bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Quantification of Seasonal Rainfall and Associated Climate–Wildfire Relationships
Authors: Slocum Matthew G. , Platt William J. , Beckage Brian , Orzell Steve L. , Taylor Wayne 
Published: August 2010

Abstract
Wildfires are often governed by rapid changes in seasonal rainfall. Therefore, measuring seasonal rainfall on a temporally finescale should facilitate the prediction of wildfire regimes. To explore this hypothesis, daily rainfall data over a 58-yr period (1950–2007) in south-central Florida were transformed into cumulative rainfall anomalies (CRAs). This transformation allowed precise estimation of onset dates and durations of the dry and wet seasons, as well as a number of other variables characterizing seasonal rainfall. These variables were compared with parameters that describe ENSO and a wildfire regime in the region (at the Avon Park Air Force Range). Onset dates and durations were found to be highly variable among years, with standard deviations ranging from 27 to 41 days. Rainfall during the two seasons was distinctive, with the dry season having half as much as the wet season despite being nearly 2 times as long. The precise quantification of seasonal rainfall led to strong statistical models describing linkages between climate and wildfires: a multiple-regression technique relating the area burned with the seasonal rainfall characteristics had an of 0.61, and a similar analysis examining the number of wildfires had an of 0.56. Moreover, the CRA approach was effective in outlining how seasonal rainfall was associated with ENSO, particularly during the strongest and most unusual events (e.g., El Niño of 1997/98). Overall, the results presented here show that using CRAs helped to define the linkages among seasonality, ENSO, and wildfires in south-central Florida, and they suggest that this approach can be used in other fire-prone ecosystems.
A Higher-Order Ray Approximation Applied to Orographic Gravity Waves: Gaussian Beam Approximation
Authors: Pulido Manuel , Rodas Claudio 
Published: August 2010

Abstract
Ray techniques are a promising tool for developing orographic gravity wave drag schemes. However, the modeling of the propagation of orographic waves using standard ray theory in realistic background wind conditions usually encounters several regions, called caustics, where the first-order ray approximation breaks down. In this work the authors develop a higher-order approximation than standard ray theory, named the Gaussian beam approximation, for orographic gravity waves in a background wind that depends on height. The analytical results show that this formulation is free of the singularities that arise in ray theory. Orographic gravity waves that propagate in a background wind that turns with height—the same conditions as in the work of Shutts—are examined under the Gaussian beam approximation. The evolution of the amplitude is well defined in this approximation even at caustics and at the forcing level. When comparing results from the Gaussian beam approximation with high-resolution numerical simulations that compute the exact solution, there is good agreement of the amplitude and phase fields. Realistic orography is represented by means of a superposition of multiple Gaussians in wavenumber space that fit the spectrum of the orography. The technique appears to give a good representation of the disturbances generated by flow over realistic orography.
Analysis of the Meridional Energy Transport by Atmospheric Overturning Circulations
Authors: Döös Kristofer , Nilsson Johan 
Published: August 2010

Abstract
The atmospheric meridional overturning circulation is computed using the interim European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-Interim) data. Meridional mass transport streamfunctions are calculated not only using pressure as a vertical coordinate but also using temperature, specific humidity, and geopotential height as generalized vertical coordinates. Moreover, mass transport streamfunctions are calculated using the latent, the dry static, or the moist static energy as generalized vertical coordinates. The total meridional energy transport can be obtained by integrating these streamfunctions “vertically” over their entire energy range. The time-averaged mass transport streamfunctions are also decomposed into mean-flow and eddy-induced components. The meridional mass transport streamfunctions with temperature and specific humidity as independent variables yield a two-cell structure with a tropical Hadley-like cell and a pronounced extratropical Ferrel-like cell, which carries warm and moist air poleward. These Ferrel-like cells are much stronger than the Eulerian zonal-mean Ferrel cell, a feature that can be understood by considering the residual circulation related to specific humidity or temperature. Regardless of the generalized vertical coordinate, the present meridional mass transport streamfunctions yield essentially a two-layer structure with one poleward and one equatorward branch. The strongest meridional overturning in the midlatitudes is obtained when the specific humidity or the moist static energy is used as the vertical coordinate, indicating that the specific humidity is the variable that best distinguishes between poleward- and equatorward-moving air in the lower troposphere.
An Enhancement of Low-Frequency Variability in the Kuroshio–Oyashio Extension in CCSM3 owing to Ocean Model Biases
Authors: Thompson Lu Anne , Kwon Young-Oh 
Published: August 2010

Abstract
Enhanced decadal variability in sea surface temperature (SST) centered on the Kuroshio Extension (KE) has been found in the Community Climate System Model version 3 (CCSM3) as well as in other coupled climate models. This decadal peak has higher energy than is found in nature, almost twice as large in some cases. While previous analyses have concentrated on the mechanisms for such decadal variability in coupled models, an analysis of the causes of excessive SST response to changes in wind stress has been missing. Here, a detailed comparison of the relationships between interannual changes in SST and sea surface height (SSH) as a proxy for geostrophic surface currents in the region in both CCSM3 and observations, and how these relationships depend on the mean ocean circulation, temperature, and salinity, is made. We use observationally based climatological temperature and salinity fields as well as satellite-based SSH and SST fields for comparison. The primary cause for the excessive SST variability is the coincidence of the mean KE with the region of largest SST gradients in the model. In observations, these two regions are separated by almost 500 km. In addition, the too shallow surface oceanic mixed layer in March north of the KE in the subarctic Pacific contributes to the biases. These biases are not unique to CCSM3 and suggest that mean biases in current, temperature, and salinity structures in separated western boundary current regions can exert a large influence on the size of modeled decadal SST variability.
Dynamics of the West African Westerly Jet
Authors: Pu Bing , Cook Kerry H. 
Published: August 2010

Abstract
The West African westerly jet (WAWJ) is a low-level westerly jet located at 8°–11°N over the eastern Atlantic and the West African coast. It is clearly distinguished from the monsoon westerly flow by its structure and dynamics, and plays an important role in transporting moisture from the tropical eastern Atlantic to Sahelian West Africa during boreal summer.
The WAWJ develops in early June, sustains maximum wind speeds of 5–6 m s−1 from late July to early September, and weakens and dissipates by mid-October. In its mature stage, the WAWJ is located within the Atlantic ITCZ. It extends from the surface to 700 hPa, with maximum speed at 925 hPa. The jet has a weak semidiurnal cycle, with maxima at 0500 and 1700 local time.
A momentum budget analysis reveals that the WAWJ forms when a region of strong westerly acceleration is generated by the superposition of the Atlantic ITCZ and the westward extension of the continental thermal low. The WAWJ is supergeostrophic at its maximum, with zonal pressure gradient and Coriolis accelerations both pointing eastward. While much of the WAWJ’s seasonal variation can be explained by the geostrophic wind, the ageostrophic wind contributes more than 40% of the wind speed during the jet’s formation and demise.
The westward extension of the thermal low is associated with the formation of an offshore low, which is related to seasonal warming of the ocean between 6° and 18°N along the coast. The coastal SSTs vary in response to a net surface heating pattern with warming to the north and cooling to the south, which is mainly controlled by solar radiative and latent heat fluxes.
Analysis of Apparent Coupling between an Oceanic Kelvin Wave and Atmospheric Convection during the Winter of 1986/87
Authors: Gribble-Verhagen Lynn , Roundy Paul E. 
Published: August 2010

Abstract
This study analyzes the apparent coupling between an intraseasonal oceanic Kelvin wave in the Pacific Ocean and atmospheric moist deep convection for a particularly high-amplitude event during the winter of 1986/87. This wave was initiated initially by westerly wind bursts that developed in association with the Madden–Julian oscillation (MJO). After initiation by the MJO, the active convective anomaly slowed to roughly 1.5 m s−1, suggesting that the event became distinct from the MJO, which usually propagates at roughly 5–7 m s−1. This study demonstrates how surface winds, currents, SST anomalies, fluxes of sensible and latent heat across the sea surface, and atmospheric convection evolve throughout the event. Results suggest that the convective envelope and oceanic Kelvin wave are mutually beneficial and serve to prolong and enhance each other.
Examining the Effects of Dust Aerosols on Satellite Sea Surface Temperatures in the Mediterranean Sea Using the Medspiration Matchup Database
Authors: Ruescas Ana B. , Arbelo Manuel , Sobrino Jose A. , Mattar Cristian 
Published: August 2010

Abstract
Dust aerosol plumes from the Sahara cover the Mediterranean Sea regularly during the summer months (June–August) and occasionally during other seasons. Dust can absorb infrared longwave radiation, thus causing a drop in sea surface temperature (SST) retrievals from satellite. To quantify the magnitude of this absorption and to understand the sources of the biases that might be introduced when trying to validate SST algorithms with in situ bulk temperatures, the effects of the dust absorption are studied using the Medspiration Match-up Database. This database provides in situ and satellite SSTs derived from the Advanced Very High Resolution Radiometer (AVHRR) and the Advanced Along-Track Scanning Radiometer (AATSR), and the difference between skin and bulk measurements is calculated in order to obtain errors or residuals, which are classified by ranges and compared to an aerosol optical thickness product derived from the sensors. The behavior of the residuals is studied and there is clear correspondence between higher residual values and higher aerosol concentrations, though in some cases this relation is not so evident, especially during autumn months. Residuals for this period are then related to other atmospheric effects and layer boundary physical processes by using ancillary data (e.g., soundings).
Observations of Elevated Convection Initiation Leading to a Surface-Based Squall Line during 13 June IHOP_2002
Authors: Marsham John H. , Trier Stanley B. , Weckwerth Tammy M. , Wilson James W. 
Published: August 2010

AbstractThe evolution of a mesoscale convective system (MCS) observed during the International H2O Project that took place on the Great Plains of the United States is described. The MCS formed at night in a frontal zone, with four initiation episodes occurring between approximately 0000 and 0400 local time. Radar, radiosonde, and surface data together show that at least three of the initiation episodes were elevated, occurring from moist conditionally unstable layers located above the boundary layer, which had been stabilized by previous MCSs. Initiation occurred in northwest–southeast-oriented lines where a southerly nocturnal low-level jet terminated, generating elevated convergence. One initiation episode was observed using the S-band dual-polarization Doppler radar (S-Pol) and occurred at the intersection of this convergence zone with a propagating wave. Calculations of the Scorer parameter were consistent with wave trapping. Downdrafts from the developing convection generated both waves and bores, which propagated ahead of the cold pool, initiating further convection. Between 0700 and 1000 local time, the structure and orientation of the MCS evolved to a southwest–northeast-oriented squall line, which built a cold-pool outflow that could lift near-surface air to its level of free convection. The weaker cold pool in the eastern part of the domain was consistent with the greater impacts of a previous MCS there. To the authors’ knowledge, this case study provides the first detailed observational investigation of elevated initiation leading to surface-based convection, a process that appears to be an important mechanism for the generation of long-lived MCSs from elevated initiation.
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans
Authors: Esparza Mario , Cárdenas Juan Pablo , Bowien Botho , Jedlicki Eugenia , Holmes David S 
Published: August 2010

Abstract

Background

Acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low pH (pH 1-2). Although a substantial amount of information is available regarding CO2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study.

Results
Four gene clusters (termed cbb1-4) in the A. ferrooxidans genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson-Bassham (CBB) cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC 4.1.1.39) and the CO2-concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon cbb1 is divergently transcribed from a gene, cbbR, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma70-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N11-A/TNA-N7TNA) were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs) confirmed that purified CbbR is able to bind to the upstream regions of the cbb1, cbb2 and cbb3 operons, demonstrating that the predicted CbbR-binding sites are functional in vitro. However, CbbR failed to bind the upstream region of the cbb4 operon that contains cbbP, encoding phosphoribulokinase (EC 2.7.1.19). Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The cbb3 operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO2 fixation and tryptophan biosynthesis. The presence of a form II RubisCO could promote the ability of A. ferrooxidans to fix CO2 at different concentrations of CO2.

Conclusions

A. ferrooxidans has features of cbb gene organization for CO2-assimilating functions that are characteristic of obligate chemolithoautotrophs and distinguish this group from facultative autotrophs. The most conspicuous difference is a separate operon for the cbbP gene. It is hypothesized that this organization may provide greater flexibility in the regulation of expression of genes involved in inorganic carbon assimilation.
Leucine-rich repeat protein PRAME: expression, potential functions and clinical implications for leukaemia
Authors: Wadelin Frances , Fulton Joel , McEwan Paul A , Spriggs Keith A , Emsley Jonas , Heery David M 
Published: August 2010

Abstract
PRAME/MAPE/OIP4 is a germinal tissue-specific gene that is also expressed at high levels in haematological malignancies and solid tumours. The physiological functions of PRAME in normal and tumour cells are unknown, although a role in the regulation of retinoic acid signalling has been proposed. Sequence homology and structural predictions suggest that PRAME is related to the leucine-rich repeat (LRR) family of proteins, which have diverse functions. Here we review the current knowledge of the structure/function of PRAME and its relevance in leukaemia.
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Authors: Betel Doron , Koppal Anjali , Agius Phaedra , Sander Chris , Leslie Christina 
Published: August 2010

AbstractmirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.
Spectral and polarization sensitivity of juvenile Atlantic salmon (Salmo salar): phylogenetic considerations
Authors: Hawryshyn C. W. , Ramsden S. D. , Betke K. M. , Sabbah S. 
Published: August 2010

SUMMARY
We were interested in comparing the characteristics of polarization sensitivity in Atlantic salmon to those in Pacific salmon. Here we show that the common ancestor to the clade containing Salmo salar, Oncorhynchus mykiss, O. nerka, O. clarkii and Salvelinus fontinalis has the trait of ultraviolet polarization sensitivity. We examined spectral and polarization sensitivity of juvenile Atlantic salmon (Salmo salar) using both optic nerve compound action potential (CAP) and electroretinogram (ERG) recordings. Our experiments employed photic manipulation to adjust the sensitivity of the four cone mechanisms of Atlantic salmon. A spectrally broad background was used to ensure a contribution of all cone mechanisms to both spectral and polarization sensitivity. Chromatic adaptation was used to isolate the sensitivity of each of the four cone mechanisms for both spectral and polarization sensitivity. Under spectrally broad conditions, UV sensitive (UVS), mid wavelength sensitive (MWS) and long wavelength sensitive (LWS) cone mechanisms contributed to polarization sensitivity. CAP recordings produced the typical ‘W’ shaped polarization sensitivity curve reflecting two active polarization detectors with peaks at e-vector orientations of 0 deg, 90 deg and 180 deg, and troughs at 30 deg and 150 deg. ERG recordings produced a four-peaked polarization sensitivity curve reflecting two active polarization detectors and negative feedback activity, with peaks at e-vectors 0 deg, 45 deg, 90 deg, 135 deg and 180 deg, and troughs at 30 deg, 60 deg, 120 deg and 150 deg. Polarization-sensitivity measurements of isolated cone mechanisms revealed two orthogonal polarization detector mechanisms in Atlantic salmon, identical to that found in rainbow trout and other Pacific salmonid fishes. Moreover, under spectrally broad background conditions, CAP and ERG polarization sensitivity of Atlantic salmon did not differ significantly from that reported in Pacific salmonids.
AMP-activated protein kinase controls metabolism and heat production during embryonic development in birds
Authors: Walter Isabel , Hegarty Bronwyn , Seebacher Frank 
Published: August 2010

SUMMARY
During embryonic and early juvenile development, endotherms must balance energy allocation between growth and heat production. Failure to either match the ATP demand of growing tissue or produce heat at the correct developmental stage will lead to damage of the organism. We tested the hypothesis that AMP-activated protein kinase (AMPK) is involved in the regulation of energy metabolism and heat production during development in the chicken (Gallus gallus). We show that mRNA concentrations of regulatory and catalytic AMPK subunits, AMPK total protein, and AMPK phosphorylation increase during development [3 days (–3 days) and one day (–1 day) before hatching, and +1 day and +8 days after hatching] in liver, and to a lesser extent in skeletal muscle. Chronic stimulation with 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) significantly increases AMPK phosphorylation in skeletal muscle and in liver. This increase was paralleled by significant increases in heat production, glucose utilization, and liver and skeletal muscle mitochondrial capacity (citrate synthase activity). The effects of AMPK are likely to be mediated by inhibition of acetyl CoA carboxylase (ACC) after hatching, when ACC protein concentration increases significantly, and by a significant AMPK-induced increase in PGC-1α mRNA concentration (at +1 day), but not in NRF-1 mRNA concentration. AMPK phosphorylation is under the control of thyroid hormone, and AMPK phosphorylation decreases significantly following the induction of hypothyroidism. We propose AMPK as a principal regulatory mechanism during the transition from ectothermy to endothermy in birds, and show that AMPK function in birds is similar to that observed in mammals.
Audiogram of a formerly stranded long-finned pilot whale (Globicephala melas) measured using auditory evoked potentials
Authors: Pacini A. F. , Nachtigall P. E. , Kloepper L. N. , Linnenschmidt M. , Sogorb A. , Matias S. 
Published: August 2010

SUMMARY
Long-finned pilot whales are highly social odontocetes found in temperate and subpolar regions. This species is particularly known for its interaction with fisheries as well as its mass strandings. Recent tagging work has provided some information about pilot whales in the wild but, even though they have been successfully kept in captivity, little is known about their sensory capabilities. This study investigates the hearing abilities of a rehabilitated 2 year old male long-finned pilot whale. A complete audiogram was collected using auditory evoked potential techniques that included measurements of nine frequencies from 4 to 100 kHz presented as sinusoidally amplitude-modulated tones. The results indicated that the region of best hearing was between 11.2 and 50 kHz and the subject had relatively poor high frequency hearing compared with other odontocete species. This study emphasizes the importance of collecting basic hearing measurements from new species, understanding diagnostic life histories as well as continuously increasing the sample size of audiometry measurements within and between odontocete species as animals become available.