bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of livestock breed diversity
Authors: Barker J.S.F. 
Published: August 2011

SUMMARYMankind uses some 40 species of animals as domestic livestock to meet our needs for food, clothing, power, etc. Within these species, there are in total some 4,500 breeds that are referred to as the global animal genetic resources. Each breed comprises a unique set of genes. More than 30% of breeds are estimated to be at risk of extinction, and many more, particularly in developing countries, are threatened by inefficient utilization. The Food and Agriculture Organization of the United Nations has been mandated by its member nations to manage the global animal genetic resources, and major progress has been made in the last few years. However, resources are limited, and priorities will have to be set for breed conservation, for breed development programmes and for evaluation studies. Breeds that are taxonomically distinct should be favoured for conservation, the objective being to maintain maximum genetic diversity of each livestock species. Genetic distances and phylogenetic diversity provide the best available objective criterion, and microsatellites are the current markers of choice for obtaining the genetic data. Microsatellite-based genetic distances will describe breed similarities due to common ancestry, but cannot account for consequences of artificial or natural selection. Phylogenetic trees for 11 water buffalo populations in southeast Asia, constructed using 25 polymorphic protein coding loci or 21 microsatellite loci, show differences in both topology and branch lengths, but the microsatellite tree is a better representation of the similarities due to common ancestry. Thus phylogenetic diversity, based on microsatellite loci, should be used as an initial guide in making conservation decisions for livestock breeds.
The Early Carboniferous volcanic outliers of Little Cumbrae and south Bute: implications for westward attenuation of the Clyde Lava Plateau
Authors: Caldwell W. G. E. , Young G. M. 
Published: August 2011

ABSTRACTLittle Cumbrae and south Bute are the closest outliers of Early Carboniferous Clyde Plateau volcanic rocks to those forming the plateau itself, and the only ones with the potential to reveal how the volcanic succession of the plateau becomes attenuated westward beneath the Firth of Clyde. Closest links are to the Renfrewshire Hills Block of the plateau proper, where the Clyde Plateau Volcanic Formation attains its greatest thickness and widest extent.Basal lavas in both outliers can be correlated to the lower part of the Strathgryfe Member of the Clyde Plateau Volcanic Formation (Viséan, Holkerian), which rests disconformably on the Clyde Sandstone Formation (Tournaisian, Chadian). Relative to the Renfrewshire Hills Block, this implies intervening overlap of three older members of the Clyde Plateau Formation and overstep of a varied sedimentary foundation. Higher lavas and pyroclastic accumulations in south Bute are correlative to the Misty Law Trachytic Member and upper part of the Strathgryfe Member. Thin lavas that cap the Renfrewshire Hills Block on its eastern flank probably never accumulated as far west as the present Firth of Clyde.Southwestward from the Renfrewshire Hills, the Clyde Plateau lavas lose about two thirds of their 1000-m thickness in 25–30 km – a rate of thinning that implies they may extend no farther than the Sound of Bute or northeastern Arran.
Imaging Action Potentials with Calcium Indicators
Authors: Yuste Rafael , MacLean Jason , Vogelstein Joshua , Paninski Liam 
Published: August 2011

INTRODUCTIONThe understanding of neuronal circuits has been greatly advanced by the ability to simultaneously image action-potential generation within large populations of neurons. This protocol describes bulk loading of brain slices with acetoxymethyl (AM) ester calcium indicators to monitor action-potential activity in functional neuronal circuits. The imaging of calcium influx into neurons provides an indirect but accurate measure of action-potential generation within individual neurons. The key advantage of the technique is that it allows the researcher to densely sample the activity of a large population of neurons with single-cell resolution.
Blastomere Injection of Cleavage-Stage Zebrafish Embryos and Imaging of Labeled Cells
Authors: England Samantha J. , Adams Richard J. 
Published: August 2011

INTRODUCTIONZebrafish embryos are useful for studying morphogenesis. Their foremost advantage is their optical transparency. Because the embryos are small, they can be imaged as whole-mount preparations. Crucially, this preserves both the mechanical and the molecular integrity of the embryo. This protocol describes the preparation of live zebrafish embryos for the collection of movies using four-dimensional time-lapse confocal microscopy. Methods are presented for the labeling of cells, for the orientation and immobilization of embryos, and for establishing a robust reproducible imaging environment with which to acquire high-resolution dynamic movies of cell behaviors during morphogenesis. These methods concentrate on the visualization of notochord morphogenesis in the zebrafish embryo. However, they also apply to the analysis of many other developing tissues. Factors that can influence the success of time-lapse confocal microscopy are discussed, such as the choice of cell label, the effects of genetic manipulation, and the consequences of environmental variation during imaging—all of which may influence the rate of development.
Immunolabeling of Drosophila Embryos and Tissues
Authors: Swedlow Jason 
Published: August 2011

INTRODUCTIONThe fruit fly Drosophila melanogaster has long been used to study the genetic factors involved in development. The ability to localize molecules within an organism that allow genetic manipulation can be quite useful. This article provides a standard method for preparing various Drosophila tissues for analysis by immunofluorescence microscopy. Specific methods are also presented for the handling of embryos, because these are used frequently and require special consideration.
Post‐orogenic evolution of the Mesozoic Micang Shan Foreland Basin system, central China
Authors: Tian Yuntao , Kohn Barry P. , Zhu Chuanqing , Xu Ming , Hu Shengbiao , Gleadow Andrew J. W. 
Published: August 2011

Abstract[Correction added after online publication 3 August 2010 ‐ ‘prelate’ has been changed to ‘pre‐late’ throughout the text]. Using apatite fission track and (U‐Th‐Sm)/He thermochronology, we report the low‐temperature thermal history of the Mesozoic Micang Shan Foreland Basin system, central China. This system, comprising the Hannan Dome hinterland, the northern Sichuan Foreland Basin and the intermediate frontal thrust belt (FB), shares a common boundary with three major tectonic terrains – Mesozoic Qinling‐Dabie Orogen, Mesozoic Sichuan Foreland Basin and Cenozoic elevated Tibetan Plateau. Results show: (1) a relatively rapid pre‐late Cretaceous cooling episode in the Hannan Dome; (2) a mid‐Cenozoic cooling phase (ca. 50°C at ca. 30 ± 5 Ma) within the northern Sichuan Basin; and (3) possible late Cenozoic cooling (ca. 25°C at ca. 16 ± 4 Ma) within the Hannan Dome‐FB, a phase which has also been reported previously from adjacent regions. The pre‐late Cretaceous cooling episode in the Hannan Dome is attributed to coeval tectonism in nearby regions. Mid‐Cenozoic cooling in the northern Sichuan Basin can possibly be attributed to either one of or a combination of shortening of the basin, onset of the Asian monsoon and drainage adjustment of the Yangtze River system, all of which are related to growth of the Tibetan Plateau. Possible late Cenozoic cooling in the hinterland and nearby regions is also probably related to the northeastward growth of the Tibetan Plateau. However, previous studies suggest a northeastward propagation for onset of cooling from the eastern Tibetan Plateau to western Qinling in response to northeastward lower crust flow from the central Tibetan Plateau. The timing of apparent late Cenozoic cooling in the Hannan Dome hinterland, at an intermediate locality, is not consistent with this trend, and supports a previous model suggesting northeastern growth of the Tibetan Plateau through reactivation of WE trending strike‐slip faults.
Seismic time‐lapse effects of solution salt mining – a feasibility study
Authors: Drijkoningen Guy , van Noort Guus , Arts Rob , Bullen Joren , Thorbecke Jan 
Published: August 2011

ABSTRACTThis article addresses the question whether time‐lapse seismic reflection techniques can be used to follow and quantify the effects of solution salt mining. Specifically, the production of magnesium salts as mined in the north of the Netherlands is considered. The use of seismic time‐lapse techniques to follow such a production has not previously been investigated. For hydrocarbon production and CO2 storage, time‐lapse seismics are used to look at reservoir changes mainly caused by pressure and saturation changes in large reservoirs, while for solution mining salt is produced from caverns with a limited lateral extent, with much smaller production volumes and a fluid (brine) replacing a solid (magnesium salt).In our approach we start from the present situation of the mine and then study three different production scenarios, representing salt production both in vertical and lateral directions of the mine. The present situation and future scenarios have been transformed into subsurface models that were input to an elastic finite‐difference scheme to create synthetic seismic data. These data have been analysed and processed up to migrated seismic images, such that time‐lapse analyses of intermediate and final results could be done.From the analyses, it is found that both vertical and lateral production is visible well above the detection threshold in difference data, both at pre‐imaging and post‐imaging stages. In quantitative terms, an additional production of the mine of 6 m causes time‐shifts in the order of 2 ms (pre‐imaging) and 4 ms (post‐imaging) and amplitude changes of above 20% in the imaged sections. A laterally oriented production causes even larger amplitude changes at the edge of the cavern due to replacement of solid magnesium salt with brine introducing a large seismic contrast. Overall, our pre‐imaging and post‐imaging time‐lapse analysis indicates that the effects of solution salt mining can be observed and quantified on seismic data. The effects seem large enough to be observable in real seismic data containing noise.
Survival and virulence properties of multiple antibiotic‐resistant Salmonella Typhimurium under simulated gastrointestinal conditions
Authors: He Xinlong , Ahn Juhee 
Published: August 2011

SummaryThe transit tolerance and relative gene expression (acrA, acrB, tolC, stn, hilA and ompD) were observed in antibiotic‐sensitive Salmonella Typhimurium (ASST) and antibiotic‐resistant S. Typhimurium (ARST) exposed to simulated gastric juices (pH 2.0, pH 3.0 and pH 5.0) for 1 or 4 h, followed by small intestinal juices (0.1% and 0.5% bile salts) for 2 h. The relative expression of acrA, acrB, tolC, stn, hilA and ompD in the ARST was upregulated after exposure to simulated gastrointestinal juices. The expression of AcrAB‐TolC efflux system in ARST was highly correlated with the expression of stn and hilA encoding virulence factor and regulator. The cross‐protective effect was observed in ARST against the gastric acid and bile salts. The AcrAB‐TolC involved in enhanced survival and virulence potential, resulting in increased in pathogenicity of ARST. This study provides useful information for assessing the gastrointestinal transit tolerance and virulence potential of multiple antibiotic‐resistant pathogens.
Exploring the use of actigraphy to investigate sleep problems in older people with intellectual disability
Authors: van Dijk E. , Hilgenkamp T. I. M. , Evenhuis H. M. , Echteld M. A. 
Published: August 2011

AbstractBackground  The aim of this study was to explore the use of actigraphy to investigate sleep problems in a convenience sample of clients of Dutch intellectual disability (ID) care providers. Based on data obtained in a large multi‐centre study on healthy ageing in people with ID, research questions were: ‘To what degree are actigraphic measurements successful in this population?’ and ‘What is the influence of different sensitivity settings of the Actiwatch Sleep Analysis software on the distribution of sleep variables in this group?’Methods  Data were collected in a cross‐sectional descriptive study design. We included 563 participants, aged 50 years or older, with borderline to profound ID. Sleep‐wake data were measured continuously during 14 days and nights using the Actiwatch AW7. A complete measurement of at least 7 days and nights, including at least one weekend day, was considered successful. Objective variables of sleep were analysed using different sensitivity settings of the Actiwatch AW7 Sleep Analysis software.Results  In 200 participants (35.5%), a successful measurement was obtained. Unsuccessful measurements were caused primarily by problems with wearing the device and incomplete information on bed time and get up time. Of 382 participants who started wearing the Actiwatch, 354 (92.3%) wore it for at least 7 days. Application of different sensitivity settings of the Sleep Analysis software resulted in clear differences of all sleep parameters.Conclusions  Further research is needed into the validity of objective sleep parameters, as measured with the Actiwatch, for screening and epidemiological research in older people with ID. It needs to be investigated which sensitivity setting of the Actiwatch gives most valid results in this specific group, whereas reference data on sleep parameters and cut‐off values are to be obtained.
Validation of personal digital photography to assess dietary quality among people with intellectual disabilities
Authors: Elinder L. S. , Brunosson A. , Bergström H. , Hagströmer M. , Patterson E. 
Published: August 2011

AbstractBackground  Dietary assessment is a challenge in general, and specifically in individuals with intellectual disabilities (ID). This study aimed to evaluate personal digital photography as a method of assessing different aspects of dietary quality in this target group.Method  Eighteen adults with ID were recruited from community residences and activity centres in Stockholm County. Participants were instructed to photograph all foods and beverages consumed during 1 day, while observed. Photographs were coded by two raters. Observations and photographs of meal frequency, intake occasions of four specific food and beverage items, meal quality and dietary diversity were compared. Evaluation of inter‐rater reliability and validity of the method was performed by intra‐class correlation analysis.Results  With reminders from staff, 85% of all observed eating or drinking occasions were photographed. The inter‐rater reliability was excellent for all assessed variables (ICC ≥ 0.88), except for meal quality where ICC was 0.66. The correlations between items assessed in photos and observations were strong to almost perfect with ICC values ranging from 0.71 to 0.92 and all were statistically significant.Conclusion  Personal digital photography appears to be a feasible, reliable and valid method for assessing dietary quality in people with mild to moderate ID, who have daily staff support.
Characterization of the elongasome core PBP2 : MreC complex of Helicobacter pylori
Authors: El Ghachi Meriem , Matteï Pierre‐Jean , Ecobichon Chantal , Martins Alexandre , Hoos Sylviane , Schmitt Christine , Colland Frédéric , Ebel Christine , Prévost Marie‐Christine , Gabel Frank , England Patrick , Dessen Andréa , Boneca Ivo G. 
Published: August 2011

SummaryThe definition of bacterial cell shape is a complex process requiring the participation of multiple components of an intricate macromolecular machinery. We aimed at characterizing the determinants involved in cell shape of the helical bacterium Helicobacter pylori. Using a yeast two‐hybrid screen with the key cell elongation protein PBP2 as bait, we identified an interaction between PBP2 and MreC. The minimal region of MreC required for this interaction ranges from amino acids 116 to 226. Using recombinant proteins, we showed by affinity and size exclusion chromatographies and surface plasmon resonance that PBP2 and MreC form a stable complex. In vivo, the two proteins display a similar spatial localization and their complex has an apparent 1:1 stoichiometry; these results were confirmed in vitro by analytical ultracentrifugation and chemical cross‐linking. Small angle X‐ray scattering analyses of the PBP2 : MreC complex suggest that MreC interacts directly with the C‐terminal region of PBP2. Depletion of either PBP2 or MreC leads to transition into spherical cells that lose viability. Finally, the specific expression in trans of the minimal interacting domain of MreC with PBP2 in the periplasmic space leads to cell rounding, suggesting that the PBP2/MreC complex formation in vivo is essential for cell morphology.
Histology as a treatment effect modifier in advanced non‐small cell lung cancer: A systematic review of the evidence
Authors: STANDFIELD LACHLAN , WESTON ADÈLE R. , BARRACLOUGH HELEN , VAN KOOTEN MAXIMILIANO , PAVLAKIS NICK 
Published: August 2011

ABSTRACTBackground and objective:  We conducted a systematic review of prospective, randomized, controlled trials (RCT) to examine whether histology had a treatment modifying effect (TME) on the efficacy outcomes of chemotherapeutic agents in patients with advanced (stage IIIB‐IV) non‐small cell lung cancer (NSCLC).Methods:  Potentially pertinent publications were reviewed in full to determine if there was any TME by histology for overall survival (OS), progression‐free survival (PFS) or treatment response rate (TRR).Results:  Data from three pemetrexed RCT, comparing (i) pemetrexed versus docetaxel, (ii) pemetrexed and cisplatin versus gemcitabine and cisplatin, and (iii) pemetrexed versus placebo, showed a statistically significant TME by histology for OS and PFS. One trial comparing pemetrexed and carboplatin versus gemcitabine and carboplatin found no significant associations between histology and OS. The results of this systematic review indicate that pemetrexed appears to have the most consistent treatment‐by‐histology interaction effect on the efficacy outcomes of chemotherapeutic agents in patients with advanced or metastatic NSCLC. Patients with non‐squamous histology gain the greatest benefit from treatment with pemetrexed. Conversely, patients with squamous cell disease appeared to experience poorer OS when pemetrexed was compared with other active treatments, and similar OS when compared with placebo. Reproducible patterns of TME effect by histology with other chemotherapeutic agents are less clear.Conclusions:  We consider that the historical approach to treating all NSCLC patients with the same chemotherapy regimen is now no longer acceptable.
Burden of obstructive lung disease in a rural setting in the Philippines
Authors: IDOLOR LUISITO F. , DE GUIA TERESITA S. , FRANCISCO NORBERTO A. , ROA CAMILO C. , AYUYAO FERNANDO G. , TADY CECIL Z. , TAN DANIEL T. , BANAL‐YANG SYLVIA , BALANAG JR VINCENT M. , REYES MARIA TERESITA N. , DANTES RENATO B. 
Published: August 2011

ABSTRACTBackground and objective:  The aim of this study was to determine the prevalence of and risk factors associated with COPD in a rural setting in the Philippines.Methods:  The study was conducted in two municipalities in Nueva Ecija province in the Philippines. Using the Burden of Obstructive Lung Disease (BOLD) protocol and study design, non‐hospitalized men or women, aged 40 years or older, were recruited by multi‐stage random sampling procedures. Participants completed questionnaires on respiratory symptoms and exposure to potential risk factors for COPD, including smoking, occupation and exposure to burning of biomass fuel. Spirometry was performed according to American Thoracic Society criteria.Results:  Of the 1188 individuals selected for recruitment, 722 had acceptable post‐bronchodilator spirometry and were classified according to Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage. The overall prevalence of COPD for all stages was 20.8%. The prevalence of COPD at GOLD Stage I or higher was greater in men compared with women (26.5% vs 15.3%), and increased between the ages of 40 to >70 years. Logistic regression analysis showed a significant association between all stages of COPD and farming for >40 years (odds ratio (OR) 2.48, 95% confidence interval (CI): 1.43–4.30), use of firewood for cooking for >60 years (OR 3.48, 95% CI: 1.57–7.71), a smoking history of ≥20 pack‐years (OR 2.86; 95% CI: 1.78–4.60), and a history of tuberculosis (OR 6.31, 95% CI: 2.67–15.0).Conclusions:  The prevalence COPD in a rural community in Nueva Ecija, Philippines was 20.8% for GOLD Stage I or higher, and 16.7% for GOLD Stage II or higher. In addition to smoking history, the use of firewood for cooking, working on a farm and a history of tuberculosis were significantly associated with fixed airflow obstruction, as assessed by spirometry.
Failure mode of laser welds in lap‐shear specimens of high strength low alloy (HSLA) steel sheets
Authors: ASIM K. , LEE J. , PAN J. 
Published: August 2011

ABSTRACTIn this paper, the failure mode of laser welds in lap‐shear specimens of non‐galvanized SAE J2340 300Y high strength low alloy steel sheets under quasi‐static loading conditions is examined based on experimental observations and finite element analyses. Laser welded lap‐shear specimens with reduced cross sections were made. Optical micrographs of the cross sections of the welds in the specimens before and after tests are examined to understand the microstructure and failure mode of the welds. Micro‐hardness tests were also conducted to provide an assessment of the mechanical properties in the base metal, heat‐affected and fusion zones. The micrographs indicate that the weld failure appears to be initiated from the base metal near the boundary of the base metal and the heat‐affected zone at a distance away from the pre‐existing crack tip, and the specimens fail due to the necking/shear of the lower left load carrying sheets. Finite element analyses based on non‐homogenous multi‐zone material models were conducted to model the ductile necking/shear failure and to obtain the J integral solutions for the pre‐existing cracks. The results of the finite element analyses are used to explain the ductile failure initiation sites and the necking/shear of the lower left load carrying sheets. The J integral solutions obtained from the finite element analyses based on the 3‐zone finite element model indicate that the J integral for the pre‐existing cracks at the failure loads are low compared to the fracture toughness and the specimens should fail in a plastic collapse or necking/shear mode. The effects of the sheet thickness on the failure mode were then investigated for laser welds with a fixed ratio of the weld width to the thickness. For the given non‐homogenous material model, the J integral solutions appear to be scaled by the sheet thickness. With consideration of the plastic collapse failure mode and fracture initiation failure mode, a critical thickness can be obtained for the transition of the plastic collapse or necking/shear failure mode to the fracture initiation failure mode. Finally, the failure load is expressed as a function of the sheet thickness according to the governing equations based on the two failure modes. The results demonstrate that the failure mode of welds of thin sheets depends on the sheet thickness, ductility of the base metal and fracture toughness of the heat‐affected zone. Therefore, failure criteria based on either the plastic collapse failure mode or the fracture initiation failure mode should be used cautiously for welds of thin sheets.