bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Transport Schemes on Modeled Dust Concentrations
Authors: Vuolo Maria Raffaella , Menut Laurent , Chepfer Hélène 
Published: January 2009

Abstract
A sensitivity study is performed with the CHIMERE-DUST chemistry transport model in order to evaluate the modeled mineral dust spread due to the horizontal transport scheme accuracy. Three different schemes are implemented in the model: the simple first-order UPWIND scheme, the second-order Van Leer scheme, and the third-order parabolic piecewise method (PPM) scheme. The results showed that a large part of the uncertainty in dust modeling may be due to the transport scheme only. Compared to the PPM scheme, it is shown that, over a large domain encompassing western Africa and the North Atlantic, a significant increase in the dust plume extension is locally diagnosed (+25% with Van Leer and +48% with UPWIND) and linked to a decrease in the dust maxima (−17% with Van Leer and −32% with UPWIND) to PPM. Far from the sources, hourly surface concentration differences may be up to 30 μg m−3 in Europe, highlighting the high uncertainty of dust modeling for air quality use.
Notes on Temperature-Dependent Lidar Equations
Authors: Adam Mariana 
Published: January 2009

AbstractThe temperature dependence of molecular backscatter coefficients must be taken into account when narrowband interference filters are used in lidar measurements. Thus, the spectral backscatter differential cross section of the molecules involved in the backscattering of the radiation has to be calculated or measured and the interference filter transmission efficiency must be known. The present paper is intended to describe in an easily reproducible manner the procedure involved in calculating the temperature-dependent functions introduced in the lidar equations, including the computation of the differential cross sections for air, nitrogen, and water vapor. The temperature-dependent functions are computed for the Howard University Raman lidar (HURL). The interference filter efficiencies are given by the manufacturer. Error estimates in water vapor mixing ratio and aerosol backscatter ratio involved when temperature-dependent functions are omitted are given for measurements taken with HURL. For the data analyzed, it is found that errors in estimating the water vapor mixing ratio are up to ∼6% while in estimating the aerosol backscattering ratio the errors are up to ∼1.3% in the planetary boundary layer and ∼2.2% in cirrus clouds. Theoretical computations are performed to determine temperature-dependent functions for nitrogen, water vapor, and their ratio, using simulated Gaussian-shaped filters. The goal is to find the optimum combination of different filters that will determine the ratio profiles of the temperature-dependent functions that are either the closest to unity or the least variable. The analyses reveal that quite constant profiles can be obtained for several combinations of the filters.
A Microdrop Generator for the Calibration of a Water Vapor Isotope Ratio Spectrometer
Authors: Iannone Rosario Q. , Romanini Daniele , Kassi Samir , Meijer Harro A. J. , Kerstel Erik R. Th 
Published: January 2009

Abstract
A microdrop generator is described that produces water vapor with a known isotopic composition and volume mixing ratio for the calibration of a near-infrared diode laser water isotope ratio spectrometer. The spectrometer is designed to measure in situ the water vapor deuterium and oxygen (17O and 18O) isotope ratios from the low troposphere up to the lower stratosphere with a high temporal resolution, and is based on ultrasensitive optical-feedback cavity-enhanced absorption spectroscopy.
To calibrate the spectrometer, a commercial microdrop generator (Microdrop GmbH) is used to inject water droplets of known size at a preset repetition frequency into a stream of dry nitrogen or synthetic air. Complete evaporation of the small droplets ensures that there is no isotopic fractionation between the liquid phase and the generated moist “air.” The water mixing ratio of the synthetic air is controlled by the repetition rate and gas flow.
The current system spans a water mixing ratio range from about 10 to 5000 ppmv, representing the range of conditions expected in the lower to upper troposphere. Both lower and higher mixing ratios can be produced after small modifications to the injector’s operating conditions or the system’s design.
Four Years of Tropical ERA-40 Vorticity Maxima Tracks. Part II: Differences between Developing and Nondeveloping Disturbances
Authors: Kerns Brandon , Zipser Edward 
Published: January 2009

Abstract
Using a subset of the relative vorticity maxima (VM) tracks described in Part I, large-scale environmental fields, cold cloud area, and rainfall area are used to discriminate between developing and nondeveloping tropical disturbances in the eastern North Pacific (EPAC) and Atlantic Oceans. By using a minimum cold cloud coverage requirement, the nondeveloping VM are limited to disturbances with enhanced low-level relative vorticity and widespread deep convection. Linear discriminant analysis is used to determine the overall discrimination and the relative importance of each predictor for each basin separately. It is important to distinguish the two basins because, for many predictors, the differences between the basins are greater than the differences between developing and nondeveloping VM in each basin. Using the parametric forecast method, there is greater discrimination and prediction skill in the EPAC than in the Atlantic. There are also significant differences between the two basins in terms of the degree of discrimination provided by each of the predictors. Surprisingly, the mean vertical wind shear magnitude is greater for EPAC developing VM than for EPAC nondeveloping VM. Incorporating the satellite-derived predictors marginally improves the potential forecast skill in the EPAC but not in the Atlantic. The prediction skill (Heidke skill score) of tropical cyclogenesis in the Atlantic is similar to what has been obtained in previous studies using cloud cluster tracks. There is greater predictive skill in the EPAC.
As2O3 toxicity in rat hepatocytes: manifestation of caspase-mediated apoptosis
Authors: Ray A , Roy S , Agarwal S , Bhattacharya S 
Published: January 2009

In India, arsenic contamination in ground water is of immediate environmental concern affecting a large number of inhabitants in Kolkata. Arsenic is known to be one of the most toxic metalloids naturally occurring in the environment giving rise to severe toxic manifestations including cancer. Because arsenic is also used in chemotherapy of leukemia, it was considered worthwhile to concentrate on the mechanism of toxic action in normal hepatocytes which has not been addressed earlier. Rat hepatocytes were isolated and incubated in As2O3 at concentrations of 10, 20, and 40 μM in a time-dependent manner (0, 15, 30 min and 1, 2, and 4 h). The expression of the common stress proteins HSP 70 and 90 throughout the experimental duration confirmed the magnitude of toxic effect imposed by arsenic. Microscopic observations showed clear apoptotic changes in hepatocytes, which were further characterized by DNA ladder formation in time- and concentration-dependent manners. Apoptosis was triggered by caspase activation and over expression of bax at 10 μM As2O3 and at 20 and 40 μM concentrations of As2O3, MAP kinases were found to mediate the apoptotic pathway. Co-treatment of cells with arsenic and caspase inhibitor (Ac-DEVD-Cho) led to over expression of bcl-2, suppression of bax, and cytosolic sequestration of Bid and Bad. It is therefore concluded that caspase activation has a direct role in arsenic-induced apoptosis mediated by mitochondrial factors at 10 μM As2O3, and JUN N-terminal kinase (JNK) and P38 activation are the major mediators of apoptosis at the higher test concentrations (20 and 40 μM) of As2O3.
Constitutive JAK3 activation induces lymphoproliferative syndromes in murine bone marrow transplantation models
Authors: Cornejo Melanie G. , Kharas Michael G. , Werneck Miriam B. , Bras Séverine Le , Moore Sandra A. , Ball Brian , Beylot-Barry Marie , Rodig Scott J. , Aster Jon C. , Lee Benjamin H. , Cantor Harvey , Merlio Jean-Philippe , Gilliland D. Gary , Mercher Thomas 
Published: January 2009

AbstractThe tyrosine kinase JAK3 plays a well-established role during normal lymphocyte development and is constitutively phosphorylated in several lymphoid malignancies. However, its contribution to lymphomagenesis remains elusive. In this study, we used the newly identified activating JAK3A572V mutation to elucidate the effect of constitutive JAK3 signaling on murine lymphopoiesis. In a bone marrow transplantation model, JAK3A572V induces an aggressive, fatal, and transplantable lymphoproliferative disorder characterized by the expansion of CD8+TCRαβ+CD44+CD122+Ly-6C+ T cellsthat closely resemble an effector/memory T-cell subtype. Compared with wild-type counterparts, these cells show increased proliferative capacities in response to polyclonal stimulation, enhanced survival rates with elevated expression of Bcl-2, and increased production of interferon-γ (IFNγ) and tumor necrosis factor-α (TNFα), correlating with enhanced cytotoxic abilities against allogeneic target cells. Of interest, the JAK3A572V disease is epidermotropic and produces intraepidermal microabscesses. Taken together, these clinical features are reminiscent of those observed in an uncommon but aggressive subset of CD8+ human cutaneous T-cell lymphomas (CTCLs). However, we also observed a CD4+ CTCL-like phenotype when cells are transplanted in an MHC-I–deficient background. These data demonstrate that constitutive JAK3 activation disrupts T-cell homeostasis and induces lymphoproliferative diseases in mice.
The Rac activator Tiam1 controls efficient T-cell trafficking and route of transendothelial migration
Authors: Gérard Audrey , van der Kammen Rob A. , Janssen Hans , Ellenbroek Saskia I. , Collard John G. 
Published: January 2009

AbstractMigration toward chemoattractants is a hallmark of T-cell trafficking and is essential to produce an efficient immune response. Here, we have analyzed the function of the Rac activator Tiam1 in the control of T-cell trafficking and transendothelial migration. We found that Tiam1 is required for chemokine- and S1P-induced Rac activation and subsequent cell migration. As a result, Tiam1-deficient T cells show reduced chemotaxis in vitro, and impaired homing, egress, and contact hypersensitivity in vivo. Analysis of the T-cell transendothelial migration cascade revealed that PKCζ/Tiam1/Rac signaling is dispensable for T-cell arrest but is essential for the stabilization of polarization and efficient crawling of T cells on endothelial cells. T cells that lack Tiam1 predominantly transmigrate through individual endothelial cells (transcellular migration) rather than at endothelial junctions (paracellular migration), suggesting that T cells are able to change their route of transendothelial migration according to their polarization status and crawling capacity.
Cognate CD4 help is essential for the reactivation and expansion of CD8 memory T cells directed against the hematopoietic cell–specific dominant minor histocompatibility antigen, H60
Authors: Ryu Su Jeong , Jung Kyung Min , Yoo Hyun Seung , Kim Tae Woo , Kim Sol , Chang Jun , Choi Eun Young 
Published: January 2009

AbstractIn contrast to previous notions of the help-independency of memory CD8 T cells during secondary expansion, here we show that CD4 help is indispensable for the re-expansion of once-helped memory CD8 T cells, using a hematopoietic cell–specific dominant minor histocompatibility (H) antigen, H60, as a model antigen. H60-specific memory CD8 T cells generated during a helped primary response vigorously expanded only when rechallenged under helped conditions. The help requirement for an optimal secondary response was confirmed by a reduction in peak size by CD4 depletion, and was reproduced after skin transplantation. Helpless conditions or noncognate separate help during the secondary response resulted in a significant reduction in the peak size and different response kinetics. Providing CD4 help again during a tertiary challenge restored robust memory expansion; however, the repeated deprivation of help further reduced clonal expansion. Adoptively transferred memory CD8 T cells did not proliferate in CD40L−/− hosts. In the CD40−/− hosts, marginal memory expansion was detected after priming with male H60 cells but was completely abolished by priming with peptide-loaded CD40−/− cells, suggesting the essential role of CD40 and CD40L in memory responses. These results provide insight into the control of minor H antigen-specific CD8 T-cell responses, to maximize the graft-versus-leukemia response.
Insights into the manifestations, outcomes, and mechanisms of leukemogenesis in Down syndrome
Authors: Malinge Sébastien , Izraeli Shai , Crispino John D. 
Published: January 2009

AbstractChildren with Down syndrome (DS) show a spectrum of clinical anomalies, including cognitive impairment, cardiac malformations, and craniofacial dysmorphy. Moreover, hematologists have also noted that these children commonly show macrocytosis, abnormal platelet counts, and an increased incidence of transient myeloproliferative disease (TMD), acute megakaryocytic leukemia (AMKL), and acute lymphoid leukemia (ALL). In this review, we summarize the clinical manifestations and characteristics of these leukemias, provide an update on therapeutic strategies and patient outcomes, and discuss the most recent advances in DS-leukemia research. With the increased knowledge of the way in which trisomy 21 affects hematopoiesis and the specific genetic mutations that are found in DS-associated leukemias, we are well on our way toward designing improved strategies for treating both myeloid and lymphoid malignancies in this high-risk population.
Robust discovery of periodically expressed genes using the laplace periodogram
Authors: Liang Kuo-ching , Wang Xiaodong , Li Ta-Hsin 
Published: January 2009

Abstract

Background
Time-course gene expression analysis has become important in recent developments due to the increasingly available experimental data. The detection of genes that are periodically expressed is an important step which allows us to study the regulatory mechanisms associated with the cell cycle.

Results
In this work, we present the Laplace periodogram which employs the least absolute deviation criterion to provide a more robust detection of periodic gene expression in the presence of outliers. The Laplace periodogram is shown to perform comparably to existing methods for the Sacharomyces cerevisiae and Arabidopsis time-course datasets, and to outperform existing methods when outliers are present.

Conclusion
Time-course gene expression data are often noisy due to the limitations of current technology, and may include outliers. These artifacts corrupt the available data and make the detection of periodicity difficult in many cases. The Laplace periodogram is shown to perform well for both data with and without the presence of outliers, and also for data that are non-uniformly sampled.
Cell and molecular mechanisms of keratinocyte function stimulated by insulin during wound healing
Authors: Liu Yan , Petreaca Melissa , Yao Min , Martins-Green Manuela 
Published: January 2009

Abstract

Background
Regenerative wound repair is a goal of modern medicine. This is important not only for the local repair but also for its beneficial effect to systemic physiological processes. When wounds become chronic, individuals are susceptible to generalized inflammatory cascades that can affect many organs and even lead to death. Skin is the most commonly injured tissue, and its proper repair is important for reestablishment of its barrier function.

Results
We show here that insulin, when topically applied to skin excision wounds, accelerates re-epithelialization and stimulates "maturation" of the healing tissue. These effects are dependent on the insulin receptor but independent of EGF/EGF-R; PI3K-Akt-Rac1 signaling pathways are critically involved, and healing is α3 and LN332-dependent.

Conclusion
Insulin has great potential for the treatments of chronic wounds in which re-epthelialization is impaired. Understanding of the pathways induced by insulin is important for the development of analog molecules that function strictly in healing. Because of its long history of safe use in humans for decades, this protein may prove to be a powerful therapy without major adverse effects.
Evolution of prokaryotic SPFH proteins
Authors: Hinderhofer Markus , Walker Christina A , Friemel Anke , Stuermer Claudia AO , Möller Heiko M , Reuter Alexander 
Published: January 2009

Abstract

Background
The SPFH protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. Recently the origin of the SPFH proteins has been questioned. Instead, convergent evolution has been proposed. However, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution pattern have not yet been considered.
To gain better insight into this very diverse protein family, we have analyzed the genomes of 497 microorganisms and investigated the pattern of occurrence as well as the genomic vicinity of the prokaryotic SPFH members.

Results
According to sequence and operon structure, a clear division into 12 subfamilies was evident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conserved operon structure and two additional subfamilies are linked to those three through functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsH protease). Therefore these subgroups most likely share common ancestry. The complex pattern of occurrence among the different phyla is indicative of lateral gene transfer. Organisms that do not possess a single SPFH protein are almost exclusively endosymbionts or endoparasites.

Conclusion
The conserved operon structure and functional similarities suggest that at least 5 subfamilies that encompass almost 75% of all prokaryotic SPFH members share a common origin. Their similarity to the different eukaryotic SPFH families, as well as functional similarities, suggests that the eukaryotic SPFH families originated from different prokaryotic SPFH families rather than one. This explains the difficulties in obtaining a consistent phylogenetic tree of the eukaryotic SPFH members. Phylogenetic evidence points towards lateral gene transfer as one source of the very diverse patterns of occurrence in bacterial species.
Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates
Authors: Matsui Toshiaki , Yamamoto Toshiyuki , Wyder Stefan , Zdobnov Evgeny M , Kadowaki Tatsuhiko 
Published: January 2009

Abstract

Background
Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of these ancient genes have not been addressed extensively. To understand the functions and evolutionary mechanisms of such ancient Urbilaterian genes, we carried out comprehensive expression profile analysis of genes shared between vertebrates and honey bees but not with the other sequenced ecdysozoan genomes (honey bee-vertebrate specific, HVS genes) as a model.

Results
We identified 30 honey bee and 55 mouse HVS genes. Many HVS genes exhibited tissue-selective expression patterns; intriguingly, the expression of 60% of honey bee HVS genes was found to be brain enriched, and 24% of mouse HVS genes were highly expressed in either or both the brain and testis. Moreover, a minimum of 38% of mouse HVS genes demonstrated neuron-enriched expression patterns, and 62% of them exhibited expression in selective brain areas, particularly the forebrain and cerebellum. Furthermore, gene ontology (GO) analysis of HVS genes predicted that 35% of genes are associated with DNA transcription and RNA processing.

Conclusion
These results suggest that HVS genes include genes that are biased towards expression in the brain and gonads. They also demonstrate that at least some of Urbilaterian genes retained in the specific animal lineage may be selectively maintained to support the species-specific phenotypes.
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
Authors: Valdés Jorge , Pedroso Inti , Quatrini Raquel , Dodson Robert J , Tettelin Herve , Blake Robert , Eisen Jonathan A , Holmes David S 
Published: January 2009

Abstract

Background

Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.

Results
The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.

Conclusion
Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.