bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Efficient Algorithm for Computing Hypervolume Contributions
Authors: Bringmann Karl , Friedrich Tobias 
Published: June 2010

The hypervolume indicator serves as a sorting criterion in many recent multi-objective evolutionary algorithms (MOEAs). Typical algorithms remove the solution with the smallest loss with respect to the dominated hypervolume from the population. We present a new algorithm which determines for a population of size n with d objectives, a solution with minimal hypervolume contribution in time [Formula: see text](nd/2 log n) for d > 2. This improves all previously published algorithms by a factor of n for all d > 3 and by a factor of [Formula: see text] for d = 3. We also analyze hypervolume indicator based optimization algorithms which remove λ > 1 solutions from a population of size n = μ + λ. We show that there are populations such that the hypervolume contribution of iteratively chosen λ solutions is much larger than the hypervolume contribution of an optimal set of λ solutions. Selecting the optimal set of λ solutions implies calculating [Formula: see text] conventional hypervolume contributions, which is considered to be computationally too expensive. We present the first hypervolume algorithm which directly calculates the contribution of every set of λ solutions. This gives an additive term of [Formula: see text] in the runtime of the calculation instead of a multiplicative factor of [Formula: see text]. More precisely, for a population of size n with d objectives, our algorithm can calculate a set of λ solutions with minimal hypervolume contribution in time [Formula: see text](nd/2 log n + nλ) for d > 2. This improves all previously published algorithms by a factor of nmin{λ,d/2} for d > 3 and by a factor of n for d = 3.
Rhetoric and Ideology in Egypt’s Wasaiyya Movement
Authors: Høigilt Jacob 
Published: June 2010

AbstractIslamic centrism (Wasaiyya) is commonly presented as an open-minded and dialogue-oriented form of Islamism. This article questions that view by analyzing texts written by two prominent centrists: Muammad ‘Ammāra and Fahmī Huwaydī. Focusing on rhetorical techniques, the article argues that their texts are characterized by aggressive polemics not conducive to pluralist public debate. While relying heavily on barrages of rhetorical questions and implicit arguments, they avoid serious discussion of difficult issues. These characteristics of their texts are brought out by a discourse analysis based on modern text linguistics, specifically Functional Grammar as developed by Michael Halliday. This approach to Islamism is new and helps explaining why centrism, despite its professed open-mindedness, has failed both to defuse the high ideological tension in contemporary Egyptian debates about Islam in society and to contribute to bringing those debates forward.
Features of Annexion Strings in Colloquial and Literary Arabic and Hebrew
Authors: Rosenhouse Judith 
Published: June 2010

AbstractArabic annexion is a basic and frequent nominal (phrase) structure which can be important not only in itself but also for translation and automatic text generation applications. The structure is expanded by concatenating to it more nouns, thus forming annexion strings. We examine here whether in colloquial and Modern Literary Arabic similar limitations exist, whether there are differences between them. Limitations and constraints on the number of words that can be connected in an annexion string were investigated for another Semitic language, Hebrew (Rosenhouse, “On the use”, “Construct”, and here). This study compares also Hebrew and Arabic annexion strings from the point of view of their length limitations. The article is based on literary Arabic as used in newspapers and books and on transcribed texts of colloquial Arabic. Some Hebrew journalese and spoken texts have also been examined for comparison. Our findings suggest positive answers to our questions.
Le lieu de la parole dans Awlād āritnā
Authors: Sleiman Rima 
Published: June 2010

AbstractMoment de rupture dans l’oeuvre réaliste de Nağīb Mafū, Awlād āritnā, ce roman dit « symboliste », fut précédé de cinq années de silence. Il est à l’origine de ce récit, une crise de la parole qui devient le sujet même de l’écriture. Mafū semble moins y interroger le sens des textes religieux que les regarder comme l’unique trace qui subsiste après la disparition du lieu original d’où la parole a jadis surgi. Cet article analyse les modalités d’exposition de cette quête du lieu de la parole dans Awlād āritnā. Deux conversions majeures sont opérées par Mafū pour retracer ce surgissement: d’une part, le lieu unique est converti en une pluralité d’espaces, de l’autre, la parole originelle bifurquée en discours infinis. À mesure que le référent se retire, le vide ontologique se creuse et la prolifération des discours fait écran au lieu de cette présence originelle. Mais la nostalgie du silence fondateur alimente le mythe du retour. Or, seule la représentation, une « mimésis du discours », permet de recouvrer la présence première. Cette reconversion ultime passe par les techniques de l’écriture narrative, d’une mimésis pensant désormais le spirituel, d’une métaphysique coïncidant avec le poétique.
Quasigeostrophic Dynamics of a Finite-Thickness Tropopause
Authors: Plougonven R. , Vanneste J. 
Published: June 2010

Abstract
A model of tropopause dynamics is derived that is of intermediate complexity between the three-dimensional quasigeostrophic model and the surface quasigeostrophic (SQG) model. The model assumes that a sharp transition in stratification occurs over a small but finite tropopause region separating regions of uniform potential vorticity (PV). The model is derived using a matched-asymptotics technique, with the ratio of the thickness of the tropopause region to the typical vertical scale of perturbations outside as a small parameter. It reduces to SQG to leading order in this parameter but takes into account the next-order correction. As a result it remains three-dimensional, although with a PV inversion relation that is greatly simplified compared to the Laplacian inversion of quasigeostrophic theory.
The model is applied to examine the linear dynamics of perturbations at the tropopause. Edge waves, described in the SQG approximation, are recovered, and explicit expressions are obtained for the corrections to their frequency and structure that result from the finiteness of the tropopause region. The sensitivity of these corrections to the stratification and shear profiles across the tropopause is investigated. In addition, the evolution of perturbations with near-zero vertically integrated PV is discussed. These perturbations, which are filtered out by the SQG approximation, are represented by a continuous spectrum of singular modes and evolve as sheared disturbances. The decomposition of arbitrary perturbations into edge-wave and continuous-spectrum contributions is discussed.
An Example Crossover Experiment for Testing New Vicarious Calibration Techniques for Satellite Ocean Color Radiometry
Authors: Voss Kenneth J. , McLean Scott , Lewis Marlon , Johnson Carol , Flora Stephanie , Feinholz Michael , Yarbrough Mark , Trees Charles , Twardowski Mike , Clark Dennis 
Published: June 2010

Abstract
Vicarious calibration of ocean color satellites involves the use of accurate surface measurements of water-leaving radiance to update and improve the system calibration of ocean color satellite sensors. An experiment was performed to compare a free-fall technique with the established Marine Optical Buoy (MOBY) measurement. It was found in the laboratory that the radiance and irradiance instruments compared well within their estimated uncertainties for various spectral sources. The spectrally averaged differences between the National Institute of Standards and Technology (NIST) values for the sources and the instruments were &lt;2.5% for the radiance sensors and &lt;1.5% for the irradiance sensors. In the field, the sensors measuring the above-surface downwelling irradiance performed nearly as well as they had in the laboratory, with an average difference of &lt;2%. While the water-leaving radiance Lw calculated from each instrument agreed in almost all cases within the combined instrument uncertainties (approximately 7%), there was a relative bias between the two instrument classes/techniques that varied spectrally. The spectrally averaged (400–600 nm) difference between the two instrument classes/techniques was 3.1%. However, the spectral variation resulted in the free-fall instruments being 0.2% lower at 450 nm and 5.9% higher at 550 nm. Based on the analysis of one matchup, the bias in Lw was similar to that observed for Lu(1 m) with both systems, indicating the difference did not come from propagating Lu(1 m) to Lw.
Calibration and Downscaling Methods for Quantitative Ensemble Precipitation Forecasts
Authors: Voisin Nathalie , Schaake John C. , Lettenmaier Dennis P. 
Published: June 2010

Abstract
Two approaches for downscaling and calibrating error estimates from ensemble precipitation forecasts are evaluated; the two methods are intended to be used to produce flood forecasts based on global weather forecasts in ungauged river basins. The focus of this study is on the ability of the approaches to reproduce observed forecast errors when applied to daily precipitation forecasts from the European Centre for Medium-Range Weather Forecasts (ECMWF) Ensemble Prediction System (EPS) for a 10-day forecast period. The two approaches are bias correction with spatial disaggregation (BCSD) and an analog technique. Mean forecast errors and skills are evaluated with respect to Tropical Rainfall Monitoring Mission (TRMM) observations over the Ohio River basin for the period 2002–06 for daily and 5-day accumulations and for 0.25° and 1° spatial resolutions. The Ohio River basin was chosen so that a relatively dense gauge-based observed precipitation dataset could also be used in the evaluation of the two approaches. Neither the BCSD nor the analog approach is able to improve on the forecast prediction skill resulting from a simple spatial interpolation benchmark. However, both approaches improve the forecast reliability, although more so for the analog approach. The BCSD method improves the bias for all forecast amounts (but less so for large amounts), but the downscaled precipitation patterns are unrealistic. The analog approach reduces biases over a wider range of forecast amounts, and the precipitation patterns are more realistic.
Bone density, balance and quality of life of postmenopausal women taking alendronate participating in different physical activity programs
Authors: Borba-Pinheiro Cláudio Joaquim , de Alencar Carvalho Mauro César Gurgel , Lima da Silva Nádia Souza , Janotta Drigo Alexandre , Pereira Bezerra Jani Cléria , Dantas Estélio Henrique Martin 
Published: June 2010

Background: The objective of this study was to determine the effects of different physical activity (PA) programs on bone density, balance and quality of life of postmenopausal women taking concomitant alendronate. A quasi-experimental study was conducted with 35 volunteers divided into four groups: practitioners of resistance training (RTG, n = 9, 49.8±4.2 years), judo (JUG, n = 11, 52.2±5.3 years), water aerobics (WAG, n = 8, 57.1±7.4 years) and the control group (CG, n = 7, 53.8±4.4 years). Methods: The following assessment tools were used: bone mineral density (BMD) measured by dual X-ray absorptiometry of the spine and proximal femur, the ‘Osteoporosis Assessment Questionnaire’ (OPAQ) and the ‘Static Balance Test with Visual Control’. The physical activities were planned for 12 months in cycles with different intensities. A two-way analysis of variance (ANOVA) was used for analysis between groups, and a Scheffé post-hoc test was used for multiple comparisons. Results: The multiple comparisons results showed that the RTG and JUG groups were significantly more efficient in the variables studied, including: lumbar BMD (Δ% = 6.8%, p = 0.001), balance (Δ% = 21.4%, p = 0.01), OPAQ (Δ% = 9.1%, p = 0.005) and lumbar BMD (Δ% = 6.4%, p = 0.003), balance (Δ% = 14%, p = 0.02) and OPAQ (Δ% = 16.8%, p = 0.000) compared with the CG. Furthermore, the RTG (Δ% = 4.8%, p = 0.02) was significantly better than the WAG for the neck of femur BMD, and the JUG (Δ% = 16.8, p = 0.0003) also demonstrated superiority to the WAG in the OPAQ. Conclusions: The physical activities studied appear to improve BMD, balance and quality of life of postmenopausal women taking a bisphosphonate. In this small sample, the RTG and the JUG groups were superior to the other groups.
The cell polarity PTK7 receptor acts as a modulator of the chemotherapeutic response in acute myeloid leukemia and impairs clinical outcome
Authors: Prebet Thomas , Lhoumeau Anne-Catherine , Arnoulet Christine , Aulas Anaïs , Marchetto Sylvie , Audebert Stéphane , Puppo Francesca , Chabannon Christian , Sainty Danielle , Santoni Marie-Josée , Sebbagh Michael , Summerour Virginia , Huon Yannick , Shin Won-Sik , Lee Seung-Taek , Esterni Benjamin , Vey Norbert , Borg Jean-Paul 
Published: June 2010

Abstract
The pseudo tyrosine kinase receptor 7 (PTK7) is an orphan tyrosine kinase receptor assigned to the planar cell polarity pathway. It plays a major role during embryogenesis and epithelial tissue organization. Here we found that PTK7 is also expressed in normal myeloid progenitors and CD34+ CD38− bone marrow cells in humans. We performed an immunophenotyping screen on more than 300 patients treated for hematologic malignancies. We demonstrated that PTK7 is expressed in acute myeloid leukemia (AML) and is mostly assigned to granulocytic lineage differentiation. Patients with PTK7-positive AML are more resistant to anthracycline-based frontline therapy with a significantly reduced leukemia-free survival in a multivariate analysis model. In vitro, expression of PTK7 in cultured leukemia cells promotes cell migration, cell survival, and resistance to anthracycline-induced apoptosis. The intracellular region of PTK7 is required for these effects. Furthermore, we efficiently sensitized primary AML blasts to anthracycline-mediated cell death using a recombinant soluble PTK7-Fc protein. We conclude that PTK7 is a planar cell polarity component expressed in the myeloid progenitor compartment that conveys promigratory and antiapoptotic signals into the cell and that represents an independent prognosis factor of survival in patients treated with induction chemotherapy.
AMPK α2 subunit is involved in platelet signaling, clot retraction, and thrombus stability
Authors: Randriamboavonjy Voahanginirina , Isaak Johann , Frömel Timo , Viollet Benoit , Fisslthaler Beate , Preissner Klaus T. , Fleming Ingrid 
Published: June 2010

Abstract
The adenosine monophosphate (AMP)–activated protein kinase (AMPK) is a regulator of energy balance at the cellular and whole-body levels, but little is known about the role of AMPK in platelet activation. We report that both the α1 and α2 AMPK isoforms are expressed by human and murine platelets and that thrombin elicits the phosphorylation of AMPKα as well as the upstream kinase, liver kinase B1 (LKB1). In human platelets, the kinase inhibitors iodotubercidin and compound C significantly inhibited thrombin-induced platelet aggregation and clot retraction without affecting the initial increase in [Ca2+]i. Clot retraction was also impaired in platelets from AMPKα2−/− mice but not from wild-type littermates or AMPKα1−/− mice. Moreover, rebleeding was more frequent in AMPKα2−/− mice, and the FeCl3-induced thrombi formed in AMPKα2−/− mice were unstable. Mechanistically, AMPKα2 was found to phosphorylate in vitro the Src-family kinase, Fyn, and isoform deletion resulted in the attenuated threonine phosphorylation of Fyn as well as the subsequent tyrosine phosphorylation of its substrate, β3 integrin. These data indicate that AMPKα2—by affecting Fyn phosphorylation and activity—plays a key role in platelet αIIbβ3 integrin signaling, leading to clot retraction and thrombus stability.
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking
Authors: Chou Chun-Chi , Rajasekaran M , Chen Chinpan 
Published: June 2010

Abstract

Background
Determination of protein-DNA complex structures with both NMR and X-ray crystallography remains challenging in many cases. High Ambiguity-Driven DOCKing (HADDOCK) is an information-driven docking program that has been used to successfully model many protein-DNA complexes. However, a protein-DNA complex model whereby the protein wraps around DNA has not been reported. Defining the ambiguous interaction restraints for the classical three-Cys2His2 zinc-finger proteins that wrap around DNA is critical because of the complicated binding geometry. In this study, we generated a Zif268-DNA complex model using three different sets of ambiguous interaction restraints (AIRs) to study the effect of the geometric distribution on the docking and used this approach to generate a newly reported Sp1-DNA complex model.

Results
The complex models we generated on the basis of two AIRs with a good geometric distribution in each domain are reasonable in terms of the number of models with wrap-around conformation, interface root mean square deviation, AIR energy and fraction native contacts. We derived the modeling approach for generating a three-Cys2His2 zinc-finger-DNA complex model according to the results of docking studies using the Zif268-DNA and other three crystal complex structures. Furthermore, the Sp1-DNA complex model was calculated with this approach, and the interactions between Sp1 and DNA are in good agreement with those previously reported.

Conclusions
Our docking data demonstrate that two AIRs with a reasonable geometric distribution in each of the three-Cys2His2 zinc-finger domains are sufficient to generate an accurate complex model with protein wrapping around DNA. This approach is efficient for generating a zinc-finger protein-DNA complex model for unknown complex structures in which the protein wraps around DNA. We provide a flowchart showing the detailed procedures of this approach.
Identification of scaffold/Matrix Attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia
Authors: Padmaja Sushma S , Lakshmanan Jagannathan , Gupta Ravi , Banerjee Santanu , Gautam Pennathur , Banerjee Sulagna 
Published: June 2010

Abstract

Background
Chromatin in the nucleus of all eukaryotes is organized into a system of loops and domains. These loops remain fastened at their bases to the fundamental framework of the nucleus, the matrix or the scaffold. The DNA sequences which anchor the bases of the chromatin loops to the matrix are known as Scaffold/Matrix Attachment Regions or S/MARs. Though S/MARs have been studied in yeast and higher eukaryotes and they have been found to be associated with gene organization and regulation of gene expression, they have not been reported in protists like Giardia. Several tools have been discovered and formulated to predict S/MARs from a genome of a higher eukaryote which take into account a number of features. However, the lack of a definitive consensus sequence in S/MARs and the randomness of the protozoan genome in general, make it a challenge to predict and identify such sequences from protists.

Results
Here, we have analysed the Giardia genome for the probable S/MARs predicted by the available computational tools; and then shown these sequences to be physically associated with the nuclear matrix. Our study also reflects that while no single computational tool is competent to predict such complex elements from protist genomes, a combination of tools followed by experimental verification is the only way to confirm the presence of these elements from these organisms.

Conclusion
This is the first report of S/MAR elements from the protozoan parasite Giardia lamblia. This initial work is expected to lay a framework for future studies relating to genome organization as well as gene regulatory elements in this parasite.
Gastric cancer is associated with NOS2-954G/C polymorphism and environmental factors in a Brazilian population
Authors: Jorge Yvana C , Duarte Marcia C , Silva Ana E 
Published: June 2010

AbstractBackgroundGastric cancer can progress from a chronic inflammation of the gastric mucosa resulting fromHelicobacter pyloriinfection that activates the inflammatory response of the host. Therefore, polymorphisms in genes involved in the inflammatory response, such as inducible nitric oxide synthase (NOS2), have been implicated in gastric carcinogenesis. The aim of this study was to evaluate the association ofNOS2polymorphisms Ser608Leu (rs2297518) in exon 16, -954G/C and -1173C/T, both in the promoter region, with gastric cancer and chronic gastritis and the association of cancer with risk factors such as smoking, alcohol intake andH. pyloriinfection.MethodsWe conducted a population-based case-control study in 474 Southeast Brazilian individuals (150 with gastric cancer, 160 with chronic gastritis, and 164 healthy individuals), in which we performedNOS2genotyping by PCR-RFLP.ResultsSNP Ser608Leu was not associated with risk of chronic gastritis or gastric cancer. The polymorphic allele -1173T was not found in the studied population. However, the frequency of -954GC+CC genotypes was significantly higher (p < 0.01) in the cancer group (48.7%) than in both the gastritis (28.1%) and the control (29.9%) groups. Multivariate logistic regression showed that theNOS2SNP -954G/C was associated with higher risk of gastric cancer (OR = 1.87; 95% CI = 1.12-3.13). We also observed an association with risk factors such as smoking and alcohol intake in both the gastric cancer (OR = 2.68; 95% CI = 1.58-4.53; OR = 3.60; 95% CI = 2.05-6.32, respectively) and the chronic gastritis (OR = 1.93; 95% CI = 1.19-3.13; OR = 2.79; 95% CI = 1.55-5.02, respectively) groups. This is the first report of increased risk of gastric cancer in association with the -954G/C polymorphism. These findings show that several polymorphisms in the promoter region of theNOS2gene may contribute to the susceptibility to gastric cancer.ConclusionsPolymorphismNOS2-954 G/C, along with alcohol intake and tobacco smoking, is associated with gastric cancer. However, theNOS2Ser608Leu polymorphism was not associated with gastric carcinogenesis. TheNOS2-1173C/T polymorphism was absent in the studied population.
Long persistence of EV71 specific nucleotides in respiratory and feces samples of the patients with Hand-Foot-Mouth Disease after recovery
Authors: Han Jun , Ma Xue-Jun , Wan Jun-Feng , Liu Ying-Hui , Han Yan-Ling , Chen Cao , Tian Chan , Gao Chen , Wang Miao , Dong Xiao-Ping 
Published: June 2010

Abstract

Background
EV71 is associated with the fatal cases of brain stem encephalitis during large HFMD outbreaks from 1998 to 2008. EV71 may continuously shed from upper respiratory tracts and feces of HFMD patients for relatively long time after recovery. However, the persistence of viruses in the patients' secretions and excretions is not clear.

Methods
Serial throat swabs and feces of 34 definitely diagnosed patients, including 30 mild cases and 4 severe cases, were traced and collected with the interval of 2 to 4 days for up to 32 and 48 days, respectively, and tested by a nested RT-PCR.

Results
The EV-71 specific sequences were identified by a Nested RT-PCR in all specimens of 0-4 days, and 5-8 days. The positive rates of EV71 in throat swabs dropped markedly to 42.86% during 9-12 days, and maintained at 20-30% during 13-24 days, while that in feces reduced to 71.43% during 9-12 days, and maintained roughly 20% till 37-40 days. EV71 nucleotide of 36.36% cases disappeared simultaneously both in throats and feces, 39.39% cases showed longer persistence of EV71 nucleotides in feces, and 21.21% were longer in throats. The longest duration of shedding observed was 24 days for throat swabs and 42 days for fecal specimens.

Conclusions
EV71 shedding from respiratory tract may continue for nearly four weeks after onset, but its excretion through feces can persist more than five weeks.