bluuebunny/crossref_metadata_2025 huggingface dataset:
A Baroclinic Instability that Couples Balanced Motions and Gravity Waves
Authors: Plougonven Riwal , Muraki David J. , Snyder Chris
Published: June 2005

Normal modes of a linear vertical shear (Eady shear) are studied within the linearized primitive equations for a rotating stratified fluid above a rigid lower boundary. The authors' interest is in modes having an inertial critical layer present at some height within the flow. Below this layer, the solutions can be closely approximated by balanced edge waves obtained through an asymptotic expansion in Rossby number. Above, the solutions behave as gravity waves. Hence these modes are an example of a spatial coupling of balanced motions to gravity waves.

The amplitude of the gravity waves relative to the balanced part of the solutions is obtained analytically and numerically as a function of parameters. It is shown that the waves are exponentially small in Rossby number. Moreover, their amplitude depends in a nontrivial way on the meridional wavenumber. For modes having a radiating upper boundary condition, the meridional wavenumber for which the gravity wave amplitude is maximal occurs when the tilts of the balanced edge wave and gravity waves agree.
A New Look at the Pacific Storm Track Variability: Sensitivity to Tropical SSTs and to Upstream Seeding
Authors: Orlanski Isidoro
Published: June 2005

There is a fairly well defined stationary wave and storm track response to El Niño SSTs over the Pacific. In this paper, the case is made that this response is a direct result of increased baroclinicity in the central Pacific and that changes in the stationary wave pattern farther east are primarily forced by changes in these transient eddies. There is also a lot of natural variability that is not associated with El Niño. The paper also stresses the point that much of the variability can be understood as forced by variations in the upstream seeding of the storm track. The question of whether these seeding variations should be thought of as chaotic noise or forced by identifiable mechanisms is not addressed. Thus, the claim is that the storm track variability and its feedback to the quasi-stationary circulation depends on two key parameters: mid-Pacific baroclinicity, controlled by SSTs, and the strength of the upstream seeding.

The approach is to first examine the effect of storm track seeding by waves entering from the Asian continent during normal years (non-ENSO years). The results show that two mechanisms operate to distribute eddy energy along the storm track: downstream development and baroclinic development. The large effect on baroclinic development at the storm track entrance results from a combination of factors: surface baroclinicity, land–sea contrast, and strong moist fluxes from the western subtropics. Experiments show that sensitivity to the seeding amplitude is large. The larger the seeding amplitude, the closer the more intense baroclinic waves flux energy downstream to upper-level waves. These barotropic waves tend to break anticyclonically and produce a ridge in the eastern Pacific.

Sensitivity to SST anomalies shows qualitative and quantitative similarity with the observed anomalies. Simulations show increased mid-Pacific baroclinicity because stronger convection in the midtropical Pacific enhances a large pool of warm air over the entire mideastern subtropical ocean. Waves with sources at the storm track entrance break anticyclonically and produce the ridge in the eastern Pacific. On the other hand, baroclinic waves generated or regenerated in the mid-Pacific tend to break cyclonically, produce a trough tendency, and reduce the eastern ridge amplitude in the Pacific–North American (PNA) sector.

These results strongly suggest thatthe variability of the quasi-permanent circulation indeed could be produced by the high-frequency eddy feedback, andtwo mechanisms are primarily responsible for the forcing of the quasi-permanent circulation: downstream development from the western Pacific and the anomalous baroclinicity in the mideastern Pacific.

The intensity of these counteracting forcings gives the different flavors of the El Niño response over the PNA region. Regardless of the SST anomaly strength, the PNA patterns seem unique but obviously have different intensities.
Structural Characteristics of Convective Systems over South America Related to Cold-Frontal Incursions
Authors: Siqueira Jose Ricardo , Rossow William B. , Machado Luiz Augusto Toledo , Pearl Cindy
Published: June 2005

International Satellite Cloud Climatology Project (ISCCP DX) and microwave sensor data collected by the Tropical Rainfall Measuring Mission (TRMM) are used to identify and describe structural characteristics of convective systems (CSs) over continental South America (SA) related to cold-frontal incursions in a 3-yr period. An austral wet-season climatology for CS events of the three most important types of front–tropical convection interaction is built by applying latitude–time diagrams and a cloud-tracking method to DX data. Type 1 is characterized by the penetration of a cold front over subtropical SA that interacts with convection and moves with it into lower tropical latitudes. Type 2 refers to Amazon convection and its enhancement in a quasi-stationary northwest–southeast-oriented band extending from the Amazon to subtropical SA along with the passage of a cold front in the subtropics and characterizes the synoptic formation of the South Atlantic convergence zone. A quasi-stationary cold front over subtropical SA that has only weak interaction with tropical convection corresponds to type 3.

Results show that the three types of front–tropical convection interaction strongly modulate deep convection over SA, producing mesoscale CSs with significant fractions of deep convective clouds and rain at their mature phase. Type 2 CSs (type 1 CSs) are constituted of larger deep convective cloud fractions with weaker (stronger) vertical development compared to type 1 CSs (type 3 CSs) in the Tropics (subtropics), resulting in larger rain fractions and less (more) presence of convective rain. Type 1 CSs have larger fractions of deep convective clouds and rain but with weaker vertical development in the subtropics than in the Tropics, showing that cold fronts organize convection more in area in the subtropics, but more in vertical extent in the Tropics. Life cycle variations of CS cloud and rain properties show tropical CSs with a more intense initial development and similar structural differences between the CS types and those found at their mature phase.
Calibrated Probabilistic Forecasting Using Ensemble Model Output Statistics and Minimum CRPS Estimation
Authors: Gneiting Tilmann , Raftery Adrian E. , Westveld Anton H. , Goldman Tom
Published: June 2005

Ensemble prediction systems typically show positive spread-error correlation, but they are subject to forecast bias and dispersion errors, and are therefore uncalibrated. This work proposes the use of ensemble model output statistics (EMOS), an easy-to-implement postprocessing technique that addresses both forecast bias and underdispersion and takes into account the spread-skill relationship. The technique is based on multiple linear regression and is akin to the superensemble approach that has traditionally been used for deterministic-style forecasts. The EMOS technique yields probabilistic forecasts that take the form of Gaussian predictive probability density functions (PDFs) for continuous weather variables and can be applied to gridded model output. The EMOS predictive mean is a bias-corrected weighted average of the ensemble member forecasts, with coefficients that can be interpreted in terms of the relative contributions of the member models to the ensemble, and provides a highly competitive deterministic-style forecast. The EMOS predictive variance is a linear function of the ensemble variance. For fitting the EMOS coefficients, the method of minimum continuous ranked probability score (CRPS) estimation is introduced. This technique finds the coefficient values that optimize the CRPS for the training data. The EMOS technique was applied to 48-h forecasts of sea level pressure and surface temperature over the North American Pacific Northwest in spring 2000, using the University of Washington mesoscale ensemble. When compared to the bias-corrected ensemble, deterministic-style EMOS forecasts of sea level pressure had root-mean-square error 9% less and mean absolute error 7% less. The EMOS predictive PDFs were sharp, and much better calibrated than the raw ensemble or the bias-corrected ensemble.
A Comparison of the ECMWF, MSC, and NCEP Global Ensemble Prediction Systems
Authors: Buizza Roberto , Houtekamer P. L. , Pellerin Gerald , Toth Zoltan , Zhu Yuejian , Wei Mozheng
Published: June 2005

The present paper summarizes the methodologies used at the European Centre for Medium-Range Weather Forecasts (ECMWF), the Meteorological Service of Canada (MSC), and the National Centers for Environmental Prediction (NCEP) to simulate the effect of initial and model uncertainties in ensemble forecasting. The characteristics of the three systems are compared for a 3-month period between May and July 2002. The main conclusions of the study are the following:the performance of ensemble prediction systems strongly depends on the quality of the data assimilation system used to create the unperturbed (best) initial condition and the numerical model used to generate the forecasts;a successful ensemble prediction system should simulate the effect of both initial and model-related uncertainties on forecast errors; andfor all three global systems, the spread of ensemble forecasts is insufficient to systematically capture reality, suggesting that none of them is able to simulate all sources of forecast uncertainty.The relative strengths and weaknesses of the three systems identified in this study can offer guidelines for the future development of ensemble forecasting techniques.
Singular-Vector-Based Covariance Propagation in a Quasigeostrophic Assimilation System
Authors: Beck Alexander , Ehrendorfer Martin
Published: June 2005

Variational data assimilation systems require the specification of the covariances of background and observation errors. Although the specification of the background-error covariances has been the subject of intense research, current operational data assimilation systems still rely on essentially static and thus flow-independent background-error covariances. At least theoretically, it is possible to use flow-dependent background-error covariances in four-dimensional variational data assimilation (4DVAR) through exploiting the connection between variational data assimilation and estimation theory.

This paper reports on investigations concerning the impact of flow-dependent background-error covariances in an idealized 4DVAR system that, based on quasigeostrophic dynamics, assimilates artificial observations. The main emphasis is placed on quantifying the improvement in analysis quality that is achievable in 4DVAR through the use of flow-dependent background-error covariances. Flow dependence is achieved through dynamical error-covariance evolution based on singular vectors in a reduced-rank approach, referred to as reduced-rank Kalman filter (RRKF). The RRKF yields partly dynamic background-error covariances through blending static and dynamic information, where the dynamic information is obtained from error evolution in a subspace of dimension k (defined here through the singular vectors) that may be small compared to the dimension of the model’s phase space n, which is equal to 1449 in the system investigated here.

The results show that the use of flow-dependent background-error covariances based on the RRKF leads to improved analyses compared to a system using static background-error statistics. That latter system uses static background-error covariances that are carefully tuned given the model dynamics and the observational information available. It is also shown that the performance of the RRKF approaches the performance of the extended Kalman filter, as k approaches n. Results therefore support the hypothesis that significant analysis improvement is possible through the use of flow-dependent background-error covariances given that a sufficiently large number (here on the order of n/10) of singular vectors is used.
Contributions from California Coastal-Zone Surface Fluxes to Heavy Coastal Precipitation: A CALJET Case Study during the Strong El Niño of 1998
Authors: Persson P. Ola G. , Neiman P. J. , Walter B. , Bao J-W. , Ralph F. M.
Published: June 2005

Analysis of the case of 3 February 1998, using an extensive observational system in the California Bight during an El Niño winter, has revealed that surface sensible and latent heat fluxes within 150 km of the shore contributed substantially to the destabilization of air that subsequently produced strong convection and flooding along the coast. Aircraft, dropsonde, and satellite observations gathered offshore documented the sea surface temperatures (SSTs), surface fluxes, stratification, and frontal structures. These were used to extrapolate the effects of the fluxes on the warm-sector, boundary layer air ahead of a secondary cold front as this air moved toward the coast. The extrapolated structure was then validated in detail with nearshore aircraft, wind profiler, sounding, and buoy observations of the frontal convection along the coast, and the trajectory transformations were confirmed with a model simulation. The results show that the surface fluxes increased CAPE by about 26% such that the nearshore boundary layer values of 491 J kg−1 were near the upper end of those observed for cool-season California thunderstorms.

The increased CAPE due to upward sensible and latent heat fluxes was a result of the anomalously warm coastal SSTs (+1°–3°C) typical of strong El Niño events. Applications of the extrapolation method using a surface flux parameterization scheme and different SSTs suggested that convective destabilization due to nearshore surface fluxes may only occur during El Niño years when positive coastal SST anomalies are present. The fluxes may have no effect or a stabilizing effect during non–El Niño years, characterized by zero or negative coastal SST anomalies. In short, during strong El Niños, it appears that the associated coastal SST anomalies serve to further intensify the already anomalously strong storms in southern California, thus contributing to the increased flooding. This modulating effect by El Niño–Southern Oscillation (ENSO) of a mesoscale process has not been considered before in attempts at assessing the impacts of ENSO on U.S. west coast precipitation.
Using Green's Functions to Calibrate an Ocean General Circulation Model
Authors: Menemenlis Dimitris , Fukumori Ichiro , Lee Tong
Published: June 2005

Green's functions provide a simple yet effective method to test and to calibrate general circulation model (GCM) parameterizations, to study and to quantify model and data errors, to correct model biases and trends, and to blend estimates from different solutions and data products. The method is applied to an ocean GCM, resulting in substantial improvements of the solution relative to observations when compared to prior estimates: overall model bias and drift are reduced and there is a 10%–30% increase in explained variance. Within the context of this optimization, the following new estimates for commonly used ocean GCM parameters are obtained. Background vertical diffusivity is (15.1 ± 0.1) × 10−6 m2 s−2. Background vertical viscosity is (18 ± 3) × 10−6 m2 s−2. The critical bulk Richardson number, which sets boundary layer depth, is Ric = 0.354 ± 0.004. The threshold gradient Richardson number for shear instability vertical mixing is Ri0 = 0.699 ± 0.008. The estimated isopycnal diffusivity coefficient ranges from 550 to 1350 m2 s−2, with the largest values occurring at depth in regions of increased mesoscale eddy activity. Surprisingly, the estimated isopycnal diffusivity exhibits a 5%–35% decrease near the surface. Improved estimates of initial and boundary conditions are also obtained. The above estimates are the backbone of a quasi-operational, global-ocean circulation analysis system.
The July 2003 Dakota Hailswaths: Creation, Characteristics, and Possible Impacts
Authors: Parker Matthew D. , Ratcliffe Ian C. , Henebry Geoffrey M.
Published: June 2005

The authors investigate the meteorology associated with two elongated swaths of crop damage produced by severe hailstorms that crossed North Dakota and South Dakota on 4 July and 20 July 2003. These hailswaths, which were observed in a Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) image time series, each persisted for more than a month and were associated with local temperature increases, presumably owing to the enhanced Bowen ratio over dry, crop-free ground. This paper documents the creation and evolution of the convective storms that produced the hailswaths, and then presents evidence that devegetated hailswaths may impact future convective weather. Idealized numerical simulations including hailswath-like surface anomalies, as well as analogies to the extant literature, suggest that hailswaths may play a part in initiating new convective clouds, especially when the low-level winds are parallel to their long axes. Analyses of conventional operational observations also show that the 4 July hailswath may have played a part in the initiation and intensification of a convective storm on 17 July and in the temporarily deviant motion of a convective storm that crossed it on 20 July. Because devegetated hailswaths are common to the central and northern plains during the summer months, and because they have heretofore received little study, a deeper understanding of hailswaths’ impacts upon moist convection may lead to improved short-term weather prediction.
Comparison of Narrow Bipolar Events with Ordinary Lightning as Proxies for Severe Convection
Authors: Jacobson Abram R. , Heavner Mathew J.
Published: June 2005

Narrow bipolar events (NBEs) are a recently studied intracloud electrical-discharge process. It is speculated that an NBE is instigated by the extensive atmospheric shower of an energetic cosmic ray. NBEs cause significant relaxation of the charge separation within the electrified cloud in a short time, on the order of 10 μs. The current flow causes radiation of a distinctive “bipolar” low-frequency/very low frequency signal that can be recorded at locations on earth up to thousands of kilometers from the source. NBEs are preceded/accompanied by the most powerful very high frequency radio emissions seen in any kind of lightning. These intense pulsed radio emissions have been routinely detected with satellite-borne radio receivers in space. Owing to their easy detection and recognition, NBEs might be a useful remote sensing proxy for space-based global, near–real time remote sensing. However, in order for that potential to be realized, NBEs must be shown to be associated, as is ordinary lightning, with severe tropospheric convection, rather than to be just a curiosity of cosmic-ray–atmosphere interactions. This question is addressed with a detailed comparison of NBEs and ordinary lightning using a ground-based lightning-transient research facility that records signals from both ordinary lightning and NBEs, the Los Alamos Sferic-waveform Array (LASA), based in Florida. First, the data from LASA are internally compared to examine the relationship of NBEs and ordinary lightning in both position and time. Second, the relationship of both NBEs and ordinary lightning to simultaneous infrared cloud imagery is examined [from the Geostationary Operational Environmental Satellite-East (GOES-East)] in order to infer the relative affinities of NBEs and ordinary lightning for cloud signatures that are consistent with severe convection.
Western Pacific SST Prediction with an Intermediate El Niño Prediction Model
Authors: Kug Jong-Seong , Kang In-Sik , Jhun Jong-Ghap
Published: June 2005

To improve forecasting skills in the western Pacific sea surface temperature (SST), the authors utilized and modified an intermediate El Niño prediction model. The original model does not have the major SST thermodynamics for western Pacific SST variability, so it cannot simulate interannual variation in the western Pacific correctly. Therefore, the authors have introduced some modifications, such as heat flux and vertical mixing, into the dynamical model in order to capture SST thermodynamics more realistically. The modified model has better forecast skill than the original one, not only for the western Pacific but also for the eastern-central Pacific. The model has predictive skill up to 6-months lead time as judged by a correlation exceeding 0.5.
New Approach to Calculation of Atmospheric Model Physics: Accurate and Fast Neural Network Emulation of Longwave Radiation in a Climate Model
Authors: Krasnopolsky Vladimir M. , Fox-Rabinovitz Michael S. , Chalikov Dmitry V.
Published: June 2005

A new approach based on a synergetic combination of statistical/machine learning and deterministic modeling within atmospheric models is presented. The approach uses neural networks as a statistical or machine learning technique for an accurate and fast emulation or statistical approximation of model physics parameterizations. It is applied to development of an accurate and fast approximation of an atmospheric longwave radiation parameterization for the NCAR Community Atmospheric Model, which is the most time consuming component of model physics. The developed neural network emulation is two orders of magnitude, 50–80 times, faster than the original parameterization. A comparison of the parallel 10-yr climate simulations performed with the original parameterization and its neural network emulations confirmed that these simulations produce almost identical results. The obtained results show the conceptual and practical possibility of an efficient synergetic combination of deterministic and statistical learning components within an atmospheric climate or forecast model. A developmental framework and practical validation criteria for neural network emulations of model physics components are outlined.
Reciprocity and Retribution: Negotiating Gender and Power in Fin-De-Siècle Paris
Authors: Ferguson Eliza Earle
Published: June 2005

Drawing on 251 cases of “crimes of passion” from the fin-de-siècle assize court of the Seine, this article analyzes the terrain of conflict in domestic partnerships among the working poor of Paris. Read in an ethnographic light, the copious testimony in such cases from the couples, their friends, and their neighbors reveals that men and women owed each other reciprocal but incongruous obligations concerning money, sexual fidelity, and household services. When one partner failed to uphold his or her end of the implicit domestic bargain, the other partner could use violence as a form of retributive punishment that was legitimate in the eyes of the community and the court.
“To Domesticate and Civilize Wild Indians”: Allotment and the Campaign to Reform Indian Families, 1875-1887
Authors: Stremlau Rose
Published: June 2005

During the late nineteenth century, critics of Indian affairs proposed a solution to the “Indian problem,” the refusal or inability of Native people to assimilate into American society. Reformers concluded that kinship systems prevented acculturation by undermining individualism and social order, and they turned to federal policy to fracture these extended indigenous families into male-dominant, nuclear families, modeled after middle-class, Anglo-American households. Reformers advocated for allotment, the subdivision of reservations into individual homesteads and the dissolution of tribal governments, because they believed that this process would foster individualism, promote economic self-interest, defeat communalism, and instill the core values of Anglo-American culture in Native people. Reformers expected private property to provide a foundation from which Indians would raise themselves up, and by giving Indians a means for self-support, they saw themselves as tipping the first domino in a chain reaction that would allow Indian men and women to distance themselves from the familial and tribal ties that hindered their personal growth and to cultivate their attachment to American society, which encouraged individualism and materialism.
Where Has Family Time Gone? In Search of Joint Family Activities and the Role of the Family Meal in 1966 and 1999
Authors: Mestdag Inge , Vandeweyer Jessie
Published: June 2005

The idea that family meal time is disappearing is gaining growing attention in Western societies. This article investigates to what extent family time has decreased and what place the family meal has within family time. Belgian time-budget data gathered in 1966 and 1999 were used to answer these research questions. Analyses show parents were spending less time together as a family and also on family meals, especially on working days. Nevertheless, the growing number of dual-earner families was not responsible for the decline in family meal time between 1966 and 1999.
Authoritarian Fatherhood: Andrew Jackson’s Early Familial Lectures to America’s “Red Children”
Authors: Black Jason Edward
Published: June 2005

The present article questions how Andrew Jackson employed the rhetorical strategy of fatherhood to bolster American nationalism while justifying the denigration of American Indians. The author argues that Jackson’s lectures illustrate a paternalism that situated American Indians in a socially subordinate position and that privileged American nationalism—particularly by way of westward and southern expansion. This subordination was accomplished through a rhetoric of authoritarian fatherhood. That is, the father-child relationship that Jackson systematized helped forge an American nationalism. In this article, several samplings of Jackson’s lectures are analyzed to uncover the patterns of Jackson’s authoritarian fatherhood. Jackson’s rhetorical fatherhood coalesces into three themes: fatherly guidance, fatherly punishment, and fatherly demagoguery. These three themes, it will be argued, formed the core of an American paternal nationalism advanced with the rise of Jackson as a national rhetorical figure.
Anatomical Reconstruction of the Lateral Ligaments of the Ankle with a Gracilis Autograft
Authors: Takao Masato , Oae Kazunori , Uchio Yuji , Ochi Mitsuo , Yamamoto Haruyasu
Published: June 2005

Background

Few anatomical and minor invasive procedures have been reported for surgical reconstruction of the lateral ligaments to treat lateral instability of the ankle. Furthermore, there are no standards according to which ligaments should be reconstructed.

Hypothesis

A new technique for anatomically reconstructing the lateral ligaments of the ankle using an interference fit anchoring system and determining which ligaments need to be reconstructed according to the results of standard stress radiography of the talocrural and subtalar joints will be effective for treating lateral instability of the ankle.

Study Design

Case series; level of evidence, 4.

Methods

Twenty-one patients with lateral instability of the ankle underwent surgery using the proposed interference fit anchoring system. Standard stress radiographs of the subtalar joint were performed, and if the talocalcaneal angle was less than 10°, only the anterior talofibular ligament was reconstructed; if there was a 10° or greater opening of the talocalcaneal angle, both the anterior talofibular ligament and the calcaneofibular ligament were reconstructed.

Results

In the 17 patients who received only the anterior talofibular ligament reconstruction, the mean talar tilt angle on standard stress radiography of the talocrural joint was 14.5°± 1.7° before surgery and 2.6°± 0.8° 2 years after surgery (P <. 0001). For the 4 patients who had both the anterior talofibular ligament and calcaneofibular ligament reconstructed, the mean talar tilt angle was 16.5°± 1.5° before surgery and 3.0°± 0.5° 2 years after surgery (P =. 0015). The overall mean talocalcaneal angle on standard stress radiography of the subtalar joint was 11.3°± 1.4° before surgery and 3.5°± 0.8° 2 years after surgery (P =. 0060).

Conclusion

The proposed system has several advantages, including anatomical reconstruction with normal stability and range of motion restored, the need for only a small incision during the reconstruction, and sufficient strength at the tendon graft-bone tunnel junction, in comparison with the tension strength of the lateral ligaments of the ankle.
Stability of naujakasite in hyperagpaitic melts, and the petrology of naujakasite lujavrite in the llímaussaq alkaline complex, South Greenland
Authors: Andersen T. , Sørensen H.
Published: June 2005

Naujakasite (Na6(Fe,Mn)Al4Si8O26) is a characteristic, rock-forming mineral of hyperagpaitic naujakasite lujavrite (arfvedsonite + naujakasite + steenstrupine + albite ± relict nepheline ± microcline ± ussingite) from the Ilímaussaq complex, South Greenland, and is only known from this complex. The qualitative stability relationships of naujakasite-bearing, low-variance liquidus mineral assemblages at near-solidus conditions in lujavritic magma can be modelled within the six-component system Si-Al-Fe-Na-O-H. The modelling suggests that an uncommon combination of elevated water activity and low oxygen fugacity is needed to stabilize arfvedsonite + naujakasite mineral assemblages in highly sodic liquids. These conditions are incompatible with the stable coexistence of aegirine and arfvedsonite. They are met in the arfvedsonite-bearing lujavrites of Ilímaussaq, but apparently not in rocks of similar composition in the Khibina and Lovozero complexes, Kola Peninsula, where aegirine- or aegirine-arfvedsonite-bearing mineral assemblages are characteristic. Liquid lines of descent leading to crystallization of naujakasite have to pass through the albite+nepheline+arfvedsonite liquidus field in the Si-Al-Fe-Na-O-H system, reaching this field at the high-Na side of the albite-nepheline-arfvedsonite plane.
A new mineral, zincolibethenite, CuZnPO4OH, a stoichiometric species of specific site occupancy
Authors: Braithwaite R. S. W. , Pritchard R. G. , Paar W. H. , Pattrick R. A. D.
Published: June 2005

Tiny green crystals from Kabwe, Zambia, associated with hopeite and tarbuttite (and probably first recorded in 1908 but never adequately characterized because of their scarcity) have been studied by X-ray diffraction, microchemical and electron probe microanalysis, infrared spectroscopy, and synthesis experiments. They are shown to be orthorhombic, stoichiometric CuZnPO4OH, of species rank, forming the end-member of a solid-solution series to libethenite, Cu2PO4OH, and are named zincolibethenite. The libethenite structure is unwilling to accommodate any more Zn substituting for Cu at atmospheric pressure, syntheses using Zn-rich solutions precipitating a mixture of zincolibethenite with hopeite, Zn3(PO4)2.4H2O. Single-crystal X-ray data confirm that the Cu(II) occupies the Jahn-Teller distorted 6-coordinate cation site in the libethenite lattice, and the Zn(II) occupies the 5-coordinate site. The space group of zincolibethenite is Pnnm, the same as that of libethenite, with unit-cell parameters a = 8.326, b = 8.260, c = 5.877 Å , V = 404.5 Å 3, Z = 4, calculated density = 3.972 g/cm3 (libethenite has a = 8.076, b = 8.407, c = 5.898 Å , V = 400.44 Å 3, Z = 4, calculated density = 3.965 g/cm3). Zincolibethenite is biaxial negative, with 2Vα(calc.) of 49°, r<v, and α = 1.660, β = 1.705, and γ = 1.715 The mineral is named for its relationship to libethenite.
Compositional and textural variation in detrital chrome-spinels from the Murray Basin, southeastern Australia
Authors: Pownceby M.
Published: June 2005

Detrital chrome-spinels are contaminant grains within heavy-mineral concentrates found in the Murray Basin of southeastern Australia. The presence of even minor levels of chromia in the predominantly ilmenite-rich concentrates downgrades their market value as potential feedstocks for the production of titania pigment.

Compositions from a database of close to 5000 chrome-spinel analyses show a broad range in chemistry. The major element components and their ranges (wt.%) are Cr: 3.10–52.06, Al: 0.46–32.50, Fe: 3.50–44.48 and Mg: 0.03–15.79. Minor components include; Ti: 0.01–6.41, Zn: 0.00–23.00 and Mn: 0.00–5.82. The broad variation in composition suggests multiple source areas for the chrome-spinels although detailed textural examination indicates that variation has also been introduced through pre- and post-deposition alteration processes.

The Murray Basin chrome-spinel database has the potential to be used in interpreting and predicting the effects of various processing conditions used to separate the chrome-spinels from the ilmenite.
Thermal expansion of troilite and pyrrhotite determined byin situcooling (873 to 373 K) neutron powder diffraction measurements
Authors: Tenailleau C. , Etschmann B. , Wang H. , Pring A. , Grguric B. A. , Studer A.
Published: June 2005

The thermal expansion coefficients for natural troilite, FeS, Ni-rich pyrrhotite, Fe0.84Ni0.11S, and Ni-poor pyrrhotite, Fe0.87Ni0.02S, were measured during cooling by in situ neutron powder diffraction over the temperature range 873–373 K. Between 873 and 573 K, the mean thermal expansion coefficients for the three compositions are 7.4(3)×10−5{FeS}, 8.0(4)×10−5{Fe0.84Ni0.11S} and 8.5(4)×10−5K−1{Fe0.87Ni0.02S}. Below 573 down to 373 K, the first two increase considerably to 14.1(7)×10−5{FeS} and 9.3(5)×10−5{Fe0.84Ni0.11S} while the latter sample shows no significant variation, 8.4(5)×10−5K−1. Below 573 K, the thermal expansion is highly anisotropic, with Δa/100 K−1ranging from 0.89(9)% {FeS} to 0.48(12)% {Fe0.87Ni0.02S} while Δc/100 K−1ranges from −0.39(11)% {FeS} to −0.13(2)% {Fe0.87Ni0.02S}.

Upon cooling through 573 K, troilite and pyrrhotite undergo a transition where the FeS6octahedra distort and in the case of pyrrhotite, cation-vacancy clustering occurs. The thermal expansion coefficients are bigger for low cation-vacancy concentrations and decrease as the pyrrhotites become less stoichiometric. This indicates that the thermal expansion in these minerals is damped by vacancy ordering or clustering. The thermal expansion coefficients for troilite and pyrrhotite are amongst the largest reported for sulphide minerals and their role in the formation of ore textures is discussed briefly.
Multiple exposures to swine barn air induce lung inflammation and airway hyper-responsiveness
Authors: Charavaryamath Chandrashekhar , Janardhan Kyathanahalli S , Townsend Hugh G , Willson Philip , Singh Baljit
Published: June 2005

Background

Swine farmers repeatedly exposed to the barn air suffer from respiratory diseases. However the mechanisms of lung dysfunction following repeated exposures to the barn air are still largely unknown. Therefore, we tested a hypothesis in a rat model that multiple interrupted exposures to the barn air will cause chronic lung inflammation and decline in lung function.

Methods

Rats were exposed either to swine barn (8 hours/day for either one or five or 20 days) or ambient air. After the exposure periods, airway hyper-responsiveness (AHR) to methacholine (Mch) was measured and rats were euthanized to collect bronchoalveolar lavage fluid (BALF), blood and lung tissues. Barn air was sampled to determine endotoxin levels and microbial load.

Results

The air in the barn used in this study had a very high concentration of endotoxin (15361.75 ± 7712.16 EU/m3). Rats exposed to barn air for one and five days showed increase in AHR compared to the 20-day exposed and controls. Lungs from the exposed groups were inflamed as indicated by recruitment of neutrophils in all three exposed groups and eosinophils and an increase in numbers of airway epithelial goblet cells in 5- and 20-day exposure groups. Rats exposed to the barn air for one day or 20 days had more total leukocytes in the BALF and 20-day exposed rats had more airway epithelial goblet cells compared to the controls and those subjected to 1 and 5 exposures (P < 0.05). Bronchus-associated lymphoid tissue (BALT) in the lungs of rats exposed for 20 days contained germinal centers and mitotic cells suggesting activation. There were no differences in the airway smooth muscle cell volume or septal macrophage recruitment among the groups.

Conclusion

We conclude that multiple exposures to endotoxin-containing swine barn air induce AHR, increase in mucus-containing airway epithelial cells and lung inflammation. The data also show that prolonged multiple exposures may also induce adaptation in AHR response in the exposed subjects.
SplitTester : software to identify domains responsible for functional divergence in protein family
Authors: Gao Xiang , Vander Velden Kent A , Voytas Daniel F , Gu Xun
Published: June 2005

Background

Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family.

Results

Our software, SplitTester, takes a multiple protein sequences alignment as input, generated from protein members of two subgroups with known functional divergence. SplitTester was designed to construct the neighbor joining tree (a split cluster) from variable-sized sliding windows across the alignment in a process called split-clustering. SplitTester identifies the regions, whose split cluster is consistent with the functional split, but may be inconsistent with the phylogeny of the protein family. We hypothesize that at least some number of these identified regions, which are not following a random mutation process, are responsible for the observed functional split. To test our method, we used reverse transcriptase from a group of Pseudoviridae retrotransposons: to identify residues specific for diverged primer recognition. Candidate regions were then mapped onto the three dimensional structures of reverse transcriptase. The locations of these amino acids within the enzyme are consistent with their biological roles.

Conclusion

SplitTester aims to identify specific domain sequences responsible for functional divergence of subgroups within a protein family. From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection.
An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences
Authors: Brochier Céline , Forterre Patrick , Gribaldo Simonetta
Published: June 2005

Background

The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets.

Results

We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives.

Conclusion

To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life.
Inferring haplotypes at the NAT2 locus: the computational approach
Authors: Sabbagh Audrey , Darlu Pierre
Published: June 2005

Background

Numerous studies have attempted to relate genetic polymorphisms within the N-acetyltransferase 2 gene (NAT2) to interindividual differences in response to drugs or in disease susceptibility. However, genotyping of individuals single-nucleotide polymorphisms (SNPs) alone may not always provide enough information to reach these goals. It is important to link SNPs in terms of haplotypes which carry more information about the genotype-phenotype relationship. Special analytical techniques have been designed to unequivocally determine the allocation of mutations to either DNA strand. However, molecular haplotyping methods are labour-intensive and expensive and do not appear to be good candidates for routine clinical applications. A cheap and relatively straightforward alternative is the use of computational algorithms. The objective of this study was to assess the performance of the computational approach inNAT2haplotype reconstruction from phase-unknown genotype data, for population samples of various ethnic origin.

Results

We empirically evaluated the effectiveness of four haplotyping algorithms in predicting haplotype phases atNAT2, by comparing the results with those directly obtained through molecular haplotyping. All computational methods provided remarkably accurate and reliable estimates forNAT2haplotype frequencies and individual haplotype phases. The Bayesian algorithm implemented in the PHASE program performed the best.

Conclusion

This investigation provides a solid basis for the confident and rational use of computational methods which appear to be a good alternative to infer haplotype phases in the particular case of theNAT2gene, where there is near complete linkage disequilibrium between polymorphic markers.
Genome-wide screening for genes whose deletions confer sensitivity to mutagenic purine base analogs in yeast
Authors: Stepchenkova Elena I , Kozmin Stanislav G , Alenin Vladimir V , Pavlov Youri I
Published: June 2005

Background

N-hydroxylated base analogs, such as 6-hydroxylaminopurine (HAP) and 2-amino-6-hydroxylaminopurine (AHA), are strong mutagens in various organisms due to their ambiguous base-pairing properties. The systems protecting cells from HAP and related noncanonical purines in Escherichia coli include specialized deoxyribonucleoside triphosphatase RdgB, DNA repair endonuclease V, and a molybdenum cofactor-dependent system. Fewer HAP-detoxification systems have been identified in yeast Saccharomyces cerevisiae and other eukaryotes. Cellular systems protecting from AHA are unknown. In the present study, we performed a genome-wide search for genes whose deletions confer sensitivity to HAP and AHA in yeast.

Results

We screened the library of yeast deletion mutants for sensitivity to the toxic and mutagenic action of HAP and AHA. We identified novel genes involved in the genetic control of base analogs sensitivity, including genes controlling purine metabolism, cytoskeleton organization, and amino acid metabolism.

Conclusion

We developed a method for screening the yeast deletion library for sensitivity to the mutagenic and toxic action of base analogs and identified 16 novel genes controlling pathways of protection from HAP. Three of them also protect from AHA.
Optimization of culture conditions to obtain maximal growth of penicillin-resistant Streptococcus pneumoniae
Authors: Restrepo Andrea V , Salazar Beatriz E , Agudelo María , Rodriguez Carlos A , Zuluaga Andres F , Vesga Omar
Published: June 2005

Background

Streptococcus pneumoniae, particularly penicillin-resistant strains (PRSP), constitute one of the most important causes of serious infections worldwide. It is a fastidious microorganism with exquisite nutritional and environmental requirements to grow, a characteristic that prevents the development of useful animal models to study the biology of the microorganism. This study was designed to determine optimal conditions for culture and growth of PRSP.

Results

We developed a simple and reproducible method for culture of diverse strains of PRSP representing several invasive serotypes of clinical and epidemiological importance in Colombia. Application of this 3-step culture protocol consistently produced more than 9 log10 CFU/ml of viable cells in the middle part of the logarithmic phase of their growth curve.

Conclusion

A controlled inoculum size grown in 3 successive steps in supplemented agar and broth under 5% CO2 atmosphere, with pH adjustment and specific incubation times, allowed production of great numbers of PRSP without untimely activation of autolysis mechanisms.
Carbon monoxide production from five volatile anesthetics in dry sodalime in a patient model: halothane and sevoflurane do produce carbon monoxide; temperature is a poor predictor of carbon monoxide production
Authors: Keijzer Christiaan , Perez Roberto SGM , De Lange Jaap J
Published: June 2005

Background

Desflurane and enflurane have been reported to produce substantial amounts of carbon monoxide (CO) in desiccated sodalime. Isoflurane is said to produce less CO and sevoflurane and halothane should produce no CO at all.

The purpose of this study is to measure the maximum amounts of CO production for all modern volatile anesthetics, with completely dry sodalime. We also tried to establish a relationship between CO production and temperature increase inside the sodalime.

Methods

A patient model was simulated using a circle anesthesia system connected to an artificial lung. Completely desiccated sodalime (950 grams) was used in this system. A low flow anesthesia (500 ml/min) was maintained using nitrous oxide with desflurane, enflurane, isoflurane, halothane or sevoflurane. For immediate quantification of CO production a portable gas chromatograph was used. Temperature was measured within the sodalime container.

Results

Peak concentrations of CO were very high with desflurane and enflurane (14262 and 10654 ppm respectively). It was lower with isoflurane (2512 ppm). We also measured small concentrations of CO for sevoflurane and halothane. No significant temperature increases were detected with high CO productions.

Conclusion

All modern volatile anesthetics produce CO in desiccated sodalime. Sodalime temperature increase is a poor predictor of CO production.