bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternatives in Paleocene exploration West of Shetland: a case study
Authors: Smallwood John R. , Prescott David , Kirk Wayne 
Published: January 2010

Synopsis
This paper illustrates oil exploration in the West of Shetlands area from 1995 to 2001 by documenting the history of Block 205/9, awarded in the UK 16th Licensing Round in 1995. Good quality Paleocene sands had been encountered in the 1989 well 205/9-1 in the down-dip part of the block, and equivalent sands were absent on the adjacent Flett Ridge to the SE, setting up the possibility of a pinchout play. The first well testing the play, 205/8-1, was drilled on the overall pinchout on 2D seismic data, but 3D seismic data were acquired across the area to better delineate the depositional systems. The first well drilled on the 3D data to test the sand pinchout, 205/14-3, failed to encounter sands in communication with those in 205/9-1, so attention turned to alternative stratigraphic traps highlighted by seismic amplitude anomalies. Detailed evaluation of the seismic data revealed that the attractive seismic amplitude response of one potential prospect was actually an artefact associated with overlying basalt. Further analysis of the 3D seismic attributes identified a tongue of sand south of 205/9-1, and analysis of magnetic fabrics from core data in 205/9-1 revealed that sand was input to this area from the NE, contrary to previous models. Unfortunately the seismic attributes, supported by fluid inclusion data, suggested that the sand was water-wet. As a result of the evaluation work, the block was relinquished in 1999 without further drilling. While there is undoubtedly scope for stratigraphic traps in the area to prove hydrocarbon-bearing, experience on the 205/9 block and other studies led to a refocusing on dip-closed structures, and a resulting discovery, the first in the Faroes, consisted of 170 m of hydrocarbon-bearing sands in the T10 Paleocene interval.
A groundwater recharge methodology for Water Framework Directive initial characterization in Scotland
Authors: Church Richard 
Published: January 2010

Synopsis
Estimation of recharge to groundwater is an important component in the characterization of groundwater bodies for the Water Framework Directive (WFD). The time scale allowed for the WFD initial characterization required a pragmatic methodology for efficient assessment of recharge to each delineated groundwater body. An assessment methodology was developed through a project funded by the Scotland and Northern Ireland Forum for Environmental Research, although it has application throughout the UK. Few recharge calculations have previously been attempted in Scotland. The environmental influences on recharge processes differ from much of the rest of the UK and the ability of the groundwater body to accept recharge is a key criteria.
The method proposed is based on a water budget approach which estimates direct and indirect recharge flow components. It includes estimation of effective rainfall, actual evapotranspiration, surface run-off and interflow in addition to the potential impacts of snow-melt, bypass flows, urban recharge and surface water leakage where appropriate. This is calculated on a daily or monthly time step with the use of a spreadsheet software tool. The degree of uncertainty in the recharge estimation increases with the scarcity of data available to the groundwater body. Many recharge estimations in Scotland will rely on national-scale mapping of climatic, land use, soil and aquifer properties. It is important that the confidence in the estimation is balanced against the perceived risk of stress to the groundwater body. Validation of the recharge calculations is ongoing and the assessment of bypass flow and interflow has been determined as critical to the accuracy of the calculation.
Theropod dinosaur and other footprints from the Valtos Sandstone Formation (Bathonian, Middle Jurassic) of the Isle of Skye
Authors: Marshall Paul 
Published: January 2010

Synopsis
Three to four footprints, including a tridactyl pes print attributed to a small bipedal theropod, are recorded from the Valtos Sandstone Formation (Bathonian, Middle Jurassic) on the Strathaird peninsula, southern Skye. The prints are preserved in a very fine-grained, well-sorted, silty sandstone that was deposited in a lagoonal, microtidal flat palaeoenvironmental setting, associated with a bay-head delta system. Two of the prints may form a short, narrow trackway reflecting a walking to gently trotting gait of a small theropod animal. These are the first dinosaur footprints recorded from southern Skye.
Constraining the maximum age of movements in the Moine Thrust Belt: dating the Canisp Porphyry
Authors: Goodenough K. M. , Evans J. A. , Krabbendam M. 
Published: January 2010

Synopsis
The Moine Thrust Belt of the Northwest Highlands of Scotland represents the front of the Caledonian Orogeny. The exact age of this thrust belt is the source of continuing debate, and has not been fully resolved either by dating of igneous rocks within the thrust belt or by direct dating of mylonites. The Canisp Porphyry sills are porphyritic quartz–microsyenite intrusions, found in the Foreland to the Moine Thrust Belt in the Assynt region. The sills occur close to the lowest thrust, but are never seen within the thrust belt. They are thus considered to predate movement on the lowest thrusts. This paper presents a U–Pb (TIMS) zircon date of 437 ± 4.8 Ma for the Canisp Porphyry, and thus movement on the lower thrusts of the Moine Thrust Belt is constrained as having occurred after that date.
A Lower Carboniferous sipunculan from the Granton Shrimp Bed, Edinburgh
Authors: Muir L. A. , Botting J. P. 
Published: January 2010

Synopsis
Sipunculans are sedentary marine worms, believed to represent either an early coelomate grade or a later offshoot of the annelids, but are unmineralized and extremely rare in the fossil record. Here we describe an example from the Granton Shrimp Bed, a Lower Carboniferous Konservat-Lagerstätte. This is the third known occurrence of Palaeozoic sipunculans, although they may have been previously overlooked. The recognition of fossil sipunculans is discussed, based partly on cuticle deformation due to the underlying muscle arrangement.
Quaternary geology of part of the Kale Water catchment, Western Cheviot Hills, southern Scotland
Authors: Mitchell W. A. 
Published: January 2010

Synopsis
This study reports on a survey of the middle part of the Kale Water, one of the western Cheviot catchments. Field mapping has revealed the presence of weathered andesite bedrock on many hillslopes. Conversely, evidence for glaciation is limited and restricted to a few exposures of till and meltwater channels suggesting that the last (Late Devensian) ice sheet in this area was cold-based, creating a frozen patch that lay to the east of a thermal boundary related to the Tweed ice stream. A well developed solifluction sheet is found on the lower valley slopes, indicating remobilization of former glacial sediments under periglacial conditions when head formed on the upper slopes. A particular feature is the presence of stratified fine gravels forming an upper lithofacies on many hillslopes which appear to be due to reworking of weathered material. Although there has been no dating of these sediments, it is suggested that the upper part of the sequence dates from Late Devensian deglaciation with the soliflucted sediments related to periglacial processes and paraglacial adjustment in association with permafrost degradation at the end of the Dimlington Stadial, and the stratified gravels related to fluvio-nivational processes associated with snowmelt during the subsequent Loch Lomond Stadial.
Simulation study on hydronic balancing to improve individual room control for radiant floor heating system
Authors: Rhee KN , Ryu SR , Yeo MS , Kim KW 
Published: January 2010

Recently, the application of radiant floor heating systems has significantly increased in many countries, resulting in the improvement of thermal comfort and energy efficiency. When it comes to the control method, individual room control is highly recommended because it can ensure thermal comfort and energy saving more successfully than that of central control, which had been widely adopted in the early days of radiant floor heating systems. To maximise the performance of individual room control, it is significantly important to adopt hydronic balancing, especially if a building is composed of rooms with diverse heating loads and floor areas. In this study, the necessity and the effect of hydronic balancing on individual room control are investigated through computer simulations. In addition, secondary problems caused by current hydronic balancing are also studied. Finally, this paper presents a new balancing method to improve an individual room control for a radiant floor heating system. Practical applications: In terms of the life cycle of a radiant floor heating system, good operation is as important as good design to maximise the system performance. Hydronic balancing is an essential procedure for the successful operation and optimisation of a radiant floor heating system. The results of this paper can be applied to the improvement of hydronic balancing, which ensures good operation and enhances the performance of a radiant floor heating system adopting individual room control. This paper could provide useful information for commissioning engineers; testing, adjusting and balancing practitioners; control equipment manufacturers; and researchers.
CC chemokine receptor 5 gene polymorphisms in beryllium disease
Authors: Sato H. , Silveira L. , Spagnolo P. , Gillespie M. , Gottschall E.B. , Welsh K.I. , Du Bois R.M. , Newman L.S. , Maier L.A. 
Published: January 2010

CC chemokine receptor 5 (CCR5) is expressed on type-1 T-helper cells, which are involved in the pathogenesis of the granulomatous lung disease chronic beryllium disease (CBD). CCR5 gene (CCR5) polymorphisms are associated with sarcoidosis severity. The present study explores associations betweenCCR5polymorphisms and CBD and its disease progression.EightCCR5polymorphisms were genotyped in CBD (n = 88), beryllium sensitisation (BeS; n = 86) and beryllium-exposed nondiseased controls (n = 173) using PCR with sequence-specific primers. Pulmonary function and bronchoalveolar lavage data were examined for associations with genotypes.There were no significant differences in genotype and allele frequency between CBD, BeS individuals and controls. In CBD, associations were found with decline in forced expiratory volume in 1 s and forced vital capacity and theCCR5-3458 thymidine (T)T genotype (p<0.0001), and an increase in alveolar–arterial oxygen tension difference at rest (p = 0.003) and at maximum exercise (p = 0.01) and the -5663 adenine allele. Increased bronchoalveolar lavage lymphocyte numbers were associated withCCR5-2459 guanine/-2135T (p = 0.01) only in the combined CBD and BeS group.This is the first study showing thatCCR5polymorphisms are associated with worsening pulmonary function over time in CBD, suggesting thatCCR5is important in the progression of pulmonary function in CBD. Further studies would be useful to clarify the mechanism whereby CCR5 polymorphisms affect progression of CBD.
Genetic and environmental influences on objective intermediate asthma phenotypes in Dutch twins
Authors: Wu T. , Boezen H.M. , Postma D.S. , Los H. , Postmus P.E. , Snieder H. , Boomsma D.I. 
Published: January 2010

It is unclear to what extent the same set of environmental or genetic factors regulate objective intermediate asthma phenotypes. We examined heritabilities of these phenotypes and estimated their environmental and genetic overlap.We studied baseline lung function (forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC), bronchial hyperresponsiveness, number of positive skin prick tests (SPT) to 11 allergens, serum total immunoglobulin (Ig)E, number of positive specific IgE tests to four allergens and eosinophil counts. 103 twin pairs were studied (46 monozygotic and 57 dizygotic; mean age: 22.5 yrs, range: 17.0–27.0 yrs). Univariate and bivariate genetic analyses were performed after adjustment for significant covariates.All intermediate asthma phenotypes showed significant heritabilities (47–83%). Most phenotypes were substantially correlated, which was mainly due to shared genetic factors. Pairs of phenotypes with the largest genetic correlations were specific IgE and SPT (0.98), and total IgE with specific IgE (0.87), with SPT (0.72), and with eosinophils (0.62). SPT showed significant environmental correlations with total IgE (0.65), specific IgE (0.70) and bronchial hyperresponsiveness (0.44).Genetic effects explain the majority of the variation in objective intermediate asthma phenotypes. Additionally, correlations between pairs of these traits are also mainly explained by genetic rather than environmental factors.
Effectiveness of the pneumococcal polysaccharide vaccine in preventing pneumonia in the elderly
Authors: Domínguez A. , Izquierdo C. , Salleras L. , Ruiz L. , Sousa D. , Bayas J-M. , Nebot M. , Varona W. , Celorrio J-M. , Carratalà J. 
Published: January 2010

The objective of our study was to evaluate the effectiveness of the 23-valent pneumococcal polysaccharide vaccine (PPV) in preventing hospital admission for community-acquired pneumonia (CAP) in people ≥65 yrs of age.We conducted a matched case–control study in patients with CAP admitted to five Spanish hospitals. Cases were persons aged ≥65 yrs admitted to hospital through the emergency department, who presented a clinical and radiological pattern compatible with pneumonia, assessed using established criteria. We matched each case with three control subjects by sex, age (±5 yrs), date of hospitalisation (±30 days) and underlying disease. The study period was May 1, 2005 to January 31, 2007. The PPV immunisation status of cases and controls was investigated. Adjusted ORs for vaccination were calculated using logistic regression analysis.A total of 489 cases and 1,467 controls were included in the final analysis. The overall adjusted vaccination effectiveness for all patients was 23.6% (95% CI 0.9–41.0). The adjusted vaccination effectiveness for immunosuppressed patients was 21.0% (95% CI -18.7–47.5).Our results suggest that the PPV may potentially reduce hospitalisations for pneumonia in the elderly and supports vaccination programmes in this age group.
Characterization of the Six1 homeobox gene in normal mammary gland morphogenesis
Authors: Coletta Ricardo D , McCoy Erica L , Burns Valerie , Kawakami Kiyoshi , McManaman James L , Wysolmerski John J , Ford Heide L 
Published: January 2010

AbstractBackgroundTheSix1homeobox gene is highly expressed in the embryonic mammary gland, continues to be expressed in early postnatal mammary development, but is lost when the mammary gland differentiates during pregnancy. However,Six1is re-expressed in breast cancers, suggesting that its re-instatement in the adult mammary gland may contribute to breast tumorigenesis via initiating a developmental process out of context. Indeed, recent studies demonstrate that Six1 overexpression in the adult mouse mammary gland is sufficient for initiating invasive carcinomas, and that its overexpression in xenograft models of mammary cancer leads to metastasis. These data demonstrate that Six1 is causally involved in both breast tumorigenesis and metastasis, thus raising the possibility that it may be a viable therapeutic target. However, because Six1 is highly expressed in the developing mammary gland, and because it has been implicated in the expansion of mammary stem cells, targeting Six1 as an anti-cancer therapy may have unwanted side effects in the breast.ResultsWe sought to determine the role of Six1 in mammary development using two independent mouse models. To study the effect of Six1 loss in early mammary development when Six1 is normally expressed,Six1-/-embryonic mammary glands were transplanted intoRag1-/-mice. In addition, to determine whether Six1 downregulation is required during later stages of development to allow for proper differentiation, we overexpressed Six1 during adulthood using an inducible, mammary-specific transgenic mouse model. Morphogenesis of the mammary gland occurred normally in animals transplanted withSix1-/-embryonic mammary glands, likely through the redundant functions of other Six family members such asSix2andSix4, whose expression was increased in response to Six1 loss. Surprisingly, inappropriate expression of Six1 in the adult mammary gland, when levels are normally low to absent, did not inhibit normal mammary differentiation during pregnancy or lactation.ConclusionsSix1 is not critical for normal mammary gland development, since neither loss nor inappropriate overexpression of Six1 adversely affects normal mammary gland development or function. However, as bothSix2andSix4levels are increased inSix1-/-mammary glands, we postulate that these Six family members are functionally redundant in the gland, as is true of many homeobox gene families. This data, in conjunction with recent findings that Six1 is capable of promoting breast cancer initiation and progression, suggest that Six1 may serve as a reasonable chemotherapeutic target in a clinical setting, particularly for those women diagnosed with breast cancer in their childbearing years.
New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome
Authors: Feng Jihua , Dai Xianhua , Xiang Qian , Dai Zhiming , Wang Jiang , Deng Yangyang , He Caisheng 
Published: January 2010

Abstract

Background
Recently, a number of high-resolution genome-wide maps of nucleosome locations in S. cerevisiae have been derived experimentally. However, nucleosome positions are determined in vivo by the combined effects of numerous factors. Consequently, nucleosomes are not simple static units, which may explain the discrepancies in reported nucleosome positions as measured by different experiments. In order to more accurately depict the genome-wide nucleosome distribution, we integrated multiple nucleosomal positioning datasets using a multi-angle analysis strategy.

Results
To evaluate the contribution of chromatin structure to transcription, we used the vast amount of available nucleosome analyzed data. Analysis of this data allowed for the comprehensive identification of the connections between promoter nucleosome positioning patterns and various transcription-dependent properties. Further, we characterised the function of nucleosome destabilisation in the context of transcription regulation. Our results indicate that genes with similar nucleosome occupancy patterns share general transcription attributes. We identified the local regulatory correlation (LRC) regions for two distinct types of nucleosomes and we assessed their regulatory properties. We also estimated the nucleosome reproducibility and measurement accuracy for high-confidence transcripts. We found that by maintaining a distance of ~13 bp between the upstream border of the +1 nucleosome and the transcription start sites (TSSs), the stable +1 nucleosome may form a barrier against the accessibility of the TSS and shape an optimum chromatin conformation for gene regulation. An in-depth analysis of nucleosome positioning in normally growing and heat shock cells suggested that the extent and patterns of nucleosome sliding are associated with gene activation.

Conclusions
Our results, which combine different types of data, suggest that cross-platform information, including discrepancy and consistency, reflects the mechanisms of nucleosome packaging in vivo more faithfully than individual studies. Furthermore, nucleosomes can be divided into two classes according to their stable and dynamic characteristics. We found that two different nucleosome-positioning characteristics may significantly impact transcription programs. Besides, some positioned-nucleosomes are involved in the transition from stable state to dynamic state in response to abrupt environmental changes.
The transforming acidic coiled coil (TACC1) protein modulates the transcriptional activity of the nuclear receptors TR and RAR
Authors: Guyot Romain , Vincent Séverine , Bertin Julie , Samarut Jacques , Ravel-Chapuis Patrick 
Published: January 2010

Abstract

Background
The transcriptional activity of Nuclear hormone Receptors (NRs) is regulated by interaction with coactivator or corepressor proteins. Many of these cofactors have been shown to have a misregulated expression or to show a subcellular mislocalization in cancer cell lines or primary tumors. Therefore they can be factors involved in the process of oncogenesis.

Results
We describe a novel NR coregulator, TACC1, which belongs to the Transforming Acidic Coiled Coil (TACC) family. The interaction of TACC1 with Thyroid Hormone Receptors (TR) and several other NRs has been shown in a yeast two-hybrid screen and confirmed by GST pulldown, colocalization and co-immunoprecipitation experiments. TACC1 interacts preferentially with unliganded NRs. In F9 cells, endogenous TACC1 localized in the chromatin-enriched fraction of the nucleus and interacted with Retinoid Acid Receptors (RARα) in the nucleus. TACC1 depletion in the cell led to decreased RARα and TRα ligand-dependent transcriptional activity and to delocalization of TR from the nucleus to the cytoplasm.

Conclusions
From these experimental studies we propose that TACC1 might be a scaffold protein building up a transcriptional complex around the NRs we studied. This function of TACC1 might account for its involvement in several forms of tumour development.
Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda
Authors: Gupta Vinay , Dorsey Grant , Hubbard Alan E , Rosenthal Philip J , Greenhouse Bryan 
Published: January 2010

Abstract

Background
Molecular genotyping is performed in anti-malarial trials to determine whether recurrent parasitaemia after therapy represents a recrudescence (treatment failure) or new infection. The use of capillary instead of agarose gel electrophoresis for genotyping offers technical advantages, but it is unclear whether capillary electrophoresis will result in improved classification of anti-malarial treatment outcomes.

Methods
Samples were genotyped using both gel and capillary electrophoresis from randomized trials of artemether-lumefantrine (AL) vs. dihydroartemisinin-piperaquine (DP) performed in two areas of Uganda: Kanungu, where transmission is moderate, and Apac, where transmission is very high. Both gel and capillary methods evaluated polymorphic regions of the merozoite surface protein 1 and 2 and glutamine rich protein genes.

Results
Capillary electrophoresis detected more alleles and provided higher discriminatory power than agarose gel electrophoresis at both study sites. There was only moderate agreement between classification of outcomes with the two methods in Kanungu (kappa = 0.66) and poor agreement in Apac (kappa = 0.24). Overall efficacy results were similar when using gel vs. capillary methods in Kanungu (42-day risk of treatment failure for AL: 6.9% vs. 5.5%, p = 0.4; DP 2.4% vs. 2.9%, p = 0.5). However, the measured risk of recrudescence was significantly higher when using gel vs. capillary electrophoresis in Apac (risk of treatment failure for AL: 17.0% vs. 10.7%, p = 0.02; DP: 8.5% vs. 3.4%, p = 0.03). Risk differences between AL and DP were not significantly different whether gel or capillary methods were used.

Conclusions
Genotyping with gel electrophoresis overestimates the risk of recrudescence in anti-malarial trials performed in areas of high transmission intensity. Capillary electrophoresis provides more accurate outcomes for such trials and should be performed when possible. In areas of moderate transmission, gel electrophoresis appears adequate to estimate comparative risks of treatment failure.