bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Magnitude of Decadal and Multidecadal Variability in North American Precipitation*,+
Authors: Ault Toby R. , St. George Scott 
Published: September 2009

Abstract
The authors use singular spectrum analysis to investigate the relative magnitude of decadal to multidecadal (D2M) variability in annual and seasonal precipitation anomalies across North America. In most places, decadal (10–20 yr) or multidecadal (20–50 yr) variability makes up less than 10% of the total variance in either annual or seasonal precipitation, with interannual variability or secular trends having much greater importance. Decadal variability is most prominent (contributing 25%–30% of the total variance) in Minnesota and northern California during winter, and the central Rocky Mountains in autumn. Eastern Québec is the only major region where precipitation exhibits significant variance in the multidecadal band. Precipitation across much of Canada exhibits significant variance at extremely low frequencies (greater than 50 yr), but variability at these time scales cannot be separated from secular trends because of the limited length of instrumental climate records. Decadal signals in the discharge of the Sacramento River and, to a lesser degree, the Colorado River are coherent and in phase with similar signals in regional precipitation. Prominent D2M signals do not resemble the low-frequency components of major climate modes such as ENSO or the PDO, which suggests that this behavior is not a product of a simple linear translation of a single climate forcing.
Scale-Dependent Uncertainties in Global QPFs and QPEs from NWP Model and Satellite Fields
Authors: Lu C. , Yuan H. , Tollerud E. I. , Wang N. 
Published: September 2009

Abstract
Global precipitation forecasts from numerical weather prediction (NWP) models can be verified using the near-global coverage of satellite precipitation retrievals. However, inaccuracies in satellite precipitation analyses complicate the interpretation of forecast errors that result from verification of an NWP model against satellite observations. In this study, assessments of both a global quantitative precipitation estimate (QPE) from a satellite precipitation product and corresponding global quantitative precipitation forecast (QPF) from a global NWP model are conducted using available global land-based gauge data. A scale decomposition technique is devised, coupled with seasonal and spatial classifications, to evaluate these inaccuracies. The results are then analyzed in context with various physical precipitation systems, including heavy monsoonal rains, light Mediterranean winter rains, and North American convective-related and midlatitude cyclone–related precipitation.
In general, global model results tend to consistently overforecast rainfall, whereas satellite measurements present a mixed pattern, underestimating many large-scale precipitation systems while overestimating many convective-scale precipitation systems. Both global model QPF and satellite-retrieved QPE showed better correlation scores in large-scale precipitation systems when verified with gauge measurements. In this case, model-based QPF tends to outperform satellite-retrieved QPE. At convective scales, there are significant drops in both model QPF and satellite QPE correlation scores, but satellite QPE performs slightly better than model QPF. These general results also showed regional and seasonal variation. For example, in tropical monsoon systems, satellite QPE tended to outperform model-based QPF at both scales. Overall, the results suggest potential improvements for both satellite estimates and weather forecast systems, in particular as applied to global precipitation forecasts.
What Is the True Value of Forecasts?
Authors: Millner Antony 
Published: September 2009

Abstract
Understanding the economic value of weather and climate forecasts is of tremendous practical importance. Traditional models that have attempted to gauge forecast value have focused on a best-case scenario, in which forecast users are assumed to be statistically sophisticated, hyperrational decision makers with perfect knowledge and understanding of forecast performance. These models provide a normative benchmark for assessing forecast value, but say nothing about the value that actual forecast users realize. Real forecast users are subject to a variety of behavioral effects and informational constraints that violate the assumptions of normative models. In this paper, one of the normative assumptions about user behavior is relaxed—users are no longer assumed to be in possession of a perfect statistical understanding of forecast performance. In the case of a cost–loss decision, it is shown that a model of users’ forecast use choices based on the psychological theory of reinforcement learning leads to a behavioral adjustment factor that lowers the relative value score that the user achieves. The dependence of this factor on the user’s decision parameters (the ratio of costs to losses) and the forecast skill is deduced. Differences between the losses predicted by the behavioral and normative models are greatest for users with intermediate cost–loss ratios, and when forecasts have intermediate skill. The relevance of the model as a tool for directing user education initiatives is briefly discussed, and a direction for future research is proposed.
Characterizing environmental and phenotypic associations using information theory and electronic health records
Authors: Wang Xiaoyan , Hripcsak George , Friedman Carol 
Published: September 2009

Abstract

Background
The availability of up-to-date, executable, evidence-based medical knowledge is essential for many clinical applications, such as pharmacovigilance, but executable knowledge is costly to obtain and update. Automated acquisition of environmental and phenotypic associations in biomedical and clinical documents using text mining has showed some success. The usefulness of the association knowledge is limited, however, due to the fact that the specific relationships between clinical entities remain unknown. In particular, some associations are indirect relations due to interdependencies among the data.

Results
In this work, we develop methods using mutual information (MI) and its property, the data processing inequality (DPI), to help characterize associations that were generated based on use of natural language processing to encode clinical information in narrative patient records followed by statistical methods. Evaluation based on a random sample consisting of two drugs and two diseases indicates an overall precision of 81%.

Conclusion
This preliminary study demonstrates that the proposed method is effective for helping to characterize phenotypic and environmental associations obtained from clinical reports.
Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia
Authors: O'Grady Eoin P , Viteri Duber F , Malott Rebecca J , Sokol Pamela A 
Published: September 2009

Abstract

Background

Burkholderia cenocepacia belongs to a group of closely related organisms called the B. cepacia complex (Bcc) which are important opportunistic human pathogens. B. cenocepacia utilizes a mechanism of cell-cell communication called quorum sensing to control gene expression including genes involved in virulence. The B. cenocepacia quorum sensing network includes the CepIR and CciIR regulatory systems.

Results
Global gene expression profiles during growth in stationary phase were generated using microarrays of B. cenocepacia cepR, cciR and cepRcciIR mutants. This is the first time CciR was shown to be a global regulator of quorum sensing gene expression. CepR was primarily responsible for positive regulation of gene expression while CciR generally exerted negative gene regulation. Many of the genes that were regulated by both quorum sensing systems were reciprocally regulated by CepR and CciR. Microarray analysis of the cepRcciIR mutant suggested that CepR is positioned upstream of CciR in the quorum sensing hierarchy in B. cenocepacia. A comparison of CepIR-regulated genes identified in previous studies and in the current study showed a substantial amount of overlap validating the microarray approach. Several novel quorum sensing-controlled genes were confirmed using qRT-PCR or promoter::lux fusions. CepR and CciR inversely regulated flagellar-associated genes, the nematocidal protein AidA and a large gene cluster on Chromosome 3. CepR and CciR also regulated genes required for iron transport, synthesis of extracellular enzymes and surface appendages, resistance to oxidative stress, and phage-related genes.

Conclusion
For the first time, the influence of CciIR on global gene regulation in B. cenocepacia has been elucidated. Novel genes under the control of the CepIR and CciIR quorum sensing systems in B. cenocepacia have been identified. The two quorum sensing systems exert reciprocal regulation of many genes likely enabling fine-tuned control of quorum sensing gene expression in B. cenocepacia strains carrying the cenocepacia island.
Intestinal parasitic infections in relation to HIV/AIDS status, diarrhea and CD4 T-cell count
Authors: Assefa Shimelis , Erko Berhanu , Medhin Girmay , Assefa Zelalem , Shimelis Techalew 
Published: September 2009

Abstract

Background
HIV infection has been modifying both the epidemiology and outcome of parasitic infections. Hence, this study was undertaken to determine the prevalence of intestinal parasitic infection among people with and without HIV infection and its association with diarrhea and CD4 T-cell count.

Methods
A cross-sectional study was conducted at Hawassa Teaching and Referral Hospital focusing on HIV positive individuals, who gave blood for CD4 T-cell count at their first enrolment and clients tested HIV negative from November, 2008 to March, 2009. Data on socio-demographic factors and diarrhea status were obtained by interviewing 378 consecutive participants (214 HIV positive and 164 HIV negative). Stool samples were collected from all study subjects and examined for parasites using direct, formol-ether and modified acid fast stain techniques.

Results
The prevalence of any intestinal parasitic infection was significantly higher among HIV positive participants. Specifically, rate of infection with Cryptosporidium, I. belli, and S. stercoralis were higher, particularly in those with CD4 count less than 200 cells/μL. Diarrhea was more frequent also at the same lower CD4 T-cell counts.

Conclusion
Immunodeficiency increased the risk of having opportunistic parasites and diarrhea. Therefore; raising patient immune status and screening at least for those treatable parasites is important.
A combination of transposable elements and magnetic cell sorting provides a very efficient transgenesis system for chicken primary erythroid progenitors
Authors: Mejia-Pous Camila , Viñuelas José , Faure Claudine , Koszela Joanna , Kawakami Koichi , Takahashi Yoshiko , Gandrillon Olivier 
Published: September 2009

Abstract

Background
Stable transgenesis is an undeniable key to understanding any genetic system. Retrovirus-based insertional strategies, which feature several technical challenges when they are used, are often limited to one particular species, and even sometimes to a particular cell type as the infection depends on certain cellular receptors. A universal-like system, which would allow both stable transgene expression independent of the cell type and an efficient sorting of transfected cells, is required when handling cellular models that are incompatible with retroviral strategies.

Results
We report here on the combination of a stable insertional transgenesis technique, based on the Tol2 transposon system together with the magnetic cell sorting (MACS) technique, which allows specific selection of cells carrying the transgene in an efficient, reliable and rapid way.

Conclusion
This new Tol2/MACS system leads to stable expression in a culture of primary chicken erythroid cells highly enriched in cells expressing the transgene of interest. This system could be used in a wide variety of vertebrate species.
Proteome analysis of the Escherichia coli heat shock response under steady-state conditions
Authors: Lüders Svenja , Fallet Claas , Franco-Lara Ezequiel 
Published: September 2009

Abstract
In this study a proteomic approach was used to investigate the steady-state response of Escherichia coli to temperature up-shifts in a cascade of two continuously operated bioreactors. The first reactor served as cell source with optimal settings for microbial growth, while in the second chemostat the cells were exposed to elevated temperatures. By using this reactor configuration, which has not been reported to be used for the study of bacterial stress responses so far, it is possible to study temperature stress under well-defined, steady-state conditions. Specifically the effect on the cellular adaption to temperature stress using two-dimensional gel electrophoresis was examined and compared at the cultivation temperatures of 37°C and 47.5°C. As expected, the steady-state study with the double bioreactor configuration delivered a different protein spectrum compared to that obtained with standard batch experiments in shaking flasks and bioreactors. Setting a high cut-out spot-to-spot size ratio of 5, proteins involved in defence against oxygen stress, functional cell envelope proteins, chaperones and proteins involved in protein biosynthesis, the energy metabolism and the amino acid biosynthesis were found to be differently expressed at high cultivation temperatures. The results demonstrate the complexity of the stress response in a steady-state culture not reported elsewhere to date.
Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis
Authors: Fomekong-Nanfack Yves , Postma Marten , Kaandorp Jaap A 
Published: September 2009

Abstract

Background
Inverse modelling of gene regulatory networks (GRNs) capable of simulating continuous spatio-temporal biological processes requires accurate data and a good description of the system. If quantitative relations between genes cannot be extracted from direct measurements, an efficient method to estimate the unknown parameters is mandatory. A model that has been proposed to simulate spatio-temporal gene expression patterns is the connectionist model. This method describes the quantitative dynamics of a regulatory network in space. The model parameters are estimated by means of model-fitting algorithms. The gene interactions are identified without making any prior assumptions concerning the network connectivity. As a result, the inverse modelling might lead to multiple circuits showing the same quantitative behaviour and it is not possible to identify one optimal circuit. Consequently, it is important to address the quality of the circuits in terms of model robustness.

Results
Here we investigate the sensitivity and robustness of circuits obtained from reverse engineering a model capable of simulating measured gene expression patterns. As a case study we use the early gap gene segmentation mechanism in Drosophila melanogaster. We consider the limitations of the connectionist model used to describe GRN Inferred from spatio-temporal gene expression. We address the problem of circuit discrimination, where the selection criterion within the optimization technique is based of the least square minimization on the error between data and simulated results.

Conclusion
Parameter sensitivity analysis allows one to discriminate between circuits having significant parameter and qualitative differences but exhibiting the same quantitative pattern. Furthermore, we show that using a stochastic model derived from a deterministic solution, one can introduce fluctuations within the model to analyze the circuits' robustness. Ultimately, we show that there is a close relation between circuit sensitivity and robustness to fluctuation, and that circuit robustness is rather modular than global. The current study shows that reverse engineering of GRNs should not only focus on estimating parameters by minimizing the difference between observation and simulation but also on other model properties. Our study suggests that multi-objective optimization based on robustness and sensitivity analysis has to be considered.
Brazilian Network for HIV Drug Resistance Surveillance: a survey of individuals recently diagnosed with HIV
Authors: Inocencio Lilian A , Pereira Anderson A , Sucupira Maria Cecilia A , Fernandez José Carlos C , Jorge Célia P , Souza Denise FC , Fink Helena T , Diaz Ricardo S , Becker Irina M , Suffert Theodoro A , Arruda Monica B , Macedo Olinda , Simão Mariangela BG , Tanuri Amilcar 
Published: September 2009

Use of antiretrovirals is widespread in Brazil, where more than 200,000 individuals are under treatment. Although general prevalence of primary antiretroviral resistance in Brazil is low, systematic sampling in large metropolitan areas has not being performed.The HIV Threshold Survey methodology (HIV‐THS, WHO) was utilized, targeting Brazil's four major regions and selecting the six most populated state capitals: Sao Paulo, Rio de Janeiro, Salvador, Porto Alegre, Brasilia and Belem. We were able to sequence samples from 210 individuals with recent HIV diagnosis, 17 of them (8.1%) carrying HIV isolates with primary antiretroviral resistance mutations. Five, nine and four isolates showed mutations related to resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non‐nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs), respectively. Using HIV‐THS, we could find an intermediate level of transmitted resistance (5% to 15%) in Belem/Brasilia, Sao Paulo and Rio de Janeiro. Lower level of transmitted resistance (<5%) were observed in the other areas. Despite the extensive antiretroviral exposure and high rates of virologic antiretroviral failure in Brazil, the general prevalence of primary resistance is still low. However, an intermediate level of primary resistance was found in the four major Brazilian cities, confirming the critical need to start larger sampling surveys to better define the risk factors associated with transmission of resistant HIV.
Laboratory Investigation of Misaligned Dowel Behavior
Authors: Hoegh Kyle , Khazanovich Lev 
Published: September 2009

Abstract
Dowels are inserted at the mid-depth of joints in jointed concrete pavements that are exposed to heavy loading to provide load transfer and reduce pumping and faulting. Dowel alignment tolerances in North America have traditionally been strict, although not based on substantial performance data. In this paper, new laboratory testing methods are proposed for evaluation of the effects of dowel misalignment on concrete joint behavior. In these tests, dowels with various levels of rotations and translations were subjected to pullout and shear loading. It was found that dowel misalignment does not have a significant effect on pullout and shear forces for certain ranges of misalignments, which far exceed the tolerances recommended by the Federal Highway Administration. At the same time, it was found that extreme cases and combinations of misalignment resulted in a significant decrease in initial stiffness and shear capacity. Therefore, there is a need for the establishment of rational alignment tolerances. The results of this study provide important information for the development of such tolerances.
Hydrogen as a probe into 5f-magnetism
Authors: Mašková Silvie , Havela Ladislav , Šantavá Eva , Miliyanchuk Khrystyna 
Published: September 2009

Abstract
We performed magnetic measurements on the hydrogenated system (U, Th)CoSn as part of an investigation of UTX compounds (T – transitional metal, X – p-metal). The U1–x
ThxCoSn compounds crystallize in the hexagonal structure (ZrNiAl type, space group P 2m). Hydrogen absorption of approximately 1 H/f. u. could be achieved. The hydrogenation does not change the crystal structure. In all cases it leads to a unit-cell expansion by 3.0 % to 3.6 %. Studies of the temperature dependence of the magnetic susceptibility indicate a certain increase in the Curie temperature TC in the hydrides, but the Th concentration at which ferromagnetism vanishes remains practically unchanged (U0.2Th0.8CoSn has a paramagnetic ground state).
Magnetism in PrPdSn and NdPdSn studied on single crystals
Authors: Mihalik Matúš , Kitazawa Hideaki , Diviš Martin , Sechovský Vladimír 
Published: September 2009

Abstract
We present the results of specific heat, magnetization and susceptibility measurements performed on single crystals of PrPdSn and NdPdSn intermetallic compounds. Both compounds crystallize in the orthorhombic TiNiSi-type crystal structure and order antiferromagnetically at TN = 4.2(1) K (PrPdSn) and TN = 3.5(1) K (NdPdSn). NdPdSn also undergoes an order-to-order phase transition at T1 = 1.95(3) K. Both compounds exhibit high magnetocrystalline anisotropy at low temperatures and a complicated magnetic structure, which is underlined by the metamagnetic phase transitions of both compounds.
Magnetic properties of fcc Ni-based transition metal alloys
Authors: Kudrnovský Josef , Drchal Václav 
Published: September 2009

Abstract
Finite-temperature magnetism of Ni-based transition metal alloys with the face-centered cubic structure is studied theoretically in the framework of the first-principles approach. Calculated total and local magnetic moments agree well with experiment. The mean-field approximation, the random-phase approximation (RPA), as well as the renormalized RPA extended to random alloys are used to estimate the Curie temperature. The most satisfactory agreement with the experiment for a broad class of Ni-based alloys Ni (M = Cu, Fe, and Mn) over the whole concentration range isobtained by using the renormalized RPA approach.
Severe plastic deformation in Gum Metal with composition at the structural stability limit
Authors: Furuta Tadahiko , Hara Masashi , Horita Zenji , Kuramoto Shigeru 
Published: September 2009

Abstract
The effects of severe plastic deformation on the mechanical properties and deformation behavior of Gum Metal with a nominal composition of Ti-36Nb-2Ta-3Zr-0.3O (mass.%) were investigated using high-pressure torsion (HPT). Applying the HPT process, the alloy shows ultra-low Young's modulus, high strength, extended elastic limit, high ductility, and very low hardening during HPT. The tensile strength of Gum Metal increases with increasing equivalent strain, while work hardening is much smaller than reported values for other common metallic materials. The deformation structure is composed of ultrafine grains produced by transgranular shear through application of HPT. These results suggest that the strengthening mechanism of Gum Metal is attributable to a unique plastic deformation which operates in the region where the local stress reaches values close to that of ideal strength.