bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of western Sicily, central Mediterranean
Authors: Catalano R. , Merlini S. , Sulli A. 
Published: November 2010

Western Sicily is part of the Sicilian chain, a sector of the SE-verging Alpine orogenic belt in the central Mediterranean. Interpretation of seismic reflection profiles, boreholes and recent inland geological data, have enabled us to assess the deep structural grain. A wedge of flat-lying Mesozoic–Miocene carbonate and terrigenous rocks (pre-Panormide nappes) is superimposed on NW-trending, 7–8 km thick, Mesozoic–Paleogene carbonate thrust ramps (Trapanese units), arranged in two structural levels extending from the Tyrrhenian coast to western offshore Sicily. Upper Miocene to Pleistocene terrigenous strata, often deformed, fill syntectonic basins above the thrust pile. The main tectonic transport of the thrust pile, developing from Early Miocene to Early–Middle Pleistocene times, was towards the east and southeast.
Initial stacking and deformation of the pre-Panormide allochthon is bracketed between Early and Late Miocene. The Late Miocene–Early Pleistocene underthrusting of the Trapanese–Saccense units, that acted through more recent deep-seated thrusts in the carbonate platform layer, induced late stage refolding and further shortening in the early emplaced pre-Panormide nappe. Previously formed structures appear to have been dissected or reactivated by a right oblique transpression during the Late Pliocene–Pleistocene. The geometry of the carbonate bodies opens new potential perspectives on the existence of structural traps, but the uncertainties of source rock occurrence remain.
Determination of facies from well logs using modular neural networks
Authors: Bhatt Alpana , Helle Hans B. 
Published: November 2010

Zonation of well logs and the correlation of zones between wells are primary tasks in sub-surface geological and engineering analysis. We propose in this paper an artificial neural network (ANN) approach for objective clustering and identification of facies from well logs. The method relies upon combining back-propagation neural networks in ensembles and modular systems, where the multi-class classification problem of facies identification has effectively been reduced to a number of two-class problems.
Based on the neural network responses using synthetic logs from a realistic model, we optimized the architecture and training procedure of the component networks in the modular system, where the building blocks are simple three-layer back-propagation ANNs. Ensembles of ANNs are trained on disjoint sets of patterns using soft overtraining to ensure diversity and generalization. Recurrent ANNs are shown to enhance the facies continuity by effectively removing ambiguous or spurious classifications.
The performance of the technique was demonstrated using synthetic data and it was then used to detect four different facies within the Ness Formation in the North Sea. An average hit rate of above 90% in wells not used for training the network is slightly to significantly better than the performance published for similar classification experiments.
Well-bore reservoir evaluation technologies to optimize field revitalization
Authors: Bryant I. D. 
Published: November 2010

The economic success of field revitalization projects depends upon draining reservoir compartments that frequently contain smaller reserves volumes than those targeted by the initial field development, in a cost-effective manner. Well-bore measurements can contribute to risk management of redevelopment by identifying and monitoring the drainage of remaining hydrocarbons. Applications of cased-hole and open-hole measurements to optimizing field redevelopment are illustrated using case studies from the Brent Field, UK; Block IV, Venezuela and the T&J Ashworth Lease, USA.
Cased-hole logging using nuclear tools has evolved from time-lapse monitoring to detect changes in saturation to also include through-casing formation evaluation. Where deep invasion prevents the use of these nuclear methods, through-casing resistivity tools can successfully detect hydrocarbons.
Open-hole formation pressures can significantly impact redevelopment strategies, as can evaluation of filtrate invasion using open-hole array resistivity tools. Emerging permanent sensor technologies enable continuous monitoring of both water saturation and formation pressure, thereby offering the potential to improve the performance of future field revitalization projects.
Balder and Jotun – two sides of the same coin? A comparison of two Tertiary oil fields in the Norwegian North Sea
Authors: Bergslien D.a.g. 
Published: November 2010

The Balder and Jotun fields are located on the western flank of the Utsira High, close to the eastern pinch-out of a Tertiary submarine fan system. Although similar in many aspects, the fields display important depositional, structural and stratigraphic differences which influence the choice of development strategy. The subsurface development strategy for the fields has been designed to optimize oil capture and minimize risk based on the interpreted reservoir geology. Therefore, differences between the exploration histories and reservoir geology are reflected in the development strategy of the two fields.
Both fields comprise Tertiary reservoir sands shed from the East Shetland Platform and transported across the Viking Graben area onto the Utsira High by sandy debris flows and turbidites. These distal gravity flow deposits display both thin-bedded sands and thicker more massive sandstones (>100 m). In the Balder Field, an intricate interaction between deposition and soft sediment deformation processes generated a complex network of reservoir compartments with common fluid contacts. In the Jotun Field, the oil–water contact is also common between all three structures, but a gas cap is restricted to one of the structures.
Tumor Suppressor CHK2: Regulator of DNA Damage Response and Mediator of Chromosomal Stability
Authors: Stolz Ailine , Ertych Norman , Bastians Holger 
Published: November 2010

Abstract
CHK2 is a multiorgan tumor susceptibility gene that encodes for a serine/threonine protein kinase involved in the response to cellular DNA damage. After ATM-mediated phosphorylation, the activated Chk2 kinase can act as a signal transducer and phosphorylate a variety of substrates, including the Cdc25 phosphatases, p53, PML, E2F-1, and Brca1, which has been associated with halting the cell cycle, the initiation of DNA repair, and the induction of apoptosis after DNA damage. In addition, recent work has revealed another, DNA-damage–independent function of Chk2 during mitosis that is required for proper mitotic spindle assembly and maintenance of chromosomal stability. This novel role involves a mitotic phosphorylation of the tumor suppressor Brca1 by the Chk2 kinase. On the basis of its role during DNA damage response, Chk2 has been suggested as an anticancer therapy target, but given its recently discovered new function and its role as a tumor suppressor, it is questionable whether inhibition of Chk2 is indeed beneficial for anticancer treatment. However, investigators may be able to exploit the loss of CHK2 in human tumors to develop novel therapies based on synthetic lethal interactions. Clin Cancer Res; 17(3); 401–5. ©2010 AACR.
Telomerase Deficiency in Bone Marrow–Derived Cells Attenuates Angiotensin II–Induced Abdominal Aortic Aneurysm Formation
Authors: Findeisen Hannes M. , Gizard Florence , Zhao Yue , Cohn Dianne , Heywood Elizabeth B. , Jones Karrie L. , Lovett David H. , Howatt Deborah A. , Daugherty Alan , Bruemmer Dennis 
Published: November 2010

Objective—
Abdominal aortic aneurysms (AAA) are an age-related vascular disease and an important cause of morbidity and mortality. In this study, we sought to determine whether the catalytic component of telomerase, telomerase reverse transcriptase (TERT), modulates angiotensin (Ang) II–induced AAA formation.

Methods and Results—
Low-density lipoprotein receptor–deficient (LDLr−/−) mice were lethally irradiated and reconstituted with bone marrow–derived cells from TERT-deficient (TERT−/−) mice or littermate wild-type mice. Mice were placed on a diet enriched in cholesterol, and AAA formation was quantified after 4 weeks of Ang II infusion. Repopulation of LDLr−/− mice with TERT−/− bone marrow–derived cells attenuated Ang II–induced AAA formation. TERT-deficient recipient mice revealed modest telomere attrition in circulating leukocytes at the study end point without any overt effect of the donor genotype on white blood cell counts. In mice repopulated with TERT−/− bone marrow, aortic matrix metalloproteinase-2 (MMP-2) activity was reduced, and TERT−/− macrophages exhibited decreased expression and activity of MMP-2 in response to stimulation with Ang II. Finally, we demonstrated in transient transfection studies that TERT overexpression activates the MMP-2 promoter in macrophages.

Conclusion—
TERT deficiency in bone marrow–derived macrophages attenuates Ang II–induced AAA formation in LDLr−/− mice and decreases MMP-2 expression. These results point to a previously unrecognized role of TERT in the pathogenesis of AAA.
Computed Tomographic Angiography and Venography for Young or Nonhypertensive Patients With Acute Spontaneous Intracerebral Hemorrhage
Authors: Wong George Kwok Chu , Siu Deyond Yung Woon , Abrigo Jill Morales , Poon Wai Sang , Tsang Federick Chun Pong , Zhu Xian Lun , Yu Simon Chun Ho , Ahuja Anil Tejbhan 
Published: November 2010

Background and Purpose—
We compared the effectiveness of using computed tomographic angiography and venography (CTAV) with digital subtraction angiography (DSA) in young or nonhypertensive patients with acute spontaneous intracerebral hemorrhage.

Methods—
We prospectively recruited 109 young (age between 18 and 45 years) or nonhypertensive patients with acute spontaneous intracerebral hemorrhage for this comparative study. All patients had CTAV using multidetector CT with 64 detectors. They were then scheduled to have catheter angiography the next day. Radiological data were collected for blinded analysis.

Results—
DSA-positive pathologies causing hemorrhage were identified in 37 (33%) patients, which included cerebral arteriovenous malformation in 22 cases. The positive and negative predictive values of CTAV for DSA-positive pathologies causing hemorrhage were 97.3% (95% CI, 88.3%–99.9%) and 100% (95% CI, 95.9%–100%), respectively.

Conclusions—
CTAV was able to detect DSA-positive pathologies causing acute spontaneous intracerebral hemorrhage in young (age between 18 and 45 years) or nonhypertensive patients with high positive and negative predictive values.
Drivers of Residual Estuarine Circulation in Tidally Energetic Estuaries: Straight and Irrotational Channels with Parabolic Cross Section
Authors: Burchard Hans , Hetland Robert D. , Schulz Elisabeth , Schuttelaars Henk M. 
Published: November 2010

Abstract
The generation of residual circulation in a tidally energetic estuary with constant longitudinal salinity gradient and parabolic cross section is examined by means of a two-dimensional cross-sectional numerical model, neglecting river runoff and Stokes drift. It is shown how the longitudinal and lateral residual circulation can be decomposed into contributions from various processes such as tidal straining circulation, gravitational circulation, advectively driven circulation, and horizontal mixing circulation. The sensitivity of the residual circulation and its components from various processes to changes in forcing is investigated by varying the Simpson number (nondimensional longitudinal buoyancy gradient) and the unsteadiness parameter (nondimensional tidal frequency), as well as the bed roughness and the width of the estuary. For relatively weak salinity gradient forcing, the tidal straining circulation dominates the residual exchange circulation in support of classical estuarine circulation (up-estuary flow near the bed and down-estuary flow near the surface). The strength of the longitudinal estuarine circulation clearly increases with increased salinity gradient forcing. However, when the Simpson number exceeds 0.15, the relative contributions of both gravitational circulation and advectively driven circulation to estuarine circulation increase substantially. Lateral residual circulation is relatively weak for small Simpson numbers and becomes flood oriented (divergent flow near the bed and convergent flow near the surface) for larger Simpson numbers because of increasing contributions from gravitational and advectively driven circulation. Increasing the unsteadiness number leads to decreased longitudinal and lateral residual circulation. Although changes in bed roughness result in relatively small changes in residual circulation, results are sensitive to the width of the estuary, mainly because of changes in residual exchange circulation driven by tidal straining.
Access to and use of reproductive health information among in-school adolescent girls in Lagos State, Nigeria
Authors: Nwalo K I N , Anasi Stella N I 
Published: November 2010

Objective: This study investigated access to and use of reproductive health information among in-school adolescent girls in Lagos State, Nigeria. Design: Descriptive survey research design was adopted for the study. Setting: The study sample consisted of 1,800 girls randomly selected from18 public senior secondary schools in Lagos State. Method: Data were collected with a questionnaire. Descriptive and inferential statistics were used for data analysis. Result: Parents were the most accessible source of reproductive health information while the Internet was the least accessible. More than 50 per cent of the respondents were not using reproductive health-related information regularly. There is no statistically-significant difference in access to and use of reproductive health information among girls in single sex and co-educational schools in Lagos State, Nigeria. Conclusion: The National Comprehensive Sexuality Education Curriculum should be implemented in all the secondary schools in Lagos State and elsewhere in Nigeria. Access to and use of reproductive health information should be promoted through regular workshops, seminars, symposia, lectures and talks for parents, teachers, and students.
Employment status influences suicide mortality in Europe
Authors: Yur’yev Andriy , Värnik Airi , Värnik Peeter , Sisask Merike , Leppik Lauri 
Published: November 2010

Background: The present study attempted to assess the relationship between suicide mortality and employment status in Europe. Methods: Suicide trends were obtained from the World Health Organization, employment rates from the Conference Board Total Economy Database, and questions about citizens’ attitudes towards employment from the European Social Survey. Correlations were analysed. Differences between mean scores for attitudes in Western and Eastern Europe were calculated. Results: Employment and suicide trends are negatively correlated in most countries. Suicide mortality is associated with unemployment risk and expectations of inadequate financial resources during unemployment, and negatively correlated with an assured high sdard of living for the unemployed. Suicide mortality and the degree of conviction that the government should ensure jobs for all are weakly correlated. Attitudes towards employment and unemployment in Eastern and Western Europe diverge. Conclusions: Changes in employment rates influence suicide mortality in many European countries. Factors that increase suicide mortality include lack of confidence in employment status and unemployed people’s expectations of insufficient income and low living standards. Suicidal behaviour is more strongly related to attitudes linked with employment status among males than females. In Eastern Europe the status of being unemployed is feared more, and people rely more on the government.
Epithin/PRSS14 proteolytically regulates angiopoietin receptor Tie2 during transendothelial migration
Authors: Kim Chungho , Seon Lee Hyo , Lee Deokjae , Lee Sang Don , Cho Eun-Gyung , Yang Soo Jung , Kim Sang Bum , Park Dongeun , Kim Moon Gyo 
Published: November 2010

Abstract
Epithin/PRSS14, a type II transmembrane serine protease, is involved in normal epithelial development and tumor progression. Here we report, as an interacting substrate of epithin, a receptor tyrosine kinase Tie2 that is well known for important roles in the vessel stability. Epithin interacts with and degrades the Tie2 extracellular portion that contains the ligand-binding domain. Epithin is located in the neighbor of Tie2-expressing vessels in normal tissue. Furthermore, epithin can cleave and degrade Tie2 not only in the same cell but also from neighboring cells nearby, resulting in the degradation of the Tie2 ectodomain. The remaining Tie2 fragment was highly phosphorylated and was able to recruit a downstream effector, phosphatidylinositol 3-kinase. Knocking down epithin expression using short hairpin RNA in thymoma cell severely impaired the migration through endothelial cells that show the actin rearrangement during the process. The diminution of epithin protein expression in 4T1 breast cancer cells caused the significant decrease in the number of transendothelial migrating cells in vitro as well as in those of metastasizing tumor nodules in vivo, Therefore, we propose that epithin, which regulates endothelial Tie2 functions, plays a critical role in the fine tuning of transendothelial migration for normal and cancer cells.
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency
Authors: Weng Francis C , Su Chien-Hao , Hsu Ming-Tsung , Wang Tse-Yi , Tsai Huai-Kuang , Wang Daryi 
Published: November 2010

Abstract

Background
Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.

Results
Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.

Conclusions
Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.
The genomic underpinnings of apoptosis in the silkworm, Bombyx mori
Authors: Zhang Jin-Ye , Pan Min-Hui , Sun Zhi-Ya , Huang Shu-Jing , Yu Zi-Shu , Liu Di , Zhao Dan-Hong , Lu Cheng 
Published: November 2010

Abstract

Background
Apoptosis is regulated in an orderly fashion by a series of genes, and has a crucial role in important physiological processes such as growth development, immunological response and so on. Recently, substantial studies have been undertaken on apoptosis in model animals including humans, fruit flies, and the nematode. However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system. Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.

Results
From the newly assembled genome databases, a genome-wide analysis of apoptosis-related genes in Bombyx mori was performed using both nucleotide and protein Blast searches. Fifty-two apoptosis-related candidate genes were identified, including five caspase family members, two tumor necrosis factor (TNF) superfamily members, one Bcl-2 family member, four baculovirus IAP (inhibitor of apoptosis) repeat (BIR) domain family members and 1 RHG (Reaper, Hid, Grim, and Sickle; Drosophila cell death activators) family member. Moreover, we identified a new caspase family member, BmCaspase-New, two splice variants of BmDronc, and Bm3585, a mammalian TNF superfamily member homolog. Twenty-three of these apoptosis-related genes were cloned and sequenced using cDNA templates isolated from BmE-SWU1 cells. Sequence analyses revealed that these genes could have key roles in apoptosis.

Conclusions

Bombyx mori possesses potential apoptosis-related genes. We hypothesized that the classic intrinsic and extrinsic apoptotic pathways potentially are active in Bombyx mori. These results lay the foundation for further apoptosis-related study in Bombyx mori.
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome
Authors: Reese Justin T , Childers Christopher P , Sundaram Jaideep P , Dickens C Michael , Childs Kevin L , Vile Donald C , Elsik Christine G 
Published: November 2010

AbstractBackgroundA goal of the Bovine Genome Database (BGD;http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project.Results and DiscussionBGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD.ConclusionsWe have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.