environments for microbiological activity
Authors: West J. M. , Chilton P. J. 
Published: November 2007

Abstract
The ability of an aquifer to support microbiological activity depends on several factors: the availability of nutrients and energy sources for microbial use; the physical characteristics of the aquifer itself (such as the groundwater flow regime); and the environmental conditions experienced by the organisms (such as temperature and pH). These factors will be reviewed and their implications discussed in relation to groundwater quality and to the geological disposal of radioactive wastes.
Individual Differences in Sentence Comprehension: A Functional Magnetic Resonance Imaging Investigation of Syntactic and Lexical Processing Demands
Authors: Prat Chantel S. , Keller Timothy A. , Just Marcel Adam 
Published: November 2007

Abstract
Language comprehension is neurally underpinned by a network of collaborating cortical processing centers; individual differences in comprehension must be related to some set of this network's properties. This study investigated the neural bases of individual differences during sentence comprehension by examining the network's response to two variations in processing demands: reading sentences containing words of high versus low lexical frequency and having simpler versus more complex syntax. In a functional magnetic resonance imaging study, readers who were independently identified as having high or low working memory capacity for language exhibited three differentiating properties of their language network, namely, neural efficiency, adaptability, and synchronization. First, greater efficiency (defined as a reduction in activation associated with improved performance) was manifested as less activation in the bilateral middle frontal and right lingual gyri in high-capacity readers. Second, increased adaptability was indexed by larger lexical frequency effects in high-capacity readers across bilateral middle frontal, bilateral inferior occipital, and right temporal regions. Third, greater synchronization was observed in high-capacity readers between left temporal and left inferior frontal, left parietal, and right occipital regions. Synchronization interacted with adaptability, such that functional connectivity remained constant or increased with increasing lexical and syntactic demands in high-capacity readers, whereas low-capacity readers either showed no reliable differentiation or a decrease in functional connectivity with increasing demands. These results are among the first to relate multiple cortical network properties to individual differences in reading capacity and suggest a more general framework for understanding the relation between neural function and individual differences in cognitive performance.
Neural Correlates of Morphological Decomposition during Visual Word Recognition
Authors: Gold Brian T. , Rastle Kathleen 
Published: November 2007

Abstract
Considerable behavioral research has demonstrated that the visual word recognition system is sensitive to morphological structure. It has typically been assumed that analysis of morphologically complex words occurs only when the meaning of these words can be derived from the meanings of their constituents (e.g., hunter = hunt + er). However, results from recent behavioral research using the masked priming technique have demonstrated that morphological analysis can occur at an earlier orthographic level, in cases in which the meanings of complex words cannot be derived from their constituents (e.g., corner = corn + er). Here, we combine the logic of behavioral masked priming with the neurophysiological phenomenon of functional magnetic resonance imaging priming suppression to look for evidence of nonsemantic morphological priming at the neural level. Both behavioral and functional magnetic resonance imaging results indicated priming effects associated with the mere appearance of morphological structure (corner—CORN). In addition, these effects were distinguishable from lexical-semantic effects (bucket—PAIL) and orthographic effects (brothel—BROTH). Three left-lateralized occipito-temporal regions showed sensitivity to early morphological components of visual word recognition. Two of these regions also showed orthographic priming (∼BA 37, peak: −48 −60 −17; ∼BA 19, peak: −40 −77 −1), whereas one was sensitive only to morphological similarity between primes and targets (∼BA 19, peak: ∼37 ∼67 ∼7). These findings provide a neurobiological basis for a purely structural morphemic segmentation mechanism operating at early stages of visual word recognition.
Performance Monitoring in the Anterior Cingulate is Not All Error Related: Expectancy Deviation and the Representation of Action-Outcome Associations
Authors: Oliveira Flavio T. P. , McDonald John J. , Goodman David 
Published: November 2007

Abstract
Several converging lines of evidence suggest that the anterior cingulate cortex (ACC) is selectively involved in error detection or evaluation of poor performance. Here we challenge this notion by presenting event-related potential (ERP) evidence that the feedback-elicited error-related negativity, an ERP component attributed to the ACC, can be elicited by positive feedback when a person is expecting negative feedback and vice versa. These results suggest that performance monitoring in the ACC is not limited to error processing. We propose that the ACC acts as part of a more general performance-monitoring system that is activated by violations in expectancy. Further, we propose that the common observation of increased ACC activity elicited by negative events could be explained by an overoptimistic bias in generating expectations of performance. These results could shed light into neurobehavioral disorders, such as depression and mania, associated with alterations in performance monitoring and also in judgments of self-related events.
On the Tip-of-the-Tongue: Neural Correlates of Increased Word-finding Failures in Normal Aging
Authors: Shafto Meredith A. , Burke Deborah M. , Stamatakis Emmanuel A. , Tam Phyllis P. , Tyler Lorraine K. 
Published: November 2007

AbstractTip-of-the-tongue (TOT) experiences are frustrating word-finding failures where people are temporarily unable to produce a word they are certain they know. TOT frequency increases with normal aging during adulthood, and behavioral evidence suggests that the underlying deficit is in retrieving the complete phonology of the target word during production. The present study investigated the neural correlates of this phonological retrieval deficit. We obtained 3-D T1-weighted structural magnetic resonance images (MRI) for healthy participants between 19 and 88 years old and used voxel-based morphometry to measure gray matter density throughout the brain. In a separate session, participants named celebrities cued by pictures and descriptions, indicating when they had a TOT, and also completed Raven's Progressive Matrices (RPM), a task that does not involve phonological production. The number of TOTs increased with age and also with gray matter atrophy in the left insula, an area implicated in phonological production. The relation between TOTs and left insula atrophy cannot be attributed to the correlation of each variable with age because TOTs were related to insula atrophy even with age effects removed. Moreover, errors on the RPM increased with age, but performance did not correlate with gray matter density in the insula. These results provide, for the first time, an association between a region in the neural language system and the rise in age-related word-finding failures and suggest that age-related atrophy in neural regions important for phonological production may contribute to age-related word production failures.
New Scales for Assessing Contribution Ratio of Pollutant Sources to Indoor Air Quality
Authors: Kim Taeyeon , Kato Shinsuke , Murakami Shuzo 
Published: November 2007

The aim of this study was to provide effective design and control methods for indoor air quality (IAQ). For this it was important to identify each pollutant source and have an understanding of the room air distribution. To design a good system for IAQ both the pollutant sources as well as the ventilation system must be controlled effectively. In this paper, new scales for IAQ that assess the contribution of pollutant sources, that we have named the Contribution Ratio of Pollutant Sources (CRPSs), are developed. The contribution of each pollutant source in a room can be analyzed by evaluating the CRPSs. These new scales assume that the pollutant concentration due to different sources can be added linearly and the airflow is at steady-state. Using CRPS, the contribution of each pollutant sources in a model room air-conditioned by a displacement ventilation system could be analyzed. The CRPSs were all calculated using the method of computational fluid dynamics (CFD), which can accurately analyze the distribution of the air velocity, temperature, and pollution in the room. The concept of CRPS was found to be very useful in this study.
Filamin repeat segments required for photosensory signalling in Dictyostelium discoideum
Authors: Annesley Sarah J , Bandala-Sanchez Esther , Ahmed Afsar U , Fisher Paul R 
Published: November 2007

AbstractBackgroundFilamin is an actin binding protein which is ubiquitous in eukaryotes and its basic structure is well conserved – an N-terminal actin binding domain followed by a series of repeated segments which vary in number in different organisms.D. discoideumis a well established model organism for the study of signalling pathways and the actin cytoskeleton and as such makes an excellent organism in which to study filamin. Ddfilamin plays a putative role as a scaffolding protein in a photosensory signalling pathway and this role is thought to be mediated by the unusual repeat segments in the rod domain.ResultsTo study the role of filamin in phototaxis, a filamin null mutant, HG1264, was transformed with constructs each of which expressed wild type filamin or a mutant filamin with a deletion of one of the repeat segments. Transformants expressing the full length filamin to wild type levels completely rescued the phototaxis defect in HG1264, however if filamin was expressed at lower than wild type levels the phototaxis defect was not restored. The transformants lacking any one of the repeat segments 2–6 retained defective phototaxis and thermotaxis phenotypes, whereas transformants expressing filaminΔ1 exhibited a range of partial complementation of the phototaxis phenotype which was related to expression levels. Immunofluorescence microscopy showed that filamin lacking any of the repeat segments still localised to the same actin rich areas as wild type filamin. Ddfilamin interacts with RasD and IP experiments demonstrated that this interaction did not rely upon any single repeat segment or the actin binding domain.ConclusionThis paper demonstrates that wild type levels of filamin expression are essential for the formation of functional photosensory signalling complexes and that each of the repeat segments 2–6 are essential for filamins role in phototaxis. By contrast, repeat segment 1 is not essential provided the mutated filamin lacking repeat segment 1 is expressed at a high enough level. The defects in photo/thermosensory signal transduction caused by the absence of the repeats are due neither to mislocalisation of filamin nor to the loss of RasD recruitment to the previously described photosensory signalling complex.
Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids
Authors: Zhu Xin-Yu , Chase Mark W , Qiu Yin-Long , Kong Hong-Zhi , Dilcher David L , Li Jian-Hua , Chen Zhi-Duan 
Published: November 2007

AbstractBackgroundRosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrialmatRgene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility ofmatRin rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes includingmatR, two plastid genes (rbcL,atpB), and one nuclear gene (18S rDNA).ResultsComparison of mitochondrialmatRand two plastid genes (rbcLandatpB) showed that the synonymous substitution rate inmatRwas approximately four times slower than those ofrbcLandatpB; however, the nonsynonymous substitution rate inmatRwas relatively high, close to its synonymous substitution rate, indicating that thematRhas experienced a relaxed evolutionary history. Analyses of ourmatRsequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.ConclusionCompared to plastid genes such asrbcLandatpB, slowly evolvingmatRproduced less homoplasious but not less informative substitutions. Thus,matRappears useful in higher-level angiosperm phylogenetics. Analysis ofmatRalone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.
An optimized procedure greatly improves EST vector contamination removal
Authors: Chen Yi-An , Lin Chang-Chun , Wang Chin-Di , Wu Huan-Bin , Hwang Pei-Ing 
Published: November 2007

Abstract

Background
The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious concern to researchers. Removal of vector contamination is one of the most significant operations to obtain accurate sequence data containing only a cDNA insert from the basecalls output by an automatic DNA sequencer. Popular bioinformatics programs to accomplish vector trimming include LUCY, cross_match and SeqClean.

Results
In a recent study, where the program SeqClean was used to remove vector contamination from our test set of EST data compiled through various library construction systems, however, a significant number of errors remained after preliminary trimming. These errors were later almost completely corrected by simply using a re-linearized form of the cloning vector to compare against the target ESTs. The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. Using SeqClean with a re-linearized form of the cloning vector significantly surpassed the other two programs in all tested conditions, while the performance of the other two programs was not influenced by the modified procedure. Vector contamination in dbEST was also investigated in this study: 2203 out of the 48212 ESTs sampled from dbEST (2007-04-18 freeze) were found to match sequences in UNIVEC.

Conclusion
Vector contamination remains a serious concern to the data quality in the public sequence database nowadays. Based on the results presented here, we feel that our modified procedure with SeqClean should be recommended to all researchers for the task of vector removal from EST or genomic sequences.
Age at developmental cortical injury differentially Alters corpus callosum volume in the rat
Authors: Threlkeld Steven W , Rosen Glenn D , Fitch R Holly 
Published: November 2007

Abstract

Background
Freezing lesions to developing rat cortex induced between postnatal day (P) one and three (P1 – 3) lead to malformations similar to human microgyria, and further correspond to reductions in brain weight and cortical volume. In contrast, comparable lesions on P5 do not produce microgyric malformations, nor the changes in brain weight seen with microgyria. However, injury occurring at all three ages does lead to rapid auditory processing deficits as measured in the juvenile period. Interestingly, these deficits persist into adulthood only in the P1 lesion case [1]. Given prior evidence that early focal cortical lesions induce abnormalities in cortical morphology and connectivity [1–4], we hypothesized that the differential behavioral effects of focal cortical lesions on P1, P3 or P5 may be associated with underlying neuroanatomical changes that are sensitive to timing of injury. Clinical studies indicate that humans with perinatal brain injury often show regional reductions in corpus callosum size and abnormal symmetry, which frequently correspond to learning impairments [5–7]. Therefore, in the current study the brains of P1, 3 or 5 lesion rats, previously evaluated for brain weight, and cortical volume changes and auditory processing impairments (P21-90), were further analyzed for changes in corpus callosum volume.

Results
Results showed a significant main effect of Treatment on corpus callosum volume [F (1,57) = 10.2, P < .01], with lesion subjects showing significantly smaller callosal volumes as compared to shams. An Age at Treatment × Treatment interaction [F(2,57) = 3.2, P < .05], indicated that corpus callosum size decreased as the age of injury decreased from P5 to P1. Simple effects analysis showed significant differences between P1 and P3 [F(1,28) = 8.7, P < .01], and P1 and P5 [F(1,28) = 15.1, P < .001], subjects. Rats with P1 injury resulting in microgyria had the greatest reduction in corpus callosum volume (22% reduction), followed by the P3 group (11% reduction), which showed a significant reduction in corpus callosum volume compared to shams [F(1,31) = 5.9, P < .05]. Finally, the P5 lesion group did not significantly differ from the sham subjects in callosal volume.

Conclusion
Decrements in corpus callosum volume in the P1 and 3 lesion groups are consistent with the reductions in brain weight and cortical volume previously reported for microgyric rats [1, 8]. Current results suggest that disruption to the cortical plate during early postnatal development may lead to more widely dispersed neurovolumetric anomalies and subsequent behavioral impairments [1], compared with injury that occurs later in development. Further, these results suggest that in a human clinical setting decreased corpus callosum volume may represent an additional marker for long-term behavioral outcome.