bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Monthly Upper-Air Dataset for North America Back to 1922 from the Monthly Weather Review
Authors: Ewen Tracy , Grant Andrea , Brönnimann Stefan 
Published: May 2008

AbstractUpper-air observations with kites, aircraft, and radiosondes were performed in the United States operationally since the 1890s. In this paper, the authors present a reevaluation of newly digitized monthly mean values from the Monthly Weather Review back to 1922. Data from 46 U.S. weather stations are presented with a focus on early kite and aircraft observations during the 1922–38 period. A quality assessment of the data, based on reconstructed reference series, is carried out and the quality of the monthly mean data is found to be sufficient for analysis of variability in upper-level circulation. Anomalies of upper-level temperatures from the reevaluated station data, together with surface fields, are shown for selected periods.
Assimilation of MODIS Cloud Optical Depths in the ECMWF Model
Authors: Benedetti Angela , Janisková Marta 
Published: May 2008

Abstract
At the European Centre for Medium-Range Weather Forecasts (ECMWF), a large effort has recently been devoted to define and implement moist physics schemes for variational assimilation of rain- and cloud-affected brightness temperatures. This study expands on the current application of the new linearized moist physics schemes to assimilate cloud optical depths retrieved from the Moderate Resolution Imaging Spectroradiometer (MODIS) on board the Aqua platform for the first time in the ECMWF operational four-dimensional assimilation system. Model optical depths are functions of ice water and liquid water contents through established parameterizations. Linearized cloud schemes in turn link these cloud variables with temperature and humidity. A bias correction is applied to the optical depths to minimize the differences between model and observations. The control variables in the assimilation are temperature, humidity, winds, and surface pressure. One-month assimilation experiments for April 2006 demonstrated an impact of the assimilated MODIS cloud optical depths on the model fields, particularly temperature and humidity. Comparison with independent observations indicates a positive effect of the cloud information assimilated into the model, especially on the amount and distribution of the ice water content. The impact of the cloud assimilation on the medium-range forecast is neutral to slightly positive. Most importantly, this study demonstrates that global assimilation of cloud observations in ECMWF four-dimensional variational assimilation system (4DVAR) is technically doable but a continued research effort is necessary to achieve clear positive impacts with such data.
Computationally Efficient Spatial Forecast Verification Using Baddeley’s Delta Image Metric
Authors: Gilleland Eric , Lee Thomas C. M. , Halley Gotway John , Bullock R. G. , Brown Barbara G. 
Published: May 2008

Abstract
An important focus of research in the forecast verification community is the development of alternative verification approaches for quantitative precipitation forecasts, as well as for other spatial forecasts. The need for information that is meaningful in an operational context and the importance of capturing the specific sources of forecast error at varying spatial scales are two primary motivating factors. In this paper, features of precipitation as identified by a convolution threshold technique are merged within fields and matched across fields in an automatic and computationally efficient manner using Baddeley’s metric for binary images.
The method is carried out on 100 test cases, and 4 representative cases are shown in detail. Results of merging and matching objects are generally positive in that they are consistent with how a subjective observer might merge and match features. The results further suggest that the Baddeley metric may be useful as a computationally efficient summary metric giving information about location, shape, and size differences of individual features, which could be employed for other spatial forecast verification methods.
A Local Ensemble Prediction System for Fog and Low Clouds: Construction, Bayesian Model Averaging Calibration, and Validation
Authors: Roquelaure Stevie , Bergot Thierry 
Published: May 2008

Abstract
At main international airports, air traffic safety and economic issues related to poor visibility conditions are crucial. Meteorologists face the challenge of supplying airport authorities with accurate forecasts of fog and cloud ceiling. These events are difficult to forecast because conditions evolve on short space and time scales during their life cycle. To obtain accurate forecasts of fog and low clouds, the Code de Brouillard à l’Echelle Locale (the local scale fog code)–Interactions between Soil, Biosphere, and Atmosphere (COBEL–ISBA) local numerical forecast system was implemented at Charles de Gaulle International Airport in Paris. However, even with dedicated observations and initialization, uncertainties remain in both initial conditions and mesoscale forcings. A local ensemble prediction system (LEPS) has been designed around the COBEL–ISBA numerical model and tested to assess the predictability of low visibility procedures events, defined as a visibility less than 600 m and/or a ceiling below 60 m. This work describes and evaluates a local ensemble strategy for the prediction of low visibility procedures. A Bayesian model averaging method has been applied to calibrate the ensemble. The study shows that the use of LEPS for specific local event prediction is well adapted and useful for low visibility prediction in the aeronautic context. Moreover, a wide range of users, especially those with low cost–loss ratios, can expect economic savings with the use of this probabilistic system.
The Equatorial Pacific Cold Tongue Bias in a Coupled Climate Model
Authors: Misra Vasubandhu , Marx L. , Brunke M. , Zeng X. 
Published: May 2008

AbstractA set of multidecadal coupled ocean–atmosphere model integrations are conducted with different time steps for coupling between the atmosphere and the ocean. It is shown that the mean state of the equatorial Pacific does not change in a statistically significant manner when the coupling interval between the atmospheric general circulation model (AGCM) and the ocean general circulation model (OGCM) is changed from 1 day to 2 or even 3 days. It is argued that because the coarse resolution of the AGCM precludes resolving realistic “weather” events, changing the coupling interval from 1 day to 2 or 3 days has very little impact on the mean coupled climate.On the other hand, reducing the coupling interval to 3 h had a much stronger impact on the mean state of the equatorial Pacific and the concomitant general circulation. A novel experiment that incorporates a (pseudo) interaction of the atmosphere with SST at every time step of the AGCM was also conducted. In this unique coupled model experiment, the AGCM at every time step mutually interacts with the skin SST. This skin SST is anchored to the bulk SST, which is updated from the OGCM once a day. Both of these experiments reduced the cold tongue bias moderately over the equatorial Pacific Ocean with a corresponding reduction in the easterly wind stress bias relative to the control integration. It is stressed from the results of these model experiments that the impact of high-frequency air–sea coupling is significant on the cold tongue bias.The interannual variation of the equatorial Pacific was less sensitive to the coupling time step between the AGCM and the OGCM. Increasing (reducing) the coupling interval of the air–sea interaction had the effect of weakening (marginally strengthening) the interannual variations of the equatorial Pacific Ocean.It is argued that the low-frequency response of the upper ocean, including the cold tongue bias, is modulated by the atmospheric stochastic forcing on the coupled ocean–atmosphere system. This effect of the atmospheric stochastic forcing is affected by the frequency of the air–sea coupling and is found to be stronger than the rectification effect of the diurnal variations of the air–sea interaction on the low frequency. This may be a result of a limitation in the coupled model used in this study in which the OGCM has an inadequate vertical resolution in the mixed layer to sustain diurnal variations in the upper ocean.
Deep Atmospheric Response to the North Pacific Oceanic Subtropical Front in Spring
Authors: Kobashi Fumiaki , Xie Shang-Ping , Iwasaka Naoto , Sakamoto Takashi T. 
Published: May 2008

Abstract
The North Pacific subtropical front (STF) is a zone of high sea surface temperature (SST) gradients located around 25°N in the western basin and is most pronounced in spring. The STF’s atmospheric effects are investigated using satellite observations and an atmospheric reanalysis. During April–May along the STF, surface wind stress curl turns weakly cyclonic in the general background of anticyclonic curls. Atmospheric column-integrated water vapor displays a pronounced meridional maximum along this surface trough, suggesting a deep vertical structure. Cyclonic wind curls occur intermittently at intervals of a few days along the STF in subsynoptic low pressure systems accompanying larger, synoptic highs in the main storm track to the north. In the subsynoptic surface lows, convective rain takes place with deep upward motion moistening the entire troposphere. The lows are enhanced by condensational heating, leading to the formation of weak cyclonic wind curls. The lows display vertical structure characteristic of baroclinic instability, suggesting that they are triggered by the passage of synoptic migratory highs and grow on the baroclinicity anchored by the SST front. The cyclonic wind curls appear to be related to a cloud/rainband associated with the so-called pre-baiu/meiyu front in May.
The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis
Authors: Kamesh N , Aradhyam Gopala K , Manoj Narayanan 
Published: May 2008

Abstract

Background
G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. The genome of the protochordate Ciona intestinalis has a compact size with an ancestral complement of many diversified gene families of vertebrates and is a good model system for studying protochordate to vertebrate diversification. An analysis of the Ciona repertoire of GPCRs from a comparative genomic perspective provides insight into the evolutionary origins of the GPCR signalling system in vertebrates.

Results
We have identified 169 gene products in the Ciona genome that code for putative GPCRs. Phylogenetic analyses reveal that Ciona GPCRs have homologous representatives from the five major GRAFS (Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin) families concomitant with other vertebrate GPCR repertoires. Nearly 39% of Ciona GPCRs have unambiguous orthologs of vertebrate GPCR families, as defined for the human, mouse, puffer fish and chicken genomes. The Rhodopsin family accounts for ~68% of the Ciona GPCR repertoire wherein the LGR-like subfamily exhibits a lineage specific gene expansion of a group of receptors that possess a novel domain organisation hitherto unobserved in metazoan genomes.

Conclusion
Comparison of GPCRs in Ciona to that in human reveals a high level of orthology of a protochordate repertoire with that of vertebrate GPCRs. Our studies suggest that the ascidians contain the basic ancestral complement of vertebrate GPCR genes. This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. Our analysis provides a framework to perform future experimental and comparative studies to understand the roles of the ancestral chordate versions of GPCRs that predated the divergence of the urochordates and the vertebrates.
The perception of stress alters adaptive behaviours inLymnaea stagnalis
Authors: Lukowiak Ken , Martens Kara , Rosenegger David , Browning Kim , de Caigny Pascaline , Orr Mike 
Published: May 2008

SUMMARYStress can alter adaptive behaviours, and as well either enhance or diminish learning, memory formation and/or memory recall. We show here that two different stressors have the ability to alter such behaviours in our model system, Lymnaea stagnalis. One, a naturally occurring stressor– the scent of a predator (crayfish) – and the other an artificially controlled one – 25 mmoll–1 KCl –significantly alter adaptive behaviours. Both the KCl stressor and predator detection enhance long-term memory (LTM) formation; additionally predator detection alters vigilance behaviours. The predator-induced changes in behaviour are also accompanied by specific and significant alterations in the electrophysiological properties of RPeD1 – a key neuron in mediating both vigilance behaviours and memory formation. Naive lab-bred snails exposed to crayfish effluent (CE; i.e. the scent of the predator) prior to recording from RPeD1 demonstrated both a significantly reduced spontaneous firing rate and fewer bouts of bursting activity compared with non-exposed snails. Importantly, in the CE experiments we used laboratory-reared snails that have not been exposed to a naturally occurring predator for over 250 generations. These data open a new avenue of research, which may allow a direct investigation from the behavioral to the neuronal level as to how relevant stressful stimuli alter adaptive behaviours, including memory formation and recall.
Seeing in the dark: vision and visual behaviour in nocturnal bees and wasps
Authors: Warrant Eric J. 
Published: May 2008

SUMMARYIn response to the pressures of predation, parasitism and competition for limited resources, several groups of (mainly) tropical bees and wasps have independently evolved a nocturnal lifestyle. Like their day-active (diurnal)relatives, these insects possess apposition compound eyes, a relatively light-insensitive eye design that is best suited to vision in bright light. Despite this, nocturnal bees and wasps are able to forage at night, with many species capable of flying through a dark and complex forest between the nest and a foraging site, a behaviour that relies heavily on vision and is limited by light intensity. In the two best-studied species – the Central American sweat bee Megalopta genalis (Halictidae) and the Indian carpenter bee Xylocopa tranquebarica (Apidae) – learned visual landmarks are used to guide foraging and homing. Their apposition eyes,however, have only around 30 times greater optical sensitivity than the eyes of their closest diurnal relatives, a fact that is apparently inconsistent with their remarkable nocturnal visual abilities. Moreover, signals generated in the photoreceptors, even though amplified by a high transduction gain, are too noisy and slow to transmit significant amounts of information in dim light. How have nocturnal bees and wasps resolved these paradoxes? Even though this question remains to be answered conclusively, a mounting body of theoretical and experimental evidence suggests that the slow and noisy visual signals generated by the photoreceptors are spatially summed by second-order monopolar cells in the lamina, a process that could dramatically improve visual reliability for the coarser and slower features of the visual world at night.
Sensory ecology on the high seas: the odor world of the procellariiform seabirds
Authors: Nevitt Gabrielle A. 
Published: May 2008

SUMMARYProcellariiform seabirds wander the world's oceans aided by olfactory abilities rivaling those of any animal on earth. Over the past 15 years, I have been privileged to study the sensory ecology of procellariiforms,focusing on how olfaction contributes to behaviors, ranging from foraging and navigation to individual odor recognition, in a broader sensory context. We have developed a number of field techniques for measuring both olfactory- and visually based behaviors in chicks and adults of various species. Our choice of test odors has been informed by long-term dietary studies and geochemical data on the production and distribution of identifiable, scented compounds found in productive waters. This multidisciplinary approach has shown us that odors provide different information over the ocean depending on the spatial scale. At large spatial scales (thousands of square kilometers), an olfactory landscape superimposed upon the ocean surface reflects oceanographic or bathymetric features where phytoplankton accumulate and an area-restricted search for prey is likely to be successful. At small spatial scales (tens to hundreds of square kilometers), birds use odors and visual cues to pinpoint and capture prey directly. We have further identified species-specific,sensory-based foraging strategies, which we have begun to explore in evolutionary and developmental contexts. With respect to chemical communication among individuals, we have shown that some species can distinguish familiar individuals by scent cues alone. We are now set to explore the mechanistic basis for these discriminatory abilities in the context of kin recognition, and whether or not the major histocompatibility complex is involved.
Barriers to Care-Seeking for Depressed African Americans
Authors: Cruz Mario , Pincus Harold Alan , Harman Jeffreys , Reynolds Charles F. , Post Edward P. 
Published: May 2008

Objective: We explored perceived barriers to mental health care-seeking for depressed, low-income African Americans who are already engaged in psychotherapy. Methods: During a trial to improve psychotherapy appointment adherence, we asked all African-American participants, “Research shows African Americans with emotional or psychological problems use mental health services at half the rate of whites with similar problems. Why do you think that is?” Responses were captured verbatim. Results: Of 53 African Americans enrolled, 43 completed the study. We analyzed their responses in the hope of identifying modifiable responses. We used qualitative analytic methods, with four raters achieving consensus in coding responses into 13 thematic categories. Stigma was the most frequent response, followed by dysfunctional coping behavior, shame, denial, and “don't know.” Conclusion: While this study supports several barriers to care-seeking reported in the extant literature, our data also underscores the prominence of shame and denial, together with their complex interrelationships to public stigma and depression, respectively. Future research should assess the relationships between these factors to mental health care-seeking behavior in low-income African Americans and ways of modifying them.
Cross‐Species Genetic Toxicity Assessment Accomplished by Flow Cytometric Analysis of Blood
Authors: Bemis Jeffrey C. , Torous Dorothea K. , Tometsko Carol R. , Dertinger Stephen D. 
Published: May 2008

AbstractThe formation of micronuclei in blood cells has been an established indicator of genotoxicity for decades. Standard microscopy methods are time‐consuming and lack the objectivity that fully automated methods can provide. The ability of flow cytometric technology to rapidly and objectively survey thousands of cells for micronuclei can significantly improve the value of this endpoint. In addition, since many more cells can be scored, and specific populations can be targeted, species that historically have been difficult to obtain micronucleus data from, such as humans, can now be readily evaluated using this methodology. This unit describes a procedure for fixation, staining, and analysis of blood samples using materials supplied in MicroFlow kits (Litron Laboratories) and a single‐laser flow cytometer. This methodology provides a reliable, robust assessment of chromosome damage that is used in basic science research as well as drug‐safety screening programs at large pharmaceutical and chemical companies. Curr. Protoc. Toxicol. 36:2.14.1‐2.14.15. © 2008 by John Wiley & Sons, Inc.
Analysis of Modulation of Immunoglobulin Gene Expression
Authors: Sulentic Courtney E. W. 
Published: May 2008

AbstractImmunoglobulins (Ig) are critical in maintaining host immunity to a variety of pathogens. Regulation of Ig expression is a complex process involving transcriptional regulation of different Ig gene loci by many transcription factors and transcriptional regulatory regions. This complexity suggests many possible molecular targets for immunotoxicants. Therefore, thorough evaluation of chemical‐induced modulation of Ig expression may necessitate multiple experimental approaches evaluating: (1) number of B cells secreting antibodies by antibody‐forming cell response or plaque assay; (2) concentration of total secreted antibodies by enzyme‐linked immunosorbent assay (ELISA); (3) cellular proliferation and viability by cell count measurements, [3H] thymidine incorporation, and trypan blue exclusion; (4) Ig mRNA expression by quantitative real‐time reverse transcriptase–polymerase chain reaction (RT‐PCR); (5) transcriptional activity of specific Ig regulatory regions by reporter gene analysis; and (6) transcription factor binding to specific Ig regulatory regions by electrophoretic mobility shift (EMSA) and chromatin immunoprecipitation (ChIP). These experimental approaches are discussed in the unit, with detailed description of EMSA, EMSA‐western analysis, and isolation of nuclear protein. Curr. Protoc. Toxicol. 36:18.14.1‐18.14.21. © 2008 by John Wiley & Sons, Inc.
Neutral Red Uptake Cytotoxicity Tests for Estimating Starting Doses for Acute Oral Toxicity Tests
Authors: Stokes William S. , Casati Silvia , Strickland Judy , Paris Michael 
Published: May 2008

AbstractIn vitro cytotoxicity assays can be used as alternative toxicity tests to reduce the total number of animals needed for acute oral toxicity tests. This unit describes two methods for determining the in vitro cytotoxicity of test substances using neutral red uptake (NRU) and using the in vitro data to determine starting doses for in vivo acute oral systemic toxicity tests, e.g., the up‐and‐down procedure or the acute toxic class method. The use of the NRU methods to determine starting doses for acute oral toxicity tests may reduce the number of animals required, and for relatively toxic substances, this approach may also reduce the number of animals that die or require humane euthanasia due to severe toxicity. An interlaboratory validation study has demonstrated that the methods are useful and reproducible for these purposes. Two standardized protocols provide details for performing NRU tests with rodent and human cells. Curr. Protoc. Toxicol. 36:20.4.1‐20.4.20. © 2008 by John Wiley & Sons, Inc.
Affinity Purification of Natural Ligands
Authors: Luong John H.T. , Scouten William H. 
Published: May 2008

AbstractImmobilization of proteins, nucleic acids, and other bioligands is not always straightforward since they are often large molecules with numerous chemically reactive groups that can all participate in the immobilization process through physical adsorption, ionic binding, or covalent linkage. Protocols for some of the most frequently used matrix‐activation systems are described in this unit. For agarose, protocols are given for cyanogen bromide, p‐nitrophenyl chloroformate, tresyl chloride, and cyanuric chloride. Tosyl chloride is used to activate cellulose, and cyanuric chloride is also used to activate aminopropyl silica gel. Activation of magnetic beads with cyanogen bromide is described, and a protocol is provided for reacting the aldehyde groups of glyoxal agarose beads with the primary amine groups of ligands, with subsequent reduction of the formed Schiff base to yield a stable matrix‐ligand bond. Curr. Protoc. Protein Sci. 52:9.3.1‐9.3.22. © 2008 by John Wiley & Sons, Inc.