bluuebunny/crossref_metadata_2025_split huggingface dataset:
A wireless real‐time coastal observation network
Authors: Ruberg Steven , Brandt Stephen , Muzzi Ronald , Hawley Nathan , Leshkevich George , Lane John , Miller Terry , Bridgeman Thomas 
Published: September 2007

A new integrated coastal observation system is providing preliminary data from the North American Great Lakes. This system can be implemented in other coastal regions. To date, it has been successfully deployed on Lakes Michigan, Huron, and Erie to make seabed to sea surface measurements of chemical, biological, and physical parameters, which are transmitted wirelessly through buoys and permanent stations.Called the Real‐Time Coastal Observation Network (ReCON), the new system leverages existing networking technology to provide universal access to a wide variety of instrumentation through the use of an underwater Ethernet port server [Austin, 2002]. A team of NOAA engineers and scientists has completed the development and testing of this integrated coastal observation network.
Examining chemical transport into the stratosphere
Authors: Zielinski Sarah 
Published: September 2007

This month, NASA will launch a coordinated field campaign centered in Costa Rica that will use satellite, ground‐based, balloon, and aircraft measurements to investigate how chemicals in the air move into the stratosphere and how this movement might affect cloud formation, climate, and ozone.Scheduled to run from 16 July through 8 August, the Tropical Composition, Cloud, and Climate Coupling (TC4) campaign “is an unprecedented opportunity to use NASA's complete suite of satellite and airborne Earth‐observing capabilities to investigate a largely unexplored region of the atmosphere,” said Michael Kurylo, a TC4 program scientist at NASA headquarters.
Kenneth R. Weiss and Usha Lee McFarling receive the 2007 AGU Walter Sullivan Award
Authors: Clifford Frank , McFarling Usha Lee , Weiss Kenneth R. 
Published: September 2007

Several 2007 AGU Awards were presented at the Joint Assembly in Acapulco, Mexico. Winners were introduced by President Tim Killeen in a formal ceremony held on 25 May 2007. An honors fiesta followed the ceremony.It is my pleasure to nominate Kenneth R. Weiss and Usha Lee McFarling of the Los Angeles Times, and their five‐part series “Altered Oceans,” for the AGU Walter Sullivan Award for Excellence in Science Journalism—Features.
Betsy Mason receives the 2007 AGU Perlman Award
Authors: Borenstein Daniel , Mason Betsy 
Published: September 2007

Californians live in a state of denial. The 100th anniversary of the 1906 San Francisco earthquake provided a window of opportunity—a time for journalists to remind Bay Area residents of the dangers of the next “Big One.”We were fortunate to have on our staff a talented journalist who happens to also be a scientist. With calm clarity, Betsy Mason alerted readers to the dangers ahead, shaking us out of our cocoons.
Mark Abbott named as NSF Assistant Director for Geosciences
Authors: Anonymous  
Published: September 2007

Mark Abbott, AGU member and dean of Oregon State University's College of Oceanic and Atmospheric Sciences, has been appointed assistant director for the Geosciences Directorate of the National Science Foundation. He will assume his new NSF position on 1 October 2007.Abbott is professor of biological oceanography at OSU. He joined the OSU faculty in 1988 and became dean in 2001.
Update on digital library project
Authors: Anonymous  
Published: September 2007

AGU is on track to deliver by the end of this year access to all articles published throughout its history and in the predecessor to JGR, Terrestrial Magnetism and Electricity, from vol. 1, no. 1 (1896) of that journal. To date, more than two thirds of journal articles (∼65,000) have been scanned. Books and Eos issues will be completed next.When introduced, this digital library will feature searching and linking capabilities for both abstracts and reference lists and will be integrated with the current publications.
Advancing the Frontiers of Earthquake Science: Fifth International Workshop on Statistical Seismology, Erice, Sicily, Italy, 31 May to 6 June 2007
Authors: Hauksson Egill , Cocco Massimo , Console Rodolfo , Wiemer Stefan 
Published: September 2007

Statistical seismology has been emerging as a new discipline at the interface between earthquake physics, earthquake statistics, hazard assessment, and society. A workshop in Italy was sponsored by the Italian Istituto Nazionale di Geofisica e Vulcanologia (INGV), the Swiss Federal Institute of Technology Zurich (ETH), and the Japanese Institute of Statistical Mathematics (ISM), to discuss the state of the art and future directions.Conference participants discussed how to use available tools and techniques of statistical seismology to advance earthquake science. Building increasingly accurate timedependent earthquake forecast models at various spatial and temporal scales is widely recognized as an important challenge, and various such models were presented and discussed at the workshop. Exploiting time dependence for hazard assessment requires us to develop a detailed understanding of the behavior of regional fault systems and corresponding earthquake catalogs spanning decades. We can no longer analyze individual faults or earthquake sequences in isolation.
Ancient sundials and maps reveal historical geomagnetic declination values
Authors: Mandea Mioara , Korte Monika 
Published: September 2007

Long records of the evolution of Earth's magnetic field help in the understanding of the field's generating mechanism. Archeomagnetism and palaeomagnetism supply valuable low‐resolution information about the field over time ranges of centuries to millions of years. Higher spatial resolution can come from direct measurements of the field, but these are restricted to the past few hundred years.In some places, such as London, Rome, or Paris, declination and inclination were frequently measured over the past four centuries [Malin and Barracogh, 1981; Cafarella et al., 1992; Alexandrescu et al., 1996]. In the early nineteenth century, measurements of field intensity became available, and the first magnetic observatory recording three field components (declination, inclination, and horizontal intensity) was installed by C.F. Gauss, in Göttingen, Germany, in 1832. Since then, continuous observations of the vector magnetic field have been made by some 200 worldwide observatories, thus making it possible to obtain good, though still incomplete, knowledge of the detailed field morphology and temporal evolution.
Southern Ocean mapping program restarts
Authors: Ott Norbert , Schenke Hans Werner 
Published: September 2007

The International Bathymetric Chart of the Southern Ocean (IBCSO) mapping program restarted at the end of 2006 after a 2‐year break. The program is based at the Alfred Wegener Institute for Polar and Marine Research, in Bremerhaven, Germany.Since the program restarted, some important topics have been revised and updated: New bathymetric data are being collected by various cruises with R/V Polarstern; new expeditions are being planned and have been carried out to Antarctic waters; a mailing list for improved communication is being established at the National Geophysical Data Center; the IBCSO expert group is being revitalized; and the conceptual design and implementation of the program's geo‐database and metadata structure conceptual design and implementation are under way.
Eutrophication stresses U.S. estuaries
Authors: Showstack Randy 
Published: September 2007

A 31 July NOAA report on estuarine eutrophication, or nutrient pollution, indicates moderate to high level nutrient‐related impacts in 64 of 99 U.S. estuaries that had adequate data for evaluation. Lead author Suzanne Bricker of NOAA's Center for Coastal Monitoring and Assessment said that most problems in the estuaries are related to human activities. The report, completed in partnership with the University of Maryland Center for Environmental Science, calls for improved management, monitoring, research, and communication efforts.The report, “Effects of Nutrient Enrichment in the Nation's Estuaries,” is available at the Web site: http://ccma.nos.noaa.gov/publications/eutroupdate/
Your subscription options for 2008
Authors: Holoviak Judy C. 
Published: September 2007

The big news for 2008 subscriptions is AGU's digital library.Members and institutions will be able to subscribe to the complete library of AGU journals and most books in electronic form. The library will include all AGU journals from volume I, issue I, through material published in 2002 and almost all books older than 5 years. The books and pre‐2002 journal articles will be scanned pdf's with html versions of titles, author information, and references. The references will be hotlinked to the abstracts of cited AGU articles and in some cases the abstracts of other cited publications. Full‐text searching of the material in the library will be available. The 2002 journal articles will be available in both html and pdf just as they were originally published.
Trends in socioeconomic differences in sickness absence among Finnish municipal employees 1990—99
Authors: Piha Kustaa , Martikainen Pekka , Rahkonen Ossi , Roos Eva , Lahelma Eero 
Published: September 2007

Aims: This study examined the associations of key dimensions of socioeconomic status and long sickness absence spells as well as their changes over time from 1990 to 1999. Methods: Municipal employees of the City of Helsinki, Finland, aged 25— 59 were studied. The number of participants varied yearly from 24,029 women and 6,523 men to 27,861 women and 7,521 men. Socioeconomic status was assessed by education, occupational class, and individual income. The outcome was the number of over three days' sickness absence spells/100 person years, for which the employer requires medical certification. Results: Low education, occupational class, and individual income were consistently associated with a 2—3 times higher sickness absence rates among both men and women. The age-adjusted sickness absence rates were relatively stable from 1990 to 1994 but increased from 1994 to 1999 among men and women. Socioeconomic differences in sickness absence rates tended to increase. Conclusions: The increase in the level of socioeconomic differences in sickness absence took place during a period of declining unemployment and staff increases at the City of Helsinki, which indicates that labour market conditions play a role in sickness absence.
An error model for protein quantification
Authors: Kreutz C. , Rodriguez M.M. Bartolome , Maiwald T. , Seidl M. , Blum H.E. , Mohr L. , Timmer J. 
Published: September 2007

AbstractMotivation: Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility of protein quantification by immunoprecipitation and immunoblotting.Results: Based on a large data set with more than 3600 data points, we unravel that the main sources of biological variability and experimental noise are multiplicative and log-normally distributed. Therefore, we suggest a log-transformation of the data to obtain additive normally distributed noise. After this transformation, common statistical procedures can be applied to analyze the data.An error model is introduced to account for technical as well as biological variability. Elimination of these systematic errors decrease variability of measurements and allow for a more precise estimation of underlying dynamics of protein concentrations in cellular signaling.The proposed error model is relevant for simulation studies, parameter estimation and model selection, basic tools of systems biology.Availability: Matlab and R code is available from the authors on request. The data can be downloaded from our website www.fdm.uni-freiburg.de/∼ckreutz/data.Contact: ckreutz@fdm.uni-freiburg.de
Effect of Proofing Time and Wheat Flour Strength on Bleaching, Sensory Characteristics, and Volume of French Breads with Added Soybean Lipoxygenase
Authors: Junqueira Roberto M. , Rocha Fabrício , Moreira Maurílio A. , Castro Inar A. 
Published: September 2007

ABSTRACTSoybean lipoxygenase addition in wheat bread doughs is widely used to improve the crumb color and rheology but little is known about the variability of the activity of lipoxygenase under diverse breadmaking conditions. Thus the objective of this study was to evaluate how soybean lipoxygenase can affect bleaching, volume, and sensory characteristics of French breads when proofing time and wheat flour strength varies. A 3‐factor Box‐Behnken design was used in this study containing one block and three independent variables or factors designated by exogenous lipoxygenase activity (x1 = 0–71 unit/μg of protein), wheat flour deformation energy (x2 = 231–258 × 10–4 J), and proofing time (x3 = 2–6 hr). Breads were randomly prepared and all assays were repeated three times. Specific volume (from 5.8 ± 0.4 to 9.9 ± 0.4 cm3/g), sensory quality (from 5.2 ± 0.8 to 8.3 ± 0.6), and yellow hue (from 12.6 ± 0.5 to 16.2 ± 0.3) significantly changed (P < 0.01) among the treatments. Specific volume of the breads increased with higher values of wheat flour strength and proofing time (ŷvs = 7.5 + 0.9 x2 + 1.2 x3 +0.5 x2x3). Sensory quality improved at higher values of wheat flour strength and shorter proofing time (ŷsq = 7.8 + 0.7 x2 – 0.2 x3 – 0.4 x22 – 0.6x32 + 0.5 x2x3), while lower and more desirable values of yellow hue were achieved at longer proofing time, higher activity of lipoxygenase, and using stronger wheat flours (ŷb = 13.7 – 1.2 x1 – 0.5 x2 – 0.2 x3 + 1.0 x12 – 0.3 x1x2). All regression models showed a good fitness to the experimental data (lack‐of‐fit P > 0.05) and the difference between predicted and observed values were also not significant (P < 0.05). Our results suggested that proofing time and wheat flour strength have a greater effect on volume and sensory quality of French breads than soybean lipoxygenase. However, the bleaching effect of this enzyme showed positive interaction with proofing time and wheat flour strength, suggesting its application even when strong wheat flours are used for the manufacture of French breads.
Tyrosine Phosphorylation Site Identification by MALDI-MS
Authors: Sickmann Albert , Meyer Helmut E. 
Published: September 2007

INTRODUCTIONIn this protocol, radiolabeled proteins are separated using SDS-PAGE and digested in-gel. The phosphopeptides are subjected to two-dimensional LC and identified by MALDI-MS and MALDI-PSD. The identification of eight tyrosine phosphorylation sites in the human Gab-1 protein is provided as an example of the method’s utility. The expression and phosphorylation of human Gab-1 with the insulin receptor kinase in vitro are summarized as an example of this approach to identifying phosphorylated tyrosine residues.
Serine/Threonine Phosphorylation Site Identification by ESI-MS: Figure 1.
Authors: Sickmann Albert , Meyer Helmut E. 
Published: September 2007

INTRODUCTIONMuch of the protein phosphorylation within cells is mediated by the activity of independent kinases. However, autophosphorylation of proteins is another way signal transduction pathways are regulated. This protocol is designed to distinguish between autophosphorylation and endogenous phosphorylation. For the localization of all endogenous phosphorylation sites, the protein is digested with trypsin and the peptides are analyzed by on-line coupling of nano-HPLC and ESI-MS. To determine the autophosphorylation sites, the protein is incubated with radioactive ATP prior to digestion with trypsin. Only 20 pmol of protein is used for each experiment. The stoichiometry of phosphorylated protein is below 5% of the total protein. Prior to analysis, the protein is separated by 10% SDS-PAGE and the protein band is excised. Before digestion, the protein is reduced and alkylated in both cases.
Isolating Total RNA from Mouse Embryos or Fetal Tissues
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: September 2007

INTRODUCTIONThis RNA isolation procedure is suitable for tissue of almost any size, and is particularly useful for fetal organs or whole embryos from mice, as it can be performed in volumes as small as 0.5 mL. The minimum amount of tissue used should be ten 7.5-dpc (days post-coitum) embryos, one or two 8.5-dpc embryos, or approximately one-tenth of a 12.5-dpc embryo. If smaller amounts of tissue are homogenized in a 0.5-mL volume, the recovery of RNA may be less efficient.
Observational Methods Used to Assess Rat Behavior: Neurological Testing
Authors: Paul Carol Ann , Beltz Barbara , Berger-Sweeney Joanne 
Published: September 2007

INTRODUCTIONThe rat is the most frequently used animal for behavioral experiments, and several methods can be used to assess behavioral changes that result from modifications to its nervous system. Objective neurological tests can be used to establish a “behavioral baseline” for a normal animal, and to study the effects of drugs or a lesion on behavior. Neurological tests should be administered much like a doctor would administer a battery of tests after a trauma, with objective observation, precise documentation, and repeated measurements by the same experimenter. This protocol outlines a series of neurological tests designed to assess reflex movements in the rat. Male or female rats may be used, although data should be analyzed separately to determine if sex differences exist.
Observational Methods Used to Assess Rat Behavior: General Activity
Authors: Paul Carol Ann , Beltz Barbara , Berger-Sweeney Joanne 
Published: September 2007

INTRODUCTIONThe activity-inactivity continuum is an important parameter of behavior, and quantification of overall locomotor activity in the rat should identify it as a naturally nocturnal animal. Disruptions in nocturnal activity can be caused by damage in visual inputs to the brain or damage in the hypothalamus. Many commercial devices are available to measure activity automatically; some can be integrated with a computer to allow overnight monitoring in the absence of an observer. A less sophisticated but still accurate method of measuring activity is to create a home-made activity chamber by replacing the bottom of a box with Plexiglas or by marking lines on the bottom of a clean rat cage so that the observer can record rat activity by noting when the lines are crossed, while simultaneously recording other behaviors. Activity in rat pups can be observed as soon as they are 10 days old using smaller activity chambers. This protocol describes the construction of a home-made activity chamber and how to measure four activities: locomotion, rearing, circling, and grooming.
Rehydration of Drosophila Embryos
Authors: Rothwell Wendy F. , Sullivan William 
Published: September 2007

INTRODUCTIONFixed Drosophila embryos stored in methanol must be rehydrated before staining. Rehydration methods differ slightly for embryos fixed in methanol versus embryos fixed in formaldehyde; techniques for both are presented. An alternative, gentler rehydration method is also presented for studies where a new probe or antibody is being used.
In Vivo Retrograde Labeling of Neurons in the Zebrafish Embryo or Larva with Rhodamine Dextran
Authors: Volkmann Katrin , Köster Reinhard W. 
Published: September 2007

INTRODUCTIONApplication of a fluorescent dye to a target area of axons or dendrites allows the identification of individual neurons projecting to the area and reconstruction of the tract of the neurite by retrograde labeling. For the red fluorescent dye tetramethylrhodamine dextran, the labeling occurs by active retrograde transport inside the cell. This protocol describes a method for applying tetramethylrhodamine dextran to living zebrafish embryos and larvae (2-7 dpf [days post-fertilization]) via microinjection. It may be adapted for use with green or yellow fluorescent dextran conjugates.
Generation of Transgenic Xenopus laevis: I. High-Speed Preparation of Egg Extracts
Authors: Ishibashi Shoko , Kroll Kristin L. , Amaya Enrique 
Published: September 2007

INTRODUCTIONManipulating genes specifically during later stages of amphibian embryonic development requires fine control over the time and place of expression. These protocols describe an efficient nuclear-transplantation-based method of transgenesis developed for Xenopus laevis. The approach enables stable expression of cloned gene products in Xenopus embryos. Because the transgene integrates into the genome prior to fertilization, the resulting embryos are not chimeric, eliminating the need to breed to the next generation to obtain nonmosaic transgenic animals. The procedure is based on restriction-enzyme-mediated integration (REMI) and can be divided into three parts: (I) high-speed preparation of egg extracts, (II) sperm nuclei preparation, and (III) nuclear transplantation. This protocol describes the method for the high-speed preparation of egg extracts. Briefly, a crude, cytostatic factor (CSF)-arrested egg extract (i.e., cytoplasm arrested in meiotic metaphase) is prepared. These extracts are driven into the interphase stage of the cell cycle by addition of calcium, and high-speed centrifugation is performed to obtain a purer cytoplasmic fraction. This fraction promotes swelling of sperm nuclei, but does not promote DNA replication. By adding the egg extract to the reaction, the sperm chromatin partially decondenses, facilitating integration of plasmid DNA into the genome.
Generation of Transgenic Xenopus laevis: II. Sperm Nuclei Preparation
Authors: Ishibashi Shoko , Kroll Kristin L. , Amaya Enrique 
Published: September 2007

INTRODUCTIONManipulating genes specifically during later stages of amphibian embryonic development requires fine control over the time and place of expression. These protocols describe an efficient nuclear-transplantation-based method of transgenesis developed for Xenopus laevis. The approach enables stable expression of cloned gene products in Xenopus embryos. Because the transgene integrates into the genome prior to fertilization, the resulting embryos are not chimeric, eliminating the need to breed to the next generation to obtain nonmosaic transgenic animals. The procedure is based on restriction-enzyme-mediated integration (REMI) and can be divided into three parts: (I) high-speed preparation of egg extracts, (II) sperm nuclei preparation, and (III) nuclear transplantation. This protocol describes a method for the preparation of sperm nuclei from Xenopus laevis. Sperm suspensions are prepared by filtration and centrifugation, and then treated with lysolecithin to disrupt the plasma membrane of the cells. Sperm nuclei can be stored frozen in small aliquots at -80°C.
Genotyping by Allele-Specific Amplification (KASPar)
Authors: Cuppen Edwin 
Published: September 2007

INTRODUCTIONThis protocol describes the use of allele-specific amplification followed by fluorescence detection (KASPar) for genotyping. The method is compatible with any real-time PCR setup and has the advantage that no specifically labeled oligonucleotides are needed.
Genotyping by Oligonucleotide Ligation Assay (OLA)
Authors: Macdonald Stuart J. 
Published: September 2007

INTRODUCTIONThis protocol describes the oligonucleotide ligation assay (OLA), which uses a set of three oligonucleotides, in combination with a thermostable Taq DNA ligase enzyme, to discriminate single-nucleotide polymorphism (SNP) alleles. Sixteen-plex OLA genotyping reactions are carried out, and allele-specific OLA products are detected on membrane arrays using radiolabeled probes.