bluuebunny/crossref_metadata_2025_split huggingface dataset:
A U.S. CLIVAR Project to Assess and Compare the Responses of Global Climate Models to Drought-Related SST Forcing Patterns: Overview and Results
Authors: Schubert Siegfried , Gutzler David , Wang Hailan , Dai Aiguo , Delworth Tom , Deser Clara , Findell Kirsten , Fu Rong , Higgins Wayne , Hoerling Martin , Kirtman Ben , Koster Randal , Kumar Arun , Legler David , Lettenmaier Dennis , Lyon Bradfield , Magana Victor , Mo Kingtse , Nigam Sumant , Pegion Philip , Phillips Adam , Pulwarty Roger , Rind David , Ruiz-Barradas Alfredo , Schemm Jae , Seager Richard , Stewart Ronald , Suarez Max , Syktus Jozef , Ting Mingfang , Wang Chunzai , Weaver Scott , Zeng Ning 
Published: May 2009

Abstract
The U.S. Climate Variability and Predictability (CLIVAR) working group on drought recently initiated a series of global climate model simulations forced with idealized SST anomaly patterns, designed to address a number of uncertainties regarding the impact of SST forcing and the role of land–atmosphere feedbacks on regional drought. The runs were carried out with five different atmospheric general circulation models (AGCMs) and one coupled atmosphere–ocean model in which the model was continuously nudged to the imposed SST forcing. This paper provides an overview of the experiments and some initial results focusing on the responses to the leading patterns of annual mean SST variability consisting of a Pacific El Niño–Southern Oscillation (ENSO)-like pattern, a pattern that resembles the Atlantic multidecadal oscillation (AMO), and a global trend pattern.
One of the key findings is that all of the AGCMs produce broadly similar (though different in detail) precipitation responses to the Pacific forcing pattern, with a cold Pacific leading to reduced precipitation and a warm Pacific leading to enhanced precipitation over most of the United States. While the response to the Atlantic pattern is less robust, there is general agreement among the models that the largest precipitation response over the United States tends to occur when the two oceans have anomalies of opposite signs. Further highlights of the response over the United States to the Pacific forcing include precipitation signal-to-noise ratios that peak in spring, and surface temperature signal-to-noise ratios that are both lower and show less agreement among the models than those found for the precipitation response. The response to the positive SST trend forcing pattern is an overall surface warming over the world’s land areas, with substantial regional variations that are in part reproduced in runs forced with a globally uniform SST trend forcing. The precipitation response to the trend forcing is weak in all of the models.
It is hoped that these early results, as well as those reported in the other contributions to this special issue on drought, will serve to stimulate further analysis of these simulations, as well as suggest new research on the physical mechanisms contributing to hydroclimatic variability and change throughout the world.
Cloud and Precipitation Parameterization in a Meso-Gamma-Scale Operational Weather Prediction Model
Authors: Gerard Luc , Piriou Jean-Marcel , Brožková Radmila , Geleyn Jean-François , Banciu Doina 
Published: May 2009

Abstract
The paper assesses the difficulties of running an operational NWP model in the resolution range of 3–8 km. In this case, deep convection cells are neither much smaller than the grid box as assumed by most parameterization schemes, nor completely resolved as would be required for them to be treated explicitly. A specific approach is proposed, with an integrated sequential treatment of resolved condensation, deep convection, and microphysics together with the use of prognostic variables. It currently allows for the production of consistent and realistic results at resolutions ranging from a few tens of kilometers down to less than 4 km. Model skill scores and an example of an operational forecast at different resolutions are presented.
A Two-Step Adams–Bashforth–Moulton Split-Explicit Integrator for Compressible Atmospheric Models
Authors: Wicker Louis J. 
Published: May 2009

Abstract
Split-explicit integration methods used for the compressible Navier–Stokes equations are now used in a wide variety of numerical models ranging from high-resolution local models to convection-permitting climate simulations. Models are now including more sophisticated and complicated physical processes, such as multimoment microphysics parameterizations, electrification, and dry/aqueous chemistry. A wider range of simulation problems combined with the increasing physics complexity may place a tighter constraint on the model’s time step compared to the fluid flow’s Courant number (e.g., the choice of the integration time step based solely on advective Courant number considerations may generate unacceptable errors associated with the parameterization schemes). The third-order multistage Runge–Kutta scheme has been very successful as the split-explicit integration method; however, its efficiency arises partially in its ability to use a time step that is 20%–40% larger than more traditional integration schemes. In applications in which the time step is constrained by other considerations, alternative integration schemes may be more efficient. Here a two-step third-order Adams–Bashforth–Moulton integrator is stably split in a similar manner as the split Runge–Kutta scheme. For applications in which the large time step is not constrained by the advective Courant number it requires less computational effort. Stability is demonstrated through eigenvalue analysis of the linear coupled one-dimensional velocity–pressure equations, and full two-dimensional nonlinear solutions from a standard test problem are shown to demonstrate solution accuracy and efficiency.
Enhanced development of CD4+ γδ T cells in the absence of Itk results in elevated IgE production
Authors: Qi Qian , Xia Mingcan , Hu Jianfang , Hicks Elizabeth , Iyer Archana , Xiong Na , August Avery 
Published: May 2009

AbstractThe Tec kinase Itk is critical for the development of αβ T cells as well as differentiation of CD4+ T cells into Th2 cells. Itk null mice have defects in the production of Th2 cytokines; however, they paradoxically have significant elevations in serum IgE. Here we show that Itk null mice have increased numbers of γδ T cells in the thymus and spleen. This includes elevated numbers of CD4+ γδ T cell, the majority of which carry the Vγ1.1 and Vδ6.2/3 γδ T-cell receptor with a distinct phenotype. The development of these CD4+ γδ T cells is T cell intrinsic, independent of either major histocompatibility complex class I or class II, and is favored during development in the absence of Itk. Itk null CD4+ γδ T cells secrete significant amounts of Th2 cytokines and can induce the secretion of IgE by wild-type B cells. Our data indicate that Itk plays important role in regulating γδ T-cell development and function. In addition, our data indicate that the elevated IgE observed in Itk-deficient mice is due in part to the enhanced development of CD4+ γδ T cells in the absence of Itk.
F18-fluorodeoxyglucose positron emission tomography in the context of other imaging techniques and prognostic factors in multiple myeloma
Authors: Bartel Twyla B. , Haessler Jeff , Brown Tracy L. Y. , Shaughnessy John D. , van Rhee Frits , Anaissie Elias , Alpe Terri , Angtuaco Edgardo , Walker Ronald , Epstein Joshua , Crowley John , Barlogie Bart 
Published: May 2009

AbstractF18-fluorodeoxyglucose positron emission tomography (FDG-PET) is a powerful tool to investigate the role of tumor metabolic activity and its suppression by therapy for cancer survival. As part of Total Therapy 3 for newly diagnosed multiple myeloma, metastatic bone survey, magnetic resonance imaging, and FDG-PET scanning were evaluated in 239 untreated patients. All 3 imaging techniques showed correlations with prognostically relevant baseline parameters: the number of focal lesions (FLs), especially when FDG-avid by PET-computed tomography, was positively linked to high levels of β-2-microglobulin, C-reactive protein, and lactate dehydrogenase; among gene expression profiling parameters, high-risk and proliferation-related parameters were positively and low-bone-disease molecular subtype inversely correlated with FL. The presence of more than 3 FDG-avid FLs, related to fundamental features of myeloma biology and genomics, was the leading independent parameter associated with inferior overall and event-free survival. Complete FDG suppression in FL before first transplantation conferred significantly better outcomes and was only opposed by gene expression profiling-defined high-risk status, which together accounted for approximately 50% of survival variability (R2 test). Our results provide a rationale for testing the hypothesis that myeloma survival can be improved by altering treatment in patients in whom FDG suppression cannot be achieved after induction therapy.
Titrated sedation with propofol or midazolam for flexible bronchoscopy: a randomised trial
Authors: Clark G. , Licker M. , Younossian A. B. , Soccal P. M. , Frey J-G. , Rochat T. , Diaper J. , Bridevaux P-O. , Tschopp J-M. 
Published: May 2009

In this study, we questioned whether propofol provided clinical benefits compared with midazolam in terms of neuropsychometric recovery, safety profile and patient tolerance.Patients, aged >18 yrs, were randomised to receive midazolam or propofol, given by non-anaesthetist physicians to achieve moderate levels of sedation as assessed by the electroencephalographic bispectral index (BIS; between 70 and 85). The primary end-point was the time delay until recovery of the BIS above 90. Other end-points included a neuropsychometric continuous performance test (CPT), serious respiratory adverse events, patient tolerance and physician satisfaction.Neuropsychometric recovery was improved in the propofol compared to the midazolam group as evidenced by faster normalisation of BIS index (5.4±4.7 minversus11.7±10.2 min; p = 0.001) and better results at the CPT. In the midazolam group, 15% of patients presented profound sedation precluding CPT completion and one patient required mechanical ventilatory support. Patient tolerance was significantly better in the propofol group, whereas the operator’s assessment was comparable in both groups.Compared with midazolam, propofol provided a higher quality of sedation in terms of neuropsychometric recovery and patient tolerance. BIS-guided propofol administration represents a safe sedation technique that can be performed by the non-anaesthesiologist.
Determinants of asthma phenotypes in supermarket bakery workers
Authors: Baatjies R. , Lopata A. L. , Sander I. , Raulf-Heimsoth M. , Bateman E. D. , Meijster T. , Heederik D. , Robins T. G. , Jeebhay M. F. 
Published: May 2009

While baker's asthma has been well described, various asthma phenotypes in bakery workers have yet to be characterised. Our study aims to describe the asthma phenotypes in supermarket bakery workers in relation to host risk factors and self-reported exposure to flour dust.A cross-sectional study of 517 supermarket bakery workers in 31 bakeries used a questionnaire, skin prick tests, and specific immunoglobulin E to wheat, rye and fungal α-amylase and methacholine challenge testing.The prevalence of probable occupational asthma (OA, 13%) was higher than atopic (6%), nonatopic (6%) and work-aggravated asthma (WAA, 3%) phenotypes. Previous episodes of high exposure to dusts, fumes and vapours causing asthma symptoms were more strongly associated with WAA (OR 5.8, 95% CI 1.7–19.2) than OA (2.8, 1.4–5.5). Work-related ocular–nasal symptoms were significantly associated with WAA (4.3, 1.3–13.8) and OA (3.1, 1.8–5.5). Bakers with OA had an increased odds ratio of reporting adverse reactions to ingested grain products (6.4, 2.0–19.8).OA is the most common phenotype among supermarket bakery workers. Analysis of risk factors contributes to defining clinical phenotypes, which will guide ongoing medical surveillance and clinical management of bakery workers.
RNAi in the cereal weevil Sitophilusspp: Systemic gene knockdown in the bacteriome tissue
Authors: Vallier Agnès , Vincent-Monégat Carole , Laurençon Anne , Heddi Abdelaziz 
Published: May 2009

Abstract

Background
The weevils Sitophilus spp. are among the most important cosmopolitan pests of stored cereal grains. However, their biology and physiology are poorly understood, mainly because the insect developmental stages take place within cereal grains and because of the lack of gene specific molecular manipulation.

Results
To gain access to the different insect developmental stages, weevil females were allowed to lay their eggs on starch pellets and hatched embryos were collected by dissolving starch with water. Embryos were transferred between two Glass Plates filled with packed Flour (GPF) to mimic compact texture of the cereal grain, and this system allowed us to recover specific developmental stages. To knockdown the gene expressed in the bacteria-bearing organ (the bacteriome), whole larvae were injected with dsRNA to target the wpgrp1 gene and they were then left to develop for a further 4 days period. Quantitative RT-PCR and Western blot analyses on the bacteriome of these animals revealed a down-regulation of the wpgrp1 expression, both at transcript and protein levels.

Conclusion
These results demonstrate that whole larval injection with dsRNA results in a high and systemic decrease of both mRNA and protein in the bacteriome tissue. This, along with the possibility of access to the insect developmental stages, opens up a new research avenue for exploring gene specific functions in the cereal weevils.
The little we know on the structure and machinery of V-ATPase
Authors: Saroussi Shai , Nelson Nathan 
Published: May 2009

SUMMARY
The life of every eukaryotic cell depends on the function of vacuolar H+-ATPase (V-ATPase). Today we know that V-ATPase is vital for many more physiological and biochemical processes than it was expected three decades ago when the enzyme was discovered. These range from a crucial role in the function of internal organelles such as vacuoles, lysosomes, synaptic vesicles, endosomes, secretory granules and the Golgi apparatus to the plasma membrane of several organisms and specific tissues, and specialized cells. The overall structure and mechanism of action of the V-ATPase is supposed to be similar to that of the well-characterized F-type ATP synthase (F-ATPase). Both consist of a soluble catalytic domain (V1 or F1) that is coupled to a membrane-spanning domain (Vo or Fo) by one or more `stalk' components. Owing to the complexity and challenging properties of V-ATPase its study is lagging behind that of its relative F-ATPase. Time will tell whether V-ATPase shares an identical mechanism of action with F-ATPase or its mode of operation is unique.
NhaA crystal structure: functional–structural insights
Authors: Padan Etana , Kozachkov Lena , Herz Katia , Rimon Abraham 
Published: May 2009

SUMMARY
Na+/H+ antiporters are integral membrane proteins that exchange Na+ for H+ across the cytoplasmic membrane and many intracellular membranes. They are essential for Na+, pH and volume homeostasis, which are crucial processes for cell viability. Accordingly, antiporters are important drug targets in humans and underlie salt-resistance in plants. Many Na+/H+ antiporters are tightly regulated by pH. Escherichia coli NhaA Na+/H+ antiporter, a prototype pH-regulated antiporter,exchanges 2 H+ for 1 Na+ (or Li+). The NhaA crystal structure has provided insights into the pH-regulated mechanism of antiporter action and opened up new in silico and in situavenues of research. The monomer is the functional unit of NhaA yet the dimer is essential for the stability of the antiporter under extreme stress conditions. Ionizable residues of NhaA that strongly interact electrostatically are organized in a transmembrane fashion in accordance with the functional organization of the cation-binding site, `pH sensor', the pH transduction pathway and the pH-induced conformational changes. Remarkably,NhaA contains an inverted topology motive of transmembrane segments, which are interrupted by extended mid-membrane chains that have since been found to vary in other ion-transport proteins. This novel structural fold creates a delicately balanced electrostatic environment in the middle of the membrane,which might be essential for ion binding and translocation. Based on the crystal structure of NhaA, a model structure of the human Na+/H+ exchanger (NHE1) was constructed, paving the way to a rational drug design.
Carbonic anhydrases and anion transport in mosquito midgut pH regulation
Authors: Linser Paul J. , Smith Kristin E. , Seron Terri J. , Neira Oviedo Marco 
Published: May 2009

SUMMARYMosquito larvae use a digestive strategy that is relatively rare in nature. The anterior half of the larval mosquito midgut has a luminal pH that ranges between 10.5 and 11.5. Most other organisms, both large and small, initiate digestion in an acid medium. The relative uniqueness of the highly alkaline digestive strategy has been a long-standing research focus in larval lepidopterans. More recently, the disease vector potential of mosquitoes has fueled specific interest in larval mosquito biology and the alkaline digestive environment in the midgut. The probable principle anion influencing the highly alkaline gut lumen is bicarbonate/carbonate. Bicarbonate/carbonate is regulated at least in part by the activity of carbonic anhydrases. Hence, we have focused attention on the carbonic anhydrases of the mosquito larva. Anopheles gambiae, the major malaria mosquito of Africa, is an organism with a published genome which has facilitated molecular analyses of the 12 carbonic anhydrase genes annotated for this mosquito. Microarray expression analyses, tissue-specific quantitative RT-PCR, and antibody localization have been used to generate a picture of carbonic anhydrase distribution in the larval mosquito. Cytoplasmic, GPI-linked extracellular membrane-bound and soluble extracellular carbonic anhydrases have been located in the midgut and hindgut. The distribution of the enzymes is consistent with an anion regulatory system in which carbonic anhydrases provide a continuous source of bicarbonate/carbonate from the intracellular compartments of certain epithelial cells to the ectoperitrophic space between the epithelial cells and the acellular membrane separating the food bolus from the gut cells and finally into the gut lumen. Carbonic anhydrase in specialized cells of the hindgut (rectum) probably plays a final role in excretion of bicarbonate/carbonate into the aquatic environment of the larva. Detection and characterization of classic anion exchangers of the SLC4A family in the midgut has been problematic. The distribution of carbonic anhydrases in the system may obviate the requirement for such transporters, making the system more dependent on simple carbon dioxide diffusion and ionization via the activity of the enzyme.
Modular structure of sodium-coupled bicarbonate transporters
Authors: Boron Walter F. , Chen Liming , Parker Mark D. 
Published: May 2009

SUMMARYMammalian genomes contain 10 SLC4 genes that, between them, encode three Cl–HCO3 exchangers, five Na+-coupled HCO3 transporters (NCBTs), one reported borate transporter, and what is reported to be a fourth Cl–HCO3 exchanger. The NCBTs are expressed throughout the body and play important roles in maintaining intracellular and whole-body pH, as well as contributing to transepithelial transport processes. The importance of NCBTs is underscored by the genetic association of dysfunctional NCBT genes with blindness, deafness, epilepsy,hypertension and metal retardation. Key to understanding the action and regulation of NCBTs is an appreciation of the diversity of NCBT gene products. The transmembrane domains of human NCBT paralogs are 50–84% identical to each other at the amino acid level, and are capable of a diverse range of actions, including electrogenic Na/HCO3 cotransport (i.e. NBCe1 and NBCe2) and electroneutral Na/HCO3 cotransport (i.e. NBCn1 and NBCn2), as well as Na+-dependent Cl–HCO3 exchange(i.e. NDCBE). Furthermore, by the use of alternative promoters and alternative-splicing events, individual SLC4 genes have the potential to generate multiple splice variants (as many as 16 in the case of NBCn1), each of which could have unique temporal and spatial patterns of distribution, unitary transporter activity (i.e. flux mediated by one molecule), array of protein-binding partners, and complement of regulatory stimuli. In the first section of this review, we summarize our present knowledge of the function and distribution of mammalian NCBTs and their multiple variants. In the second section of this review we consider the molecular consequences of NCBT variation.
Epithelial ultrastructure and cellular mechanisms of acid and base transport in theDrosophilamidgut
Authors: Shanbhag Shubha , Tripathi Subrata 
Published: May 2009

SUMMARYThere is a resurgence of interest in the Drosophila midgut on account of its potential value in understanding the structure, development and function of digestive organs and related epithelia. The recent identification of regenerative or stem cells in the adult gut of Drosophila has opened up new avenues for understanding development and turnover of cells in insect and mammalian gastrointestinal tracts. Conversely, the physiology of the Drosophila gut is less well understood as it is a difficult epithelial preparation to study under controlled conditions. Recent progress in microperfusion of individual segments of the Drosophila midgut, in both larval and adult forms, has enabled ultrastructural and electrophysiological study and preliminary characterization of cellular transport processes in the epithelium. As larvae are more active feeders, the transport rates are higher than in adults. The larval midgut has at least three segments: an anterior neutral zone, a short and narrow acid-secreting middle segment and a long and wider posterior segment (which is the best studied) that secretes base (probably HCO3–) into the lumen. The posterior midgut has a lumen-negative transepithelial potential(35–45 mV) and a high resistance (800–1400 Ω.cm2)that correlates with little or no lateral intercellular volume. The primary transport system driving base secretion into the lumen appears to be a bafilomycin-A1-sensitive, electrogenic H+ V-ATPase located on the basal membrane, which extrudes acid into the haemolymph, as inferred from the extracellular pH gradients detected adjacent to the basal membrane. The adult midgut is also segmented (as inferred from longitudinal gradients of pH dye-indicators in the lumen) into anterior, middle and posterior regions. The anterior segment is probably absorptive. The middle midgut secretes acid (pH&lt;4.0), a process dependent on a carbonic-anhydrase-catalysed H+ pool. Cells of the middle segment are alternately absorptive (apically amplified by ≈9-fold, basally amplified by &gt;90-fold) and secretory (apically amplified by &gt;90-fold and basally by ≈10-fold). Posterior segment cells have an extensively dilated basal extracellular labyrinth, with a volume larger than that of anterior segment cells, indicating more fluid reabsorption in the posterior segment. The luminal pH of anterior and posterior adult midgut is 7–9. These findings in the larval and adult midgut open up the possibility of determining the role of plasma membrane transporters and channels involved in driving not only H+ fluxes but also secondary fluxes of other solutes and water in Drosophila.