bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Contributions of Tidal Straining and Gravitational Circulation to Residual Circulation in Periodically Stratified Tidal Estuaries
Authors: Burchard Hans , Hetland Robert D. 
Published: February 2010

Abstract
This numerical modeling study quantifies for the first time the contribution of various processes to estuarine circulation in periodically stratified tidal flow under the impact of a constant horizontal buoyancy gradient. The one-dimensional water column equations with periodic forcing are first cast into nondimensional form, resulting in a multidimensional parameter space spanned by the modified inverse Strouhal number and the modified horizontal Richardson number, as well as relative wind speed and wind direction and the residual runoff. The along-tide momentum equation is then solved for the tidal-mean velocity profile in such a way that it is equated to the sum of the contributions of tidal straining (resulting from the temporal correlation between eddy viscosity and vertical shear), gravitational circulation (resulting from the depth-varying forcing by a constant horizontal buoyancy gradient), wind straining, and depth-mean residual flow (resulting from net freshwater runoff). This definition of tidal straining does not only account for tidal asymmetries resulting from horizontal buoyancy gradients but also from wind straining and residual runoff. For constant eddy viscosity, the well-known estuarine circulation analytical solution with polynomial residual profiles is directly obtained. For vertically parabolic and constant-in-time eddy viscosity, a new analytic solution with logarithmic residual profiles is found, showing that the intensity of the gravitational circulation scales with the horizontal Richardson number. For scenarios with realistic spatially and temporally varying eddy viscosity, a numerical water column model equipped with a state-of-the-art two-equation turbulence closure model is applied to quantify the individual contributions of the various processes to estuarine circulation. The fundamental outcome of this study is that, for irrotational flow with periodic stratification and without wind forcing and residual runoff, the tidal straining is responsible for about two-thirds and gravitational circulation is responsible for about one-third of the estuarine circulation, proportionally dependent on the horizontal Richardson number, and weakly dependent on the Strouhal number. This new and robust result confirms earlier estimates by H. Burchard and H. Baumert, who suggested that tidal straining is the major generation mechanism for estuarine turbidity maxima. However, a sensitivity analysis of the model results to details of the turbulence closure model shows some uncertainty with respect to the parameterization of sheared convection during flood. Increasing down-estuary wind straining and residual runoff reduce the quantitative contribution of tidal straining. For relatively small horizontal Richardson numbers, the tidal straining contribution to estuarine circulation may even be reversed by down-estuary wind straining.
The Impact of Spume Droplets and Wave Stress Parameterizations on Simulated Near-Surface Maritime Wind and Temperature
Authors: Innocentini Valdir , Gonçalves Iury Angelo 
Published: February 2010

AbstractThe influence of ocean gravity waves on the wind and temperature above the surface is investigated using a one-dimensional boundary layer model. The effect of the wave-induced stress is evaluated using three parameterizations: wave age (WaAg), wave steepness (WaSt), and wind action on the wave spectrum (WiAc). It is found that while the WaAg is more effective in reducing the wind for young waves, in the WaSt approach the maximum reduction is for old waves. On the other hand, the WiAc is very sensitive to the energy present in high frequencies corresponding to periods less than 2 s, which are found in both young and mature spectra. Since observations show that most of the wave stress is due to the small-period wave energy, in this aspect the WaSt parameterization is not recommended; WaAg is not as accurate; and thus WiAc is the best among the three, although its computational cost is the highest.The droplet load contribution to the total surface stress can be neglected for the droplet spectrum produced by 10-m wind speeds up to 15 m s−1, but its importance increases with the speed and its magnitude becomes about ⅕ of the total stress for wind speed ∼30 m s−1.Concerning the latent and sensible heat fluxes accompanying the production of spume droplets by waves, a feasible microphysical formulation for operational use in weather forecasting models is proposed. The droplet spectrum is assumed to be a product of two functions, one depending on the windsea Reynolds number and the other on the droplet radius spectrum. The bulk effect of the latter is analytically evaluated and stored in a table as a function of air temperature Ta, relative humidity R%, and significant wave height Hs. In numerical experiments with initial sea surface temperature 5 K higher than the air surface, latent and sensible heat contributions to the air temperature are computed as a function of the wave spectra. The launched droplet spectrum (which increases the air temperature due to sensible heat) and the relative humidity (which controls the cooling due to the droplet evaporation) define the heat budget and the air temperature evolution. Although in these experiments the sea temperature is much higher than the air temperature, the results show a noticeable dominance of the evaporative cooling in the lower atmosphere mainly for smaller significant wave height. Some air warming is noticeable only from a threshold around Hs ≥ 5 m.
Evaluation of a Dynamical Basis for Advance Forecasting of the Date of Onset of Monsoon Rainfall over India
Authors: Goswami P. , Gouda K. C. 
Published: February 2010

Abstract
The onset of the Indian summer monsoon (ISM) represents one of the most dramatic transitions in the regional circulation pattern. The onset also marks the beginning of the main rainy season for India; advanced and accurate forecast of the date of the onset of monsoon (DOM) thus has application in many sectors. Although the standard deviation (σ) in DOM over the past hundred years is only 7 days, nearly 50% of the cases show large (&gt;1σ) deviations; forecasting of DOM, especially for the extreme years is thus nontrivial and is rarely attempted because of the poor skill of most GCMs in the long-range prediction of daily ISM rainfall. A primary cause for the poor skill in forecasting parameters like rainfall appears to be the loss of predictability due to noise introduced by local synoptic processes. However, sharp transitions in the regional circulation pattern and associated rainfall, which are likely to be less affected by synoptic noise, may have higher predictability, somewhat similar to the way that monthly mean parameters are more predictable. This premise is explored for advanced forecasting of the onset of ISM over Kerala, India, and it is shown that significant skill is possible in advanced forecasting of DOM. A general circulation model (GCM) with a special feature, variable resolution, and an objective debiasing of daily rainfall forecast, is used to meet the special requirements of forecasting DOM. Based on a set of objective and validated criteria, hindcasts of DOM are generated in a complete operational setting from a five-member ensemble for each year for the period 1980–2003. The hindcasts are evaluated in terms of a number of parameters; as well as against a climatological forecast (null hypothesis), for 70% of the forecasts, the mean absolute error is less than that of the climatological forecasts. Furthermore, in contrast to the climate forecasts, these forecasts capture 7 out of 9 large (&gt;1σ in observation) departures from the mean within the mean error, which implies high skill. Implications of the results for predicting certain weather and climate processes are discussed.
Warm Core Structures in Organized Cloud Clusters Developing or Not Developing into Tropical Storms Observed by the Advanced Microwave Sounding Unit
Authors: Bessho Kotaro , Nakazawa Tetsuo , Nishimura Shuji , Kato Koji 
Published: February 2010

Abstract
The temperature profiles of organized cloud clusters developing or not developing (nondeveloping) into tropical storms (TSs; maximum surface wind &gt;34 kt) over the western North Pacific in 2004 were investigated using Advanced Microwave Sounding Unit (AMSU) observations in combination with the independently created early stage Dvorak analysis. Typical temperature profiles of the developing and nondeveloping cloud clusters were compared. From this comparison, positive upper-troposphere temperature anomalies were found in both cluster types; however, the spatial extent of the temperature anomalies for the developing cloud clusters was larger than those of the nondeveloping cloud clusters. Statistical analysis was performed on the temperature anomalies near the center of all clusters retrieved from AMSU observational data. Findings indicate that the area-average temperature anomalies increased along with the intensity of the clusters indicated by the Dvorak T-number classification. Using time series analysis of upper-level temperature anomalies associated with these cloud clusters, a definition of warm core structures showing the temperature anomaly greater than a threshold (WCT) was created. WCT exists when the area averaged temperature anomaly exceeds 0.9 K. Using this definition, almost 70% of the cloud clusters that had WCTs later became TSs, while 85% of those that did not have WCTs eventually dissipated without being classified as a TS. For the WCT clusters that developed into TSs, the lead time from the detection of their AMSU-based WCT to their classification as TSs was 27.7 h. These results indicate that there is a good possibility that the detection and forecasting of tropical cyclone formation, particularly those storms that later may become classified as TSs, will be improved using temperature anomalies derived from AMSU data.
Evolutionary Optimization of an Ice Accretion Forecasting System
Authors: Pytlak Pawel , Musilek Petr , Lozowski Edward , Arnold Dan 
Published: February 2010

AbstractThe ability to model and forecast accretion of ice on structures is very important for many industrial sectors. For example, studies conducted by the power transmission industry indicate that the majority of failures are caused by icing on overhead conductors and other components of power networks. This paper presents an extension to the ice accretion forecasting system (IAFS) that is comprised of a numerical weather prediction model, a precipitation-type algorithm, and an ice accretion model. To optimize the performance of IAFS, the parameters of the precipitation-type algorithm are estimated using a genetic algorithm. The system is developed by hindcasting a well-documented freezing-rain event and calibrated using four additional ice storms. Subsequently, the system is tested using three independent storms. The results show a significant improvement in consistency, accuracy, and skill of IAFS. The methodology described in this contribution is not limited to ice accretion modeling—it provides a general approach for setting operational parameters of data-processing algorithms to achieve interoperability of numerical weather prediction models with add-on applications based on empirical observations.
A Two-Season Impact Study of the WindSat Surface Wind Retrievals in the NCEP Global Data Assimilation System
Authors: Bi Li , Jung James A. , Morgan Michael C. , Le Marshall John F. 
Published: February 2010

Abstract
A two-season observing system experiment (OSE) was used to quantify the impacts of assimilating the WindSat surface winds product developed by the Naval Research Laboratory (NRL). The impacts of assimilating these surface winds were assessed by comparing the forecast results through 168 h for the months of October 2006 and March 2007. The National Centers for Environmental Prediction’s (NCEP) Global Data Assimilation/Global Forecast System (GDAS/GFS) was used, at a resolution of T382-64 layers, as the assimilation system and forecast model for these experiments.
A control simulation utilizing all the data types assimilated in the operational GDAS was compared to an experimental simulation that added the WindSat surface winds. Quality control procedures required to assimilate the surface winds are discussed. Anomaly correlations (ACs) of geopotential heights at 1000 and 500 hPa were evaluated for the control and experiment during both seasons. The geographical distribution of the forecast impacts (FIs) on the wind field and temperature fields at 10-m height and 500 hPa is also discussed.
The results of this study show that assimilating the surface wind retrievals from the WindSat satellite improve the NCEP GFS wind and temperature forecasts. A positive FI, which suggests that the error growth of the experiment is slower than the control, has been realized in the NCEP GDAS/GFS wind and temperature forecasts through 24 h. The WindSat experiment AC scores are similar to the control simulation AC scores until the day 6 forecasts, when the improvements in the WindSat experiment become greater for both seasons and in most of the cases.
Quantification of illite and smectite and their layer charges in sandstones and shales from shallow burial depth
Authors: Środoń J. 
Published: February 2010

AbstractPrecise measurement of the content and the layer charge of illite and smectite is an important aspect of the mineralogical calibration of geophysical well logs and of the evaluation of mechanical and chemical properties of sedimentary rocks. Ate chnique for obtaining such measurements was developed during mineralogical studies of the Miocene clastic rocks from the Carpathian Foredeep. X-ray diffraction (XRD), chemical, cation exchange capacity (CEC), H2O sorption, and ethylene glycol monoethyl ether (EGME) sorption data were obtained for 65 samples of sandstones, shales and carbonates. The illite + smectite sum, involving all detected 2:1 minerals (smectite, illite-smectite, illite, glauconite and muscovite) was measured by XRD. The content of the illitic component was evaluated separately using % K2O and accounting for % K2O in K-feldspar. The content of the smectitic component was estimated from EGME retention using the reference data for a smectite standard, and from CEC assuming the smectitic layer charge of 0.41/O10(OH)2 (Środoń et al., in press). All these measurements produced very consistent results.
Ni-sepiolite-falcondoite in garnierite mineralization from the Falcondo Ni-laterite deposit, Dominican Republic
Authors: Tauler E. , Proenza J. A. , Galí S. , Lewis J. F. , Labrador M. , García-Romero E. , Suarez M. , Longo F. , Bloise G. 
Published: February 2010

AbstractNew chemical and structural data on sepiolite-falcondoite in garnierite veins from the Falcondo Ni-laterite deposits, central Dominican Republic, are reported. Samples of Ni-sepiolite-falcondoite vary in colour from whitish green to green depending on the NiO content (wt.%) and the amount of silica present. The texture is normally schistose and friable but samples with considerable quartz and/or amorphous silica are compact and hard. Back-scattered electron images indicate that the samples are composed of at least three generations of Ni-sepiolite-falcondoite. The extreme refined cell parameters for Ni-sepiolite-falcondoite vary from 13.400(2), 27.006(4), 5.273(1) Å to 13.340(3), 27.001(6), 5.267(1) Å (space group Pncn). As the Ni content increases there is a small reduction in the a parameter. Chemical compositions determined by electron probe microanalysis cover a large interval of the Ni-sepiolite-falcondoite solid solution (Fal3 and Fal77). Individual samples show a considerable range in composition with the widest range determined in one sample from 4.63 to 22.40 wt.% NiO.
Adult T-cell leukemia/lymphoma development in HTLV-1–infected humanized SCID mice
Authors: Banerjee Prabal , Tripp Adam , Lairmore Michael D. , Crawford Lindsey , Sieburg Michelle , Ramos Juan Carlos , Harrington William , Beilke Mark A. , Feuer Gerold 
Published: February 2010

AbstractThe molecular and genetic factors induced by human T-lymphotropic virus type-1 (HTLV-1) that initiate adult T-cell leukemia/lymphoma (ATLL) remain unclear, in part from the lack of an animal model that accurately recapitulates leukemogenesis. HTLV-1–infected humanized nonobese diabetic severe combined immunodeficiency (HU-NOD/SCID) mice were generated by inoculation of NOD/SCID mice with CD34+ hematopoietic progenitor and stem cells (CD34+ HP/HSCs) infected ex vivo with HTLV-1. HTLV-1-HU-NOD/SCID mice exclusively developed CD4+ T-cell lymphomas with characteristics similar to ATLL and elevated proliferation of infected human stem cells (CD34+CD38−) in the bone marrow were observed in mice developing malignancies. Purified CD34+ HP/HSCs from HTLV-1–infected patient peripheral blood mononuclear cells revealed proviral integrations suggesting viral infection of human bone marrow–derived stem cells. NOD/SCID mice reconstituted with CD34+ HP/HSCs transduced with a lentivirus vector expressing the HTLV-1 oncoprotein (Tax1) also developed CD4+ lymphomas. The recapitulation of a CD4+ T-cell lymphoma in HU-NOD/SCID mice suggests that HSCs provide a viral reservoir in vivo and act as cellular targets for cell transformation in humans. This animal model of ATLL will provide an important tool for the identification of molecular and cellular events that control the initiation and progression of the lymphoma and potential therapeutic targets to block tumor development.
The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations
Authors: Widmann Michael , Radloff Robert , Pleiss Jürgen 
Published: February 2010

Abstract

Background
Thiamine diphosphate (ThDP)-dependent enzymes form a vast and diverse class of proteins, catalyzing a wide variety of enzymatic reactions including the formation or cleavage of carbon-sulfur, carbon-oxygen, carbon-nitrogen, and especially carbon-carbon bonds. Although very diverse in sequence and domain organisation, they share two common protein domains, the pyrophosphate (PP) and the pyrimidine (PYR) domain. For the comprehensive and systematic comparison of protein sequences and structures the Thiamine diphosphate (ThDP)-dependent Enzyme Engineering Database (TEED) was established.

Description
The TEED http://www.teed.uni-stuttgart.de contains 12048 sequence entries which were assigned to 9443 different proteins and 379 structure entries. Proteins were assigned to 8 different superfamilies and 63 homologous protein families. For each family, the TEED offers multisequence alignments, phylogenetic trees, and family-specific HMM profiles. The conserved pyrophosphate (PP) and pyrimidine (PYR) domains have been annotated, which allows the analysis of sequence similarities for a broad variety of proteins. Human ThDP-dependent enzymes are known to be involved in many diseases. 20 different proteins and over 40 single nucleotide polymorphisms (SNPs) of human ThDP-dependent enzymes were identified in the TEED.

Conclusions
The online accessible version of the TEED has been designed to serve as a navigation and analysis tool for the large and diverse family of ThDP-dependent enzymes.
Trastuzumab with either docetaxel or vinorelbine as first-line treatment for patients with HER2-positive advanced breast cancer: a retrospective comparison
Authors: Redana Stefania , Donadio Michela , Nolè Franco , Jacomuzzi Maria Elena , Beano Alessandra , Martinello Rossella , Sapino Anna , Viale Giuseppe , Aglietta Massimo , Montemurro Filippo 
Published: February 2010

Abstract

Background
Combinations of trastuzumab with either docetaxel or vinorelbine are considered valuable treatment options for HER2-positive metastatic breast cancer patients. We performed a retrospective comparison of the clinical outcomes associated with either one of these combinations.

Methods
From a multi-institutional database we retrieved 179 patients treated with either docetaxel or vinorelbine plus trastuzumab as first-line therapy for HER2-positive advanced breast cancer.

Results
Docetaxel-trastuzumab was superior to vinorelbine-trastuzumab in terms of response rate (RR: 77 vs 57%, p = 0.01) and median overall survival (OS: 35 vs 23 months, p = 0.04), but not in median time to progression (TTP: 12 vs 10 months, p = 0.53). At multivariate analysis, type of treatment was not associated with TTP but was an independent predictor of OS, with a significant reduction in the risk of death in favor of docetaxel-trastuzumab (HR 0.474, 95% IC 0,303-0.742, p < 0.01).

Conclusion
Docetaxel or vinorelbine, when combined with trastuzumab, provide excellent rates of tumor control in patients with previously untreated HER2-positive advanced breast cancer. Docetaxel may offer some advantage in terms of response rate and resulted in a significantly prolonged overall survival, which, because of the retrospective design of our study, deserves further investigation in prospective trials.
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues
Authors: Wu Shirley , Liu Tianyun , Altman Russ B 
Published: February 2010

Abstract

Background
The emergence of structural genomics presents significant challenges in the annotation of biologically uncharacterized proteins. Unfortunately, our ability to analyze these proteins is restricted by the limited catalog of known molecular functions and their associated 3D motifs.

Results
In order to identify novel 3D motifs that may be associated with molecular functions, we employ an unsupervised, two-phase clustering approach that combines k-means and hierarchical clustering with knowledge-informed cluster selection and annotation methods. We applied the approach to approximately 20,000 cysteine-based protein microenvironments (3D regions 7.5 Å in radius) and identified 70 interesting clusters, some of which represent known motifs (e.g. metal binding and phosphatase activity), and some of which are novel, including several zinc binding sites. Detailed annotation results are available online for all 70 clusters at http://feature.stanford.edu/clustering/cys.

Conclusions
The use of microenvironments instead of backbone geometric criteria enables flexible exploration of protein function space, and detection of recurring motifs that are discontinuous in sequence and diverse in structure. Clustering microenvironments may thus help to functionally characterize novel proteins and better understand the protein structure-function relationship.