bluuebunny/crossref_metadata_2025_split huggingface dataset:
The History and Prehistory of Pearling in the Persian Gulf
Authors: Carter Robert 
Published: June 2005

AbstractThe paper presents an analysis and synthesis of historical and archaeological data on pearl fishing in the Persian Gulf. The history of pearling in the region is reviewed, from the earliest possible references to the mid 20th century. Economic data from the 18th–20th centuries CE is analysed in detail, to de fine the economic course of the pearling industry during that time, and assess the impact on human settlement in the region. The archaeological data for pearl fishing are then examined, from the 6th millennium BCE onwards, and compared to the historical evidence. The results of archaeological survey in the Abu Dhabi islands region are then taken as a case study, and changes in settlement patterns are related to the historical trajectory of the pearling industry. It is observed that the regional economy became overwhelmingly dependent on the pearl trade in recent centuries, and was increasingly subject to the demands of the global market. Cette étude présente une analyse et une synthèse des données historiques et archéologiques sur la pêche des perles dans le Golfe arabo-persique. L'histoire de la pêche des perles dans la région est passée en revue, depuis les plus anciennes références connues qui remontent au milieu du 20e siècle. Les données économiques du 18e au 20e siècle sont analysées en détail pour dé finir l'évolution de l'industrie perlière pendant cette période et évaluer son incidence sur le peuplement de la région. Les données archéologiques sur la pêche des perles, examinées depuis le 6ème millénaire avant J.-C., ont été comparées aux données historiques. Les résultats des reconnaissances archéologiques dans les îles de la région d'Abu Dhabi sont alors présentées comme étude de cas et les modi fications de con figuration de l'habitat sont reliées à l'évolution historique de l'industrie perlière. On remarque que l'économie de cette région est devenue presque entièrement dépendante du commerce des perles dans les siècles récents, et qu'elle était de plus en plus assujettie à la demande du marché mondial.
Reflections on State-Making and History-Making in South India, 1500-1800
Authors: Subrahmanyam Sanjay 
Published: June 2005

AbstractThis paper is concerned with early modern southern India, and in particular, the areas ruled over by Vijayanagara, the Nayakas of Senji and the Nawwabs of Arcot. Its primary intention is to point out that states as diverse as these produced important narratives that served as points of self-definition. Positivist historians have often struggled to understand what to do with these texts, asking in effect whether they are “truths” or “lies,” and often rejecting them wholsesale for the ostensibly more “reliable” stone and copper-plate based inscriptions.The paper argues against the divide in south Indian history between “textualists,” who read narrative texts, and “epigraphers,” who prefer the “hard” evidence of inscriptions, and contends that any general historical analysis must of necessity be based on a reading of both forms of materials. In this context, the paper develops the argument for the emergence of a certain historical self-consciousness in early modern south India, both in the Perso-Islamic and the vernacular traditions, and in their interface. It would naturally be tempting to see matters in terms of a succession of expressive forms, each one successfully and finally displacing its predecessors, but it is proposed that the realities one encounters are rather more complex than this model would suggest.
Social Hierarchy and Merchant Philanthropy as Perceived in Several Late-Ming and Early-Qing Texts
Authors: Handlin Smith Joanna 
Published: June 2005

AbstractFollowing the fall of the Ming dynasty in 1644, literati questioned the social hierarchy, acknowledged merchants as philanthropists, and revised their understanding of gifts and donations. Using several texts (by Tang Zhen and Wei Xi, in particular), this paper proposes that early-Qing literati reconceptualized some of the goals of philanthropy. Where late-Ming philanthropy aimed (among other things) to spread moral instruction and affirm the superior status of scholar-officials, the early-Qing Wei Xi condoned merchant use of philanthropy to build social connections. Thus, the high moralizing of late-Ming philanthropy gave way to perceptions that the recipients of aid were directly obligated to their benefactors. The weakening of the moral purpose of philanthropy and the intensification of donor-beneficiary relations sparked a trend to routinize philanthropy (through forced donations and quasi-taxation), thereby diminishing the room for and significance of individual initiative.
Decadal Changes in the South Indian Ocean Thermocline
Authors: McDonagh Elaine L. , Bryden Harry L. , King Brian A. , Sanders Richard J. , Cunningham Stuart A. , Marsh Robert 
Published: June 2005

Abstract
A significant change in properties of the thermocline is observed across the whole Indian Ocean 32°S section between 1987 and 2002. This change represents a reversal of the pre-1987 freshening and decreasing oxygen concentrations of the upper thermocline that had been interpreted as a fingerprint of anthropogenic climate change. The thermocline at the western end of the section (40°–70°E) is occupied by a single variety of mode water with a potential temperature of around 13°C. The thermocline at the eastern end of the 32°S section is occupied by mode waters with a range of properties cooling from ∼11°C at 80°E to ∼9°C near the Australian coast. The change in θ–S properties between 1987 and 2002 is zonally coherent east of 80°E, with a maximum change on isopycnals at 11.6°C. Ages derived from helium–tritium data imply that the mode waters at all longitudes take about the same time to reach 32°S from their respective ventilation sites. Dissolved oxygen concentration changes imply that all of the mode water reached the section ∼20% faster in 2002 than in 1987.
Terrestrial Carbon Cycle Dynamics under Recent and Future Climate Change
Authors: Matthews H. Damon , Weaver Andrew J. , Meissner Katrin J. 
Published: June 2005

AbstractThe behavior of the terrestrial carbon cycle under historical and future climate change is examined using the University of Victoria Earth System Climate Model, now coupled to a dynamic terrestrial vegetation and global carbon cycle model. When forced by historical emissions of CO2 from fossil fuels and land-use change, the coupled climate–carbon cycle model accurately reproduces historical atmospheric CO2 trends, as well as terrestrial and oceanic uptake for the past two decades. Under six twenty-first-century CO2 emissions scenarios, both terrestrial and oceanic carbon sinks continue to increase, though terrestrial uptake slows in the latter half of the century. Climate–carbon cycle feedbacks are isolated by comparing a coupled model run with a run where climate and the carbon cycle are uncoupled. The modeled positive feedback between the carbon cycle and climate is found to be relatively small, resulting in an increase in simulated CO2 of 60 ppmv at the year 2100. Including non-CO2 greenhouse gas forcing and increasing the model’s climate sensitivity increase the effect of this feedback to 140 ppmv. The UVic model does not, however, simulate a switch from a terrestrial carbon sink to a source during the twenty-first century, as earlier studies have suggested. This can be explained by a lack of substantial reductions in simulated vegetation productivity due to climate changes.
Quantifying Uncertainty in Projections of Regional Climate Change: A Bayesian Approach to the Analysis of Multimodel Ensembles
Authors: Tebaldi Claudia , Smith Richard L. , Nychka Doug , Mearns Linda O. 
Published: June 2005

Abstract
A Bayesian statistical model is proposed that combines information from a multimodel ensemble of atmosphere–ocean general circulation models (AOGCMs) and observations to determine probability distributions of future temperature change on a regional scale. The posterior distributions derived from the statistical assumptions incorporate the criteria of bias and convergence in the relative weights implicitly assigned to the ensemble members. This approach can be considered an extension and elaboration of the reliability ensemble averaging method. For illustration, the authors consider the output of mean surface temperature from nine AOGCMs, run under the A2 emission scenario from the Synthesis Report on Emission Scenarios (SRES), for boreal winter and summer, aggregated over 22 land regions and into two 30-yr averages representative of current and future climate conditions. The shapes of the final probability density functions of temperature change vary widely, from unimodal curves for regions where model results agree (or outlying projections are discounted) to multimodal curves where models that cannot be discounted on the basis of bias give diverging projections. Besides the basic statistical model, the authors consider including correlation between present and future temperature responses, and test alternative forms of probability distributions for the model error terms. It is suggested that a probabilistic approach, particularly in the form of a Bayesian model, is a useful platform from which to synthesize the information from an ensemble of simulations. The probability distributions of temperature change reveal features such as multimodality and long tails that could not otherwise be easily discerned. Furthermore, the Bayesian model can serve as an interdisciplinary tool through which climate modelers, climatologists, and statisticians can work more closely. For example, climate modelers, through their expert judgment, could contribute to the formulations of prior distributions in the statistical model.
PentaPlot: A software tool for the illustration of genome mosaicism
Authors: Hamel Lutz , Zhaxybayeva Olga , Gogarten J Peter 
Published: June 2005

Abstract
Background
Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix.

Results
The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families.

Conclusion
PentaPlot is being made publicly available as an open source project at http://pentaplot.sourceforge.net.
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
Authors: Cooper James W , Kershenbaum Aaron 
Published: June 2005

Abstract
Background
The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest.

Results
This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a set of easily implemented rules. Applying these techniques to 12,300 abstracts, a precision of 0.61 and a recall of 0.97 were obtained, (f = 0.74) and when allowing for two-hop and three-hop relations discovered by graphical analysis, the precision was 0.74 (f = 0.83).

Conclusion
This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches.
Haplotypes at the Tas2r locus on distal chromosome 6 vary with quinine taste sensitivity in inbred mice
Authors: Nelson Theodore M , Munger Steven D , Boughter John D 
Published: June 2005

Abstract

Background
The detection of bitter-tasting compounds by the gustatory system is thought to alert animals to the presence of potentially toxic food. Some, if not all, bitter stimuli activate specific taste receptors, the T2Rs, which are expressed in subsets of taste receptor cells on the tongue and palate. However, there is evidence for both receptor-dependent and -independent transduction mechanisms for a number of bitter stimuli, including quinine hydrochloride (QHCl) and denatonium benzoate (DB).

Results
We used brief-access behavioral taste testing of BXD/Ty recombinant inbred (RI) mouse strains to map the major quantitative trait locus (QTL) for taste sensitivity to QHCl. This QTL is restricted to a ~5 Mb interval on chromosome 6 that includes 24 genes encoding T2Rs (Tas2rs). Tas2rs at this locus display in total 307 coding region single nucleotide polymorphisms (SNPs) between the two BXD/Ty RI parental strains, C57BL/6J (quinine-sensitive) and DBA/2J (quinine insensitive); approximately 50% of these mutations are silent. Individual RI lines contain exclusively either C57BL/6J or DBA/2J Tas2r alleles at this locus, and RI lines containing C57BL/6J Tas2r alleles are more sensitive to QHCl than are lines containing DBA/2J alleles. Thus, the entire Tas2r cluster comprises a large haplotype that correlates with quinine taster status.

Conclusion
These studies, the first using a taste-salient assay to map the major QTL for quinine taste, indicate that a T2R-dependent transduction cascade is responsible for the majority of strain variance in quinine taste sensitivity. Furthermore, the large number of polymorphisms within coding exons of the Tas2r cluster, coupled with evidence that inbred strains exhibit largely similar bitter taste phenotypes, suggest that T2R receptors are quite tolerant to variation.
Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data
Authors: Carpentier Anne-Sophie , Torrésani Bruno , Grossmann Alex , Hénaut Alain 
Published: June 2005

AbstractBackgroundAlthough the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe directly. The advent of massive hybridisation techniques opens the way to further studies of the chromosomal structure because the genes that are co-expressed, as identified by microarray experiments, probably share some spatial relationship. The use of several independent sets of gene expression data should make it possible to obtain an exhaustive view of the genes co-expression and thus a more accurate image of the structure of the chromosome.ResultsFor bothBacillus subtilisandEscherichia colithe co-expression of genes varies as a function of the distance between the genes along the chromosome. The long-range correlations are surprising: the changes in the level of expression ofanygene are correlated (positively or negatively) to the changes in the expression level of other genes located at well-defined long-range distances.This property is true for all the genes, regardless of their localisation on the chromosome.We also found short-range correlations, which suggest that the location of these co-expressed genes corresponds to DNA turns on the nucleoid surface (14–16 genes).ConclusionThe long-range correlations do not correspond to the domains so far identified in the nucleoid. We explain our results by a model of the nucleoid solenoid structure based on two types of spirals (short and long). The long spirals are uncoiled expressed DNA while the short ones correspond to coiled unexpressed DNA.
Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii
Authors: Weng Jing-Ke , Tanurdzic Milos , Chapple Clint 
Published: June 2005

Abstract

Background
The lycophyte Selaginella moellendorffii is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150–200 million years earlier than angiosperms, a group of plants that includes the well-studied flowering plant Arabidopsis thaliana. S. moellendorffii has a genome size of approximately 100 Mbp, as small or smaller than that of A. thaliana. S. moellendorffii has the potential to provide significant comparative information to better understand the evolution of vascular plants.

Results
We sequenced 2181 Expressed Sequence Tags (ESTs) from a S. moellendorffii cDNA library. One thousand three hundred and one non-redundant sequences were assembled, containing 291 contigs and 1010 singletons. Approximately 75% of the ESTs matched proteins in the non-redundant protein database. Among 1301 clusters, 343 were categorized according to Gene Ontology (GO) hierarchy and were compared to the GO mapping of A. thaliana tentative consensus sequences. We compared S. moellendorffii ESTs to the A. thaliana and Physcomitrella patens EST databases, using the tBLASTX algorithm. Approximately 60% of the ESTs exhibited similarity with both A. thaliana and P. patens ESTs; whereas, 13% and 1% of the ESTs had exclusive similarity with A. thaliana and P. patens ESTs, respectively. A substantial proportion of the ESTs (26%) had no match with A. thaliana or P. patens ESTs.

Conclusion
We discovered 1301 putative unigenes in S. moellendorffii. These results give an initial insight into its transcriptome that will aid in the study of the S. moellendorffii genome in the near future.
The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences
Authors: Brune Iris , Brinkrolf Karina , Kalinowski Jörn , Pühler Alfred , Tauch Andreas 
Published: June 2005

Abstract

Background
The genus Corynebacterium includes Gram-positive microorganisms of great biotechnologically importance, such as Corynebacterium glutamicum and Corynebacterium efficiens, as well as serious human pathogens, such as Corynebacterium diphtheriae and Corynebacterium jeikeium. Although genome sequences of the respective species have been determined recently, the knowledge about the repertoire of transcriptional regulators and the architecture of global regulatory networks is scarce. Here, we apply a combination of bioinformatic tools and a comparative genomic approach to identify and characterize a set of conserved DNA-binding transcriptional regulators in the four corynebacterial genomes.

Results
A collection of 127 DNA-binding transcriptional regulators was identified in the C. glutamicum ATCC 13032 genome, whereas 103 regulators were detected in C. efficiens YS-314, 63 in C. diphtheriae NCTC 13129 and 55 in C. jeikeium K411. According to amino acid sequence similarities and protein structure predictions, the DNA-binding transcriptional regulators were grouped into 25 regulatory protein families. The common set of DNA-binding transcriptional regulators present in the four corynebacterial genomes consists of 28 proteins that are apparently involved in the regulation of cell division and septation, SOS and stress response, carbohydrate metabolism and macroelement and metal homeostasis.

Conclusion
This work describes characteristic features of a set of conserved DNA-binding transcriptional regulators present within the corynebacterial core genome. The knowledge on the physiological function of these proteins should not only contribute to our understanding of the regulation of gene expression but will also provide the basis for comprehensive modeling of transcriptional regulatory networks of these species.
A BAC-based physical map of the Nile tilapia genome
Authors: Katagiri Takayuki , Kidd Celeste , Tomasino Elizabeth , Davis Jesse T , Wishon Cassandra , Stern Justin E , Carleton Karen L , Howe Aimee E , Kocher Thomas D 
Published: June 2005

Abstract

Background
Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical maps of the tilapia genome. Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences.

Results
We constructed a genome-wide physical map of the tilapia genome by restriction fingerprinting 35,245 bacterial artificial chromosome (BAC) clones using high-resolution capillary polyacrylamide gel electrophoresis. The map consists of 3,621 contigs and is estimated to span 1.752 Gb in physical length. An independent analysis of the marker content of four contigs demonstrates the reliability of the assembly.

Conclusion
This physical map is a powerful tool for accelerating genomic studies in cichlid fishes, including comparative mapping among fish species, long-range assembly of genomic shotgun sequences, and the positional cloning of genes underlying important phenotypic traits. The tilapia BAC fingerprint database is freely available at http://hcgs.unh.edu/fpc/image.php.
Nuclear distribution and chromatin association of DNA polymerase α-primase is affected by TEV protease cleavage of Cdc23 (Mcm10) in fission yeast
Authors: Yang Xiaowen , Gregan Juraj , Lindner Karola , Young Hedi , Kearsey Stephen E 
Published: June 2005

AbstractBackgroundCdc23/Mcm10 is required for the initiation and elongation steps of DNA replication but its biochemical function is unclear. Here, we probe its function using a novel approach in fission yeast, involving Cdc23 cleavage by the TEV protease.ResultsInsertion of a TEV protease cleavage site into Cdc23 allows in vivo removal of the C-terminal 170 aa of the protein by TEV protease induction, resulting in an S phase arrest. This C-terminal fragment of Cdc23 is not retained in the nucleus after cleavage, showing that it lacks a nuclear localization signal and ability to bind to chromatin. Using an in situ chromatin binding procedure we have determined how the S phase chromatin association of DNA polymerase α-primase and the GINS (Sld5-Psf1-Psf2-Psf3) complex is affected by Cdc23 inactivation. The chromatin binding and sub-nuclear distribution of DNA primase catalytic subunit (Spp1) is affected by Cdc23 cleavage and also by inactivation of Cdc23 using a degron allele, implying that DNA polymerase α-primase function is dependent on Cdc23. In contrast to the effect on Spp1, the chromatin association of the Psf2 subunit of the GINS complex is not affected by Cdc23 inactivation.ConclusionAn important function of Cdc23 in the elongation step of DNA replication may be to assist in the docking of DNA polymerase α-primase to chromatin.