bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discarte
Authors: Sherwood Rob , Bender Adam , Spring Neil 
Published: August 2008

Internet topology discovery consists of inferring the inter-router connectivity ("links") and the mapping from IP addresses to routers ("alias resolution"). Current topology discovery techniques use TTL-limited "traceroute" probes to discover links and use direct router probing to resolve aliases. The often-ignored record route (RR) IP option provides a source of disparate topology data that could augment existing techniques, but it is difficult to properly align with traceroute-based topologies because router RR implementations are under-standardized. Correctly aligned RR and traceroute topologies have fewer false links, include anonymous and hidden routers, and discover aliases for routers that do not respond to direct probing. More accurate and feature-rich topologies benefit overlay construction and network diagnostics, modeling, and measurement.We present DisCarte, a system for aligning and cross-validating RR and traceroute topology data using observed engineering practices DisCarte uses disjunctive logic programming (DLP), a logical inference and constraint solving technique, to intelligently merge RR and traceroute data. We demonstrate that the resultant topology is more accurate and complete than previous techniques by validating its internal consistency and by comparing to publicly-available topologies. We classify irregularities in router implementations and introduce a divide-and-conquer technique used to scale DLP to Internet-sized systems.
Interaction of Upper-Tropospheric Turbulence and Gravity Waves as Obtained from Spectral and Structure Function Analyses
Authors: Lu Chungu , Koch Steven E. 
Published: August 2008

Abstract
Spectral and structure function analyses of horizontal velocity fields observed in the upper troposphere and lower stratosphere during the Severe Clear Air Turbulence Collides with Air Traffic (SCATCAT) field program, conducted over the Pacific, were carried out in an effort to identify the scale interactions of turbulence and small-scale gravity waves. Because of the intermittent nature of turbulence, these analyses were conducted by clearly separating out the cases when turbulence did or did not occur in the data. In the presence of turbulence, transitional power spectra from k−2 to k−5/3 were found to be associated with gravity waves and turbulence, respectively. The second-order structure function analysis was able to translate these spectral slopes into r and r 2/3 scaling, consistent with the Monin and Yaglom conversion law, in physical space, which presented clearer pictures of scale interactions between turbulence and gravity waves. The third-order structure function analysis indicated the existence of a narrow region of inverse energy cascade from the scales of turbulence up to the gravity waves scales. This inverse energy cascade region was linked to the occurrence of Kelvin–Helmholtz instability and other wave-amplifying mechanisms, which were conjectured to lead to the breaking of small-scale gravity waves and the ensuing generation of turbulence. The multifractal analyses revealed further scale breaks between gravity waves and turbulence. The roughness and intermittent properties were also calculated for turbulence and gravity waves, respectively. Based on these properties, turbulence and gravity waves in a bifractal parameter space were mapped. In this way, their physical and statistical attributes were clearly manifested and understood.
Quasigeostrophic Turbulence with Explicit Surface Dynamics: Application to the Atmospheric Energy Spectrum
Authors: Tulloch Ross , Smith K. Shafer 
Published: August 2008

Abstract
The horizontal wavenumber spectra of wind and temperature near the tropopause have a steep −3 slope at synoptic scales and a shallower −5/3 slope at mesoscales, with a transition between the two regimes at a wavelength of about 450 km. Here it is demonstrated that a quasigeostrophic model driven by baroclinic instability exhibits such a transition near its upper boundary (analogous to the tropopause) when surface temperature advection at that boundary is properly resolved and forced. To accurately represent surface advection at the upper and lower boundaries, the vertical structure of the model streamfunction is decomposed into four parts, representing the interior flow with the first two neutral modes, and each surface with its Green’s function solution, resulting in a system with four prognostic equations. Mean temperature gradients are applied at each surface, and a mean potential vorticity gradient consisting both of β and vertical shear is applied in the interior. The system exhibits three fundamental types of baroclinic instability: interactions between the upper and lower surfaces (Eady type), interactions between one surface and the interior (Charney type), and interactions between the barotropic and baroclinic interior modes (Phillips type). The turbulent steady states that result from each of these instabilities are distinct, and those of the former two types yield shallow kinetic energy spectra at small scales along those boundaries where mean temperature gradients are present. When both mean interior and surface gradients are present, the surface spectrum reflects a superposition of the interior-dominated −3 slope cascade at large scales, and the surface-dominated −5/3 slope cascade at small scales. The transition wavenumber depends linearly on the ratio of the interior potential vorticity gradient to the surface temperature gradient, and scales with the inverse of the deformation scale when β = 0.
A Spectral Stochastic Kinetic Energy Backscatter Scheme and Its Impact on Flow-Dependent Predictability in the ECMWF Ensemble Prediction System
Authors: Berner J. , Shutts G. J. , Leutbecher M. , Palmer T. N. 
Published: August 2008

Abstract
Understanding model error in state-of-the-art numerical weather prediction models and representing its impact on flow-dependent predictability remains a complex and mostly unsolved problem. Here, a spectral stochastic kinetic energy backscatter scheme is used to simulate upscale-propagating errors caused by unresolved subgrid-scale processes. For this purpose, stochastic streamfunction perturbations are generated by autoregressive processes in spectral space and injected into regions where numerical integration schemes and parameterizations in the model lead to excessive systematic kinetic energy loss. It is demonstrated how output from coarse-grained high-resolution models can be used to inform the parameters of such a scheme. The performance of the spectral backscatter scheme is evaluated in the ensemble prediction system of the European Centre for Medium-Range Weather Forecasts. Its implementation in conjunction with reduced initial perturbations results in a better spread–error relationship, more realistic kinetic-energy spectra, a better representation of forecast-error growth, improved flow-dependent predictability, improved rainfall forecasts, and better probabilistic skill. The improvement is most pronounced in the tropics and for large-anomaly events.
It is found that whereas a simplified scheme assuming a constant dissipation rate already has some positive impact, the best results are obtained for flow-dependent formulations of the unresolved processes.
A Station-Based Southern Annular Mode Index from 1884 to 2005
Authors: Visbeck Martin 
Published: August 2008

Abstract
Atmospheric pressure observations from the Southern Hemisphere are used to estimate monthly and annually averaged indexes of the southern annular mode (SAM) back to 1884. This analysis groups all relevant observations in the following four regions: one for Antarctica and three in the subtropical zone. Continuous surface pressure observations are available at a number of locations in the subtropical regions since the end of the nineteenth century. However, year-round observations in the subpolar region near the Antarctic continent began only during the 1940–60 period. The shorter Antarctic records seriously compromise the length of a traditionally estimated SAM index. To improve the situation “proxy” estimates of Antarctic sea level pressure anomalies are provided based on the concept of atmospheric mass conservation poleward of 20°S. This allows deriving a longer SAM index back to 1884. Several aspects of the new record, its statistical properties, seasonal trends, and the regional pressure anomaly correlations, are presented.
Interlobular and intralobular mammary stroma: Genotype may not reflect phenotype
Authors: Fleming JM , Long EL , Ginsburg E , Gerscovich D , Meltzer PS , Vonderhaar BK 
Published: August 2008

AbstractBackgroundThe normal growth and function of mammary epithelial cells depend on interactions with the supportive stroma. Alterations in this communication can lead to the progression or expansion of malignant growth. The human mammary gland contains two distinctive types of fibroblasts within the stroma. The epithelial cells are surrounded by loosely connected intralobular fibroblasts, which are subsequently surrounded by the more compacted interlobular fibroblasts. The different proximity of these fibroblasts to the epithelial cells suggests distinctive functions for these two subtypes. In this report, we compared the gene expression profiles between the two stromal subtypes.MethodsFresh normal breast tissue was collected from reduction mammoplasty patients and immediately placed into embedding medium and frozen on dry ice. Tissue sections were subjected to laser capture microscopy to isolate the interlobular from the intralobular fibroblasts. RNA was prepared and subjected to microarray analysis using the Affymetrix Human Genome U133 GeneChip®. Data was analyzed using the Affy and Limma packages available from Bioconductor. Findings from the microarray analysis were validated by RT-PCR and immunohistochemistry.ResultsNo statistically significant difference was detected between the gene expression profiles of the interlobular and intralobular fibroblasts by microarray analysis and RT-PCR. However, for some of the genes tested, the protein expression patterns between the two subtypes of fibroblasts were significantly different.ConclusionThis study is the first to report the gene expression profiles of the two distinct fibroblast populations within the human mammary gland. While there was no significant difference in the gene expression profiles between the groups, there was an obvious difference in the expression pattern of several proteins tested. This report also highlights the importance of studying gene regulation at both the transcriptional and post-translational level.
Male sexual ornament size is positively associated with reproductive morphology and enhanced fertility in the stalk-eyed fly Teleopsis dalmanni
Authors: Rogers David W , Denniff Matthew , Chapman Tracey , Fowler Kevin , Pomiankowski Andrew 
Published: August 2008

Abstract

Background
Exaggerated male ornaments and displays often evolve in species where males only provide females with ejaculates during reproduction. Although "good genes" arguments are typically invoked to explain this phenomenon, a simpler alternative is possible if variation in male reproductive quality (e.g. sperm number, ejaculate content, mating rate) is an important determinant of female reproductive success. The "phenotype-linked fertility hypothesis" states that female preference for male ornaments or displays has been selected to ensure higher levels of fertility and has driven the evolution of exaggerated male traits. Females of the stalk-eyed fly Teleopsis dalmanni must mate frequently to maintain high levels of fertility and prefer to mate with males exhibiting large eyespan, a condition-dependent sexual ornament. If eyespan indicates male reproductive quality, females could directly increase their reproductive success by mating with males with large eyespan. Here we investigate whether male eyespan indicates accessory gland and testis length, and then ask whether mating with large eyespan males affects female fertility.

Results
Male eyespan was a better predictor of two key male reproductive traits – accessory gland and testis length – than was body size alone. This positive relationship held true over three levels of increasing environmental stress during the maturation of the adult accessory glands and testes. Furthermore, females housed with a large eyespan male exhibited higher levels of fertility than those with small eyespan males.

Conclusion
Male eyespan in stalk-eyed flies is subject to strong directional mate preference and is a reliable indicator of male reproductive quality – both because males with larger eyespan have bigger accessory glands and testes, and also as they confer higher fertility on females. Fertility enhancement may have arisen because males with larger eyespan mated more often and/or because they transferred more sperm or other substances per ejaculate. The need to ensure high levels of fertility could thus have been an important selective force in the coevolution of female preference and male eyespan in stalk-eyed flies. Our results support the phenotype-linked fertility hypothesis and suggest that it might be of general importance in explaining the evolution of exaggerated male ornaments and displays in species where males only provide females with ejaculates during reproduction.
A DNA and morphology based phylogenetic framework of the ant genus Lasius with hypotheses for the evolution of social parasitism and fungiculture
Authors: Maruyama Munetoshi , Steiner Florian M , Stauffer Christian , Akino Toshiharu , Crozier Ross H , Schlick-Steiner Birgit C 
Published: August 2008

AbstractBackgroundAnts of the genusLasiusare ecologically important and an important system for evolutionary research. Progress in evolutionary research has been hindered by the lack of a well-founded phylogeny of the subgenera, with three previous attempts disagreeing. Here we employed two mitochondrial genes (cytochrome c oxidase subunit I, 16S ribosomal RNA), comprising 1,265 bp, together with 64 morphological characters, to recover the phylogeny ofLasiusby Bayesian and Maximum Parsimony inference after exploration of potential causes of phylogenetic distortion. We use the resulting framework to infer evolutionary pathways for social parasitism and fungiculture.ResultsWe recovered two well supported major lineages. One includesAcanthomyops,Austrolasius,Chthonolasius, andLasius pallitarsis, which we confirm to represent a seventh subgenus, the other clade containsDendrolasius, andLasius sensu stricto. The subgenusCautolasius, displaying neither social parasitism nor fungiculture, probably belongs to the second clade, but its phylogenetic position is not resolved at the cutoff values of node support we apply. Possible causes for previous problems with reconstructing theLasiusphylogeny include use of other reconstruction techniques, possibly more prone to instabilities in some instances, and the inclusion of phylogenetically distorting characters.ConclusionBy establishing an updated phylogenetic framework, our study provides the basis for a later formal taxonomic revision of subgenera and for studying the evolution of various ecologically and sociobiologically relevant traits ofLasius, although there is need for future studies to include nuclear genes and additional samples from the Nearctic. Both social parasitism and fungiculture evolved twice inLasius, once in each major lineage, which opens up new opportunities for comparative analyses. The repeated evolution of social parasitism has been established for other groups of ants, though not for temporary social parasitism as found inLasius. For fungiculture, the independent emergence twice in a monophyletic group marks a novel scenario in ants. We present alternative hypotheses for the evolution of both traits, with one of each involving loss of the trait. Though less likely for both traits than later evolution without reversal, we consider reversal as sufficiently plausible to merit independent testing.
Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate
Authors: Natalang Onguma , Bischoff Emmanuel , Deplaine Guillaume , Proux Caroline , Dillies Marie-Agnès , Sismeiro Odile , Guigon Ghislaine , Bonnefoy Serge , Patarapotikul Jintana , Mercereau-Puijalon Odile , Coppée Jean-Yves , David Peter H 
Published: August 2008

Abstract

Background
Translation of the genome sequence of Plasmodium sp. into biologically relevant information relies on high through-put genomics technology which includes transcriptome analysis. However, few studies to date have used this powerful approach to explore transcriptome alterations of P. falciparum parasites exposed to antimalarial drugs.

Results
The rapid action of artesunate allowed us to study dynamic changes of the parasite transcriptome in synchronous parasite cultures exposed to the drug for 90 minutes and 3 hours. Developmentally regulated genes were filtered out, leaving 398 genes which presented altered transcript levels reflecting drug-exposure. Few genes related to metabolic pathways, most encoded chaperones, transporters, kinases, Zn-finger proteins, transcription activating proteins, proteins involved in proteasome degradation, in oxidative stress and in cell cycle regulation. A positive bias was observed for over-expressed genes presenting a subtelomeric location, allelic polymorphism and encoding proteins with potential export sequences, which often belonged to subtelomeric multi-gene families. This pointed to the mobilization of processes shaping the interface between the parasite and its environment. In parallel, pathways were engaged which could lead to parasite death, such as interference with purine/pyrimidine metabolism, the mitochondrial electron transport chain, proteasome-dependent protein degradation or the integrity of the food vacuole.

Conclusion
The high proportion of over-expressed genes encoding proteins exported from the parasite highlight the importance of extra-parasitic compartments as fields for exploration in drug research which, to date, has mostly focused on the parasite itself rather than on its intra and extra erythrocytic environment. Further work is needed to clarify which transcriptome alterations observed reflect a specific response to overcome artesunate toxicity or more general perturbations on the path to cellular death.
Functional imaging of interleukin 1 beta expression in inflammatory process using bioluminescence imaging in transgenic mice
Authors: Li Limei , Fei Zhaoliang , Ren Jianke , Sun Ruilin , Liu Zhihui , Sheng Zhejin , Wang Long , Sun Xia , Yu Jun , Wang Zhugang , Fei Jian 
Published: August 2008

AbstractBackgroundInterleukin 1 beta (IL-1β) plays an important role in a number of chronic and acute inflammatory diseases. To understand the role of IL-1β in disease processes and develop anin vivoscreening system for anti-inflammatory drugs, a transgenic mouse line was generated which incorporated the transgene firefly luciferase gene driven by a 4.5-kb fragment of the human IL-1β gene promoter. Luciferase gene expression was monitored in live mice under anesthesia using bioluminescence imaging in a number of inflammatory disease models.ResultsIn a LPS-induced sepsis model, dramatic increase in luciferase activity was observed in the mice. This transgene induction was time dependent and correlated with an increase of endogenous IL-1β mRNA and pro-IL-1β protein levels in the mice. In a zymosan-induced arthritis model and an oxazolone-induced skin hypersensitivity reaction model, luciferase expression was locally induced in the zymosan injected knee joint and in the ear with oxazolone application, respectively. Dexamethasone suppressed the expression of luciferase gene both in the acute sepsis model and in the acute arthritis model.ConclusionOur data suggest that the transgenic mice model could be used to study transcriptional regulation of the IL-1β gene expression in the inflammatory process and evaluation the effect of anti-inflammatory drugin vivo.
Physiological and molecular characterization of aluminum resistance in Medicago truncatula
Authors: Chandran Divya , Sharopova Natasha , VandenBosch Kathryn A , Garvin David F , Samac Deborah A 
Published: August 2008

Abstract

Background
Aluminum (Al) toxicity is an important factor limiting crop production on acid soils. However, little is known about the mechanisms by which legumes respond to and resist Al stress. To explore the mechanisms of Al toxicity and resistance in legumes, we compared the impact of Al stress in Al-resistant and Al-sensitive lines of the model legume, Medicago truncatula Gaertn.

Results
A screen for Al resistance in 54 M. truncatula accessions identified eight Al-resistant and eight Al-sensitive lines. Comparisons of hydroponic root growth and root tip hematoxylin staining in an Al-resistant line, T32, and an Al-sensitive line, S70, provided evidence that an inducible Al exclusion mechanism occurs in T32. Transcriptional events associated with the Al resistance response were analyzed in T32 and S70 after 12 and 48 h Al treatment using oligonucleotide microarrays. Fewer genes were differentially regulated in response to Al in T32 compared to S70. Expression patterns of oxidative stress-related genes, stress-response genes and microscopic examination of Al-treated root tips suggested a lower degree of Al-induced oxidative damage to T32 root tips compared to S70. Furthermore, genes associated with cell death, senescence, and cell wall degradation were induced in both lines after 12 h of Al treatment but preferentially in S70 after 48 h of Al treatment. A multidrug and toxin efflux (MATE) transporter, previously shown to exude citrate in Arabidopsis, showed differential expression patterns in T32 and S70.

Conclusion
Our results identified novel genes induced by Al in Al-resistant and sensitive M. truncatula lines. In T32, transcription levels of genes related to oxidative stress were consistent with reactive oxygen species production, which would be sufficient to initiate cell death of Al-accumulating cells thereby contributing to Al exclusion and root growth recovery. In contrast, transcriptional levels of oxidative stress-related genes were consistent with excessive reactive oxygen species accumulation in S70 potentially resulting in necrosis and irreversible root growth inhibition. In addition, a citrate-exuding MATE transporter could function in Al exclusion and/or internal detoxification in T32 based on Al-induced transcript localization studies. Together, our findings indicate that multiple responses likely contribute to Al resistance in M. truncatula.