bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of the Harang reversal and its dependence on plasma sheet conditions: Rice convection model simulations
Authors: Gkioulidou Matina , Wang Chih‐Ping , Lyons Larry R. , Wolf Richard A.
Published: July 2009

The goal of this paper is to understand the formation of the Harang reversal and its association with the region 2 field‐aligned current (FAC) system, which couples the plasma sheet transport to the ionosphere. We have run simulations with the Rice convection model (RCM) using the Tsyganenko 96 magnetic field model and realistic plasma sheet particle boundary conditions on the basis of Geotail observations. Our results show that the existence of an overlap in magnetic local time (MLT) of the region 2 upward and downward FAC is necessary for the formation of the Harang reversal. In the overlap region the downward FAC, which is located at lower latitudes, is associated with low‐energy ions that penetrate closer to Earth toward the dawn side, while the upward FAC, which is located at higher latitudes, is associated with high‐energy ions. Under the same enhanced convection we compare the Harang reversal resulting from a hotter and more tenuous plasma sheet with the one resulting from a colder and denser plasma sheet. For the former case the shielding of the convection electric field is less efficient than for the latter case, allowing low‐energy protons to penetrate further earthward, resulting in a Harang reversal that extends to lower latitudes, expands wider in MLT, and is located further equatorward than the upward FAC peak and the conductivity peak. The return flows of the Harang reversal in the hot and tenuous case are located in a low conductivity region. This leads to an enhancement of these westward flows, resulting in subauroral polarization streams (SAPS).
Dynamics of wind‐driven upwelling and relaxation between Monterey Bay and Point Arena: Local‐, regional‐, and gyre‐scale controls
Authors: Pringle James M. , Dever Edward P.
Published: July 2009

In north and central California, equatorward winds drive equatorward flows and the upwelling of cold dense water over the shelf during the midspring and summer upwelling season. When the winds temporarily weaken, the upwelling flows between Point Reyes and Point Arena “relax,” becoming strongly poleward over the shelf. Analytical and numerical models are used to describe the effect of alongshore variability of winds, bathymetry, and basin‐scale pressure gradients on the strength of upwelling and its relaxation. Alongshore winds weaken to the south of Point Reyes, and the shelf becomes narrower from Point Reyes to Monterey Bay. Both of these lead to reduced upwelling at and to the north of Point Reyes, causing an alongshore gradient of temperature and density on the shelf. These alongshore gradients lead to an along‐isobath pressure gradient over the shelf that drive the relaxation flows. A simple analytical model is used to explain the dynamics, magnitude, and structure of the relaxation flows. The modeling also suggests that the depth of origin of the upwelled waters, and thus their temperature, is controlled by the along‐isobath pressure gradient that exists over the continental slope. This along‐slope pressure gradient is also responsible for the California undercurrent in this region. This pressure gradient is not generated in a model of the Californian coast extending from 32°N to 42°N and integrated for several months, suggesting it is caused by dynamics whose spatial or temporal scales are larger than the Californian coast and/or longer than several months.
Analyzing the variation of Lyapunov exponents of solar and geomagnetic activity indices during coronal mass ejections
Authors: Mirmomeni M. , Lucas C.
Published: July 2009

Hostile space weather is one of the principal threats to modern human technology because of the dependency of our lives on satellites. Solar coronal mass ejections, solar flares, and high‐speed solar wind streams often cause some sequences of damaging disturbances within the Earth's magnetosphere, in the atmosphere, and even on the Earth's surface. The time‐varying Sun, as the main source of space weather causes geomagnetic storms and substorms in many ways with coronal mass ejections (CME) being possibly the most harmful among them. CMEs cause transient magnetized plasma flows as interplanetary consequences, which drive the geomagnetic storms and substorms in the Earth's magnetosphere. It is shown that the cyclic solar activity has chaotic characteristics. It seems that the chaotic modeling of solar and geomagnetic activity indices is an important approach for analysis and prediction of the solar extreme events. This is particularly useful for engineers and designers interested in space weather prediction and its applications. One of the most important tools for eliciting the chaotic trends is the “Lyapunov exponents,” which is a useful measure of the stability of a dynamic system. This paper analyzes the variation of Lyapunov exponents (LE) for three solar and geomagnetic activity indices during CMEs: the sunspot number, disturbance storm time, and proton temperature. The analysis has been carried out using the technique of adaptive LE estimation adopted from previous works; the suitable window for which has been determined via trial and error. It is shown that the LE of these solar and geomagnetic activity indices varies rapidly during CMEs. The variation in LEs creates a pattern as a precursor for the forthcoming CME. This precursor, which is an oscillation in the values of Les, begins several steps sooner than the CME's occurrence. Then, during the CME, the LEs decrease to a small positive or a negative value, which demonstrates that during an anomaly such as a CME the chaotic characteristics of solar and geomagnetic activity indices decrease and solar and geomagnetic activity indices follow more regular dynamics.
Real‐time predictions of geomagnetic storms and substorms: Use of the Solar Wind Magnetosphere‐Ionosphere System model
Authors: Mays M. L. , Horton W. , Spencer E. , Kozyra J.
Published: July 2009

A low‐dimensional, plasma physics‐based, nonlinear dynamical model of the coupled magnetosphere‐ionosphere system, called Real‐Time Solar Wind Magnetosphere‐Ionosphere System (WINDMI), is used to predict AL and Dst values approximately 1 h before geomagnetic substorm and storm event. Subsequently, every 10 min ground‐based measurements compiled by World Data Center, Kyoto, are compared with model predictions (http://orion.ph.utexas.edu/∼windmi/realtime/). WINDMI model runs are also available at the Community Coordinated Modeling Center (http://ccmc.gsfc.nasa.gov/). The performance of the Real‐Time WINDMI model is quantitatively evaluated for 22 storm/substorm event predictions from February 2006 to August 2008. Three possible input solar wind‐magnetosphere coupling functions are considered: the standard rectified coupling function, a function due to Siscoe, and a recent function due to Newell. Model AL and Dst predictions are validated using the average relative variance (ARV), correlation coefficient (COR), and root mean squared error (RMSE). The Newell input function yielded the best model AL predictions by all three measures (mean ARV, COR, and RMSE), followed by the rectified, then Siscoe input functions. Model AL predictions correlate at least 1 standard deviation better with the AL index data than a direct correlation between the input coupling functions and the AL index. The mean Dst ARV results show better prediction performance for the rectified input than the Siscoe and Newell inputs. The mean Dst COR and RMSE measures do not readily distinguish between the three input coupling functions.
Interdecadal unstationary relationship between NAO and east China's summer precipitation patterns
Authors: Gu Wei , Li Chongyin , Li Weijing , Zhou Wen , Chan Johnny C. L.
Published: July 2009

Based on a 120‐year Chinese station rainfall dataset and historical NAO indices, the interdecadal unstationary relationship between the North Atlantic Oscillation (NAO) and east China's summer precipitation patterns is revealed for the period 1880–1999. It is shown that on the interannual timescale, the March NAO is closely related to the first leading precipitation mode which exhibits an out‐of‐phase variation of the precipitation between the Yangtze River Valley and Southeast China, and the January NAO is closely related to the third leading mode which depicts the anomalous rainfall in North China and its out‐of‐phase variation in the Yangtze River Delta. Both of the two relationships are characterized by clear and consistent interdecadal variations, with almost the same transition points occurring in about 1905, 1925 and 1950, respectively. Further analyses imply that these interdecadal changes of the relationship are possibly associated with the SSTA in North Pacific and North Atlantic.
Spontaneous onset of a Madden‐Julian oscillation event in a cloud‐system‐resolving simulation
Authors: Miura Hiroaki , Satoh Masaki , Katsumata Masaki
Published: July 2009

Spontaneous onset of a Madden‐Julian Oscillation (MJO) event in November 2006 was reproduced at a proper location and time by a global cloud‐resolving model (CRM) used with a relatively coarse horizontal grid. Preconditioning of moisture was simulated about 4‐days prior to the onset in the Indian Ocean, which agreed with data obtained in an in‐situ observation. To investigate influence of zonal Sea Surface Temperature (SST) gradient in the Indian Ocean, we conducted a sensitivity study comparing composites made from five ensemble simulations. It was found that the eastward‐moving signal of this MJO event could be obscured if SST were zonally uniform in the western Indian Ocean. Zonal SST gradient has not been considered important in the previous studies about the MJO onset, but SST distribution locating cooler SST in the west side possibly help enhance convection in slow eastward‐moving envelopes of the MJO.
Magnetic flux in the magnetotail and polar cap during sawteeth, isolated substorms, and steady magnetospheric convection events
Authors: Huang Chao‐Song , DeJong Anna D. , Cai Xia
Published: July 2009

Different magnetospheric dynamic processes, such as sawtooth events, isolated substorms, and steady magnetospheric convection (SMC), can occur, depending on the solar wind condition. The purpose of this study is to calculate the magnetic flux in the magnetotail and in the polar cap during these magnetospheric modes and to establish a quantitative relation between the magnetic flux and the solar wind parameters. We use the Imager for Magnetopause‐to‐Aurora Global Exploration Far Ultraviolet Imager and Polar Ultraviolet Imager measurements to derive the magnetic flux in the polar cap and the Geotail measurements to derive the magnetic flux in the magnetotail. The average value of the magnetic flux at the sawtooth onset is ∼1 GWb in the polar cap and magnetotail, and the relative decrease of the magnetic flux from the maximum value at the sawtooth onset to the minimum value after the onset is 24–26.5%. The average magnetic flux in the polar cap at the onset of isolated substorms is 0.68 GWb and decreases by 26.5% after the expansion phase. The magnetic flux in the polar cap during SMC events varies between 0.3 and 0.8 GWb. The magnetic flux at the isolated substorm onset is at the upper limit of the magnetic flux of SMC events for the same merging electric field, and the magnetic flux at the sawtooth onset is always higher than that during isolated substorms and during SMC events. The magnetic flux in the magnetotail and polar cap during sawtooth events and isolated substorms increases gradually before the onset and then decreases rapidly after the onset, which is consistent with the traditional energy loading‐unloading scenario. However, the maximum magnetic flux at the sawtooth or isolated substorm onset is not a constant but increases with the merging electric field and with the corrected Dst index. The results also provide reasonable explanation of the relatively constant period of sawtooth events.
Is the normal heart rate “chaotic” due to respiration?
Authors: Wessel Niels , Riedl Maik , Kurths Jürgen
Published: July 2009

The incidence of cardiovascular diseases increases with the growth of the human population and an aging society, leading to very high expenses in the public health system. Therefore, it is challenging to develop sophisticated methods in order to improve medical diagnostics. The question whether the normal heart rate is chaotic or not is an attempt to elucidate the underlying mechanisms of cardiovascular dynamics and therefore a highly controversial topical challenge. In this contribution we demonstrate that linear and nonlinear parameters allow us to separate completely the data sets of the three groups provided for this controversial topic in nonlinear dynamics. The question whether these time series are chaotic or not cannot be answered satisfactorily without investigating the underlying mechanisms leading to them. We give an example of the dominant influence of respiration on heart beat dynamics, which shows that observed fluctuations can be mostly explained by respiratory modulations of heart rate and blood pressure (coefficient of determination: 96%). Therefore, we recommend reformulating the following initial question: “Is the normal heart rate chaotic?” We rather ask the following: “Is the normal heart rate ‘chaotic’ due to respiration?”
On the nature of heart rate variability in a breathing normal subject: A stochastic process analysis
Authors: Buchner Teodor , Petelczyc Monika , Żebrowski Jan J. , Prejbisz Aleksander , Kabat Marek , Januszewicz Andrzej , Piotrowska Anna Justyna , Szelenberger Waldemar
Published: July 2009

Human heart rate is moderated by the autonomous nervous system acting predominantly through the sinus node (the main cardiac physiological pacemaker). One of the dominant factors that determine the heart rate in physiological conditions is its coupling with the respiratory rhythm. Using the language of stochastic processes, we analyzed both rhythms simultaneously taking the data from polysomnographic recordings of two healthy individuals. Each rhythm was treated as a sum of a deterministic drift term and a diffusion term (Kramers–Moyal expansion). We found that normal heart rate variability may be considered as the result of a bidirectional coupling of two nonlinear oscillators: the heart itself and the respiratory system. On average, the diffusion (noise) component measured is comparable in magnitude to the oscillatory (deterministic) term for both signals investigated. The application of the Kramers–Moyal expansion may be useful for medical diagnostics providing information on the relation between respiration and heart rate variability. This interaction is mediated by the autonomous nervous system, including the baroreflex, and results in a commonly observed phenomenon—respiratory sinus arrhythmia which is typical for normal subjects and often impaired by pathology.
Three-axis rapid steering of optically propelled micro/nanoparticles
Authors: Huang Yanan , Wan Jingfang , Cheng Ming-Chieh , Zhang Zhipeng , Jhiang Sissy M. , Menq Chia-Hsiang
Published: July 2009

This paper presents the design and implementation of a three-axis steering system, wherein a micro/nanoparticle is optically trapped and propelled to serve as a measurement probe. The actuators in the system consist of a deformable mirror enabling axial steering and a two-axis acousto-optic deflector for lateral steering. The actuation range is designed and calibrated to be over 20 μm along the two lateral axes and over 10 μm along the axial direction. The actuation bandwidth of the two lateral axes is over 50 kHz and the associated resolution is 0.016 nm (1σ). The axial resolution is 0.16 nm, while the bandwidth is enhanced to over 3 kHz by model cancellation method. The performance of the three-axis steering system is illustrated by three sets of experiments. First, active Brownian motion control of the trapped probe is utilized to enhance trapping stability. Second, a large range three-dimensional (3D) steering of a 1.87 μm probe, contouring a complex 3D trajectory in a 6×6×4 μm3 volume, is demonstrated. Third, a closed-loop steering is implemented to achieve improved precision.
Effects of the mean free path and relaxation in a model for the aggregation of particles in superfluid media
Authors: Alves S. G. , Vilesov A. F. , Ferreira S. C.
Published: July 2009

In this paper, we study a two-dimensional model for the growth of molecular clusters in superfluid helium at low temperature. In the model, particles of diameter a follow random ballistic moves of length δ=a−256a. Upon attachment on the cluster surface, particles allow one-step relaxation to the nearest twofold coordinated site. Average coordination numbers of particles show that in the presence of relaxation the screening for incoming particles modifies the microscopic structure of the cluster. These results are in qualitative agreement with experimental aggregation of methane in He droplets, in which large abundance of fully coordinated sites is observed. The average coordination number increases with δ, showing that screening is relevant when relaxation is present. As the cluster size increases, the corresponding structure clusters changes from a compact to a fractal, typical of ballistic and diffusion limited models, respectively. A scaling ansatz describing the crossover between the two regimes is proposed.
Chirped pulse multiphoton ionization of nitrogen: Control of selective rotational excitation in N2+(B Σ2u+)
Authors: Plenge J. , Wirsing A. , Raschpichler C. , Meyer M. , Rühl E.
Published: July 2009

We report on fluorescence spectra of N2+(B Σ2u+)→N2+(X Σ2g+) obtained from multiphoton ionization of molecular nitrogen by 804 nm femtosecond laser pulses. The analysis of the fluorescence spectra reveals that the vibrational levels v=0 and v=4 in the B Σ2u+-state of N2+ are primarily populated. The rotational state distribution of N2+(B Σ2u+, v=0) is determined from the rotationally resolved fluorescence spectra. It is demonstrated that the linear chirp of the 804 nm femtosecond laser pulse has a strong influence on the rotational state distribution of the vibrational ground state of the molecular cation N2+(B Σ2u+, v=0). Possible mechanisms leading to the experimental results are discussed. The particular population of the vibrational levels as well as the linear chirp dependence of the fluorescence signal gives evidence for the importance of a resonant intermediate state. The N2 a Π1-state is likely involved in a resonant multiphoton excitation process. This permits to selectively control the rotational population of the cation that is formed via chirped pulse multiphoton ionization.
Crystal field theory analysis of rovibrational spectra of carbon monoxide monomers isolated in solid parahydrogen
Authors: Fajardo Mario E. , Lindsay C. Michael , Momose Takamasa
Published: July 2009

We report the first rotationally resolved and completely assigned rovibrational spectrum for a nonhydride molecule rotating in the solid phase: carbon monoxide (CO) monomers isolated in cryogenic solid parahydrogen (p-H2). We employ a modified crystal field theory model, in which the CO molecular spectroscopic constants are taken as adjustable parameters, to make good spectroscopic assignments for all the observed features. We discuss the limitations of this approach and highlight the need for improved theoretical models of molecular rotation dynamics in quantum solids.
Matrix effects on secondary ion emission from a room-temperature ionic liquid, 1-ethyl-3-methylimidazolium bis[trifluoromethanesulfonyl]imide
Authors: Souda Ryutaro
Published: July 2009

The ionization mechanism of room-temperature ionic liquids has been investigated using time-of-flight secondary ion mass spectrometry in the temperature range of 15–300 K. Analyses of 1-ethyl-3-methylimidazolium bis[trifluoromethanesulfonyl]imide ([emim][Tf2N]) deposited on a Ni(111) substrate revealed that the [emim]+ and [Tf2N]− yields increase together with the Ni+ yield at monolayer coverage; no such increase was observed for the films deposited on a D2O spacer layer. Results indicated that the [emim][Tf2N] molecule is not perfectly ionized; the Ni(111) surface accepts (for [emim]+) or donates (for [Tf2N]−) an electron with higher efficiency than the counterion because of the metal band effect. This phenomenon might be induced by electrostatic interactions between the separated cation and anion during sputtering. It is also suggested that the sputtered Ni atom can be ionized nonadiabatically by the formation of a quasimolecule with adspecies. The multilayer of [emim][Tf2N] deposited at 15 K has a porous structure, resembling that of polar molecules, because of nonionic intermolecular interactions. The phase transition is identifiable, together with the morphological change in the crystalline film, from temperature evolutions of the secondary ion yields.
Induced charge electro osmotic mixer: Obstacle shape optimization
Authors: Jain Mranal , Yeung Anthony , Nandakumar K.
Published: July 2009

Efficient mixing is difficult to achieve in miniaturized devices due to the nature of low Reynolds number flow. Mixing can be intentionally induced, however, if conducting or nonconducting obstacles are embedded within the microchannel. In the case of conducting obstacles, vortices can be generated in the vicinity of the obstacle due to induced charge electro-osmosis (ICEO) which enhances mixing of different streams: the obstacle shape affects the induced zeta potential on the conducting surface, which in turn influences the flow profile near the obstacle. This study deals with optimization of the geometric shape of a conducting obstacle for the purpose of micromixing. The obstacle boundary is parametrically represented by nonuniform rational B-spline curves. The optimal obstacle shape, which maximizes the mixing for given operating conditions, is found using genetic algorithms. Various case studies at different operating conditions demonstrated that the near right triangle shape provides optimal mixing in the ICEO flow dominant regime, whereas rectangular shape is the optimal shape in diffusion dominant regime. The tradeoff between mixing and transport is examined for symmetric and nonsymmetric obstacle shapes.
Analysis reveals when evolution favors one mode of gene regulation over another
Authors: Day Charles
Published: July 2009

Bacteria use two basic modes for controlling the expression of a gene. Which mode prevails depends on how conditions vary and on the statistical mechanics of genetic mutation.
Need for clean energy, waste transmutation revives interest in hybrid fusion–fission reactors
Authors: Feder Toni
Published: July 2009

Sweet solution or pie in the sky? Hybrids get new attention.
Special report: Obama proposes big increases for energy, climate change, and basic research
Authors: Kramer David
Published: July 2009

The president’s first budget, and a supplement from the American Recovery and Reinvestment Act, would put federal support for basic physical sciences research back on schedule for a 10-year doubling by 2016.
Industrial R&D in transition
Authors: Anderson R. Joseph , Butler Orville R.
Published: July 2009

An American Institute of Physics study completed in 2008 documents the ways in which the corporate physicist’s work has changed in the past 40 years. Here are its major findings.
Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy
Authors: Schuettpelz Eric , Pryer Kathleen M.
Published: July 2009

In today's angiosperm-dominated terrestrial ecosystems, leptosporangiate ferns are truly exceptional—accounting for 80% of the ≈11,000 nonflowering vascular plant species. Recent studies have shown that this remarkable diversity is mostly the result of a major leptosporangiate radiation beginning in the Cretaceous, following the rise of angiosperms. This pattern is suggestive of an ecological opportunistic response, with the proliferation of flowering plants across the landscape resulting in the formation of many new niches—both on forest floors and within forest canopies—into which leptosporangiate ferns could diversify. At present, one-third of leptosporangiate species grow as epiphytes in the canopies of angiosperm-dominated tropical rain forests. However, we know too little about the evolutionary history of epiphytic ferns to assess whether or not their diversification was in fact linked to the establishment of these forests, as would be predicted by the ecological opportunistic response hypothesis. Here we provide new insight into leptosporangiate diversification and the evolution of epiphytism by integrating a 400-taxon molecular dataset with an expanded set of fossil age constraints. We find evidence for a burst of fern diversification in the Cenozoic, apparently driven by the evolution of epiphytism. Whether this explosive radiation was triggered simply by the establishment of modern angiosperm-dominated tropical rain forest canopies, or spurred on by some other large-scale extrinsic factor (e.g., climate change) remains to be determined. In either case, it is clear that in both the Cretaceous and Cenozoic, leptosporangiate ferns were adept at exploiting newly created niches in angiosperm-dominated ecosystems.
A search for factors influencing etioplast–chloroplast transition
Authors: Pudelski Birgit , Soll Jürgen , Philippar Katrin
Published: July 2009

Chloroplast biogenesis in angiosperm plants requires the light-dependent transition from an etioplast stage. A key factor in this process is NADPH:protochlorophyllide oxidoreductase A (PORA), which catalyzes the light-dependent reduction of protochlorophyllide to chlorophyllide. In a recent study the chloroplast outer envelope channel OEP16 was described to be involved in etioplast to chloroplast transition by forming the translocation pore for the precursor protein of PORA [Pollmann et al. (2007)
Proc Natl Acad Sci USA
104:2019–2023]. This hypothesis was based on the finding that a single
OEP16.1
knockout mutant in
Arabidopsis thaliana
was severely affected during seedling de-etiolation and PORA protein was absent in etioplasts. In contrast, in our study the identical T-DNA insertion line greened normally and showed normal etioplast to chloroplast transition, and mature PORA was present in etioplasts [Philippar et al. (2007)
Proc Natl Acad Sci USA
104:678–683]. To address these conflicting results regarding the function of OEP16.1 for PORA import, we analyzed several lines segregating from the original
OEP16.1
T-DNA insertion line. Thereby we can unequivocally show that the loss of OEP16.1 neither correlates with impaired PORA import nor causes the observed de-etiolation phenotype. Furthermore, we found that the mutant line contains at least 2 additional T-DNA insertions in the genes for the extracellular polygalacturonase converter
AroGP1
and the plastid-localized chorismate mutase
CM1
. However, detailed examination of the de-etiolation phenotype and a genomewide transcriptional analysis revealed no direct influence of these genes on etioplast to chloroplast transition in
Arabidopsis
cotyledons.
Persistence of fear memory across time requires the basolateral amygdala complex
Authors: Poulos Andrew M. , Li Veronica , Sterlace Sarah S. , Tokushige Fonda , Ponnusamy Ravikumar , Fanselow Michael S.
Published: July 2009

Mammals evolved a potent fear-motivated defensive system capable of single-trial fear learning that shows no forgetting over the lifespan of the animal. The basolateral amygdala complex (BLA) is considered an essential component of this conditional fear learning system. However, recent studies challenge this view and suggest that plasticity within other brain regions (i.e., central nucleus of the amygdala) may be crucial for fear conditioning. In the present study, we examine the mnemonic limits of contextual fear conditioning in the absence of the BLA using overtraining and by measuring remote fear memories. After excitotoxic lesions of the BLA were created, animals underwent overtraining and were tested at recent and remote memory intervals. Here we show that animals with BLA lesions can learn normal levels of fear. However, this fear memory loses its adaptive features: it is acquired slowly and shows substantial forgetting when remote memory is tested. Collectively, these findings suggest that fear-related plasticity acquired by brain regions outside of the BLA, unlike those acquired in the intact animals, do so for a relatively time-limited period.
The role of World War II in the development of Luxembourgish as a national language
Authors: Wagner Melanie , Davies Winifred V.
Published: July 2009

This paper explores the link between explicit Luxembourgish language policy and the actual practices as well as expressed attitudes of a group of speakers of Luxembourgish, with the aim of studying the role of World War II in the advancement of Luxembourgish as Luxembourg’s national language. The first two sections introduce the theoretical approach of the paper and provide an overview of the history and present situation of Luxembourg and Luxembourgish. The following two sections present the findings of a sociolinguistic study of language choice, language values and identities, and linguistic (in)security among a group of Luxembourgish letter-writers, as well as recent interview data provided by the sole surviving correspondent. The final section brings together these results and the claims made regarding the role of World War II in the changing status of Luxembourgish and points out the complexity of this discussion.
Life after a diagnosis with endometriosis ‐ a 15 years follow‐up study
Authors: FAGERVOLD BENTE , JENSSEN MARITA , HUMMELSHOJ LONE , MOEN METTE HAASE
Published: July 2009

Objective. Previous studies have elucidated the negative impact of endometriosis on life, but the patient selection may have contributed to a skewed picture. The aim of this study was to investigate longitudinally the consequences of the disease in women diagnosed with endometriosis 15 years ago. Design. Retrospective descriptive. Setting. Trondheim 2007. Sample. One hundred thirty women diagnosed with endometriosis at St. Olav's Hospital in Trondheim between 1991 and 1993. Methods. Questionnaires. Response rate of 60%. Main outcome measures. Consequences of living with endometriosis. Results. Of the women, 19.2% never experienced pelvic pain and 21.8% did not have any further visits to the gynecological department after being diagnosed. Almost 70% had received pharmaceutical treatment and positive effect on pain was reported by 41% for NSAIDs and oral contraceptives, and by 62% for progestins and GnRH‐analogues. Satisfactory effect on pain after surgical interventions at the time of diagnosis was reported by 60.9%, and by 89.9% after later surgeries. Of the infertile patients, 75.6% succeeded in delivering one or more biological children. Half of the women reported that endometriosis had some negative impact on their lives. After menopause, 96.9% were free from pain. Conclusion. This study confirms that endometriosis is a condition that often has considerable impact on a woman's life. However, the study also found that endometriosis does not always cause pain, that treatment in many cases is effective, that infertility may be overcome, and that almost all postmenopausal women were free from endometriosis‐associated pain.
Total reflection of x-ray fluorescence (TXRF): a mature technique for environmental chemical nanoscale metrology
Authors: Borgese L , Zacco A , Bontempi E , Colombi P , Bertuzzi R , Ferretti E , Tenini S , Depero L E
Published: July 2009

Total reflection x-ray fluorescence (TXRF) is a technique well established for chemical analysis of samples deposited as a thin layer. Nowadays it is mainly employed for electronic industry quality control. Recently, very compact and economic TXRF instrumentation was proposed. Combining this with the capability to analyze liquid samples, this technique is suitable to be employed in many different applications, comprising the very critical field of environmental analysis. Comparisons with the standard atomic absorption spectroscopy (AAS) technique show that TXRF is a practical, accurate, and reliable technique. Indeed, round-robin activities have already been started. Despite the efficiency and economy of the developed portable TXRF instrumentation, this is not widely employed for chemical laboratory analysis probably because TXRF is not an officially recognized technique, i.e. it is not yet normative-subjected. This fact could also be due to the long background of analytical applications developed for AAS, ICPS or inductively coupled plasma mass spectroscopy (ICP-MS) up to now. In this paper, we present a work of environmental monitoring of an industrial site, performed by means of bioindicators (lichens). The analysis of trace elements concentration in lichen was usually conducted with spectrophotometric techniques, such as AAS and ICP-MS, which were accepted by common regulations and normative-subjected. In this study, we accomplished a comparative lichen analysis by AAS and TXRF. The reproducibility of the obtained results showed the high correspondence between the two techniques. This comparison highlighted the versatility of the TXRF apparatus that allowed more rapid and simultaneous element detection. The obtained results suggested that this portable TXRF system could be suitable for regulation to produce certificated analysis upto ppb concentrations for some elements.
Lateral genetic transfer: open issues
Authors: Ragan Mark A. , Beiko Robert G.
Published: July 2009

Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.
The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them
Authors: Doolittle W. Ford
Published: July 2009

Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.
Genome beginnings: rooting the tree of life
Authors: Lake James A. , Skophammer Ryan G. , Herbold Craig W. , Servin Jacqueline A.
Published: July 2009

A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.
Conjugative plasmids: vessels of the communal gene pool
Authors: Norman Anders , Hansen Lars H. , Sørensen Søren J.
Published: July 2009

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the termsupergenometo describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.
The Painted Turtle, Chrysemys picta: A Model System for Vertebrate Evolution, Ecology, and Human Health
Authors: Valenzuela Nicole
Published: July 2009

INTRODUCTION

Painted turtles (Chrysemys picta) are representatives of a vertebrate clade whose biology and phylogenetic position hold a key to our understanding of fundamental aspects of vertebrate evolution. These features make them an ideal emerging model system. Extensive ecological and physiological research provide the context in which to place new research advances in evolutionary genetics, genomics, evolutionary developmental biology, and ecological developmental biology which are enabled by current resources, such as a bacterial artificial chromosome (BAC) library of C. picta, and the imminent development of additional ones such as genome sequences and cDNA and expressed sequence tag (EST) libraries. This integrative approach will allow the research community to continue making advances to provide functional and evolutionary explanations for the lability of biological traits found not only among reptiles but vertebrates in general. Moreover, because humans and reptiles share a common ancestor, and given the ease of using nonplacental vertebrates in experimental biology compared with mammalian embryos, painted turtles are also an emerging model system for biomedical research. For example, painted turtles have been studied to understand many biological responses to overwintering and anoxia, as potential sentinels for environmental xenobiotics, and as a model to decipher the ecology and evolution of sexual development and reproduction. Thus, painted turtles are an excellent reptilian model system for studies with human health, environmental, ecological, and evolutionary significance.
Ants (Formicidae): Models for Social Complexity
Authors: Smith Chris R. , Dolezal Adam , Eliyahu Dorit , Holbrook C. Tate , Gadau Jürgen
Published: July 2009

INTRODUCTION

The family Formicidae (ants) is composed of more than 12,000 described species that vary greatly in size, morphology, behavior, life history, ecology, and social organization. Ants occur in most terrestrial habitats and are the dominant animals in many of them. They have been used as models to address fundamental questions in ecology, evolution, behavior, and development. The literature on ants is extensive, and the natural history of many species is known in detail. Phylogenetic relationships for the family, as well as within many subfamilies, are known, enabling comparative studies. Their ease of sampling and ecological variation makes them attractive for studying populations and questions relating to communities. Their sociality and variation in social organization have contributed greatly to an understanding of complex systems, division of labor, and chemical communication. Ants occur in colonies composed of tens to millions of individuals that vary greatly in morphology, physiology, and behavior; this variation has been used to address proximate and ultimate mechanisms generating phenotypic plasticity. Relatedness asymmetries within colonies have been fundamental to the formulation and empirical testing of kin and group selection theories. Genomic resources have been developed for some species, and a whole-genome sequence for several species is likely to follow in the near future; comparative genomics in ants should provide new insights into the evolution of complexity and sociogenomics. Future studies using ants should help establish a more comprehensive understanding of social life, from molecules to colonies.
Marking Individual Ants for Behavioral Sampling in a Laboratory Colony: Figure 1.
Authors: Holbrook C. Tate
Published: July 2009

INTRODUCTION

Ant societies are tractable and malleable, two features that make them ideal models for probing the organization of complex biological systems. The ability to identify specific individuals while they function as part of a colony permits an integrative analysis of social complexity, including self-organizational processes (i.e., how individual-level properties and social interactions give rise to emergent, colony-level attributes such as division of labor and collective decision making). Effects of genotype, nutrition, and physiology on individual behavior and the organization of work also can be investigated in this manner, through correlative and manipulative approaches. Moreover, aspects of colony demography (e.g., colony size, and age and size distributions of workers) can be altered experimentally to examine colony development and regulatory mechanisms underlying colony homeostasis and resiliency. This protocol describes how to sample the behavior of ants living in a colony under laboratory conditions. Specifically, it outlines how to identify and observe individuals within a colony, an approach that can be used to quantify individual- and colony-level patterns of behavior. When a lower-resolution measure of overall group behavior is desired, individual identities might not be required. Given the diversity of ants and their study, this protocol provides a very general methodology; the details can be modified according to the body size, colony size, and ecology of the focal species, as well as to specific research aims. These basic techniques can also be extended to more advanced experimental designs such as manipulation of colony demography and hormone treatment.
General Dissection of Female Ant Reproductive System and Brain
Authors: Dolezal Adam , Brent Colin
Published: July 2009

INTRODUCTION

Dissection of the reproductive system of ant workers and queens can be useful for answering many questions. Observations of ovarian status in both female castes can be used to identify relationships between other factors and the ovaries, determine whether an individual has laid eggs, and, with more advanced molecular techniques, identify the end product of the oocyte in question (e.g., trophic egg, viable egg, nonviable egg). In addition, dissection of queens allows for observation of the spermatheca (the sperm storage organ), and thus identification of whether an individual has mated. Sperm can also be sampled for genetic analyses. In this protocol, we describe the dissection of the female ant reproductive system. We also discuss dissection of the corpora allata glands, where juvenile hormone is produced.
GC-MS for Characterization and Identification of Ant Semiochemicals
Authors: Eliyahu Dorit
Published: July 2009

INTRODUCTION

Living in a predominantly dark environment, ants rely mostly on chemical signals for communication. Trail and alarm pheromones are the most widely studied and best characterized of all ant semiochemicals, but other such compounds can influence a variety of other behaviors, including reproductive activities, sexual development, nest mate and caste recognition, and defense. A typical worker body contains more than 10 different semiochemical-producing glands, and the surface of the cuticle is covered with lipids that serve as recognition signals. The methods of choice for collection and identification of ant semiochemicals should be determined based on results of behavioral analyses. These can indicate the source (e.g., glandular, cuticular) and the nature (volatile vs. nonvolatile) of the chemical. This protocol presents a number of different methods for collecting lipid semiochemicals. These can be followed by gas chromatography (GC) coupled with mass spectrometry (MS) to better characterize, and possibly identify, the semiochemical in question.
Using Iterative Methods for Global Multiple Sequence Alignment
Authors: Mount David W.
Published: July 2009

INTRODUCTION

Finding a global optimal alignment of more than two sequences that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time is especially difficult. The dynamic programming algorithm used for optimal alignment of pairs of sequences can be extended to global alignment of three sequences, but for more than three sequences, only a small number of relatively short sequences may be analyzed. Thus, approximate methods are used for global alignment. One class of these is iterative global alignment, which makes an initial global alignment of groups of sequences and then revises the alignment to achieve a more reasonable result. This article discusses several iterative alignment methods. In particular, steps are provided for using the Sequence Alignment by Genetic Algorithm (SAGA).
Indicators Based on Fluorescence Resonance Energy Transfer (FRET): Figure 1.
Authors: Tsien Roger Y.
Published: July 2009

INTRODUCTION

One of the major new trends in the design of indicators for optically imaging biochemical and physiological functions of living cells has been the exploitation of fluorescence resonance energy transfer (FRET). FRET is a well-known spectroscopic technique for monitoring changes in the proximity and mutual orientation of pairs of chromophores. It has long been used in biochemistry and cell biology to assess distances and orientations between specific labeling sites within a single macromolecule or between two separate molecules. More recently, macromolecules or molecular pairs have been engineered to change their FRET in response to biochemical and physiological signals such as membrane potential, cyclic AMP (cAMP), protease activity, free Ca2+ and Ca2+-calmodulin (CaM) concentrations, protein-protein heterodimerization, phosphorylation, and reporter-gene expression. Because FRET is general, nondestructive, and easily imaged, it has proven to be one of the most versatile spectroscopic readouts available to the designer of new probes. FRET is particularly amenable to emission ratioing, which is more reliably quantifiable than single-wavelength monitoring and better suited than excitation ratioing to high-speed and laser-excited imaging. This article summarizes the photophysical principles of FRET and the types of indicators used.