bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of the ETBreceptor in retinal ganglion cell death in glaucomaThis article is one of a selection of papers published in the special issue (part 1 of 2) on Forefronts in Endothelin.
Authors: Krishnamoorthy Raghu R. , Rao Vidhya R. , Dauphin Rachel , Prasanna Ganesh , Johnson Christina , Yorio Thomas 
Published: May 2008

Recent observations suggest that the vasoactive peptide endothelin-1 (ET-1) may be an important contributor to the etiology of glaucoma. ET-1 administration has been shown to produce optic nerve axonal loss and apoptosis of retinal ganglion cells. Ocular ET-1 levels are elevated in aqueous humor in response to elevated intraocular pressure both in glaucoma patients and in animal models of glaucoma; however, the precise mechanisms by which ET-1 mediates glaucomatous optic neuropathy are not clear. Presently we report that ET-1-mediated apoptosis was markedly attenuated in ETBreceptor-deficient rats, suggesting a key role for ETBreceptors in apoptosis of retinal ganglion cells by ET-1 treatment. Using virally transformed rat retinal ganglion cells (RGC-5 cells), we found that ET-1 (100 nmol/L) treatment produced apoptotic changes in these cells that was determined by flow cytometric analyses, release of mitochondrial cytochrome c to the cytosol, and increased phosphorylation of c-Jun N-terminal kinase. Pretreatment with the ETB-receptor antagonist BQ788 (1 μmol/L) was able to significantly attenuate ET-1-mediated apoptosis in RGC-5 cells. ET-1-mediated apoptotic changes in RGC-5 cells were associated with ETB-receptor activation and were accompanied by a significant upregulation of ETB-receptor expression. These studies suggest that ocular ET-1 acts through ETBreceptors to mediate apoptosis of retinal ganglion cells, a key event in glaucoma and related optic neuropathies.
Changes in Frequency of Precipitation Types Associated with Surface Air Temperature over Northern Eurasia during 1936–90
Authors: Ye Hengchun 
Published: May 2008

Abstract
Potential benefits or disadvantages of increasing precipitation in high-latitude regions under a warming climate are dependent on how and in what form the precipitation occurs. Precipitation frequency and type are equally as important as quantity and intensity to understanding the seasonality of hydrological cycles and the health of the ecosystem in high-latitude regions. This study uses daily historical synoptic observation records during 1936–90 over the former USSR to reveal associations between the frequency of precipitation types (rainfall, snowfall, mixed solid and liquid, and wet days of all types) and surface air temperatures to determine potential changes in precipitation characteristics under a warming climate. Results from this particular study show that the frequency of precipitation of all types generally increases with air temperature during winter. However, both solid and liquid precipitation days predominantly decrease with air temperature during spring with a reduction in snowfall days being most significant. During autumn, snowfall days decrease while rainfall days increase resulting in overall decreases in wet days as air temperature increases. The data also reveal that, as snowfall days increase in relationship to increasing air temperatures, this increase may level out or even decrease as mean surface air temperature exceeds −8°C in winter. In spring and autumn, increasing rainfall days switch to decreasing when the mean surface air temperature goes above 6°C. The conclusion of this study is that changes in the frequency of precipitation types are highly dependent on the location’s air temperature and that threshold temperatures exist beyond which changes in an opposite direction occur.
Influence of a New Turbulence Regime on the Global Air–Sea Heat Fluxes
Authors: Sahlée Erik , Smedman Ann-Sofi , Rutgersson Anna , Högström Ulf 
Published: May 2008

Abstract
Recent research has found that boundary layer turbulence changes its organization as the stratification approaches neutral from the unstable side. When the thermal forcing weakens in combination with wind speed above approximately 10 m s−1, detached eddies are formed in the upper part of the surface layer. These eddies effectively transport drier and colder air from aloft to the surface as they move downward, thereby enhancing the surface fluxes of sensible and latent heat. This effect has been observed over both land and sea; that is, it is not dependent on the nature of the underlying surface. Here the authors perform a sensitivity study of how this reorganization of the turbulence structure influences the global air–sea heat fluxes. Using modified bulk formulations incorporating this effect, the magnitude of the enhancement in a climatic sense was estimated by the use of 40-yr ECMWF Re-Analysis (ERA-40) data in the bulk formulas. It is found that for the 1979–2001 period, the global increase of the latent and sensible heat fluxes over the ice-free oceans is 3.6 and 1.2 W m−2, respectively. These numbers suggest that this effect is of some significance. The results also indicate that the regional and seasonal variability may be large. The largest annual increases are found over the southern oceans between 30° and 60°S where the sensible heat flux increases by 2.3 W m−2 and the latent heat flux by 6.5 W m−2. Ocean areas close to the equator experience almost no increase, whereas the latent heat flux from the Arabian Sea during the monsoon period is enhanced by 11.5 W m−2.
Energy Spectrum Characteristics of Boreal Summer Intraseasonal Oscillations: Climatology and Variations during the ENSO Developing and Decaying Phases*
Authors: Lin Ailan , Li Tim 
Published: May 2008

Abstract
The geographic-dependence characteristics of the energy spectrum of the boreal summer intraseasonal oscillation (BSISO; May–October) over the Indo–western Pacific region were analyzed using 25-yr (1979–2003) observational data. The BSISO energy spectrum distribution exhibits a distinctive regional characteristic. The stationary and eastward-propagating modes are most pronounced at the equator (5°S–5°N), while the westward-propagating modes are dominant in the off-equatorial region (10°–20°N). While the eastward intraseasonal oscillation (ISO) spectrum agglomerates on the 30–60-day period and zonal wavenumber 1, the westward mode covers wider spatial (wavenumber) and temporal (period) range. Along the Arabian Sea, Bay of Bengal, and South China Sea (SCS) latitudes, the dominant wavenumber 1 mode is the eastward (westward) propagation at the 30–60-day (10–20 day) period; for zonal wavenumber 2, the dominant mode is the westward propagation at both the 30–60-day and 10–20-day periods. Compared to the absolute amplitude of both zonal and meridional mode energy spectrum, northward propagation is the most predominant mode in boreal summer over the Indo–western Pacific regions. The strongest northward-propagating BSISO signal appears in the eastern tropical Indian Ocean.
The variation of BSISO differs significantly in the El Niño and La Niña developing and decaying phases. During the El Niño (La Niña) developing summer, the eastward propagation is enhanced (weakened) at the equator, while the northward propagation is also strengthened (weakened) over the western Pacific (east of 140°E). During the El Niño (La Niña) decaying summer, the eastward propagation weakens (strengthens) at the equator, opposite to that in the developing summer; the westward propagation off the equator and the northward propagation over SCS and the western Pacific are suppressed (enhanced). The amplitude of the BSISO variation is stronger in the decaying summer than that in the developing summer. This asymmetry in BSISO variations is primarily attributed to the asymmetry of the background mean flow change associated with the developing and decaying phases of ENSO.
The Effect of the Galápagos Islands on ENSO in Forced Ocean and Hybrid Coupled Models
Authors: Karnauskas Kristopher B. , Murtugudde Raghu , Busalacchi Antonio J. 
Published: May 2008

Abstract
An ocean general circulation model (OGCM) of the tropical Pacific Ocean is used to examine the effects of the Galápagos Islands on the El Niño–Southern Oscillation (ENSO). First, a series of experiments is conducted using the OGCM in a forced context, whereby an idealized El Niño event may be examined in cases with and without the Galápagos Islands. In this setup, the sensitivity of the sea surface temperature (SST) anomaly response to the presence of the Galápagos Islands is examined. Second, with the OGCM coupled to the atmosphere via zonal wind stress, experiments are conducted with and without the Galápagos Islands to determine how the Galápagos Islands influence the time scale of ENSO.
In the forced setup, the Galápagos Islands lead to a damped SST anomaly given an identical zonal wind stress perturbation. Mixed layer heat budget calculations implicate the entrainment mixing term, which confirms that the difference is due to the Galápagos Islands changing the background mean state, that is, the equatorial thermocline as diagnosed in a previous paper. In the hybrid coupled experiments, there is a clear shift in the power spectrum of SST anomalies in the eastern equatorial Pacific. Specifically, the Galápagos Islands lead to a shift in the ENSO time scale from a biennial to a quasi-quadrennial period. Mechanisms for the shift in ENSO time scale due to the Galápagos Islands are discussed in the context of well-known paradigms for the oscillatory nature of ENSO.
Estimating Bolus Velocities from Data—How Large Must They Be?
Authors: Killworth Peter D. 
Published: May 2008

Abstract
This paper examines the representation of eddy fluxes by bolus velocities. In particular, it asks the following: 1) Can an arbitrary eddy flux divergence of density be represented accurately by a nondivergent bolus flux that satisfies the condition of no normal flow at boundaries? 2) If not, how close can such a representation come? 3) If such a representation can exist in some circumstances, what is the size of the smallest bolus velocity that fits the data?
The author finds, in agreement with earlier authors, that the answer to the first question is no, although under certain conditions, which include a modification to the eddy flux divergence, a bolus representation becomes possible. One such condition is when the eddy flux divergence is required to balance the time-mean flux divergence. The smallest bolus flow is easily found by solving a thickness-weighted Poisson equation on each density level. This problem is solved for the North Pacific using time-mean data from an eddy-permitting model. The minimum bolus flow is found to be very small at depth but larger than is usually assumed near the surface. The magnitude of this minimum flow is of order one-tenth of the mean flow. Similar but larger results are found for a coarse-resolution model.
Data Assimilation for a Coupled Ocean–Atmosphere Model. Part II: Parameter Estimation
Authors: Kondrashov Dmitri , Sun Chaojiao , Ghil Michael 
Published: May 2008

Abstract
The parameter estimation problem for the coupled ocean–atmosphere system in the tropical Pacific Ocean is investigated using an advanced sequential estimator [i.e., the extended Kalman filter (EKF)]. The intermediate coupled model (ICM) used in this paper consists of a prognostic upper-ocean model and a diagnostic atmospheric model. Model errors arise from the uncertainty in atmospheric wind stress. First, the state and parameters are estimated in an identical-twin framework, based on incomplete and inaccurate observations of the model state. Two parameters are estimated by including them into an augmented state vector. Model-generated oceanic datasets are assimilated to produce a time-continuous, dynamically consistent description of the model’s El Niño–Southern Oscillation (ENSO). State estimation without correcting erroneous parameter values still permits recovering the true state to a certain extent, depending on the quality and accuracy of the observations and the size of the discrepancy in the parameters. Estimating both state and parameter values simultaneously, though, produces much better results. Next, real sea surface temperatures observations from the tropical Pacific are assimilated for a 30-yr period (1975–2004). Estimating both the state and parameters by the EKF method helps to track the observations better, even when the ICM is not capable of simulating all the details of the observed state. Furthermore, unobserved ocean variables, such as zonal currents, are improved when model parameters are estimated. A key advantage of using this augmented-state approach is that the incremental cost of applying the EKF to joint state and parameter estimation is small relative to the cost of state estimation alone. A similar approach generalizes various reduced-state approximations of the EKF and could improve simulations and forecasts using large, realistic models.
Elevated Convection and Castellanus: Ambiguities, Significance, and Questions
Authors: Corfidi Stephen F. , Corfidi Sarah J. , Schultz David M. 
Published: May 2008

AbstractThe term elevated convection is used to describe convection where the constituent air parcels originate from a layer above the planetary boundary layer. Because elevated convection can produce severe hail, damaging surface wind, and excessive rainfall in places well removed from strong surface-based instability, situations with elevated storms can be challenging for forecasters. Furthermore, determining the source of air parcels in a given convective cloud using a proximity sounding to ascertain whether the cloud is elevated or surface based would appear to be trivial. In practice, however, this is often not the case. Compounding the challenges in understanding elevated convection is that some meteorologists refer to a cloud formation known as castellanus synonymously as a form of elevated convection. Two different definitions of castellanus exist in the literature—one is morphologically based (cloud formations that develop turreted or cumuliform shapes on their upper surfaces) and the other is physically based (inferring the turrets result from the release of conditional instability). The terms elevated convection and castellanus are not synonymous, because castellanus can arise from surface-based convection and elevated convection exists that does not feature castellanus cloud formations. Therefore, the purpose of this paper is to clarify the definitions of elevated convection and castellanus, fostering a better understanding of the relevant physical processes. Specifically, the present paper advocates the physically based definition of castellanus and recommends eliminating the synonymity between the terms castellanus and elevated convection.
t(8;21)(q22;q22) fusion proteins preferentially bind to duplicated AML1/RUNX1 DNA-binding sequences to differentially regulate gene expression
Authors: Okumura Akiko J. , Peterson Luke F. , Okumura Fumihiko , Boyapati Anita , Zhang Dong-Er 
Published: May 2008

AbstractChromosome abnormalities are frequently associated with cancer development. The 8;21(q22;q22) chromosomal translocation is one of the most common chromosome abnormalities identified in leukemia. It generates fusion proteins between AML1 and ETO. Since AML1 is a well-defined DNA-binding protein, AML1-ETO fusion proteins have been recognized as DNA-binding proteins interacting with the same consensus DNA-binding site as AML1. The alteration of AML1 target gene expression due to the presence of AML1-ETO is related to the development of leukemia. Here, using a 25-bp random double-stranded oligonucleotide library and a polymerase chain reaction (PCR)-based DNA-binding site screen, we show that compared with native AML1, AML1-ETO fusion proteins preferentially bind to DNA sequences with duplicated AML1 consensus sites. This finding is further confirmed by both in vitro and in vivo DNA-protein interaction assays. These results suggest that AML1-ETO fusion proteins have a selective preference for certain AML1 target genes that contain multimerized AML1 consensus sites in their regulatory elements. Such selected regulation provides an important molecular mechanism for the dysregulation of gene expression during cancer development.
Multifaceted mechanisms in COPD: inflammation, immunity, and tissue repair and destruction
Authors: Chung K. F. , Adcock I. M. 
Published: May 2008

Chronic obstructive pulmonary disease is a leading global cause of morbidity and mortality that is characterised by inexorable deterioration of small airways obstruction with emphysema associated with cellular inflammation and structural remodelling. Other features include apoptosis as well as proliferation of cells, and both tissue repair and lack of tissue repair.Metalloprotease release, together with that of apoptotic factors, may underlie the emphysema, and, conversely, fibrosis of the small airways may be accounted for by the effects of growth factor activation. In advanced disease, influential factors include the development of autoimmunity, with activation of dendritic cells and T-helper cells of both type 1 and 2, and the senescence response.An inability of macrophages to ingest apoptosed cells and bacteria may exacerbate inflammatory responses. Systemic inflammation with concomitant cardiovascular disease and metabolic syndrome may reflect the effect of cigarette smoke on nonpulmonary cells. Corticosteroid resistance may be secondary to oxidative stress mechanisms, such as inactivation of histone deacetylases.The mechanisms of chronic obstructive pulmonary disease may be heterogeneous, according to severity, and clinical phenotypes need to be correlated with cellular and pathological processes. Treatments may be targeted to patients with specific mechanisms.
Severe and recurrent episodes of bronchiolitis obliterans organising pneumonia associated with indolent CD4+ CD8+ T-cell leukaemia
Authors: Martinez-Gallo M. , Puy C. , Ruiz-Hernandez R. , Rodriguez-Arias J. M. , Bofill M. , Nomdedeu J. F. , Cigudosa J. C. , Rodriguez-Sanchez J. L. , de la Calle-Martin O. 
Published: May 2008

The present study describes an adult male who has had recurrent episodes of pulmonary infiltrates with severe acute respiratory failure over a period of 10 yrs. Clinical and pathological characteristics revealed bronchiolitis obliterans with organising pneumonia (BOOP) that responded dramatically to prednisone. BOOP is characterised by inflammation of the bronchioles and surrounding tissue in the lungs. It can mimic infectious pneumonia but diagnosis is suspected when there is no response to multiple antibiotic treatment, and blood and sputum cultures are negative for microorganisms.A high proportion of double-positive (DP)-T-cells was detected in peripheral blood and in bronchoalveolar lavage, expressing CD4 and CD8αβ heterodimer with memory phenotype. These DP-T-lymphocytes expressed specific homing molecules that could explain their tropism to lung tissue, giving rise to the clinical symptoms. The patient did not present organomegaly, lymphadenopathy, lymphocytosis or other features of malignancy. However, T-cell receptor Vβ chain analysis indicated clonal rearrangement, and cytogenetic studies displayed chromosomic alterations that were similar to clonal proliferation observed in ataxia-telangiectasia and T-prolymphocytic leukaemia.The findings suggest a smouldering form of lymphoproliferation, the first sign of which was bronchiolitis obliterans organising pneumonia requiring constant corticoid treatment.
Pax7 is requisite for maintenance of a subpopulation of superior collicular neurons and shows a diverging expression pattern to Pax3 during superior collicular development
Authors: Thompson Jennifer A , Zembrzycki Andreas , Mansouri Ahmed , Ziman Mel 
Published: May 2008

Abstract

Background

Pax7 encodes a transcription factor well-established as an important determinant of mesencephalic identity and superior collicular development. Pax7 mutant mice, however, present with no obvious morphological impairments to the superior colliculus. This finding is paradoxical and has been attributed to functional redundancy afforded by its paralogue Pax3. Here we utilise Pax7 mutant mice to investigate the precise role of this important developmental regulator during superior collicular development and neuronal specification/differentiation. We also assess its spatiotemporal relationship with Pax3 during embryonic development.

Results
Analysis of the superior colliculus of Pax7 mutant and wildtype mice at a variety of developmental timepoints revealed that whilst correct initial specification is maintained, a subpopulation of dorsal mesencephalic neurons is lost at early postnatal stages. Moreover, a comparative analysis of embryonic Pax3 and Pax7 expression profiles indicate that Pax3 expression overlaps extensively with that of Pax7 initially, but their expression domains increasingly diverge as development progresses, coinciding spatiotemporally with neuronal differentiation and maturation of the tissue. Furthermore, Pax3 expression is perturbed within the CNS of embryonic Pax7 mutant mice.

Conclusion
In summary, these results demonstrate that during superior collicular development, Pax7 is required to maintain a subpopulation of dorsal, mesencephalic neurons and partially regulates, spatiotemporally, Pax3 expression within the CNS. The differential nature of Pax7 and Pax3 with respect to neuronal differentiation may have implications for future stem cell therapies aimed at exploiting their developmental capabilities.
Transcription of the extended hyp-operon in Nostocsp. strain PCC 7120
Authors: Agervald Åsa , Stensjö Karin , Holmqvist Marie , Lindblad Peter 
Published: May 2008

Abstract

Background
The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120.

Results
RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome.

Conclusion
This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.