bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Mechanisms Underlying the Positive Stringent Response of the
Bacillus subtilis ilv-leu
Operon, Involved in the Biosynthesis of Branched-Chain Amino Acids
Authors: Tojo Shigeo , Satomura Takenori , Kumamoto Kanako , Hirooka Kazutake , Fujita Yasutaro 
Published: July 2008

ABSTRACT

Branched-chain amino acids are the most abundant amino acids in proteins. The
Bacillus subtilis ilv-leu
operon is involved in the biosynthesis of branched-chain amino acids. This operon exhibits a RelA-dependent positive stringent response to amino acid starvation. We investigated this positive stringent response upon lysine starvation as well as decoyinine treatment. Deletion analysis involving various
lacZ
fusions revealed two molecular mechanisms underlying the positive stringent response of
ilv-leu
, i.e., CodY-dependent and -independent mechanisms. The former is most likely triggered by the decrease in the in vivo concentration of GTP upon lysine starvation, GTP being a corepressor of the CodY protein. So, the GTP decrease derepressed
ilv-leu
expression through detachment of the CodY protein from its
cis
elements upstream of the
ilv-leu
promoter. By means of base substitution and in vitro transcription analyses, the latter (CodY-independent) mechanism was found to comprise the modulation of the transcription initiation frequency, which likely depends on fluctuation of the in vivo RNA polymerase substrate concentrations after stringent treatment, and to involve at least the base species of adenine at the 5′ end of the
ilv-leu
transcript. As discussed, this mechanism is presumably distinct from that for
B. subtilis rrn
operons, which involves changes in the in vivo concentration of the initiating GTP.
Use of tissue ink to maintain identification of individual cores on needle biopsies of the prostate
Authors: Singh P B , Saw N K , Haq A , Blades R A , Martin F L , Matanhelia S S , Nicholson C M 
Published: July 2008

Background:There is an increasing necessity to extract the maximum amount of information, beyond even a cancer diagnosis, from prostate biopsies. Thus, maintaining site-specific information regarding individual biopsy cores might be critical.Aim:To evaluate the applicability of employing tissue ink to maintain the identity of individual prostatic biopsy cores.Method:In this ongoing study, 12 core prostate biopsy specimens are sent to the laboratory in individual pots labelled according to anatomical site. The specimens are placed in two separate multi-compartment cassettes. They are inked with different colours to identify the site of origin from each lobe. The cassettes are then processed with a single paraffin block for each side; the six cores from each side can be mounted on a single slide.Results:The different colours used adhere well to the biopsy cores, thus maintaining the identity of each core. Six cores from each side are embedded in a single paraffin block and examined on a single slide, making it cost-effective, while maintaining high quality, accurate histopathological information.Conclusion:Differential inking of prostate biopsy cores is an easily applicable method that is cost-effective and provides tumour location information. Prostate biopsy data archived to maintain individual core information might be used to determine applicability of such information to predict extra-capsular extension by correlating with imaging and radical prostatectomy findings, and for treatment planning.
Quantitative assessment of the degree of villous atrophy in patients with coeliac disease
Authors: Ciaccio E J , Bhagat G , Naiyer A J , Hernandez L , Green P H R 
Published: July 2008

Background:Endoscopy and biopsy are used to diagnose coeliac disease. There are, however, observer-dependent interpretations of the degree of villous atrophy in biopsies. A pilot study using quantitative image-processing procedures was performed to quantify the degree of villous atrophy in patients with coeliac disease.Method:The degree of villous atrophy in duodenal biopsy images was quantified by calculating the ratio of villous edge-to-piecewise arc length (E/P ratio), and this value was compared with the blinded assessment of Marsh score for degree of villous atrophy.Results:Mean E/P ratios for n = 31 biopsy images, 2.76 (SD 0.44) (Marsh IIIa), 1.91 (0.50) (Marsh IIIb) and 1.18 (0.22) (Marsh IIIc), were significantly different (p = 0.006). Based on non-parametric testing, the E/P ratios were inversely correlated with Marsh scores (Spearman coefficient ρ = −0.798, Kendall τ = −0.681; p<0.0001).Conclusions:Biopsy images quantified by image analysis correlated exceedingly well with the histopathological grade of villous atrophy. Since quantified measurements are real-numbered values and lack observer bias, measurement of villous atrophy based on image analysis lends itself to standardisation of histological grading.
Nestin is expressed in basal-like and triple negative breast cancers
Authors: Parry S , Savage K , Marchiò C , Reis-Filho J S 
Published: July 2008

Aims:To analyse the distribution of nestin expression in different breast tumours and to determine the prognostic impact of nestin expression.Methods:Nestin expression was immunohistochemically analysed in a cohort of 245 invasive breast cancer patients treated with therapeutic surgery followed by anthracycline-based chemotherapy using a semi-quantitative scoring system.Results:Nestin was exclusively expressed in grade III breast carcinoma and preferentially expressed in basal-like and triple negative cancers. Nestin-positive tumours displayed high proliferation rates and p53 nuclear expression. Lymph-node positive patients with nestin-positive cancers had a shorter breast cancer specific survival; however nestin was not an independent prognostic factor on multivariate analysis.Conclusions:Nestin expression is preferentially found in basal-like and triple negative breast carcinomas. Further studies are warranted to define the biological role played by nestin in these subgroups of breast cancers.
How promptly nonindustrial private forest landowners regenerate their lands after harvest: a duration analysis
Authors: Sun Xing , Munn Ian A. , Sun Changyou , Hussain Anwar 
Published: July 2008

Understanding factors that influence how promptly landowners regenerate their timberlands after harvest, if at all, is critical to developing policies to improve forest productivity. Mississippi forest landowners with over 100 acres (1 acre = 0.404 ha) of forestland were surveyed in 2006 to collect harvest and regeneration data from 1996 to 2006. This study investigated the length of the time interval between harvest and reforestation. Nonparametric duration analysis was used to examine how long nonindustrial private forest landowners waited to reforest after harvesting. Parametric duration analysis was used to examine factors that influenced the length of this period. The mean time elapsed from harvest to regeneration was 11 months for landowners that regenerated their lands. The instantaneous probability of regeneration reached its highest value in the 16th month after harvest and, thereafter, decreased steadily until the 28th month, after which the probability of regeneration was essentially nil. Interest in timber production, employing a consultant, and ownerships that were predominantly pine forest types were factors associated with substantially shorter reforestation times. Lower stumpage prices and higher reforestation costs were associated with substantially longer reforestation times.
Water table depth affects productivity, water use, and the response to nitrogen addition in a savanna system
Authors: Ford Chelcy R. , Mitchell Robert J. , Teskey Robert O. 
Published: July 2008

We investigated annual aboveground net primary productivity (ANPP) and transpiration (E) of the dominant plant life forms, longleaf pine (Pinus palustris Mill.) trees and wiregrass (Aristida stricta Michx.), in a fire-maintained savanna. Experimental plots spanned a natural hydrologic gradient (xeric and mesic site types) mediated by soil moisture (θ) and water table depth (WTD), and received additions of either 0 or 100 kg N·ha–1·year–1. Low rates of ANPP (1.3–2.2 Mg·ha–1) and annual E (108–380 mm) were observed in these communities. WTD and N addition explained 95% of the variation in community ANPP, whereas site type and WTD explained 83% of variation in community E. Between tree and grass life forms, longleaf pine ANPP was more coupled to WTD than wiregrass. For any given leaf area supported, ANPP of longleaf pine increased linearly with increasing water use and decreasing WTD. The longleaf pine ANPP response to N addition was greater in sites with high water use compared with those with low water use, indicating that this savanna system is colimited by nutrient and water availability and that water table depth plays a role in regulating savanna productivity.
Aerobiology of Pinus taeda pollen clouds
Authors: Williams Claire G. 
Published: July 2008

Better knowledge of aerobiological properties of pollen clouds is needed for pines and other woody perennials because these properties shape the predictive accuracy of spatially explicit pollen dispersal models. Four properties were experimentally measured in this study using processed Pinus taeda L. (loblolly pine) pollen as well as pollen concentration and viability data collected from an 18-year-old P. taeda plantation. Results showed that P. taeda pollen had a settling or terminal velocity value of 2.1 cm·s–1; that daytime pollen count from a plantation was sparse, reaching a maximum of 1480 grains·m–3 at peak pollen shed; and that pollen concentration showed no vertical gradient above or below the plantation’s canopy. Pollen sampled above and within the canopy had comparable germination rates. Surprisingly, a low concentration of viable Pinus spp. pollen was present during nighttime. Study results added further to the idea that P. taeda pollen has a higher nuisance value than either Zea mays L. (maize) or Agrostis stolonifera L. (creeping bentgrass) pollen because of its low terminal velocity value, persistent viability, and perennial production.
The Low-Frequency Relationship of the Tropical–North Pacific Sea Surface Temperature Teleconnections
Authors: Yeh Sang-Wook , Kirtman Ben P. 
Published: July 2008

Abstract
The low-frequency relationship between interannual tropical and North Pacific sea surface temperature anomalies (SSTAs) in observations and a coupled general circulation model (CGCM) is investigated. The authors use the interactive ensemble CGCM, which advances a new approach for artificially increasing the signal-to-noise ratio, making it easier to detect physical and dynamical links with much reduced interference by atmospheric noise. The results presented here suggest that decadal variations in the relationship between the dominant modes of tropical and North Pacific interannual SSTA variability result from changes of spatial manifestation of North Pacific SSTA, both in the observation and in the model.
The authors conjecture that the details of tropical Pacific SST forcing ultimately determine the tropical–North Pacific SST teleconnections, and this conjecture is examined in a much longer time series from a CGCM simulation. There are two patterns of North Pacific interannual SSTA variability in the model. The first pattern is locally forced by noise in the surface air–sea fluxes associated due to internal atmospheric dynamics. The second pattern is remotely forced by tropical SSTA. As the relationship of tropical–North Pacific SST teleconnections varies in the model, the spatial manifestation of the North Pacific SSTA changes from the atmospheric noise-forced pattern to the remotely forced pattern and vice versa. In the model, the amplitude of the tropical Pacific SSTA variance varies on decadal time scales and this largely determines the dominant structure of North Pacific SSTA variability. Furthermore, the change in location of the maximum tropical SST forcing is associated with the changes in the spatial manifestation of North Pacific interannual SSTA variability.
Shallow Meridional Circulations in the Tropical Atmosphere
Authors: Zhang Chidong , Nolan David S. , Thorncroft Christopher D. , Nguyen Hanh 
Published: July 2008

Abstract
A shallow meridional circulation (SMC) in the tropical atmosphere features a low-level (e.g., 700 hPa) flow that is in the opposite direction to the boundary layer monsoon or trade wind flow and is distinct from the meridional flow above. Representations of the SMC in three global reanalyses show both similarities and astonishing discrepancies. While the SMC over West Africa appears to be the strongest, it also exists over the eastern Atlantic and eastern Pacific Oceans, and over the Indian subcontinent, with different strength and structure. All SMCs undergo marked seasonal cycles. The SMCs are summarized into two types: one associated with the marine ITCZ and the other with the summer monsoon. The large-scale conditions for these two types of SMCs are similar: a strong meridional gradient in surface pressure linked to surface temperature distributions and an absence of deep moist convection. The processes responsible for these conditions are different for the two types of SMCs, as are their structures relative to moist convection, associated precipitation, and deep meridional overturning circulations. It is suggested that discrepancies among the representations of the SMC in the three global reanalyses stem from different treatment of physical parameterizations, especially for cumulus convection, in the models used for the data assimilation.
Two Regimes of the Equatorial Warm Pool. Part I: A Simple Tropical Climate Model
Authors: Watanabe Masahiro 
Published: July 2008

Abstract
Atmosphere–ocean coupled processes responsible for generating and maintaining the equatorial warm pool were investigated using models of different complexities. The primary focus was to answer the following question: why is the observed warm pool concentrated around the maritime continent? In this first of a two-part series, the solutions of a simple conceptual model that represents the tropical Pacific and Indian Oceans interacting via the Walker circulation are examined. When the interbasin coupling is sufficiently strong, surface wind convergence over the Maritime Continent associated with easterly trades over the Pacific acts to generate the equatorial westerly over the Indian Ocean, leading to a warm pool spontaneously emerging between the two ocean basins. The conceptual model shows that tropical climate has two equilibria, depending upon the ocean basin widths—a single warm pool regime corresponding to the current climate and a split warm pool regime that accompanies warm pools created in the western parts of each ocean basin. The latter is found to be unstable and hence exhibits large-amplitude vacillations between the ocean basins being further amplified by the Bjerknes feedback. The above two regimes of the equatorial warm pool are identified in the model incorporating the interactive Atlantic Ocean as well, wherein the mean state and variability in the three ocean basins qualitatively agree with the observations.
Reduced Atlantic Storminess during Last Glacial Maximum: Evidence from a Coupled Climate Model
Authors: Li Camille , Battisti David S. 
Published: July 2008

Abstract
The Last Glacial Maximum (LGM), 21 000 yr before present, was the time of maximum land ice extent during the last ice age. A recent simulation of the LGM climate by a state-of-the-art fully coupled global climate model is shown to exhibit strong, steady atmospheric jets and weak transient eddy activity in the Atlantic sector compared to today’s climate. In contrast, previous work based on uncoupled atmospheric model simulations has shown that the LGM jets and eddy activity in the Atlantic sector are similar to those observed today, with the main difference being a northeastward extension of their maxima. The coupled model simulation is shown to agree more with paleoclimate proxy records and thus is taken as the more reliable representation of LGM climate. The existence of this altered atmospheric circulation state during LGM in the model has implications for understanding the stability of glacial climates, for the possibility of multiple atmospheric circulation regimes, and for the interpretation of paleoclimate proxy records.
A High-Resolution Simulation of Typhoon Rananim (2004) with MM5. Part I: Model Verification, Inner-Core Shear, and Asymmetric Convection
Authors: Li Qingqing , Duan Yihong , Yu Hui , Fu Gang 
Published: July 2008

Abstract
In this study, the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) is used to simulate Typhoon Rananim (2004) at high resolution (2-km grid size). The simulation agrees well with a variety of observations, especially for intensification, maintenance, landfall, and inner-core structures, including the echo-free eye, the asymmetry in eyewall convection, and the slope of the eyewall during landfall. The asymmetric feature of surface winds is also captured reasonably well by the model, as well as changes in surface winds and pressure near the storm center.
The shear-induced vortex tilt and storm-relative asymmetric winds are examined to investigate how vertical shear affects the asymmetric convection in the inner-core region. The inner-core vertical shear is found to be nonunidirectional, and to induce a nonunidirectional vortex tilt. The distribution of asymmetric convection is, however, inconsistent with the typical downshear-left pattern for a deep-layer shear. Qualitative agreement is found between the divergence pattern and the storm-relative flow, with convergence (divergence) generally associated with asymmetric inflow (outflow) in the eyewall. The collocation of the inflow-induced lower-level convergence in the boundary layer and the lower troposphere and the midlevel divergence causes shallow updrafts in the western and southern parts of the eyewall, while the deep and strong upward motion in the southeastern portion of the eyewall is due to the collocation of the net convergence associated with the strong asymmetric flow in the midtroposphere and the inflow near 400 hPa and its associated divergence in the outflow layer above 400 hPa.
Comparison of Four Cloud Schemes in Simulating the Seasonal Mean Field Forced by the Observed Sea Surface Temperature
Authors: Shimpo Akihiko , Kanamitsu Masao , Iacobellis Sam F. , Hong Song-You 
Published: July 2008

Abstract
The impacts of four stratiform cloud parameterizations on seasonal mean fields are investigated using the global version of the Experimental Climate Prediction Center (ECPC) global-to-regional forecast system (G-RSM). The simulated fields are compared with the International Satellite Cloud Climatology Project (ISCCP) data for clouds, the Global Precipitation Climatology Project data for precipitation, the Earth Radiation Budget Experiment and the Surface Radiation Budget data for radiation, and the National Centers for Environmental Prediction (NCEP)–Department of Energy (DOE) Atmospheric Model Intercomparison Project (AMIP-II) Reanalysis (R-2) for temperature.
Compared to observations, no stratiform cloud parameterization performed better in simulating all aspects of clouds, temperature, precipitation, and radiation fluxes. There are strong interactions between parameterized stratiform clouds and boundary layer clouds and convection, resulting in changes in low-level cloudiness and precipitation in the simulations.
When the simulations are compared with ISCCP cloudiness and cloud water, and the NCEP/DOE R-2 relative humidity, the cloud amounts simulated by all four cloud schemes depend mostly on relative humidity with less dependency on the model’s cloud water, while the observed cloud amount is more strongly dependent on cloud water than relative humidity, suggesting that cloud parameterizations and the simulation of cloud water require further improvement.
A Case Study of Convective Boundary Layer Development during IHOP_2002: Numerical Simulations Compared to Observations
Authors: Conzemius Robert J. , Fedorovich Evgeni 
Published: July 2008

Abstract
Results are presented from a combined numerical and observational study of the convective boundary layer (CBL) diurnal evolution on a day of the International H2O Project (IHOP_2002) experiment that was marked by the passage of a dryline across part of the Oklahoma and Texas Panhandles. The initial numerical setup was based on observational data obtained from IHOP_2002 measurement platforms and supplementary datasets from surrounding locations. The initial goals of the study were as follows: (i) numerical investigation of the structure and evolution of the relatively shallow and homogeneous CBL east of the dryline by means of large-eddy simulation (LES), (ii) evaluation of LES predictions of the sheared CBL growth against lidar observations of the CBL depth evolution, and (iii) comparison of the simulated turbulence structures with those observed by lidar and vertically pointing radar during the CBL evolution. In the process of meeting these goals, complications associated with comparisons between LES predictions and atmospheric observations of sheared CBLs were encountered, adding an additional purpose to this study, namely, to convey and analyze these issues.
For a period during mid- to late morning, the simulated CBL evolution was found to be in fair agreement with atmospheric lidar and radar observations, and the simulated entrainment dynamics were consistent with those from previous studies. However, CBL depths, determined from lidar data, increased at a faster rate than in the simulations during the afternoon, and the wind direction veered in the simulations more than in the observations. The CBL depth discrepancy can be explained by a dryline solenoidal circulation reported in other studies of the 22 May 2002 case. The discrepancy in winds can be explained by time variation of the large-scale pressure gradient, which was not included in LES.
Analysis and Prediction of a Squall Line Observed during IHOP Using Multiple WSR-88D Observations
Authors: Sun Juanzhen , Zhang Ying 
Published: July 2008

Abstract
This paper presents a case study on the assimilation of observations from multiple Doppler radars of the Next Generation Weather Radar (NEXRAD) network. A squall-line case documented during the International H2O Project (IHOP_2002) is used for the study. Radar radial velocity and reflectivity observations from four NEXRADs are assimilated into a convection-permitting model using a four-dimensional variational data assimilation (4DVAR) scheme. A mesoscale analysis using a supplementary sounding, velocity–azimuth display (VAD) profiles, and surface observations from Meteorological Aerodrome Reports (METAR) are produced and used to provide a background and boundary conditions for the 4DVAR radar data assimilation. Impact of the radar data assimilation is assessed by verifying the skill of the subsequent very short-term (5 h) forecasts.
Assimilation and forecasting experiments are conducted to examine the impact of radar data assimilation on the subsequent precipitation forecasts. It is found that the 4DVAR radar data assimilation significantly reduces the model spinup required in the experiments without radar data assimilation, resulting in significantly improved 5-h forecasts. Additional experiments are conducted to study the sensitivity of the precipitation forecasts with respect to 4DVAR cycling configurations. Results from these experiments suggest that the forecasts with three 4DVAR cycles are improved over those with cold start, but the cycling impact seems to diminish with more cycles. The impact of observations from each of the individual radars is also examined by conducting a set of experiments in which data from each radar are alternately excluded. It is found that the accurate analysis of the environmental wind surrounding the convective cells is important in successfully predicting the squall line.