bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seismic data reconstruction using multidimensional prediction filters
Authors: Naghizadeh M. , Sacchi M.D. 
Published: April 2009

ABSTRACTIn this paper we discuss a beyond‐alias multidimensional implementation of the multi‐step autoregressive reconstruction algorithm for data with missing spatial samples. The multi‐step autoregressive method is summarized as follows: vital low‐frequency information is first regularized adopting a Fourier based method (minimum weighted norm interpolation); the reconstructed data are then used to estimate prediction filters that are used to interpolate higher frequencies. This article discusses the implementation of the multi‐step autoregressive method to data with more than one spatial dimension. Synthetic and real data examples are used to examine the performance of the proposed method. Field data are used to illustrate the applicability of multidimensional multi‐step autoregressive operators for regularization of seismic data.
Intercomparison, interpretation, and assessment of spring phenology in North America estimated from remote sensing for 1982–2006
Authors: WHITE MICHAEL A. , De BEURS KIRSTEN M. , DIDAN KAMEL , INOUYE DAVID W. , RICHARDSON ANDREW D. , JENSEN OLAF P. , O'KEEFE JOHN , ZHANG GONG , NEMANI RAMAKRISHNA R. , Van LEEUWEN WILLEM J. D. , BROWN JESSLYN F. , De WIT ALLARD , SCHAEPMAN MICHAEL , LIN XIOAMAO , DETTINGER MICHAEL , BAILEY AMEY S. , KIMBALL JOHN , SCHWARTZ MARK D. , BALDOCCHI DENNIS D. , LEE JOHN T. , LAUENROTH WILLIAM K. 
Published: April 2009

AbstractShifts in the timing of spring phenology are a central feature of global change research. Long‐term observations of plant phenology have been used to track vegetation responses to climate variability but are often limited to particular species and locations and may not represent synoptic patterns. Satellite remote sensing is instead used for continental to global monitoring. Although numerous methods exist to extract phenological timing, in particular start‐of‐spring (SOS), from time series of reflectance data, a comprehensive intercomparison and interpretation of SOS methods has not been conducted. Here, we assess 10 SOS methods for North America between 1982 and 2006. The techniques include consistent inputs from the 8 km Global Inventory Modeling and Mapping Studies Advanced Very High Resolution Radiometer NDVIg dataset, independent data for snow cover, soil thaw, lake ice dynamics, spring streamflow timing, over 16 000 individual measurements of ground‐based phenology, and two temperature‐driven models of spring phenology. Compared with an ensemble of the 10 SOS methods, we found that individual methods differed in average day‐of‐year estimates by ±60 days and in standard deviation by ±20 days. The ability of the satellite methods to retrieve SOS estimates was highest in northern latitudes and lowest in arid, tropical, and Mediterranean ecoregions. The ordinal rank of SOS methods varied geographically, as did the relationships between SOS estimates and the cryospheric/hydrologic metrics. Compared with ground observations, SOS estimates were more related to the first leaf and first flowers expanding phenological stages. We found no evidence for time trends in spring arrival from ground‐ or model‐based data; using an ensemble estimate from two methods that were more closely related to ground observations than other methods, SOS trends could be detected for only 12% of North America and were divided between trends towards both earlier and later spring.
Geometric quantification of the plant endoplasmic reticulum
Authors: BOUCHEKHIMA A.‐N. , FRIGERIO L. , KIRKILIONIS & M. 
Published: April 2009

SummaryOne of the most difficult obstacles to make biological sciences more quantitative is the lack of understanding the interplay of form and function. Each cell is full of complex‐shaped objects, which moreover change their form over time. To tackle this problem, we suggest the use of geometric invariants that are able to produce precise reference points to compare a cell's different functional elements such as organelles under fixed and varying physiological conditions. In this paper, we look at the topology of an almost static sample of the plant cortical endoplasmic reticulum (ER) under close‐to‐normal physiological conditions using a multi‐disciplinary approach combining confocal microscopy, image processing techniques, visualization, computational geometry and graph theory. Data collected from a series of optical sections taken at short, regular intervals along the optical axis are used to reconstruct the ER in three dimensions. A graph structure of the ER network is obtained after thinning the ER geometry to its essential features. The graph is the final and most abstract quantification of the ER and serves very well as a geometrical invariant, even and very importantly, in cases in which the ER sample is moving or slightly changing shape during image acquisition. Moreover, graph theoretic features, such as the number of nodes and their degrees and the number of edges and their lengths, are very robust against different kinds of small perturbations that should not change the ER function. We will also attach surface areas and volumes estimated for the plant ER network as weights to the graph, allowing an even more precise quantitative characterization of this organelle. In total, we have compared 28 different samples under similar experimental conditions. The methods used in this paper should also be applicable to the quantification of other organelles in which geometric abstraction is possible to analyse function. Finally, by the use of confocal microscopy, our techniques will be transferable to situations in which protein markers can move inside the organelle's lumen and/or on the membrane surface to test further aspects of protein distribution.
Measurements of the diameters of the great arteries and semi‐lunar valves of chick and mouse embryos
Authors: WENINGER W.J. , MAURER B. , ZENDRON B. , DORFMEISTER K. , GEYER S.H. 
Published: April 2009

SummaryThe great arteries of embryos are small channels of a complex three‐dimensional arrangement. Measurements of their diameters, as required for understanding cardiovascular morphogenesis and the genesis of malformations, cannot be performed in two‐dimensional histological sections. We present and evaluate a quick and simple method for performing highly significant and objective measurements of the diameters of blood vessels in vertebrate embryos and used this method for providing statistics of the diameter of the semi‐lunar valves and the lumina of the great arteries of early chick and mouse foetus. We employed the high‐resolution episcopic microscopy technique for generating volume data and three‐dimensional computer models of the arterial trees of 30 chick embryos (Hamburger Hamilton stage 34), 30 mouse embryos of the OF1 strain harvested on 14.5 dpc, 30 embryos of the OF1 strain harvested on 15.5 dpc and 28 mouse embryos of the PARKES strain harvested on 14.5 dpc. The three‐dimensional models (voxel size 2 μm × 2 μm × 2 μm and 3 μm × 3 μm × 3 μm) were used for defining virtual resection planes perpendicular to the longitudinal axis of the blood vessels at comparable positions. In these planes, we measured the lumen areas and the lumen perimeters. We also calculated the lumen diameter and the true lumen area from the perimeter and present statistical analysis. Finally, we evaluate and discuss the reliability and reproducibility of our method and present all measurements in a form that minimizes the influence of specimen size variation, specimen processing and data generation methods.
Visualization of BrdU‐labelled DNA in cyanobacterial cells by Hilbert differential contrast transmission electron microscopy
Authors: NITTA K. , NAGAYAMA K. , DANEV R. , KANEKO Y. 
Published: April 2009

SummaryWe have attempted to observe the native shape of DNA in rapidly frozen whole cyanobacterial cells through 5‐bromo‐2‐deoxyuridine (BrdU) incorporation and visualization with a Hilbert differential contrast transmission electron microscopy (HDC TEM). The incorporation of BrdU into the DNA of Synechococcus elongatus PCC 7942 was confirmed with fluorescently labelled anti‐BrdU antibodies and through EDX analysis of ultra‐thin sections. HDC TEM observed cells that had incorporated BrdU into their DNA exhibited electron dense areas at the location corresponding to fluorescently labelled BrdU. Since various strings and strands were observed in high contrast with the HDC TEM, we conclude that the method promises to allow us to identify and understand bulk structural changes of the in vivo DNA and the nucleoid through observation at high resolution.
Inhibition of cathelicidin activity by bacterial exopolysaccharides
Authors: Foschiatti Michela , Cescutti Paola , Tossi Alessandro , Rizzo Roberto 
Published: April 2009

SummaryThe interaction of bacterial exopolysaccharides, produced by opportunistic lung pathogens, with antimicrobial peptides of the innate primate immune system was investigated. The exopolysaccharides were produced by Pseudomonas aeruginosa, Inquilinus limosus and clinical isolates of the Burkholderia cepacia complex, bacteria that are all involved in lung infections of cystic fibrosis patients. The effects of the biological activities of three orthologous cathelicidins from Homo sapiens sapiens, Pongo pygmaeus (orangutan) and Presbitys obscurus (dusky leaf monkey) were examined. Inhibition of the antimicrobial activity of peptides was assessed using minimum inhibitory concentration assays on a reference Escherichia coli strain in the presence and absence of exopolysaccharides, whereas complex formation between peptides and exopolysaccharides was investigated by means of circular dichroism, fluorescence spectroscopy and atomic force microscopy. Biological assays revealed that the higher the negative charge of exopolysaccharides the stronger was their inhibiting effect. Spectroscopic studies indicated the formation of molecular complexes of varying stability between peptides and exopolysaccharides, explaining the inhibition. Atomic force microscopy provided a direct visualization of the molecular complexes. A model is proposed where peptides with an α‐helical conformation interact with exopolysaccharides through electrostatic and other non‐covalent interactions.
A case–control study of infant, maternal and perinatal characteristics associated with deformational plagiocephaly
Authors: McKinney Christy M. , Cunningham Michael L. , Holt Victoria L. , Leroux Brian , Starr Jacqueline R. 
Published: April 2009

SummaryDeformational plagiocephaly, an abnormal asymmetric flattening of infants' heads, is diagnosed in approximately 10% of infants. The prevalence of plagiocephaly has increased dramatically since 1992 when it was first recommended that infants be placed to sleep in a non‐prone position to reduce the risk of sudden infant death syndrome. The authors conducted a case–control study to evaluate associations between plagiocephaly and perinatal characteristics. The authors assessed whether risk factors for plagiocephaly have changed since 1992. Cases were born 1987–2002 in Washington State and diagnosed with plagiocephaly at the Craniofacial Center at Seattle Children's Hospital. Risk factor information was abstracted from birth certificate and hospital discharge data and unconditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI).Cases (n = 2764) were more likely than controls (n = 13 817) to have been injured at birth (OR 1.4; 95% CI 1.2, 1.7) or diagnosed with a congenital anomaly (OR 2.0; 95% CI 1.8, 2.3). Cases were more likely to have been male, a twin, or small‐for‐gestational‐age. This first large‐scale, case–control study of risk factors for plagiocephaly in a U.S. population provides new evidence that birth injuries and congenital anomalies are associated with plagiocephaly risk.
A new facies model for the Upper Gypsum of Sicily (Italy): chronological and palaeoenvironmental constraints for the Messinian salinity crisis in the Mediterranean
Authors: MANZI VINICIO , LUGLI STEFANO , ROVERI Marco , CHARLOTTE SCHREIBER B. 
Published: April 2009

AbstractThe Upper Gypsum unit of the Caltanissetta Basin (Sicily) records the last phase of the Messinian salinity crisis comprising the so‐called ‘Lago Mare’ event. A new facies analysis study recognizes nine to ten depositional cycles consisting of seven rhythmically interbedded primary gypsum bodies, and two to three sandstone bodies separated by marly terrigenous horizons showing laterally persistent vertical organization. A basal thin gypsum bed is overlain by a cluster of five thicker gypsum bodies. A marly interval containing two distinct sandstone horizons separates this cluster from the overlying uppermost (seventh) gypsum body. The terrigenous Arenazzolo Formation, in turn followed by the lower Pliocene Trubi Formation, is considered here to form the uppermost part of the Upper Gypsum unit. The rhythmic alternation in the sandy marls and gypsum/sandstone bodies records the response of sediments from shelfal to deltaic systems to precession‐driven arid‐wet climate fluctuations causing cyclical changes of both base‐level and water concentration. During wet climate phases (at insolation maxima) marl and sandstone were deposited in a hypohaline environment as suggested by: (i) the typical Lago Mare faunal assemblage and (ii) the negative δ18O values. During arid phases (at insolation minima) the reduced meteoric supply, recorded by higher δ18O values in the carbonate, caused the development of a negative hydrological budget leading to evaporite precipitation. At a basinal scale the Upper Gypsum unit unconformably overlies a mainly clastic evaporite unit containing carbonate breccia (the so‐called ‘Calcare di Base’) and/or clastic gypsum. Towards the basin centres, where the basal contact becomes conformable, a primary gypsum cumulate horizon is present. This layer is interpreted as a possible lateral equivalent of the Halite unit present only in the deepest depocentres. Based on astronomical calibration of the depositional cycles, the Upper Gypsum unit, including the Arenazzolo Formation, spans the interval between 5·33 and 5·53 Ma. This new age calibration allows the deposition of the Halite unit to be dated between 5·6 Ma (top of the Lower Evaporites) and 5·55 Ma (base of the Upper Evaporites) corresponding to isotopic stages TG12 and/or TG14.
Using magnetic resonance imaging for experimental analysis of fine‐sediment infiltration into gravel beds
Authors: HAYNES HEATHER , VIGNAGA ELISA , HOLMES WILLIAM M. 
Published: April 2009

AbstractSedimentologists recognize that development of a fine‐resolution, truly three‐dimensional analytical tool is essential if the internal structure of an opaque material is to be examined. This paper therefore seeks to: (i) test the viability of magnetic resonance imaging for sedimentological research; and (ii) investigate fine‐sediment infiltration into gravel beds. The results of six experiments are analysed quantitatively using ImageJ post‐processing software. Data indicate that magnetic resonance imaging‐based measurements of particle axes and volumes are comparable with standard laboratory techniques. Furthermore, the technique permits visualization and analysis of differences in the pattern of fine‐sediment infiltration (median particle diameter, d) into a framework of gravel (median particle diameter, D). Data clearly illustrate a siltation process for samples of D/d = 34 and a sealing process for samples of D/d = 7 where the seal is restricted to a depth equal to 2D. This pore‐scale visualization is valuable to the understanding of hydraulic–sediment–habitat interactions.
TNF block haplotypes associated with conserved MHC haplotypes in European, Asian and Australian Aboriginal donors
Authors: Valente F. P. , Tan C. , Phipps M. , Witt C. S. , Kaur G. , Gut I. , Allcock R. , Price P. 
Published: April 2009

AbstractAssociations between major histocompatibility complex (MHC) ancestral haplotypes (AHs) and immunopathological diseases are traditionally ascribed to human leukocyte antigen (HLA) class I or class II alleles. However, polymorphisms in TNF and nearby genes in the central MHC can influence risk. We have defined TNF block haplotypes in Asian, European and Australian Aboriginal donors and shown conservation of TNF block haplotypes in geographically distinct populations, consistent with a common evolutionary origin. Here we show that most TNF block haplotypes do not align with a single MHC AH and associations often vary with ethnicity. This suggests more recent recombination events between the TNF block and the HLA alleles.
Acute cell‐mediated rejection in orthotopic pig‐to‐mouse corneal xenotransplantation
Authors: Oh Joo Youn , Kim Mee Kum , Ko Jung Hwa , Lee Hyun Ju , Kim Youngji , Park Chan‐Sik , Park Chung‐Gyu , Kim Sang Joon , Wee Won Ryang , Lee Jin Hak 
Published: April 2009

Abstract: Background:  To investigate the role of T cells and natural killer (NK) cells in mediating corneal xenograft rejection in a pig‐to‐mouse model.Methods:  Pig corneas were orthotopically transplanted into BALB/c, C57BL/6, nude, severe combined immunodeficiency (SCID), and NOD/SCID/γcnull (NOG) mice. Graft survival was clinically assessed by slit‐lamp biomicroscopy and median survival times (MST) were calculated. The rejected grafts were histologically evaluated using antibodies against CD4, CD8, NK1.1, and F4/80.Results:  The pig corneal xenografts were acutely rejected by BALB/c and C57BL/6 mice (MST 9.0 days), while nude, SCID and NOG mice rejected pig corneas in a more delayed fashion (MST 16.0, 16.4, and 16.9 days, respectively). The majority of infiltrating cells found in rejected grafts in C57BL/6 mice were macrophages and CD4+ T cells, while CD8+ T cells and NK cells were rarely found. The grafts in nude mice had markedly decreased inflammatory infiltration with small numbers of macrophages and CD4+ T cells. Infiltration was even more modest in grafts in SCID and NOG mice.Conclusions:  T cells play an important role in acute rejection of pig corneal xenografts in mice, although acute rejection is not solely the result of T‐cell‐mediated immunity. NK cells are less likely to be involved in the rejection process.
Experimental support for the role of nest predation in the evolution of brood parasitism
Authors: SHAW R. C. , HAUBER M. E. 
Published: April 2009

AbstractIn 1965, Hamilton and Orians (HO) hypothesized that the starting point for the evolution of obligate interspecific brood parasitism in birds was the facultative laying of physiologically committed eggs in neighbouring active nests of con‐ and heterospecifics, following predation of a bird’s own nest during the laying stage. We tested this prediction of the HO hypothesis by using captive pairs of zebra finches (Taeniopygia guttata), a species with evidence for intraspecific parasitism both in the wild and in captivity. As predicted, in response to experimental nest removal, subjects laid eggs parasitically in simulated active conspecific nests above chance levels. Across subsequent trials, we detected both repeatability and directional change in laying patterns, with some subjects switching from parasitism to depositing eggs in the empty nest. Taken together, these results support the assumptions and predictions of the HO hypothesis, and indicate that the zebra finch is a potential model species for future behavioural and genetic studies in captive brood parasite research.
Nursing scholarship in Japan: Development, facilitators, and barriers
Authors: Turale Sue , Ito Misae , Murakami Kyoko , Nakao Fujiko 
Published: April 2009

AbstractThis qualitative study sought a contemporary view of the development, facilitators of, and barriers to nursing scholarship in Japan from the perspectives of the scholars. In‐depth interviews were conducted with 13 scholars across Japan, which were digitally recorded, and the data were subjected to content analysis. Five themes emerged: a spirit of collectivism; a lack of nursing control; a lack of English ability; a high workload; and collaboration. The participants considered that culturally based consensus and communication behaviors, as well as the control and dominance by the medical profession, were hampering nursing scholarship. Furthermore, Japanese nurses were not in control of the profession in a period of unprecedented growth in university nursing education and a growing nursing shortage. A lack of English‐speaking and English‐writing abilities hindered collaboration with scholars internationally and the writing of international publications. Most of the participants felt unable to compare the extent and nature of Japanese scholarship with that of their Asian neighbors. The Japanese scholars need to grasp opportunities to learn English, collaborate with other nurses nationally and internationally, learn assertion and political skills to give them the confidence to take control of nursing education, and be more involved in research collaboration and international publications.
They just don't get enough! Variable intern experience in bedside procedural skills
Authors: Boots R. J. , Egerton W. , McKeering H. , Winter H. 
Published: April 2009

AbstractBackground: Medical school and resident training programmes offer different learning opportunities and outcomes. The aim of the study was to assess medical student and intern experience in common clinical procedures.Methods: Interns employed in a metropolitan teaching hospital from 2000 to 2004 completed a survey of experience and confidence in clinical procedures at the beginning and end of their intern year. Attendance at and the contribution to procedural confidence of a voluntary procedural skill‐training programme were examined.Results: For the 314 interns, clinical experience before and during internship varied for each procedure and between year cohorts as did training programme attendance (44–84%). Student procedural confidence was predicted by pre‐intern experience either on patients or by simulation (β = 0.17, 95% confidence interval (CI) 0.02–0.21, P = 0.03) and age >30 years on commencing internship (β = 8.44, 95%CI 3.03–14.06, P = 0.003. Adjusted R2 = 0.08, P = 0.002). Intern procedural confidence by year's end was predicted by attendance at the training programme (β = 0.48, 95%CI 0.34–0.62, P < 0.001), intern experience with patient procedures (β = 0.34, 95%CI 0.21–0.47, P < 0.001) and a clear decision to enter a postgraduate training programme (β = 0.13, 95%CI 0.04–0.22, P = 0.007, Adjusted R2 = 0.50, P < 0.001).Conclusion: Interns and students receive variable experience to carry out procedural skills on patients. This makes designing training programmes difficult as training needs vary each year. Both mandatory supervision of key skills and opportunities to supplement limited experience are needed during the intern year to ensure a uniform experience.