bluuebunny/crossref_metadata_2025_split huggingface dataset:
Merged Statistical Analyses of Historical Monthly Precipitation Anomalies Beginning 1900
Authors: Smith Thomas M. , Arkin Phillip A. , Sapiano Mathew R. P. , Chang Ching-Yee 
Published: May 2010

Abstract
A monthly reconstruction of precipitation beginning in 1900 is presented. The reconstruction resolves interannual and longer time scales and spatial scales larger than 5° over both land and oceans. Because of different land and ocean data availability, the reconstruction combines two separate historical reconstructions. One analyzes interannual variations directly by fitting gauge-based anomalies to large-scale spatial modes. This direct reconstruction is used for land anomalies and interannual oceanic anomalies. The other analyzes annual and longer variations indirectly from correlations with analyzed sea surface temperature and sea level pressure. This indirect reconstruction is used for oceanic variations with time scales longer than interannual. In addition, a method of estimating reconstruction errors is also presented.
Over land the reconstruction is a filtered representation of the gauge data with data gaps filled. Over oceans the reconstruction gives an estimate of the atmospheric response to changing temperature and pressure, combined with interannual variations. The reconstruction makes it possible to evaluate global precipitation variations for periods much longer than the satellite period, which begins in 1979. Evaluations show some large-scale similarities with coupled model precipitation variations over the twentieth century, including an increasing tendency over the century. The reconstructed land and sea trends tend to be out of phase at low latitudes, similar to the out-of-phase relationship for interannual variations. This reconstruction may be used for climate monitoring, for statistical climate studies of the twentieth century, and for helping to evaluate dynamic climate models. In the future the possibility of improving the reconstruction will be explored by further improving the analysis methods and including additional data.
Assimilation of Satellite-Derived Skin Temperature Observations into Land Surface Models
Authors: Reichle Rolf H. , Kumar Sujay V. , Mahanama Sarith P. P. , Koster Randal D. , Liu Q. 
Published: May 2010

Abstract
Land surface (or “skin”) temperature (LST) lies at the heart of the surface energy balance and is a key variable in weather and climate models. In this research LST retrievals from the International Satellite Cloud Climatology Project (ISCCP) are assimilated into the Noah land surface model and Catchment land surface model (CLSM) using an ensemble-based, offline land data assimilation system. LST is described very differently in the two models. A priori scaling and dynamic bias estimation approaches are applied because satellite and model LSTs typically exhibit different mean values and variabilities. Performance is measured against 27 months of in situ measurements from the Coordinated Energy and Water Cycle Observations Project at 48 stations. LST estimates from Noah and CLSM without data assimilation (“open loop”) are comparable to each other and superior to ISCCP retrievals. For LST, the RMSE values are 4.9 K (CLSM), 5.5 K (Noah), and 7.6 K (ISCCP), and the anomaly correlation coefficients (R) are 0.61 (CLSM), 0.63 (Noah), and 0.52 (ISCCP). Assimilation of ISCCP retrievals provides modest yet statistically significant improvements (over an open loop, as indicated by nonoverlapping 95% confidence intervals) of up to 0.7 K in RMSE and 0.05 in the anomaly R. The skill of the latent and sensible heat flux estimates from the assimilation integrations is essentially identical to the corresponding open loop skill. Noah assimilation estimates of ground heat flux, however, can be significantly worse than open loop estimates. Provided the assimilation system is properly adapted to each land model, the benefits from the assimilation of LST retrievals are comparable for both models.
Nonhydrostatic Atmospheric Modeling Using a Combined Cartesian Grid
Authors: Yamazaki Hiroe , Satomura Takehiko 
Published: May 2010

Abstract
A new method for representing topography on a Cartesian grid is applied to a two-dimensional nonhydrostatic atmospheric model to achieve highly precise simulations over steep terrain. The shaved cell method based on finite-volume discretization is used along with a cell-combining approach in which small cut cells are combined with neighboring cells either vertically or horizontally. A unique staggered arrangement of variables enables quite simple computations of momentum equations by avoiding the evaluation of surface pressure and reducing the computational cost of combining cells for the velocity variables. The method successfully reproduces flows over a wide range of slopes, including steep slopes where significant errors are observed in a model using conventional terrain-following coordinates. The advantage of horizontal cell combination on extremely steep slopes is also demonstrated.
Single premedication dose of dexamethasone 20 mg IV before docetaxel administration
Authors: Chouhan Jyoti D , Herrington Jon D 
Published: May 2010

Background: The administration of docetaxel requires the use of dexamethasone for the prevention of hypersensitivity reactions (HSRs) and fluid retention reactions (FRRs). The manufacturer recommends dexamethasone for 3 days starting the day before docetaxel. This regimen has the potential for nonadherence so the utility of a single dexamethasone dose would be welcomed. Objective: To ascertain the incidence of HSRs and FRRs after receiving a single dose of intravenous dexamethasone before docetaxel administration. Design: Retrospective chart review. Setting: Data set from an oncology clinic affiliated with a large, tertiary, academic, teaching hospital. Patients: Ninety patients (median age 59 years, range 40—92 years) with cancer (primarily breast cancer, nonsmall cell lung cancer and head/neck cancer) who received docetaxel. Measurements and Results: Patients with heart failure, renal failure, chronic edema, current steroid use and/or prostate cancer were excluded from the study. Seven patients (7.8%) experienced a HSR requiring a treatment intervention (fluid bolus, oxygen, steroid, and/or diphenhydramine). Eleven patients (12.2%) had documented fluid retention. The mean docetaxel dose at the onset of fluid retention was 247.2 ± 134.5 mg/m2. Limitations: This single center evaluation with a small sample size had the potential for incomplete collection of the adverse events from the medical records due its retrospective nature. Conclusion: Hypersensitivity reactions and FRRs occurred in 7.8% and 12.2% of patients, respectively. This is lower than the rates reported by the manufacturer with the oral premedication regimen.
Differentiation of type 1 T regulatory cells (Tr1) by tolerogenic DC-10 requires the IL-10–dependent ILT4/HLA-G pathway
Authors: Gregori Silvia , Tomasoni Daniela , Pacciani Valentina , Scirpoli Miriam , Battaglia Manuela , Magnani Chiara Francesca , Hauben Ehud , Roncarolo Maria-Grazia 
Published: May 2010

AbstractType 1 T regulatory (Tr1) cells suppress immune responses in vivo and in vitro and play a key role in maintaining tolerance to self- and non–self-antigens. Interleukin-10 (IL-10) is the crucial driving factor for Tr1 cell differentiation, but the molecular mechanisms underlying this induction remain unknown. We identified and characterized a subset of IL-10–producing human dendritic cells (DCs), termed DC-10, which are present in vivo and can be induced in vitro in the presence of IL-10. DC-10 are CD14+, CD16+, CD11c+, CD11b+, HLA-DR+, CD83+, CD1a−, CD1c−, express the Ig-like transcripts (ILTs) ILT2, ILT3, ILT4, and HLA-G antigen, display high levels of CD40 and CD86, and up-regulate CD80 after differentiation in vitro. DC-10 isolated from peripheral blood or generated in vitro are potent inducers of antigen-specific IL-10–producing Tr1 cells. Induction of Tr1 cells by DC-10 is IL-10–dependent and requires the ILT4/HLA-G signaling pathway. Our data indicate that DC-10 represents a novel subset of tolerogenic DCs, which secrete high levels of IL-10, express ILT4 and HLA-G, and have the specific function to induce Tr1 cells.
High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations
Authors: Wu Yu-Chang , Kipling David , Leong Hui Sun , Martin Victoria , Ademokun Alexander A. , Dunn-Walters Deborah K. 
Published: May 2010

AbstractB-cell receptor (BCR) diversity is achieved centrally by rearrangement of Variable, Diversity, and Joining genes, and peripherally by somatic hypermutation and class-switching of the rearranged genes. Peripheral B-cell populations are subject to both negative and positive selection events in the course of their development that have the potential to shape the BCR repertoire. The origin of IgM+IgD+CD27+ (IgM memory) cells is controversial. It has been suggested that they may be a prediversified, antigen-independent, population of cells or that they are a population of cells that develop in response to T-independent antigens. Most recently, it was suggested that the majority of IgM memory cells are directly related to switched memory cells and are early emigrants from the germinal center reaction. Advances in sequencing technology have enabled us to undertake large scale IGH repertoire analysis of transitional, naive, IgM memory and switched memory B-cell populations. We find that the memory B-cell repertoires differ from the transitional and naive repertoires, and that the IgM memory repertoire is distinct from that of class-switched memory. Thus we conclude that a large proportion of IgM memory cells develop in response to different stimuli than for class-switched memory cell development.
Characterization of adipocyte differentiation from human mesenchymal stem cells in bone marrow
Authors: Qian Shu-Wen , Li Xi , Zhang You-You , Huang Hai-Yan , Liu Yuan , Sun Xia , Tang Qi-Qun 
Published: May 2010

Abstract

Background
Adipocyte hyperplasia is associated with obesity and arises due to adipogenic differentiation of resident multipotent stem cells in the vascular stroma of adipose tissue and remote stem cells of other organs. The mechanistic characterization of adipocyte differentiation has been researched in murine pre-adipocyte models (i.e. 3T3-L1 and 3T3-F442A), revealing that growth-arrest pre-adipocytes undergo mitotic clonal expansion and that regulation of the differentiation process relies on the sequential expression of three key transcription factors (C/EBPβ, C/EBPα and PPARγ). However, the mechanisms underlying adipocyte differentiation from multipotent stem cells, particularly human mesenchymal stem cells (hBMSCs), remain poorly understood. This study investigated cell cycle regulation and the roles of C/EBPβ, C/EBPα and PPARγ during adipocyte differentiation from hBMSCs.

Results
Utilising a BrdU incorporation assay and manual cell counting it was demonstrated that induction of adipocyte differentiation in culture resulted in 3T3-L1 pre-adipocytes but not hBMSCs undergoing mitotic clonal expansion. Knock-down and over-expression assays revealed that C/EBPβ, C/EBPα and PPARγ were required for adipocyte differentiation from hBMSCs. C/EBPβ and C/EBPα individually induced adipocyte differentiation in the presence of inducers; PPARγ alone initiated adipocyte differentiation but the cells failed to differentiate fully. Therefore, the roles of these transcription factors during human adipocyte differentiation are different from their respective roles in mouse.

Conclusions
The characteristics of hBMSCs during adipogenic differentiation are different from those of murine cells. These findings could be important in elucidating the mechanisms underlying human obesity further.
Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica
Authors: Cancela Martín , Ruétalo Natalia , Dell'Oca Nicolás , da Silva Edileuza , Smircich Pablo , Rinaldi Gabriel , Roche Leda , Carmona Carlos , Alvarez-Valín Fernando , Zaha Arnaldo , Tort José F 
Published: May 2010

AbstractBackgroundThe common liver flukeFasciola hepaticais the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies. Understanding the molecular mechanisms underlying the host-parasite interaction provide relevant clues in this search, while enlightening the physiological adaptations to parasitism. Genomics and transcriptomics are still in their infancy inF. hepatica, with very scarce information available from the invasive newly excysted juveniles (NEJ). Here we provide an initial glimpse to the transcriptomics of the NEJ, the first stage to interact with the mammalian host.ResultsWe catalogued more than 500 clusters generated from the analysis ofF. hepaticajuvenile expressed sequence tags (EST), several of them not detected in the adult stage. A set of putativeF. hepaticaspecific transcripts, and a group of sequences conserved exclusively in flatworms were identified. These novel sequences along with a set of parasite transcripts absent in the host genomes are putative new targets for future anti-parasitic drugs or vaccine development.Comparisons of theF. hepaticasequences with other metazoans genomes or EST databases were consistent with the basal positioning of flatworms in the bilaterian phylogeny. Notably, GC content, codon usage and amino acid frequencies are remarkably different in Schistosomes toF. hepaticaand other trematodes.Functional annotation of predicted proteins showed a general representation of diverse biological functions. Besides proteases and antioxidant enzymes expected to participate in the early interaction with the host, various proteins involved in gene expression, protein synthesis, cell signaling and mitochondrial enzymes were identified. Differential expression of secreted protease gene family members between juvenile and adult stages may respond to different needs during host colonization.ConclusionThe knowledge of the genes expressed by the invasive stage ofFasciola hepaticais a starting point to unravel key aspects of this parasite's biology. The integration of the emerging transcriptomics, and proteomics data and the advent of functional genomics tools in this organism are positioningF. hepaticaas an interesting model for trematode biology.
The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors
Authors: Yang Shihui , Pelletier Dale A , Lu Tse-Yuan S , Brown Steven D 
Published: May 2010

Abstract

Background

Zymomonas mobilis produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed Z. mobilis ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions.

Results
We generated a Z. mobilis hfq insertion mutant AcRIM0347 in an acetate tolerant strain (AcR) background and investigated its role in model lignocellulosic pretreatment inhibitors including acetate, vanillin, furfural and hydroxymethylfurfural (HMF). Saccharomyces cerevisiae Lsm protein (Hfq homologue) mutants and Lsm protein overexpression strains were also assayed for their inhibitor phenotypes. Our results indicated that all the pretreatment inhibitors tested in this study had a detrimental effect on both Z. mobilis and S. cerevisiae, and vanillin had the most inhibitory effect followed by furfural and then HMF for both Z. mobilis and S. cerevisiae. AcRIM0347 was more sensitive than the parental strain to the inhibitors and had an increased lag phase duration and/or slower growth depending upon the conditions. The hfq mutation in AcRIM0347 was complemented partially by trans-acting hfq gene expression. We also assayed growth phenotypes for S. cerevisiae Lsm protein mutant and overexpression phenotypes. Lsm1, 6, and 7 mutants showed reduced tolerance to acetate and other pretreatment inhibitors. S. cerevisiae Lsm protein overexpression strains showed increased acetate and HMF resistance as compared to the wild-type, while the overexpression strains showed greater inhibition under vanillin stress conditions.

Conclusions
We have shown the utility of the pKNOCK suicide plasmid for mutant construction in Z. mobilis, and constructed a Gateway compatible expression plasmid for use in Z. mobilis for the first time. We have also used genetics to show Z. mobilis Hfq and S. cerevisiae Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.
The Leishmania amazonensis TRF (TTAGGG repeat-binding factor) homologue binds and co-localizes with telomeres
Authors: da Silva Marcelo S , Perez Arina M , da Silveira Rita de Cássia V , de Moraes Camila E , Siqueira-Neto Jair L , Freitas-Junior Lucio H , Cano Maria Isabel N 
Published: May 2010

Abstract

Background
Telomeres are specialized structures at the end of chromosomes essential for maintaining genome stability and cell viability. The importance of telomeric proteins for telomere maintenance has increased our interest in the identification of homologues within the genus Leishmania. The mammalian TRF1 and TRF2 proteins, for example, bind double-stranded telomeres via a Myb-like DNA-binding domain and are involved with telomere length regulation and chromosome end protection. In addition, TRF2 can modulate the activity of several enzymes and influence the conformation of telomeric DNA. In this work, we identified and characterized a Leishmania protein (LaTRF) homologous to both mammalian TRF1 and TRF2.

Results
LaTRF was cloned using a PCR-based strategy. ClustalW and bl2seq sequence analysis showed that LaTRF shared sequence identity with the Trypanosoma brucei TRF (TbTRF) protein and had the same degree of sequence similarities with the dimerization (TRFH) and the canonical DNA-binding Myb-like domains of both mammalian TRFs. LaTRF was predicted to be an 82.5 kDa protein, indicating that it is double the size of the trypanosome TRF homologues. Western blot and indirect immunofluorescence combined with fluorescence in situ hybridization showed that LaTRF, similarly to hTRF2, is a nuclear protein that also associates with parasite telomeres. Native and full length LaTRF and a mutant bearing the putative Myb-like domain expressed in bacteria bound double-stranded telomeric DNA in vitro. Chromatin immunoprecipitation showed that LaTRF interacted specifically with telomeres in vivo.

Conclusion
The nuclear localization of LaTRF, its association and co-localization with parasite telomeres and its high identity with TbTRF protein, support the hypothesis that LaTRF is a Leishmania telomeric protein.
Dynamic models of pneumococcal carriage and the impact of the Heptavalent Pneumococcal Conjugate Vaccine on invasive pneumococcal disease
Authors: Melegaro Alessia , Choi Yoon Hong , George Robert , Edmunds W John , Miller Elizabeth , Gay Nigel J 
Published: May 2010

AbstractBackgroundThe 7-valent pneumococcal conjugate vaccine has been introduced in national immunisation programmes of most industrialised countries and recently in two African GAVI eligible countries (Rwanda and The Gambia). However the long term effects of PCV are still unclear, as beneficial direct and herd immunity effects might be countered by serotype replacement.MethodA dynamic, age-structured, compartmental model ofStreptococcus pneumoniaetransmission was developed to predict the potential impact of PCV7 on the incidence of invasive disease accounting for both herd immunity and serotype replacement effects. The model was parameterised using epidemiological data from England and Wales and pre and post-vaccination surveillance data from the US.ResultsModel projections showed that serotype replacement plays a crucial role in determining the overall effect of a PCV7 vaccination programme and could reduce, negate or outweigh its beneficial impact. However, using the estimate of the competition parameter derived from the US post-vaccination experience, an infant vaccination programme would prevent 39,000 IPD cases in the 20 years after PCV7 introduction in the UK. Adding a catch-up campaign for under 2 or under 5 year olds would provide a further reduction of 1,200 or 3,300 IPD cases respectively, mostly in the first few years of the programme.ConclusionsThis analysis suggests that a PCV vaccination programme would eradicate vaccine serotypes from circulation. However, the increase in carriage of non-vaccine serotypes, and the consequent increase in invasive disease, could reduce, negate or outweigh the benefit. These results are sensitive to changes in the protective effect of the vaccine, and, most importantly, to the level of competition between vaccine and non-vaccine types. The techniques developed here can be used to assess the introduction of vaccination programmes in developing countries and provide the basis for cost-effectiveness analyses.
Beneficial effect of aurothiomalate on murine malaria
Authors: Alesutan Ioana , Bobbala Diwakar , Qadri Syed M , Estremera Adriana , Föller Michael , Lang Florian 
Published: May 2010

Abstract

Background
Premature death of Plasmodium-infected erythrocytes is considered to favourably influence the clinical course of malaria. Aurothiomalate has previously been shown to trigger erythrocyte death or eryptosis, which is characterized by cell membrane scrambling leading to phosphatidylserine exposure at the cell surface. Phosphatidylserine-exposing cells are rapidly cleared from circulating blood. The present study thus tested whether sodium aurothiomalate influences the intraerythrocytic parasite development in vitro and the clinical course of murine malaria in vivo.

Methods
Human erythrocytes were infected with Plasmodium falciparum BinH in vitro and mice were infected (intraperitoneal injection of 1 × 106 parasitized murine erythrocytes) with Plasmodium berghei ANKA in vivo.

Results
Exposure to aurothiomalate significantly decreased the in vitro parasitemia of P. falciparum-infected human erythrocytes without influencing the intraerythrocytic DNA/RNA content. Administration of sodium aurothiomalate in vivo (daily 10 mg/kg b.w. s.c. from the 8th day of infection) enhanced the percentage of phosphatidylserine-exposing infected and noninfected erythrocytes in blood. All nontreated mice died within 30 days of infection. Aurothiomalate-treatment delayed the lethal course of malaria leading to survival of more than 50% of the mice 30 days after infection.

Conclusions
Sodium aurothiomalate influences the survival of Plasmodium berghei-infected mice, an effect only partially explained by stimulation of eryptosis.