bluuebunny/crossref_metadata_2025_split huggingface dataset:
Momentum Fluxes of Gravity Waves Generated by Variable Froude Number Flow over Three-Dimensional Obstacles
Authors: Eckermann Stephen D. , Lindeman John , Broutman Dave , Ma Jun , Boybeyi Zafer 
Published: March 2010

Abstract
Fully nonlinear mesoscale model simulations are used to investigate the momentum fluxes of gravity waves that emerge at a “far-field” height of 6 km from steady unsheared flow over both an axisymmetric and elliptical obstacle for nondimensional mountain heights ĥm = Fr−1 in the range 0.1–5, where Fr is the surface Froude number. Fourier- and Hilbert-transform diagnostics of model output yield local estimates of phase-averaged momentum flux, while area integrals of momentum flux quantify the amount of surface pressure drag that translates into far-field gravity waves, referred to here as the “wave drag” component. Estimates of surface and wave drag are compared to parameterization predictions and theory. Surface dynamics transition from linear to high-drag (wave breaking) states at critical inverse Froude numbers Frc−1 predicted to within 10% by transform relations. Wave drag peaks at Frc−1 &lt; ĥm ≲ 2, where for the elliptical obstacle both surface and wave drag vacillate owing to cyclical buildup and breakdown of waves. For the axisymmetric obstacle, this occurs only at ĥm = 1.2. At ĥm ≳ 2–3 vacillation abates and normalized pressure drag assumes a common normalized form for both obstacles that varies approximately as ĥm−1.3. Wave drag in this range asymptotes to a constant absolute value that, despite its theoretical shortcomings, is predicted to within 10%–40% by an analytical relation based on linear clipped-obstacle drag for a Sheppard-based prediction of dividing streamline height. Constant wave drag at ĥm ∼ 2–5 arises despite large variations with ĥm in the three-dimensional morphology of the local wave momentum fluxes. Specific implications of these results for the parameterization of subgrid-scale orographic drag in global climate and weather models are discussed.
Chaotic Behaviors in the Response of a Quasigeostrophic Oceanic Double Gyre to Seasonal External Forcing
Authors: Shimokawa Shinya , Matsuura Tomonori 
Published: March 2010

Abstract
In an oceanic double-gyre system, nonlinear oscillations of the ocean under seasonally changing external forcing are investigated using a 1.5-layer quasigeostrophic model and a simple model related to energy balance of the oceanic double gyre. In the experiments, the variable parameter is the amplitude of external seasonal forcing and the Reynolds number is fixed as 39, at which periodic shedding of inertial subgyres occurs. The authors found that entrainment (at 2 times the period of the forcing) and intermittency (on–off type), phenomena that are often seen in nonlinear systems, emerge with increasing amplitude of the forcing. They seem to be related to the generation mechanism and characteristics of long-term (from interannual to decadal) variations in the strong current region of subtropical gyres such as the Kuroshio and its extension region.
Analyzing the Image Warp Forecast Verification Method on Precipitation Fields from the ICP
Authors: Gilleland Eric , Lindström Johan , Lindgren Finn 
Published: March 2010

Abstract
Image warping for spatial forecast verification is applied to the test cases employed by the Spatial Forecast Verification Intercomparison Project (ICP), which includes both real and contrived cases. A larger set of cases is also used to investigate aggregating results for summarizing forecast performance over a long record of forecasts. The technique handles the geometric and perturbed cases with nearly exact precision, as would be expected. A statistic, dubbed here the IWS for image warp statistic, is proposed for ranking multiple forecasts and tested on the perturbed cases. IWS rankings for perturbed and real test cases are found to be sensible and physically interpretable. A powerful result of this study is that the image warp can be employed using a relatively sparse, preset regular grid without having to first identify features.
Stress Fractures of the Metacarpal Bones in Adolescent Tennis Players
Authors: Balius Ramon , Pedret Carles , Estruch Assun , Hernández Gemma , Ruiz-Cotorro Ángel , Mota Javier 
Published: March 2010

Background: There are 12 reported cases of metacarpal stress fractures in athletes, with only 4 of them involving the second metacarpal. Purpose: The authors describe stress fracture of the second metacarpal bone in teenaged tennis players and the relationship with sport intensity and type of grip used. They also demonstrate that magnetic resonance imaging is the diagnostic study of choice to differentiate this entity from the most common cause of pain in this region of the hand in tennis players—the carpal boss. Study Design: Case series; Level of evidence, 4. Methods: Seven adolescent tennis players (mean age, 16.5 years; 6 female, 1 male) with dorsal hand pain produced by playing tennis were examined by radiographs and initial magnetic resonance imaging. In 2 cases, bone scintigraphy was performed. In the first 2 cases, the presumptive diagnosis was a carpal boss, but with this experience, the diagnostic evaluation of the last 5 cases was oriented toward a stress reaction at this level. Radiologic follow-up was performed. The authors also evaluated the grip type used by each tennis player. Results: Clinical evaluation and imaging studies resulted in a diagnosis of stress injury of the second metatarsal in 6 of 7 cases, with the seventh case involving the third metacarpal. Initial imaging was positive in 3 cases, revealing an increased signal in the marrow without hairline crack and cortical thickening of the shaft or simply an increased signal in the marrow. In all cases, there was a history of recent increase in the sport training load. Six of the 7 tennis players were using a semi-Western or Western grip. Conclusion: Stress fractures of the second metacarpal are characteristic of adolescent tennis players and are associated with an increased intensity of tennis play and may be associated with use of the semi-Western or Western grip. Magnetic resonance imaging is the most useful tool for obtaining a definitive diagnosis.
‘Love it. Buy it. Sell it’
Authors: Denegri-Knott Janice , Molesworth Mike 
Published: March 2010

Our work adds to existing research on eBay by presenting it as a space where consumers’ imaginations are stimulated and where their psychological work to manufacture ever new wants and desires allows for a reflection of consumer tastes and practices. To do so, we conceptualize eBay as a digital virtual space that allows consumers to browse at length through a plethora of goods, test preferences and potentially reflect on the significance of objects and daydreams pursued. Conceptually, we draw a synthesis between desire and imagination-laden narratives within consumer research with Rob Shield’s analytic of the digital virtual and its relationship to the real and ideal. From that reading we attribute eBay with a liminoid texture that helps us account for the social dramas that some of its users, such as famed science fiction writer William Gibson, may experience. We argue that whilst eBay does not provoke the initial breach, its enormous, global, ever changing catalogue of goods, produces a crisis that invites the user to engage in redressive action. That analysis has two moments, one focusing on the eBay experience as a form of flânerie, and then, how visual and written information gathered from searching eBay can be used to craft daydreams relative to a desired good. Specifically, we consider concrete consumer practices through which consumers feed and actualize more substantive daydreams of an improved life, including bookmarking, bidding and winning (owning) desired items. We conclude that eBay’s significance as a seductive site to consume (in) lies in its ability to allow for the continuous construction of latent wants while providing consumers with the tools to react to these wants in various ways.
FOXO3A as a key molecule for all-trans retinoic acid–induced granulocytic differentiation and apoptosis in acute promyelocytic leukemia
Authors: Sakoe Yasuhiko , Sakoe Kumi , Kirito Keita , Ozawa Keiya , Komatsu Norio 
Published: March 2010

Abstract
All-trans retinoic acid (ATRA) induces granulocytic differentiation and apoptosis in acute promyelocytic leukemia (APL) cells, although the detailed mechanisms are not fully understood. We investigated ATRA-induced cellular responses mediated by the transcription factor FOXO3A in APL cells. FOXO3A was constitutively phosphorylated and localized in the cytoplasm in both APL-derived NB4 cells and primary APL cells. Upon treating the cells with ATRA, FOXO3A phosphorylation was reduced and FOXO3A translocated into the nucleus. In addition, the expression of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL), a target molecule for FOXO3A, was increased at the transcriptional and protein levels. As expected, transfection of a short hairpin RNA (shRNA) oligonucleotide specific for FOXO3A significantly inhibited ATRA-induced granulocytic differentiation and apoptosis in NB4 cells. In NB4-derived ATRA-resistant NB4/RA cells, neither FOXO3A nuclear localization nor subsequent TRAIL induction was observed after ATRA treatment. Furthermore, forced expression of active FOXO3A in the nucleus induced TRAIL production and apoptosis in NB4/RA cells. We conclude that activation of FOXO3A is an essential event for ATRA-induced cellular responses in NB4 cells. FOXO3A is a promising target for therapeutic approaches to overcome ATRA resistance in APL.
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants
Authors: Li Yunqi , Middaugh C Russell , Fang Jianwen 
Published: March 2010

Abstract

Background
The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to estimate the relative thermostability of possible mutants.

Results
We report a novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting the relative thermostability of protein mutants. The scoring function was developed based on an elaborate analysis of a set of features calculated or predicted from 540 pairs of hyperthermophilic and mesophilic protein ortholog sequences. It was constructed by a linear combination of ten important features identified by a feature ranking procedure based on the random forest classification algorithm. The weights of these features in the scoring function were fitted by a hill-climbing algorithm. This scoring function has shown an excellent ability to discriminate hyperthermophilic from mesophilic sequences. The prediction accuracies reached 98.9% and 97.3% in discriminating orthologous pairs in training and the holdout testing datasets, respectively. Moreover, the scoring function can distinguish non-homologous sequences with an accuracy of 88.4%. Additional blind tests using two datasets of experimentally investigated mutations demonstrated that the scoring function can be used to predict the relative thermostability of proteins and their mutants at very high accuracies (92.9% and 94.4%). We also developed an amino acid substitution preference matrix between mesophilic and hyperthermophilic proteins, which may be useful in designing more thermostable proteins.

Conclusions
We have presented a novel scoring function which can distinguish not only HP/MP ortholog pairs, but also non-homologous pairs at high accuracies. Most importantly, it can be used to accurately predict the relative stability of proteins and their mutants, as demonstrated in two blind tests. In addition, the residue substitution preference matrix assembled in this study may reflect the thermal adaptation induced substitution biases. A web server implementing the scoring function and the dataset used in this study are freely available at http://www.abl.ku.edu/thermorank/.
Role of casein kinase 1 in the glucose sensor-mediated signaling pathway in yeast
Authors: Pasula Satish , Chakraborty Samujjwal , Choi Jae H , Kim Jeong-Ho 
Published: March 2010

Abstract

Background
In yeast, glucose-dependent degradation of the Mth1 protein, a corepressor of the glucose transporter gene (HXT) repressor Rgt1, is a crucial event enabling expression of several HXT. This event occurs through a signaling pathway that involves the Rgt2 and Snf3 glucose sensors and yeast casein kinase 1 and 2 (Yck1/2). In this study, we examined whether the glucose sensors directly couple with Yck1/2 to convert glucose binding into an intracellular signal that leads to the degradation of Mth1.

Results
High levels of glucose induce degradation of Mth1 through the Rgt2/Snf3 glucose signaling pathway. Fluorescence microscopy analysis indicates that, under glucose-limited conditions, GFP-Mth1 is localized in the nucleus and does not shuttle between the nucleus and cytoplasm. If glucose-induced degradation is prevented due to disruption of the Rgt2/Snf3 pathway, GFP-Mth1 accumulates in the nucleus. When engineered to be localized to the cytoplasm, GFP-Mth1 is degraded regardless of the presence of glucose or the glucose sensors. In addition, removal of Grr1 from the nucleus prevents degradation of GFP-Mth1. These results suggest that glucose-induced, glucose sensor-dependent Mth1 degradation occurs in the nucleus. We also show that, like Yck2, Yck1 is localized to the plasma membrane via C-terminal palmitoylation mediated by the palmitoyl transferase Akr1. However, glucose-dependent degradation of Mth1 is not impaired in the absence of Akr1, suggesting that a direct interaction between the glucose sensors and Yck1/2 is not required for Mth1 degradation.

Conclusion
Glucose-induced, glucose sensor-regulated degradation of Mth1 occurs in the nucleus and does not require direct interaction of the glucose sensors with Yck1/2.
Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc
Authors: Sohn Philip , Cox Megan , Chen Dongquan , Serra Rosa 
Published: March 2010

Abstract

Background
Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-β superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing mouse tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-β has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-β action in these specialized joints is not known. One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing mouse IVD and to begin to understand the mechanism of TGF-β action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing mouse vertebrae and IVD. We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice as well as in sclerotome cultures treated with TGF-β or BMP4.

Results
Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/database searches resulting in a list of genes that can be used as markers of IVD. Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We also generated lists of genes regulated by TGF-β or BMP4 in cultured sclerotome. As expected, treatment with BMP4 resulted in up-regulation of cartilage marker genes including Acan, Sox 5, Sox6, and Sox9. In contrast, treatment with TGF-β1 did not regulate expression of cartilage markers but instead resulted in up-regulation of many IVD markers including Fmod and Adamtsl2.

Conclusions
We propose TGF-β has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-β that warrant further investigation as regulators of IVD development.
The role of phenotypic plasticity on the proteome differences between two sympatric marine snail ecotypes adapted to distinct micro-habitats
Authors: Martínez-Fernández Mónica , de la Cadena María Páez , Rolán-Alvarez Emilio 
Published: March 2010

AbstractBackgroundThe role of phenotypic plasticity is increasingly being recognized in the field of evolutionary studies. In this paper we look at the role of genetic determinationversusplastic response by comparing the protein expression profiles between two sympatric ecotypes adapted to different shore levels and habitats using two-dimensional protein maps.ResultsWe compared qualitative and quantitative differences in protein expression between pools of both ecotypes from different environments (field and laboratory conditions). The results suggested that ecotype differences may affect about 7% of the proteome in agreement with previous studies, and moreover these differences are basically insensitive to environmental changes. Thus, observed differences between wild ecotypes can be mainly attributed to genetic factors rather than phenotypic plasticity.ConclusionsThese results confirm the mechanism of adaptation already proposed in this species and a minor role of phenotypic plasticity in this ecological speciation process. In addition, this study provides a number of interesting protein spots potentially involved in adaptation, and therefore candidates for a future identification.
New insights into the evolution of subtilisin-like serine protease genes in Pezizomycotina
Authors: Li Juan , Yu Li , Yang Jinkui , Dong Linqian , Tian Baoyu , Yu Zefen , Liang Lianming , Zhang Ying , Wang Xu , Zhang Keqin 
Published: March 2010

Abstract

Background
Subtilisin-like serine proteases play an important role in pathogenic fungi during the penetration and colonization of their hosts. In this study, we perform an evolutionary analysis of the subtilisin-like serine protease genes of subphylum Pezizomycotina to find if there are similar pathogenic mechanisms among the pathogenic fungi with different life styles, which utilize subtilisin-like serine proteases as virulence factors. Within Pezizomycotina, nematode-trapping fungi are unique because they capture soil nematodes using specialized trapping devices. Increasing evidence suggests subtilisin-like serine proteases from nematode-trapping fungi are involved in the penetration and digestion of nematode cuticles. Here we also conduct positive selection analysis on the subtilisin-like serine protease genes from nematode-trapping fungi.

Results
Phylogenetic analysis of 189 subtilisin-like serine protease genes from Pezizomycotina suggests five strongly-supported monophyletic clades. The subtilisin-like serine protease genes previously identified or presumed as endocellular proteases were clustered into one clade and diverged the earliest in the phylogeny. In addition, the cuticle-degrading protease genes from entomopathogenic and nematode-parasitic fungi were clustered together, indicating that they might have overlapping pathogenic mechanisms against insects and nematodes. Our experimental bioassays supported this conclusion. Interestingly, although they both function as cuticle-degrading proteases, the subtilisin-like serine protease genes from nematode-trapping fungi and nematode-parasitic fungi were not grouped together in the phylogenetic tree. Our evolutionary analysis revealed evidence for positive selection on the subtilisin-like serine protease genes of the nematode-trapping fungi.

Conclusions
Our study provides new insights into the evolution of subtilisin-like serine protease genes in Pezizomycotina. Pezizomycotina subtilisins most likely evolved from endocellular to extracellular proteases. The entomopathogenic and nematode-parasitic fungi likely share similar properties in parasitism. In addition, our data provided better understanding about the duplications and subsequent functional divergence of subtilisin-like serine protease genes in Pezizomycotina. The evidence of positive selection detected in the subtilisin-like serine protease genes of nematode-trapping fungi in the present study suggests that the subtilisin-like serine proteases may have played important roles during the evolution of pathogenicity of nematode-trapping fungi against nematodes.
Transcriptome profiling of a Sinorhizobium meliloti fadD mutant reveals the role of rhizobactin 1021 biosynthesis and regulation genes in the control of swarming
Authors: Nogales Joaquina , Domínguez-Ferreras Ana , Amaya-Gómez Carol V , van Dillewijn Pieter , Cuéllar Virginia , Sanjuán Juan , Olivares José , Soto María J 
Published: March 2010

Abstract

Background
Swarming is a multicellular phenomenom characterized by the coordinated and rapid movement of bacteria across semisolid surfaces. In Sinorhizobium meliloti this type of motility has been described in a fadD mutant. To gain insights into the mechanisms underlying the process of swarming in rhizobia, we compared the transcriptome of a S. meliloti fadD mutant grown under swarming inducing conditions (semisolid medium) to those of cells grown under non-swarming conditions (broth and solid medium).

Results
More than a thousand genes were identified as differentially expressed in response to growth on agar surfaces including genes for several metabolic activities, iron uptake, chemotaxis, motility and stress-related genes. Under swarming-specific conditions, the most remarkable response was the up-regulation of iron-related genes. We demonstrate that the pSymA plasmid and specifically genes required for the biosynthesis of the siderophore rhizobactin 1021 are essential for swarming of a S. meliloti wild-type strain but not in a fadD mutant. Moreover, high iron conditions inhibit swarming of the wild-type strain but not in mutants lacking either the iron limitation response regulator RirA or FadD.

Conclusions
The present work represents the first transcriptomic study of rhizobium growth on surfaces including swarming inducing conditions. The results have revealed major changes in the physiology of S. meliloti cells grown on a surface relative to liquid cultures. Moreover, analysis of genes responding to swarming inducing conditions led to the demonstration that iron and genes involved in rhizobactin 1021 synthesis play a role in the surface motility shown by S. meliloti which can be circumvented in a fadD mutant. This work opens a way to the identification of new traits and regulatory networks involved in swarming by rhizobia.