bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why Rolls are Prevalent in the Hurricane Boundary Layer
Authors: Foster Ralph C. 
Published: September 2005

Abstract
Recent remote sensing observations show that the hurricane boundary layer flow, although energetic, is not a region of homogeneous turbulence. In fact, the observations convincingly demonstrate that a large fraction of the turbulent flow in the regions away from the deep convective rainbands is highly organized into intense horizontal roll vortices that are approximately aligned with the mean wind and span the depth of the boundary layer. These observations show that rolls strongly increase the flux of momentum between the underlying surface and the main body of the storm compared to an equivalent hurricane boundary layer flow without rolls. The linear and nonlinear dynamics of hurricane boundary layer roll formation are outlined and it is shown why rolls are, in fact, the expected basic hurricane boundary layer state. The model presented here explains the hurricane roll features currently documented in field programs and makes predictions that can be tested in future experiments. The primary effects of rolls on the boundary layer fluxes are inherently nonlocal and nongradient and hence cannot be captured by standard downgradient turbulence parameterizations used in hurricane simulations. However, the nonlinear theory is the proper starting point for developing boundary layer parameterizations that include roll modification of the turbulent fluxes.
An Assessment of the Parameterization of Subgrid-Scale Cloud Effects on Radiative Transfer. Part II: Horizontal Inhomogeneity
Authors: Wood Norman B. , Gabriel Philip M. , Stephens Graeme L. 
Published: September 2005

Abstract
The role of horizontal inhomogeneity in radiative transfer through cloud fields is investigated within the context of the two-stream approximation. Spatial correlations between cloud optical properties and the radiance field are introduced in the three-dimensional radiative transfer equation and lead to a two-stream model in which the correlations are represented by parameterizations. The behavior of the model is examined using simple single-layer single-column atmospheres. Positive correlations between extinction or scattering and the radiance field are shown to decrease transmission, increase reflection, and increase absorption within inhomogeneous media. The parameterization is used to evaluate the characteristics of inhomogeneous cloud fields observed by radar and lidar over a number of different locations and seasons, revealing that shortwave transfer is generally characterized by negative correlations between extinction and radiance, while longwave transfer is characterized by positive correlations. The results from this characterization are applied to the integration of an atmospheric general circulation model. Model surface temperatures are significantly affected, largely in response to changes in downwelling radiative fluxes at the surface induced by changes in cloud cover and water vapor distributions.
Tracer Transport in Deep Convective Updrafts: Plume Ensemble versus Bulk Formulations
Authors: Lawrence Mark G. , Rasch Philip J. 
Published: September 2005

Abstract
Two widely used approaches for parameterizing tracer transport based on convective mass fluxes are the plume ensemble formulation (PEF) and the bulk formulation (BF). Here the behavior of these two is contrasted for the specific case in which the BF airmass fluxes are derived as a direct simplification of an explicit PEF. Relative to the PEF, the BF has a greater rate of entrainment of midtropospheric air into the parcels that reach the highest altitudes, and thus is expected to compute less efficient transport of surface-layer tracers to the upper troposphere. In this study, this difference is quantified using a new algorithm for computing mass conserving, monotonic tracer transport for both the BF and PEF, along with a technique for decomposing a bulk mass flux profile into a set of consistent, discrete plumes for use in the PEF. Runs with a 3D global chemistry transport model (MATCH) show that the BF is likely to be an adequate approximation for most tracers with lifetimes of a week or longer. However, for short-lived tracers (lifetimes of a couple days or less) the BF results in significantly less efficient transport to the upper troposphere than the PEF, with differences exceeding 30% on a monthly zonal mean basis. Implications of these results for tropospheric chemistry are discussed.
Predictability in a Model of Geophysical Turbulence
Authors: Kleeman Richard , Majda Andrew 
Published: September 2005

AbstractThe nature of predictability is examined in a numerical model relevant to the midlatitude atmosphere and oceans. The approach followed is novel and uses new theoretical tools from information theory, namely entropy functionals, as measures of information content and their application to finite ensembles. Particular attention is paid here to the practical application of these methods to the problem of ensemble prediction in dynamical systems with state spaces of high dimensionality. In this case, typically only an estimate of the prediction probability distribution function is available at coarse resolution. A methodology for estimating the information loss implied by this limited knowledge is introduced and applied to the practical problem of measuring prediction information content in a model able to generate geophysical turbulence. The application studied here generates such turbulence through the mechanism of baroclinic instability via an imposed and constant mean vertical shear. In traditional studies in this area, considerable attention has been paid to variations in ensemble spread as the major determinant of how predictability may change as prediction initial conditions vary. The analysis here reveals that such a scenario neglects the important role of the so-called ensemble signal, which is related to the difference in the first moments of the prediction and climatological distributions. It is found, in fact, that this quantity is often a strong control over variations in predictability of the large-scale barotropic flow. An initial investigation of the role of non-Gaussian effects shows that for the univariate large-scale barotropic case, they are only of minor importance to variations in predictability.
Embedded Cellular Convection in Moist Flow past Topography
Authors: Fuhrer Oliver , Schär Christoph 
Published: September 2005

AbstractMarginally unstable air masses impinging upon a mountain ridge may lead to the development of a nominally stratiform orographic cloud with shallow embedded convection. Rainfall amounts and distribution are then strongly influenced by the convective dynamics. In this study, the transition from purely stratiform orographic precipitation to flow regimes with embedded convection is systematically investigated. To this end, idealized cloud-resolving numerical simulations of moist flow past a two-dimensional mountain ridge are performed in a three-dimensional domain. A series of simulations with increasing upstream potential instability shows that the convective dynamics may significantly increase precipitation amounts, intensity, and efficiency, to an extent that cannot be replicated by two-dimensional simulations. Under conditions of uniform upstream flow, the embedded convection is of the cellular type. It is demonstrated that simple stability measures of the upstream profile are poor predictors for the occurrence and depth of embedded convection. A linear stability analysis is performed to understand the linear growth of the developing convective instabilities. Embedded convection results if the growth rates of convective instabilities are compatible with the advective time scale (the time an air parcel spends inside the orographic cloud) and the microphysical time scale (time for rain production and fallout). Individual convective updrafts are anchored to the mean flow. Additional simulations serve to demonstrate that the development of embedded convection and associated precipitation may strongly depend on small-amplitude upstream perturbations. Such perturbations enhance the efficacy of the convective circulations and lead to overall stronger precipitation. The potential implications of this result for the predictability of quantitative precipitation are also discussed.
Bmi-1 is useful as a novel molecular marker for predicting progression of myelodysplastic syndrome and patient prognosis
Authors: Mihara Keichiro , Chowdhury Moniruddin , Nakaju Nanae , Hidani Sachiko , Ihara Akihiro , Hyodo Hideo , Yasunaga Shin'ichiro , Takihara Yoshihiro , Kimura Akiro 
Published: September 2005

Abstract
The International Prognostic Scoring System (IPSS) has been widely used to predict the prognosis of patients with myelodysplastic syndrome (MDS). However, IPSS does not always provide a sufficiently precise evaluation of patients to allow the appropriate choice of clinical interventions. Here, we analyzed the expression of Bmi-1, which is required to regulate the self-renewal in CD34+ cells from 51 patients with cases of MDS and acute myeloid leukemia preceded by MDS (MDS-AML). Higher positivity rate of Bmi-1 was preferentially seen in refractory anemia with excess blasts (RAEB), RAEB in transformation (RAEB-T), and MDS-AML compared with refractory anemia (RA) and RA with ringed sideroblasts (RARS). IPSS score was positively correlated with the percentage of Bmi-1 expression. Patients with RA and RARS with a higher percentage of Bmi-1+ cells showed disease progression to RAEB. Here, we propose Bmi-1 as a novel molecular marker to predict the progression and prognosis of MDS.
Microcytic anemia and hepatic iron overload in a child with compound heterozygous mutations in DMT1 (SCL11A2)
Authors: Iolascon Achille , d'Apolito Maria , Servedio Veronica , Cimmino Flora , Piga Antonio , Camaschella Clara 
Published: September 2005

Abstract
Divalent metal transporter 1 (DMT1) mediates apical iron uptake in duodenal enterocytes and iron transfer from the transferrin receptor endosomal cycle into the cytosol in erythroid cells. Both mk mice and Belgrade rats, which carry an identical DMT1 mutation, exhibit severe microcytic anemia at birth and defective intestinal iron use and erythroid iron use. We report the hematologic phenotype of a child, compound heterozygote for 2 DMT1 mutations, who was affected by severe anemia since birth and showed hepatic iron overload. The novel mutations were a 3-bp deletion in intron 4 (c.310-3_5del CTT) resulting in a splicing abnormality and a C>T transition at nucleotide 1246(p. R416C). A striking reduction of DMT1 protein in peripheral blood mononuclear cells was demonstrated by Western blot analysis. The proband required blood transfusions until erythropoietin treatment allowed transfusion independence when hemoglobin levels between 75 and 95 g/L (7.5 and 9.5 g/dL) were achieved. Hematologic data of this patient at birth and in the first years of life strengthen the essential role of DMT1 in erythropoiesis. The early onset of iron overload indicates that, as in animal models, DMT1 is dispensable for liver iron uptake, whereas its deficiency in the gut is likely bypassed by the up-regulation of other pathways of iron use.
KSHV viral cyclin inactivates p27KIP1 through Ser10 and Thr187 phosphorylation in proliferating primary effusion lymphomas
Authors: Sarek Grzegorz , Järviluoma Annika , Ojala Päivi M. 
Published: September 2005

AbstractKaposi sarcoma herpesvirus (KSHV) infection is consistently associated with primary effusion lymphomas (PELs) that are non-Hodgkin lymphomas of B-cell origin. All PEL cells are latently infected with KSHV and express latent viral proteins such as the viral cyclin (v-cyclin), which has previously been implicated in down-regulation of cell-cycle inhibitor p27KIP1 levels via phosphorylation on Thr187. PEL cells retain high levels of p27KIP1 but yet proliferate actively, which has left the biologic significance of this p27KIP1 destabilization somewhat elusive. We have recently demonstrated that v-cyclin and p27KIP1 stably associate in PEL cells. Here we demonstrate that v-cyclin together with its kinase partner CDK6 phosphorylates the associated p27KIP1 in PEL cells, which represent a biologically relevant model system for KSHV pathobiology. During latent viral replication p27KIP1 was phosphorylated by v-cyclin-CDK6 predominantly on Ser10, which enhances its cytoplasmic localization. Interestingly, upon reactivation of KSHV lytic cycle, v-cyclin-CDK6 phosphorylated p27KIP1 on Thr187, which resulted in down-regulation of p27KIP1 protein levels. These findings indicate that v-cyclin modulates the cell-cycle inhibitory function of p27KIP1 by phosphorylation in PELs, and also suggest a novel role for v-cyclin in the lytic reactivation of KSHV. (Blood. 2006;107:725-732)
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Authors: Sczyrba Alexander , Beckstette Michael , Brivanlou Ali H , Giegerich Robert , Altmann Curtis R 
Published: September 2005

Abstract

Background
Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems.

Description
Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined.

Conclusion
The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches.
Supplementary material can be found at http://bibiserv.techfak.uni-bielefeld.de/xendb/.
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene
Authors: Liang Ping , Nair Jayakumar R , Song Lei , McGuire John J , Dolnick Bruce J 
Published: September 2005

Abstract

Background
The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSα and rTSβ. The rTSβ isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown.

Results
Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSβ. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSγ, which is absent in rTSβ. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSγ and rTSβ proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events.

Conclusion
The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.
Differential effects of intragastric acid and capsaicin on gastric emptying and afferent input to the rat spinal cord and brainstem
Authors: Holzer Peter , Painsipp Evelin , Schuligoi Rufina 
Published: September 2005

Abstract

Background
Hydrochloric acid (HCl) is a potential threat to the integrity of the gastric mucosa and is known to contribute to upper abdominal pain. We have previously found that gastric mucosal challenge with excess HCl is signalled to the rat brainstem, but not spinal cord, as visualized by expression of c-fos messenger ribonucleic acid (mRNA), a surrogate marker of neuronal excitation. This study examined whether gastric mucosal exposure to capsaicin, a stimulant of nociceptive afferents that does not damage the gastric mucosa, is signalled to both brainstem and spinal cord and whether differences in the afferent signalling of gastric HCl and capsaicin challenge are related to different effects on gastric emptying.

Results
Rats were treated intragastrically with vehicle, HCl or capsaicin, activation of neurons in the brainstem and spinal cord was visualized by in situ hybridization autoradiography for c-fos mRNA, and gastric emptying deduced from the retention of intragastrically administered fluid. Relative to vehicle, HCl (0.5 M) and capsaicin (3.2 mM) increased c-fos transcription in the nucleus tractus solitarii by factors of 7.0 and 2.1, respectively. Capsaicin also caused a 5.2-fold rise of c-fos mRNA expression in lamina I of the caudal thoracic spinal cord, although the number of c-fos mRNA-positive cells in this lamina was very small. Thus, on average only 0.13 and 0.68 c-fos mRNA-positive cells were counted in 0.01 mm sections of the unilateral lamina I following intragastric administration of vehicle and capsaicin, respectively. In contrast, intragastric HCl failed to induce c-fos mRNA in the spinal cord. Measurement of gastric fluid retention revealed that HCl suppressed gastric emptying while capsaicin did not.

Conclusion
The findings of this study show that gastric mucosal exposure to HCl and capsaicin is differentially transmitted to the brainstem and spinal cord. Since only HCl blocks gastric emptying, it is hypothesized that the two stimuli are transduced by different afferent pathways. We infer that HCl is exclusively signalled by gastric vagal afferents whereas capsaicin is processed both by gastric vagal and intestinal spinal afferents.
Mortality following Campylobacter infection: a registry-based linkage study
Authors: Ternhag Anders , Törner Anna , Svensson Åke , Giesecke Johan , Ekdahl Karl 
Published: September 2005

Abstract

Background
Campylobacteriosis is one of the most commonly identified causes of bacterial diarrheal disease and a common cause of gastroenteritis in travellers from developed nations. Despite the widespread occurrence, there is little information on Campylobacter mortality.

Methods
Mortality among a cohort of Campylobacter cases were compared with the general population 0–1, 1–3, 3–12 and more than 12 month after the onset of the illness. The cases were sub-grouped according to if they had been infected domestically or abroad.

Results
The standardized mortality ratio for cases infected domestically was 2.9 (95% CI: 1.9–4.0) within the first month following the illness. The risk then gradually diminished and approached 1.0 after one year or more have passed since the illness. This initial excess risk was not attributable to any particular age group (such as the oldest).
In contrast, for those infected abroad, a lower standardized mortality ratio 0.3 (95% CI: 0.04–0.8) was shown for the first month after diagnosis compared to what would be expected in the general population.

Conclusion
Infection with Campylobacter is associated with an increased short-term risk of death among those who were infected domestically. On the contrary, for those infected abroad a lower than expected risk of death was evident. We suggest that the explanation behind this is a "healthy traveler effect" among imported cases, and effects of a more frail than average population among domestic cases.
Artesunate plus sulfadoxine-pyrimethamine for treatment of uncomplicated Plasmodium falciparum malaria in Sudan
Authors: Elamin Sakina B , Malik Elfatih M , Abdelgadir Tarig , Khamiss Ammar H , Mohammed Mamoun M , Ahmed Elderderi S , Adam Ishag 
Published: September 2005

Abstract

Background
Early diagnosis and effective treatment with an appropriate drug form the main components of the World Health Organization's strategy to reduce malaria related mortality. The few available drugs might be safeguarded if combined with artesunate. The addition of artesunate to a standard antimalarial treatment substantially reduces treatment failure, recrudescence and gametocyte carriage.

Methods
During late 2004, the efficacy of artesunate (4 mg/kg. day, on days 0–2) plus sulfadoxine-pyrimethamine (25 mg/kg, on day 0) for the treatment of uncomplicated Plasmodium falciparum malaria was investigated in four sentinel areas in Sudan, with different malaria transmission (Damazin, Kassala, Kosti, and Malakal).

Results
Two hundreds and sixty-nine patients completed the 28-day follow-up. On day one, 60 (22.3%) patients were febrile and 15 (5.5%) patients were parasitaemic. On day three, all the patients were afebrile and aparasitaemic. While two patients (0.7%, Kassala) showed late Clinical and Parasitological Failures, the rest (99.3%) of the patients demonstrated Adequate Clinical and Parasitological Response. A gametocytaemia were detected during the follow-up in one patient (0.37%, Kassala). Adverse drug effects were detected in 32 (11.9%) patients

Conclusion
The study showed that AS plus SP is an effective, safe drug in the treatment of uncomplicated P. falciparum malaria in Sudan.
Natural history and treatment of hepatitis B virus and hepatitis C virus coinfection
Authors: Crockett Seth D , Keeffe Emmet B 
Published: September 2005

AbstractHepatitis B virus (HBV) and hepatitis C virus (HCV) coinfection is not uncommon as a result of similar routes of infection. Patients who are coinfected represent a unique group with diverse serologic profiles. Combined chronic hepatitis B and C leads to more severe liver disease and an increased risk of hepatocellular carcinoma. Furthermore, coinfected patients represent a treatment challenge. No standard recommendations exist for treatment of viral hepatitis due to dual HBV/HCV infection, and therefore treatment must be individualized based on patient variables such as serologic and virologic profiles, patient's prior exposure to antiviral treatment, and the presence of other parenterally transmitted viruses such as hepatitis D virus and human immunodeficiency virus. The natural history and treatment of patients with HBV and HCV coinfection is reviewed.