bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Theory of Baroclinic Turbulence
Authors: Farrell Brian F. , Ioannou Petros J. 
Published: February 2009

Abstract
Understanding the physical mechanism maintaining fluid turbulence remains a fundamental theoretical problem. The two-layer model is an analytically and computationally simple system in which the dynamics of turbulence can be conveniently studied; in this work, a maximally simplified model of the statistically steady turbulent state in this system is constructed to isolate and identify the essential mechanism of turbulence. In this minimally complex turbulence model the effects of nonlinearity are parameterized using an energetically consistent stochastic process that is white in both space and time, turbulent fluxes are obtained using a stochastic turbulence model (STM), and statistically steady turbulent states are identified using stochastic structural stability theory (SSST). These turbulent states are the fixed-point equilibria of the nonlinear SSST system. For parameter values typical of the midlatitude atmosphere, these equilibria predict the emergence of marginally stable eddy-driven baroclinic jets. The eddy variances and fluxes associated with these jets and the power-law scaling of eddy variances and fluxes are consistent with observations and simulations of baroclinic turbulence. This optimally simple model isolates the essential physics of baroclinic turbulence: maintenance of variance by transient perturbation growth, replenishment of the transiently growing subspace by nonlinear energetically conservative eddy–eddy scattering, and equilibration to a statistically steady state of marginal stability by a combination of nonlinear eddy-induced mean jet modification and eddy dissipation. These statistical equilibrium states provide a theory for the general circulation of baroclinically turbulent planetary atmospheres.
Evidence for Submesoscale Barriers to Horizontal Mixing in the Ocean from Current Measurements and Aerial Photographs
Authors: Gildor Hezi , Fredj Erick , Steinbuck Jonah , Monismith Stephen 
Published: February 2009

Abstract
Ocean submesoscale (∼2–20 km) mixing processes play a major role in ocean dynamics, in physical–biological interactions (e.g., in the dispersion of larvae), and in the dispersion of pollutants. In this paper, horizontal mixing on a scale of a few kilometers is investigated, from observations of surface currents, using highly resolved (300 m) high-frequency radar. These results show the complexity of ocean mixing on scales of a few kilometers and the existence of temporary barriers to mixing that can affect the dispersion of biological materials and pollutants. These barriers are narrow [O(100 m)] and can survive for a few days. The existence of these barriers is supported in simultaneous aerial photographs. The barriers observed here may require a new approach to the way horizontal mixing is parameterized in ocean and climate models.
An Ocean Circulation Model Based on Operator-Splitting, Hamiltonian Brackets, and the Inclusion of Sound Waves
Authors: Salmon Rick 
Published: February 2009

Abstract
This paper offers a simple, entirely prognostic, ocean circulation model based on the separation of the complete dynamics, including sound waves, into elementary Poisson brackets. For example, one bracket corresponds to the propagation of sound waves in a single direction. Other brackets correspond to the rotation of the velocity vector by individual components of the vorticity and to the action of buoyancy force. The dynamics is solved by Strang splitting of the brackets. Key features of the method are the assumption that the sound waves propagate exactly one grid distance in a time step and the use of Riemann invariants to solve the sound-wave dynamics exactly. In these features the method resembles the lattice Boltzmann method, but the flexibility of more conventional methods is retained. As in the lattice Boltzmann method, very short time steps are required to prevent unrealistically strong coupling between the sound waves and the slow hydrodynamic motions of primary interest. However, the disadvantage of small time steps is more than compensated by the model’s extreme simplicity, even in the presence of very complicated boundaries, and by its massively parallel form. Numerical tests and examples illustrate the practicality of the method.
Eddy Formation and Shedding in a Separating Boundary Current
Authors: Pichevin Thierry , Herbette Steven , Floc’h France 
Published: February 2009

Abstract
This study deals with the separation of western boundary currents within a reduced-gravity framework, and it analyzes the formation of eddies in the separation region and the conditions of their shedding into the open ocean. It shows that the separation point of the current oscillates along the coast so that the retroflected eastward current develops meanders. These meanders grow, drift westward under the influence of β, and finally hit the coastal current, which leads to the periodic formation of eddies. This study also highlights the impact by the geometrical configurations of the flow and coastline upon the existence or lack of a subsequent shedding of these eddies: a shedding occurs when no obstacle hinders the β-induced westward drift of the eddies. This happens when either (i) the current retroflects far enough beyond the tip of the coast so that, because of β, the eddies can propagate westward without being blocked, or (ii) the tilt of the coast is small enough so that the alongshore component of the β-induced velocity is enhanced and the eddies can escape from the retroflection region.
Differentiation therapy of leukemia: 3 decades of development
Authors: Nowak Daniel , Stewart Daphne , Koeffler H. Phillip 
Published: February 2009

AbstractA characteristic feature of leukemia cells is a blockade of differentiation at a distinct stage in cellular maturation. In the 1970s and 1980s, studies demonstrating the capabilities of certain chemicals to induce differentiation of hematopoietic cell lines fostered the concept of treating leukemia by forcing malignant cells to undergo terminal differentiation instead of killing them through cytotoxicity. The first promising reports on this notion prompted a review article on this subject by us 25 years ago. In this review, we revisit this interesting field of study and report the progress achieved in the course of nearly 3 decades. The best proof of principle for differentiation therapy has been the treatment of acute promyelocytic leukemia with all-trans retinoic acid. Attempts to emulate this success with other nuclear hormone ligands such as vitamin D compounds and PPARγ agonists or different classes of substances such as hematopoietic cytokines or compounds affecting the epigenetic landscape have not been successful on a broad scale. However, a multitude of studies demonstrating partial progress and improvements and, finally, the new powerful possibilities of forward and reverse engineering of differentiation pathways by manipulation of transcription factors support the continued enthusiasm for differentiation therapy of leukemia in the future.
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
Authors: Orsi Renato H , Borowsky Mark L , Lauer Peter , Young Sarah K , Nusbaum Chad , Galagan James E , Birren Bruce W , Ivy Reid A , Sun Qi , Graves Lewis M , Swaminathan Bala , Wiedmann Martin 
Published: February 2009

AbstractBackgroundWhile increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses on fourListeria monocytogenes, including human and food isolates from both a 1988 case of sporadic listeriosis and a 2000 listeriosis outbreak, which had been linked to contaminated food from a single processing facility. All four isolates had been shown to have identical subtypes, suggesting that a specificL. monocytogenesstrain persisted in this processing plant over at least 12 years. While a genome sequence for the 1988 food isolate has been reported, we sequenced the genomes of the 1988 human isolate as well as a human and a food isolate from the 2000 outbreak to allow for comparative genome analyses.ResultsThe twoL. monocytogenesisolates from 1988 and the two isolates from 2000 had highly similar genome backbone sequences with very few single nucleotide (nt) polymorphisms (1 – 8 SNPs/isolate; confirmed by re-sequencing). While no genome rearrangements were identified in the backbone genome of the four isolates, a 42 kb prophage inserted in the chromosomalcomKgene showed evidence for major genome rearrangements. The human-food isolate pair from each 1988 and 2000 had identical prophage sequence; however, there were significant differences in the prophage sequences between the 1988 and 2000 isolates. Diversification of this prophage appears to have been caused by multiple homologous recombination events or possibly prophage replacement. In addition, only the 2000 human isolate contained a plasmid, suggesting plasmid loss or acquisition events. Surprisingly, besides the polymorphisms found in thecomKprophage, a single SNP in the tRNA Thr-4 prophage represents the only SNP that differentiates the 1988 isolates from the 2000 isolates.ConclusionOur data support the hypothesis that the 2000 human listeriosis outbreak was caused by aL. monocytogenesstrain that persisted in a food processing facility over 12 years and show that genome sequencing is a valuable and feasible tool for retrospective epidemiological analyses. Short-term evolution ofL. monocytogenesin non-controlled environments appears to involve limited diversification beyond plasmid gain or loss and prophage diversification, highlighting the importance of phages in bacterial evolution.
The extracellular EXO protein mediates cell expansion in Arabidopsis leaves
Authors: Schröder Florian , Lisso Janina , Lange Peggy , Müssig Carsten 
Published: February 2009

Abstract

Background
The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth. It is part of a gene family with eight members in Arabidopsis. EXO gene expression is under control of BR, and EXO overexpression promotes shoot and root growth. In this study, the consequences of loss of EXO function are described.

Results
The exo loss of function mutant showed diminished leaf and root growth and reduced biomass production. Light and scanning electron microscopy analyses revealed that impaired leaf growth is due to reduced cell expansion. Epidermis, palisade, and spongy parenchyma cells were smaller in comparison to the wild-type. The exo mutant showed reduced brassinolide-induced cotyledon and hypocotyl growth. In contrast, exo roots were significantly more sensitive to the inhibitory effect of synthetic brassinolide. Apart from reduced growth, exo did not show severe morphological abnormalities. Gene expression analyses of leaf material identified genes that showed robust EXO-dependent expression. Growth-related genes such as WAK1, EXP5, and KCS1, and genes involved in primary and secondary metabolism showed weaker expression in exo than in wild-type plants. However, the vast majority of BR-regulated genes were normally expressed in exo. HA- and GFP-tagged EXO proteins were targeted to the apoplast.

Conclusion
The EXO gene is essential for cell expansion in leaves. Gene expression patterns and growth assays suggest that EXO mediates BR-induced leaf growth. However, EXO does not control BR-levels or BR-sensitivity in the shoot. EXO presumably is involved in a signalling process which coordinates BR-responses with environmental or developmental signals. The hypersensitivity of exo roots to BR suggests that EXO plays a diverse role in the control of BR responses in the root.
Cytoplasmic CXCR4 expression in breast cancer: induction by nitric oxide and correlation with lymph node metastasis and poor prognosis
Authors: Yasuoka Hironao , Tsujimoto Masahiko , Yoshidome Katsuhide , Nakahara Masaaki , Kodama Rieko , Sanke Tokio , Nakamura Yasushi 
Published: February 2009

Abstract

Background
Lymph nodes constitute the first site of metastasis for most malignancies, and the extent of lymph node involvement is a major criterion for evaluating patient prognosis. The CXC chemokine receptor 4 (CXCR4) has been shown to play an important role in lymph node metastasis. Nitric oxide (NO) may also contribute to induction of metastatic ability in human cancers.

Methods
CXCR4 expression was analyzed in primary human breast carcinoma with long-term follow-up. The relationship between nitrotyrosine levels (a biomarker for peroxynitrate formation from NO in vivo) and lymph node status, CXCR4 immunoreactivity, and other established clinico-pathological parameters, as well as prognosis, was analyzed. Nitrite/nitrate levels and CXCR4 expressions were assessed in MDA-MB-231 and SK-BR-3 breast cancer cell lines after induction and/or inhibition of NO synthesis.

Results
CXCR4 staining was predominantly cytoplasmic; this was observed in 50%(56/113) of the tumors. Cytoplasmic CXCR4 expression was significantly correlated with nitrotyrosine levels and lymph node metastasis. Kaplan-Meier survival curves showed that cytoplasmic CXCR4 expression was associated with reduced disease-free and overall survival. In multivariate analysis, cytoplasmic CXCR4 expression emerged as a significant independent predictor for overall and disease-free survival. Cytoplasmic expression of functional CXCR4 in MDA-MB-231 and SK-BR-3 cells was increased by treatment with the NO donor DETA NONOate. This increase was abolished by L-NAME, an inhibitor of NOS.

Conclusion
Our data showed a role for NO in stimulating cytoplasmic CXCR4 expression in vitro. Formation of the biomarker nitrotyrosine was also correlated with CXCR4 expression and lymph node metastasis in vivo. In addition, cytoplasmic CXCR4 expression may serve as a significant prognostic factor for long-term survival in breast cancer.
Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes
Authors: Park Chungoo , Makova Kateryna D 
Published: February 2009

Abstract
Background
Gene expression divergence is one manifestation of functional differences between duplicate genes. Although rapid accumulation of expression divergence between duplicate gene copies has been observed, the driving mechanisms behind this phenomenon have not been explored in detail.

Results
We examine which factors influence expression divergence between human duplicate genes, utilizing the latest genome-wide data sets. We conclude that the turnover of transcription start sites between duplicate genes occurs rapidly after gene duplication and that gene pairs with shared transcription start sites have significantly higher expression similarity than those without shared transcription start sites. Moreover, we find that most (55%) duplicate gene pairs do not retain the same coding sequence structure between the two duplicate copies and this also contributes to divergence in their expression. Furthermore, the proportion of aligned sequences in cis-regulatory regions between the two copies is positively correlated with expression similarity. Surprisingly, we find no effect of copy-specific transposable element insertions on the divergence of duplicate gene expression.

Conclusions
Our results suggest that turnover of transcription start sites, structural heterogeneity of coding sequences, and divergence of cis-regulatory regions between copies play a pivotal role in determining the expression divergence of duplicate genes.
Crucial Roles for Interactions between MLL3/4 and INI1 in Nuclear Receptor Transactivation
Authors: Lee Seunghee , Kim Dae-Hwan , Goo Young Hwa , Lee Young Chul , Lee Soo-Kyung , Lee Jae W. 
Published: February 2009

AbstractNuclear receptor (NR) transactivation involves multiple coactivators, and the molecular basis for how these are functionally integrated needs to be determined to fully understand the NR action. Activating signal cointegrator-2 (ASC-2), a transcriptional coactivator of many NRs and transcription factors, forms a steady-state complex, ASCOM (for ASC-2 complex), which contains histone H3-lysine-4 (H3K4) methyltransferase MLL3 or its paralog MLL4. Here, we show that ASCOM requires a functional cross talk with the ATPase-dependent chromatin remodeling complex Swi/Snf for efficient NR transactivation. Our results reveal that ASCOM and Swi/Snf are tightly colocalized in the nucleus and that ASCOM and Swi/Snf promote each other’s binding to NR target genes. We further show that the C-terminal SET domain of MLL3 and MLL4 directly interacts with INI1, an integral subunit of Swi/Snf. Our mutational analysis demonstrates that this interaction underlies the mutual facilitation of ASCOM and Swi/Snf recruitment to NR target genes. Importantly, this study uncovers a specific protein-protein interaction as a novel venue to couple two distinct enzymatic coactivator complexes during NR transactivation.
Urea transporter and glutamine synthetase regulation and localization in gulf toadfish gill
Authors: McDonald M. Danielle , Vulesevic Branka , Perry Steve F. , Walsh Patrick J. 
Published: February 2009

SUMMARYThe goal of the present study was to investigate the role of circulating cortisol and urea in the transcriptional regulation of branchial glutamine synthetase (GS), which incorporates NH3 into glutamate to form glutamine, and the toadfish urea transporter, tUT, which is involved in urea excretion across the gill of the gulf toadfish. GS (of which there are two isoforms, LGS and GGS) and tUT mRNA expression and activity were measured in toadfish exposed to treatments that would induce variable stress responses. In addition, the role of circulating urea in tUT regulation was investigated by infusing toadfish with urea alone or in combination with intraperitoneal injection of RU486, a corticosteroid type II receptor antagonist. There was a 4.8-fold upregulation in the mRNA expression of the gill-specific GS isoform(GGS) in response to cortisol infusion and a similar upregulation in the more ubiquitous isoform (LGS). Furthermore, there was a significant 1.9-fold and 3.3-fold upregulation in the mRNA expression of the toadfish urea transporter,tUT, in response to stress through crowding or exogenous cortisol loading through infusion, respectively. In addition, tUT was found to have a urea-sensitive component to transcriptional regulation that was independent of circulating cortisol concentrations. However, the changes measured in mRNA expression of GGS, LGS and tUT did not correspond with changes in protein activity. To determine the cell type(s) involved in glutamine production and urea excretion, we attempted to localize GGS, LGS and tUT using in situ hybridization. This study is the first to show that GGS and tUT expression appear to occur in gill mitochondria-rich cells of toadfish,suggesting that these cells play a combined glutamine production and urea excretion role, which may have implications for predator avoidance.
Skeletal muscle fiber types in the ghost crab,Ocypode quadrata:implications for running performance
Authors: Perry Michael J. , Tait Jennifer , Hu John , White Scott C. , Medler Scott 
Published: February 2009

SUMMARYGhost crabs possess rapid running capabilities, which make them good candidates for comparing invertebrate exercise physiology with that of more extensively studied vertebrates. While a number of studies have examined various aspects of running physiology and biomechanics in terrestrial crabs,none to date have defined the basic skeletal muscle fiber types that power locomotion. In the current study, we investigated skeletal muscle fiber types comprising the extensor and flexor carpopodite muscles in relation to running performance in the ghost crab. We used kinematic analyses to determine stride frequency and muscle shortening velocity and found that both parameters are similar to those of comparably sized mammals but slower than those observed in running lizards. Using several complementary methods, we found that the muscles are divided into two primary fiber types: those of the proximal and distal regions possess long sarcomeres (6.2±2.3 μm) observed in crustacean slow fibers and have characteristics of aerobic fibers whereas those of the muscle mid-region have short sarcomeres (3.5±0.4 μm)characteristic of fast fibers and appear to be glycolytic. Each fiber type is characterized by several different myofibrillar protein isoforms including multiple isoforms of myosin heavy chain (MHC), troponin I (TnI), troponin T(TnT) and a crustacean fast muscle protein, P75. Three different isoforms of MHC are differentially expressed in the muscles, with fibers of the mid-region always co-expressing two isoforms at a 1:1 ratio within single fibers. Based on our analyses, we propose that these muscles are functionally divided into a two-geared system, with the aerobic fibers used for slow sustained activities and the glycolytic mid-region fibers being reserved for explosive sprints. Finally, we identified subtle differences in myofibrillar isoform expression correlated with crab body size, which changes by several orders of magnitude during an animal's lifetime.
Losing stability: tail loss and jumping in the arboreal lizardAnolis carolinensis
Authors: Gillis Gary B. , Bonvini Lauren A. , Irschick Duncan J. 
Published: February 2009

SUMMARYVoluntary loss of an appendage, or autotomy, is a remarkable behavior that is widespread among many arthropods and lower vertebrates. Its immediate benefit, generally escape from a predator, is balanced by various costs,including impaired locomotor performance, reproductive success and long-term survival. Among vertebrates, autotomy is most widespread in lizards, in which tail loss has been documented in close to 100 species. Despite numerous studies of the potential costs of tail autotomy in lizards, none have focused on the importance of the tail in jumping. Using high-speed video we recorded jumps from six lizards (Anolis carolinensis) both before and after removing 80% of the tail to test the hypothesis that tail loss has a significant effect on jumping kinematics. Several key performance metrics, including jump distance and takeoff velocity, were not affected by experimental tail removal,averaging 21 cm and 124 cm s–1, respectively, in both tailed and tailless lizards. However, in-air stability during jumping was greatly compromised after tail removal. Lizards without tails rotated posteriorly more than 30 deg., on average, between takeoff and landing (and sometimes more than 90 deg.) compared with an average of 5 deg. of rotation in lizards with intact tails. Such exaggerated posterior rotation prevents coordinated landing, which is critical for animals that spend much of their time jumping to and from small branches. This work augments recent experiments demonstrating the importance of the tail as a mid-air stabilizer during falling in geckos, and emphasizes new and severe functional costs associated with tail autotomy in arboreal lizards.