bluuebunny/crossref_metadata_2025 huggingface dataset:
Global Distribution of Tropical Deep Convection: Different Perspectives from TRMM Infrared and Radar Data
Authors: Liu Chuntao , Zipser Edward J. , Nesbitt Stephen W.
Published: February 2007

Cold cloud features (CCFs) are defined by grouping six full years of Tropical Rainfall Measuring Mission (TRMM) infrared pixels with brightness temperature at 10.8-μm wavelength (TB11) less than or equal to 210 and 235 K. Then the precipitation radar (PR)-observed precipitation area and reflectivity profiles inside CCFs are summarized and compared with the area and minimum temperature of the CCFs. Comparing the radar with the infrared data, significant regional differences are found, quantified, and used to describe regional differences in selected properties of deep convective systems in the Tropics. Inside 4 million CCFs, 35% (57%) of cold cloud area with TB11 ≤ 235 K (210 K) have rain detected by the PR near the surface. Only ∼1% of the area of TB11 ≤ 210 K have 20 dBZ reaching 14 km. CCFs colder than 210 K occur most frequently over the west Pacific Ocean, but 20-dBZ echoes extending above 10 km in this region are disproportionately rare by comparison to many continental regions. Ratios of PR-detected raining area to area of TB11 ≤ 235 K are higher over central Africa, Argentina, and India than over tropical oceans. After applying these ratios to the climatological Global Precipitation Index (GPI) tropical rainfall estimates, the regional distribution is more consistent with the rainfall retrieval from the PR. This suggests that the discrepancy between GPI- and PR-retrieved rainfall can be partly explained with the nonraining anvil. Categorization of CCFs based on the minimum TB11, size of CCFs, and 20-dBZ heights demonstrates that 20-dBZ echoes above 17 km occur most frequently over land, while the coldest clouds occur most frequently over the west Pacific. The vertical distances between the cloud-top heights determined from TB11 and PR 20-dBZ echo-top heights are smaller over land than over ocean and may be considered as another proxy for convective intensity.
The Predictability of Extratropical Storm Tracks and the Sensitivity of Their Prediction to the Observing System
Authors: Froude Lizzie S. R. , Bengtsson Lennart , Hodges Kevin I.
Published: February 2007

A new method for assessing forecast skill and predictability that involves the identification and tracking of extratropical cyclones has been developed and implemented to obtain detailed information about the prediction of cyclones that cannot be obtained from more conventional analysis methodologies. The cyclones were identified and tracked along the forecast trajectories, and statistics were generated to determine the rate at which the position and intensity of the forecasted storms diverge from the analyzed tracks as a function of forecast lead time. The results show a higher level of skill in predicting the position of extratropical cyclones than the intensity. They also show that there is potential to improve the skill in predicting the position by 1–1.5 days and the intensity by 2–3 days, via improvements to the forecast model. Further analysis shows that forecasted storms move at a slower speed than analyzed storms on average and that there is a larger error in the predicted amplitudes of intense storms than the weaker storms. The results also show that some storms can be predicted up to 3 days before they are identified as an 850-hPa vorticity center in the analyses. In general, the results show a higher level of skill in the Northern Hemisphere (NH) than the Southern Hemisphere (SH); however, the rapid growth of NH winter storms is not very well predicted. The impact that observations of different types have on the prediction of the extratropical cyclones has also been explored, using forecasts integrated from analyses that were constructed from reduced observing systems. A terrestrial, satellite, and surface-based system were investigated and the results showed that the predictive skill of the terrestrial system was superior to the satellite system in the NH. Further analysis showed that the satellite system was not very good at predicting the growth of the storms. In the SH the terrestrial system has significantly less skill than the satellite system, highlighting the dominance of satellite observations in this hemisphere. The surface system has very poor predictive skill in both hemispheres.
Cycling the Representer Algorithm for Variational Data Assimilation with the Lorenz Attractor
Authors: Ngodock H. E. , Smith S. R. , Jacobs G. A.
Published: February 2007

Realistic dynamic systems are often strongly nonlinear, particularly those for the ocean and atmosphere. Applying variational data assimilation to these systems requires a tangent linearization of the nonlinear dynamics about a background state for the cost function minimization. The tangent linearization may be accurate for limited time scales. Here it is proposed that linearized assimilation systems may be accurate if the assimilation time period is less than the tangent linear accuracy time limit. In this paper, the cycling representer method is used to test this assumption with the Lorenz attractor. The outer loops usually required to accommodate the linear assimilation for a nonlinear problem may be dropped beyond the early cycles once the solution (and forecast used as the background in the tangent linearization) is sufficiently accurate. The combination of cycling the representer method and limiting the number of outer loops significantly lowers the cost of the overall assimilation problem. In addition, this study shows that weak constraint assimilation corrects tangent linear model inaccuracies and allows extension of the limited assimilation period. Hence, the weak constraint outperforms the strong constraint method. Assimilated solution accuracy at the first cycle end is computed as a function of the initial condition error, model parameter perturbation magnitude, and outer loops. Results indicate that at least five outer loops are needed to achieve solution accuracy in the first cycle for the selected error range. In addition, this study clearly shows that one outer loop in the first cycle does not preclude accuracy convergence in future cycles.
The Impact of Assimilating SSM/I and QuikSCAT Satellite Winds on Hurricane Isidore Simulations
Authors: Chen Shu-Hua
Published: February 2007

Three observational datasets of Hurricane Isidore (in 2002) were analyzed and compared: the Special Sensor Microwave Imager (SSM/I), the Quick Scatterometer (QuikSCAT) winds, and dropsonde winds. SSM/I and QuikSCAT winds were on average about 1.9 and 0.3 m s−1 stronger, respectively, than dropsonde winds. With more than 20 000 points of data, SSM/I wind speed was about 2.2 m s−1 stronger than QuikSCAT. Comparison of the wind direction observed by QuikSCAT with those from the dropsondes showed that the quality of QuikSCAT data is good. The effect of assimilating SSM/I wind speeds and/or QuikSCAT wind vectors for the analysis of Hurricane Isidore was assessed using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) and its three-dimensional variational data assimilation system. For the Hurricane Isidore case study, it was found that the assimilation of either satellite winds strengthened the cyclonic circulation in the analysis. However, the increment of the QuikSCAT wind analysis is more complicated than that from the SSM/I analysis due to the correction of the storm location, a positive result from the assimilation of wind vectors. The increase in low-level wind speeds enhanced the air–sea interaction processes and improved the simulated intensity for Isidore. In addition, the storm structure was better simulated. Assimilation of QuikSCAT wind vectors clearly improved simulation of the storm track, in particular during the later period of the simulation, but lack of information about the wind direction from SSM/I data prevented it from having much of an effect. Assessing the assimilation of QuikSCAT wind speed versus wind vector data confirmed this hypothesis. The track improvement partially resulted from the relocation of the storm’s initial position after assimilation of the wind vectors. For this case study, it was found that the assimilation of SSM/I or QuikSCAT data had the greatest impact on the Hurricane Isidore simulation during the first 2 days.
The Impact of Multisatellite Data on the Initialization and Simulation of Hurricane Lili’s (2002) Rapid Weakening Phase
Authors: Zhang Xiaoyan , Xiao Qingnong , Fitzpatrick Patrick J.
Published: February 2007

Numerical experiments have been conducted to examine the impact of multisatellite data on the initialization and forecast of the rapid weakening of Hurricane Lili (in 2002) from 0000 UTC to landfall in Louisiana on 1300 UTC 3 October 2002. Fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) 4DVAR sensitivity runs were conducted separately with QuikSCAT surface winds, the Geostationary Operational Environmental Satellite-8 (GOES-8) cloud drift–water vapor winds, and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) temperature–dewpoint sounding data to investigate their individual impact on storm track and intensity. The results were compared against a simulation initialized from a Global Forecast System background interpolated to the MM5 grid. Assimilating QuikSCAT surface wind data improves the analyzed outer-core surface winds, as well as the inner-core low-level temperature and moisture fields. Substantial adjustments of winds are noted on the periphery of the hurricane by assimilating GOES-8 satellite-derived upper-level winds. Both track forecasts initialized at 1200 UTC 2 October 2002 with four-dimensional variational data assimilation (4DVAR) of QuikSCAT and GOES-8 show improvement compared to those initialized with the model background. Assimilating Aqua MODIS sounding data improves the outer-core thermodynamic features. The Aqua MODIS data has a slight impact on the track forecast, but more importantly shows evidence of impacting the model intensity predicting by retarding the incorrect prediction of intensification. All three experiments also show that bogusing of an inner-core wind vortex is required to depict the storm’s initial intensity.

To properly investigate Lili’s weakening, data assimilation experiments that incorporate bogusing vortex, QuikSCAT winds, GOES-8 winds, and Aqua MODIS sounding data were performed. The 4DVAR satellite-bogus data assimilation is conducted in two consecutive 6-h windows preceding Lili’s weakening. Comparisons of the results between the experiments with and without satellite data indicated that the satellite data, particularly the Aqua MODIS sounding information, makes an immediate impact on the hurricane intensity change beyond normal bogusing procedures. The track forecast with the satellite data is also more accurate than just using bogusing alone. This study suggests that dry air intrusion played an important role in Lili’s rapid weakening. It also demonstrates the potential benefit of using satellite data in a 4DVAR context—particularly high-resolution soundings—on unusual cases like Hurricane Lili.
Estimating and Correcting Global Weather Model Error
Authors: Danforth Christopher M. , Kalnay Eugenia , Miyoshi Takemasa
Published: February 2007

The purpose of the present study is to explore the feasibility of estimating and correcting systematic model errors using a simple and efficient procedure, inspired by papers by Leith as well as DelSole and Hou, that could be applied operationally, and to compare the impact of correcting the model integration with statistical corrections performed a posteriori. An elementary data assimilation scheme (Newtonian relaxation) is used to compare two simple but realistic global models, one quasigeostrophic and one based on the primitive equations, to the NCEP reanalysis (approximating the real atmosphere). The 6-h analysis corrections are separated into the model bias (obtained by time averaging the errors over several years), the periodic (seasonal and diurnal) component of the errors, and the nonperiodic errors. An estimate of the systematic component of the nonperiodic errors linearly dependent on the anomalous state is generated.

Forecasts corrected during model integration with a seasonally dependent estimate of the bias remain useful longer than forecasts corrected a posteriori. The diurnal correction (based on the leading EOFs of the analysis corrections) is also successful. State-dependent corrections using the full-dimensional Leith scheme and several years of training actually make the forecasts worse due to sampling errors in the estimation of the covariance. A sparse approximation of the Leith covariance is derived using univariate and spatially localized covariances. The sparse Leith covariance results in small regional improvements, but is still computationally prohibitive. Finally, singular value decomposition is used to obtain the coupled components of the correction and forecast anomalies during the training period. The corresponding heterogeneous correlation maps are used to estimate and correct by regression the state-dependent errors during the model integration. Although the global impact of this computationally efficient method is small, it succeeds in reducing state-dependent model systematic errors in regions where they are large. The method requires only a time series of analysis corrections to estimate the error covariance and uses negligible additional computation during a forecast. As a result, it should be suitable for operational use at relatively small computational expense.
Scale-Selective Bias Correction in a Downscaling of Global Analysis Using a Regional Model
Authors: Kanamaru Hideki , Kanamitsu Masao
Published: February 2007

Systematic large-scale errors are often found within the regional domain in the regional dynamical downscaling procedure. This paper proposes a method to suppress such errors using a combination of spectral tendency damping and area average correction of temperature, humidity, and surface pressure in the Regional Spectral Model. The proposed scale-selective bias-correction method reduces the time tendency of the zonal and meridional wind components for the physical scale greater than a predetermined length. In addition, the area mean perturbations of temperature and humidity are forced to zero. The surface pressure difference between the model field and the global field is adjusted from the hydrostatic equation using the mean elevation difference between the two fields and the area mean temperature. Each of these three components of the technique is necessary for the model to effectively reduce large-scale errors in the regional domain. With this method, the downscaled field becomes less dependent on the domain size. Furthermore, the downscaled precipitation compares better with observations, as do the near-surface temperature and wind fields. The scheme allows much weaker lateral boundary relaxation, although it is still an essential part of the regional model. The use of a similar scheme is recommended for any regional model in the application of dynamical downscaling of analysis for climate studies.
Predictability of June–September Rainfall in Ethiopia
Authors: Korecha Diriba , Barnston Anthony G.
Published: February 2007

In much of Ethiopia, similar to the Sahelian countries to its west, rainfall from June to September contributes the majority of the annual total, and is crucial to Ethiopia’s water resource and agriculture operations. Drought-related disasters could be mitigated by warnings if skillful summer rainfall predictions were possible with sufficient lead time. This study examines the predictive potential for June–September rainfall in Ethiopia using mainly statistical approaches. The skill of a dynamical approach to predicting the El Niño–Southern Oscillation (ENSO), which impacts Ethiopian rainfall, is assessed. The study attempts to identify global and more regional processes affecting the large-scale summer climate patterns that govern rainfall anomalies. Multivariate statistical techniques are applied to diagnose and predict seasonal rainfall patterns using historical monthly mean global sea surface temperatures and other physically relevant predictor data. Monthly rainfall data come from a newly assembled dense network of stations from the National Meteorological Agency of Ethiopia. Results show that Ethiopia’s June–September rainy season is governed primarily by ENSO, and secondarily reinforced by more local climate indicators near Africa and the Atlantic and Indian Oceans. Rainfall anomaly patterns can be predicted with some skill within a short lead time of the summer season, based on emerging ENSO developments. The ENSO predictability barrier in the Northern Hemisphere spring poses a major challenge to providing seasonal rainfall forecasts two or more months in advance. Prospects for future breakthroughs in ENSO prediction are thus critical to future improvements to Ethiopia’s summer rainfall prediction.
Impact of Configurations of Rapid Intermittent Assimilation of WSR-88D Radar Data for the 8 May 2003 Oklahoma City Tornadic Thunderstorm Case
Authors: Hu Ming , Xue Ming
Published: February 2007

Various configurations of the intermittent data assimilation procedure for Level-II Weather Surveillance Radar-1988 Doppler radar data are examined for the analysis and prediction of a tornadic thunderstorm that occurred on 8 May 2003 near Oklahoma City, Oklahoma. Several tornadoes were produced by this thunderstorm, causing extensive damages in the south Oklahoma City area. Within the rapidly cycled assimilation system, the Advanced Regional Prediction System three-dimensional variational data assimilation (ARPS 3DVAR) is employed to analyze conventional and radar radial velocity data, while the ARPS complex cloud analysis procedure is used to analyze cloud and hydrometeor fields and adjust in-cloud temperature and moisture fields based on reflectivity observations and the preliminary analysis of the atmosphere. Forecasts for up to 2.5 h are made from the assimilated initial conditions. Two one-way nested grids at 9- and 3-km grid spacings are employed although the assimilation configuration experiments are conducted for the 3-km grid only while keeping the 9-km grid configuration the same. Data from the Oklahoma City radar are used. Different combinations of the assimilation frequency, in-cloud temperature adjustment schemes, and the length and coverage of the assimilation window are tested, and the results are discussed with respect to the length and evolution stage of the thunderstorm life cycle. It is found that even though the general assimilation method remains the same, the assimilation settings can significantly impact the results of assimilation and the subsequent forecast. For this case, a 1-h-long assimilation window covering the entire initial stage of the storm together with a 10-min spinup period before storm initiation works best. Assimilation frequency and in-cloud temperature adjustment scheme should be set carefully to add suitable amounts of potential energy during assimilation. High assimilation frequency does not necessarily lead to a better result because of the significant adjustment during the initial forecast period. When a short assimilation window is used, covering the later part of the initial stage of storm and using a high assimilation frequency and a temperature adjustment scheme based on latent heat release can quickly build up the storm and produce a reasonable analysis and forecast. The results also show that when the data from a single Doppler radar are assimilated with properly chosen assimilation configurations, the model is able to predict the evolution of the 8 May 2003 Oklahoma City tornadic thunderstorm well for up to 2.5 h. The implications of the choices of assimilation settings for real-time applications are discussed.
Sensitivity of Mesoscale Gravity Waves to the Baroclinicity of Jet-Front Systems
Authors: Wang Shuguang , Zhang Fuqing
Published: February 2007

This study investigates the sensitivity of mesoscale gravity waves to the baroclinicity of the background jet-front systems by simulating different life cycles of baroclinic waves with a high-resolution mesoscale model. Four simulations are made starting from two-dimensional baroclinic jets having different static stability and wind shear in order to obtain baroclinic waves with significantly different growth rates. In all experiments, vertically propagating mesoscale gravity waves are simulated in the exit region of upper-tropospheric jet streaks. A two-dimensional spectral analysis demonstrates that these gravity waves have multiple components with different wave characteristics. The short-scale wave components that are preserved by a high-pass filter with a cutoff wavelength of 200 km have horizontal wavelengths of 85–161 km and intrinsic frequencies of 3–11 times the Coriolis parameter. The medium-scale waves that are preserved by a bandpass filter (with 200- and 600-km cutoff wavelengths) have horizontal wavelengths of 250–350 km and intrinsic frequencies less than 3 times the Coriolis parameter. The intrinsic frequencies of these gravity waves tend to increase with the growth rate of the baroclinic waves; gravity waves with similar frequency are found in the experiments with similar average baroclinic wave growth rate but with significantly different initial tropospheric static stability and tropopause geometry. The residuals of the nonlinear balance equation are used to assess the flow imbalance. In all experiments, the developing background baroclinic waves evolve from an initially balanced state to the strongly unbalanced state especially near the exit region of upper-level jet fronts before mature mesoscale gravity waves are generated. It is found that the growth rate of flow imbalance also correlates well to the growth rate of baroclinic waves and thus correlates to the frequency of gravity waves.
An Analytic Longwave Radiation Formula for Liquid Layer Clouds
Authors: Larson Vincent E. , Kotenberg Kurt E. , Wood Norman B.
Published: February 2007

Many Global Energy and Water Cycle Experiment (GEWEX) Cloud System Study (GCSS) intercomparisons of boundary layer clouds have used a convenient but idealized longwave radiation formula for clouds in their large-eddy simulations (LESs). Under what conditions is this formula justified? Can it be extended to midlevel layer clouds? This note first derives the GCSS formula using an alternative method to effective emissivity. A key simplifying assumption is that the cloud is isothermal in the vertical (and horizontal). However, this assumption does not turn out to be overly restrictive in practice. Then the GCSS formula is compared with a detailed numerical code, BugsRad. Sensitivity studies are performed in which cloud properties, cloud altitude, and thermodynamic profiles are modified. Here, the focus is primarily on midlevel, altostratocumulus layers. The results here show that the GCSS formula can be successfully extended to liquid (ice free), midlevel clouds. The GCSS formula produces remarkably accurate radiative profiles if the parameters are adjusted on a case-by-case basis. However, the formula needs to be calibrated using a more general radiative transfer code.
Individual and School Predictors of Middle School Aggression
Authors: Reis Janet , Trockel Mickey , Mulhall Peter
Published: February 2007

Hierarchical linear modeling is used to assess individual student, family, and school predictors of aggression in 111,662 students in sixth, seventh, and eighth grades. Nine measures of problem-solving strategies, quality of family and peer interaction, and perceptions of school climate are analyzed at the individual student level. Eight measures of school climate are included in the analysis at the school level. Aggression is operationalized with student self-report of the previous 6-month frequency of hitting others, being mean to others, and getting into a fight. At the level of the individual student, measures of problem solving were most strongly predictive of aggression. Inclusion of students in policy and rule processes, cultural sensitivity education, and teaching that emphasizes understanding over memorization were significant predictors of aggression at the school level. The potential for abatement of student aggression across individual and school levels offers opportunities for further testing of interventions for the child and the school.
Risk Comparison Among Youth Who Report Sex With Same-Sex Versus Both-Sex Partners
Authors: Moon Martha W. , Fornili Katherine , O'Briant Amanda L.
Published: February 2007

This article examines risk behavior among youth attending support groups for sexual minority youth in Richmond, Virginia, using a structured survey, with particular attention to partner selection and its relationship to risk. Within this generally high-risk group, youth reporting sex partners of both sexes had significantly higher risk profiles, including histories of drug use, suicide attempts, sexual victimization, and having run away from or been removed from the home, than those reporting only same-sex partners.
“I Wanna Have a Good Future”: Teen Mothers' Rise in Educational Aspirations, Competing Demands, and Limited School Support
Authors: SmithBattle Lee
Published: February 2007

This longitudinal study examined teen mothers' descriptions of being students before and after giving birth and the impact of mothering on their educational goals and school progress. Nineteen teens and at least one of their parents were interviewed six times from the third trimester of pregnancy to 10 months postpartum. Regardless of their school status prior to pregnancy, the anticipation of motherhood led teens to reevaluate their priorities and motivated them to remain in or return to school. The transformed meaning and significance of school in the lives of these teens was apparent in improved grades, in their resolve to graduate, and in their new interest in attending college. Their renewed commitment to school was often thwarted by competing work demands, family responsibilities, and school policies and practices. These findings suggest that professionals are missing a critical opportunity to promote teen mothers' educational goals and their long-term success.
Differential Response to an Exclusive Breastfeeding Peer Counseling Intervention: The Role of Ethnicity
Authors: Anderson Alex K. , Damio Grace , Chapman Donna J. , Pérez-Escamilla Rafael
Published: February 2007

The authors analyzed data from a trial assessing the efficacy of breastfeeding peer counseling (PC) for increasing exclusive breastfeeding (EBF) to (1) examine whether different ethnic groups responded differently to the intervention and (2) document the determinants of EBF. At 2 months postpartum, the prevalence of EBF in the intervention group was 11.4% among Puerto Ricans compared to 44.4% among non-Puerto Ricans ( P = .008). Multivariate logistic regression analyses showed that women who had the intention prenatally to engage in EBF were more likely to do so and those whose mothers lived in the United States were less likely to engage in EBF at hospital discharge. At 2 months postpartum, mothers who were breastfed as children were more likely to engage in EBF, whereas non-Puerto Ricans had a significantly greater response to the intervention than Puerto Ricans (odds ratio, 6.40; 95% confidence interval, 1.45-28.33). There is a need for further studies to determine why different ethnic groups respond differently to EBF promotion interventions.
Normal Nipple Position in Term Infants Measured on Breastfeeding Ultrasound
Authors: Jacobs Lorili Audrey , Dickinson Jan E. , Hart Philip David , Doherty Dorota A. , Faulkner Shani Jean
Published: February 2007

Nipple position is believed to influence breastfeeding success. To investigate this belief, submental ultrasound images were obtained during breastfeeding of normal term infants. This study measured nipple to hard-soft palate distance (NHSPD) in 18 mother-infant pairs during the first and fourth weeks of life. Median NHSPD was 5 mm (interquartile: 4, 6 mm). There were no significant differences in median NHSPD between first, second, and fifth minutes of feeding ( P = .675) or between week 1 and week 4 ( P = .320). The nipple was not stationary during feeding, with mean nipple movement of 4.0 ∓ 1.3 mm. Further research is required with more infants to confirm the boundaries of normality for ultrasound measurements of nipple position during successful breastfeeding.
Changes in Breast Skin Temperature During the Course of Breastfeeding
Authors: Kimura Chisato , Matsuoka Megumi
Published: February 2007

Breast skin temperature was measured during breastfeeding in 11 mothers on a total of 47 occasions, using a Coretemp CM-210 (Terumo Corp, Tokyo, Japan), to examine the changes of breast skin temperature during the course of breastfeeding. In both breasts, the breast skin temperature was significantly higher than the baseline skin temperature from the beginning of suckling up to 5 minutes after completion of suckling, and the mean breast skin temperature before breastfeeding between 4 days and 8 weeks postpartum was significantly higher than that on the first 1 to 2 days postpartum. These results show that the breast skin temperature increases between the first 1 to 2 days and 4 to 5 days postpartum and that breast skin temperature remains high during suckling and up to 5 minutes after the completion of suckling. These findings will be useful for educating mothers during the perinatal period on the normal course of breastfeeding by individual instruction or in classes.
Low Prepregnant Body Mass Index and Breastfeeding Practices
Authors: Giovannini Marcello , Radaelli Giovanni , Riva Enrica , Banderali Giuseppe
Published: February 2007

The relationship of low prepregnant body mass index with breastfeeding was investigated in 1272 women who delivered a term infant with birthweight ≥ 2500 g at the San Paolo Hospital in Milan, Northern Italy. Underweight was defined using the Institute of Medicine’s cutoff of 19.8 kg/m2. Women were interviewed via telephone through 12 months postdelivery about breastfeeding practices. Education level (high versus low, odds ratio [OR], 1.41), primiparity (OR, 1.35), vaginal delivery (OR, 0.74), and birthweight of the infant (normal versus high, OR, 1.89) were associated with low, as opposed to normal, pre-pregnant body mass index. After adjustment for these confounders, no difference was found between underweight and normal weight women for initiation or duration of breastfeeding (mean adjusted difference, 0.4; 95% confidence interval [95% CI], -0.1 to 0.9 months) or exclusive breastfeeding (0.1 [95% CI, -0.1 to 0.3] months). Underweight mothers of healthy term infants may not be at increased risk for not initiating or shorter breastfeeding.
Chronic GvHD decreases antiviral immune responses in allogeneic BMT
Authors: Hossain Mohammad S. , Roback John D. , Pollack Brian P. , Jaye David L. , Langston Amelia , Waller Edmund K.
Published: February 2007

Chronic graft-versus-host disease (cGvHD) is associated with functional immunodeficiency and an increased risk of opportunistic infections in allogeneic bone marrow transplantation (BMT). We used a parent to F1 model of allogeneic BMT to test the hypothesis that cGvHD leads to impaired antigen-specific antiviral immunity and compared BM transplant recipients with cGvHD to control groups of allogeneic BM transplant recipients without GvHD. Mice with and without cGvHD received a nonlethal dose of murine cytomegalovirus (MCMV) +100 days after transplantation. Recipients with cGvHD had more weight loss and higher viral loads in the spleen and liver. MCMV infection led to greater than 25-fold expansion of donor spleen–derived MCMV peptide–specific tetramer-positive CD8+ T cells in blood of transplant recipients with and without cGvHD, but mice with cGvHD had far fewer antigen-specific T cells in peripheral tissues and secondary lymphoid organs. The immunosuppression associated with cGvHD was confirmed by vaccinating transplant recipients with and without cGvHD using a recombinant Listeria expressing MCMV early protein (Lm-MCMV). Secondary adoptive transfer of lymphocytes from donor mice with or without cGvHD into lymphopenic congenic recipients showed that cGvHD impaired tissue-specific homing of antigen-specific T cells. These results indicate that cGvHD causes an intrinsic immunosuppression and explain, in part, the functional immunodeficiency in allogeneic transplant recipients.
New thrombopoietic growth factors
Authors: Kuter David J.
Published: February 2007

Although development of first-generation thrombopoietic growth factors (recombinant human thrombopoietin [TPO] and pegylated recombinant human megakaryocyte growth and development factor [PEG-rHuMGDF]) was stopped due to development of antibodies to PEG-rHuMGDF, nonimmunogenic second-generation thrombopoietic growth factors with unique pharmacologic properties have been developed. TPO peptide mimetics contain TPO receptor-activating peptides inserted into complementarity-determining regions of Fab (Fab 59), attached to the IgG Fc region (AMG 531), or pegylated (Peg-TPOmp). Orally available, TPO nonpeptide mimetics (eltrombopag, AKR-501) bind and activate the TPO receptor by a mechanism different from TPO and may have an additive effect to TPO. TPO agonist antibodies are monoclonal antibodies activating the TPO receptor but modified in size [TPO minibodies; ie, VB22B sc(Fv)2] or immunoglobuln type (domain subclass-converted TPO agonist antibodies; ie, MA01G4G344). All second-generation thrombopoietic growth factors stimulate growth of TPO-dependent cell lines via JAK2/STAT signaling pathways and increase platelet counts in animals. When tested in healthy humans, TPO peptide and nonpeptide mimetics produced a dose-dependent rise in platelet count. AMG 531 and eltrombopag markedly increase platelet counts in patients with immune thrombocytopenic purpura, without significant adverse effects. One or more second-generation thrombopoietic growth factors should soon be clinically available for treating thrombocytopenic disorders.
Treatment-related risk factors of inhibitor development in previously untreated patients with hemophilia A: the CANAL cohort study
Authors: Gouw Samantha C. , van der Bom Johanna G. , Marijke van den Berg H.
Published: February 2007

The CANAL Study (Concerted Action on Neutralizing Antibodies in severe hemophilia A) was designed to describe the relationship between treatment characteristics and inhibitor development in previously untreated patients with severe hemophilia A. This multicenter retrospective cohort study investigated 366 consecutive patients born between 1990 and 2000. The outcome was clinically relevant inhibitor development, defined as the occurrence of at least 2 positive inhibitor titers combined with a decreased recovery. Eighty-seven (24%) patients developed inhibitors (69 high titer [19%]). The incidence of inhibitors appeared to be associated with age at first treatment, decreasing from 41% for those treated within the first month of age to 18% in those treated after 18 months; after adjustment for treatment intensity, this association largely disappeared. Surgical procedures and peak treatment moments at start of treatment increased inhibitor risk (relative risk [RR], 3.7; 95% confidence interval [CI], 2.0-7.1; and RR, 3.3; CI, 2.1-5.3, respectively). Regular prophylaxis was associated with a 60% lower risk than on-demand treatment (RR, 0.4; CI, 0.2-0.8). Our findings suggest that the previously reported associated between an early age at first exposure and the risk of inhibitor development is largely explained by early, intensive treatment. The latter appears to be an independent risk factor for inhibitor development. In addition, early, regular prophylaxis may protect patients with hemophilia against the development of inhibitors.
Interaction between B7-H1 and PD-1 determines initiation and reversal of T-cell anergy
Authors: Tsushima Fumihiko , Yao Sheng , Shin Tahiro , Flies Andrew , Flies Sarah , Xu Haiying , Tamada Koji , Pardoll Drew M. , Chen Lieping
Published: February 2007

Although self-reactive T-cell precursors can be eliminated upon recognition of self-antigen presented in the thymus, this central tolerance process is often incomplete, and additional mechanisms are required to prevent autoimmunity. Recent studies indicates that the interaction between B7-H1 and its receptor PD-1 on activated T cells plays an important role in the inhibition of T-cell responses in peripheral organs. Here, we show that, before their exit to the periphery, T cells in lymphoid organs rapidly up-regulate PD-1 upon tolerogen recognition. Ablation of the B7-H1 and PD-1 interaction when T cells are still in lymphoid organs prevents anergy. Furthermore, blockade of B7-H1 and PD-1 interaction could render anergic T cells responsive to antigen. Our results thus reveal previously unappreciated roles of B7-H1 and PD-1 interaction in the control of initiation and reversion of T-cell anergy.
The peritoneal micromilieu commits B cells to home to body cavities and the small intestine
Authors: Berberich Simon , Förster Reinhold , Pabst Oliver
Published: February 2007

The distinct combination of homing receptors such as selectins, chemokine receptors, and integrins directs the migration of lymphocytes throughout the body. Upon activation lymphocytes irreversibly switch their set of homing receptors, now guiding them to entirely different destinations. Here we report that exposure of naive B cells to the microenvironment of the peritoneal cavity modulates their migration propensities in the absence of antigenic stimulation. B1 and B2 cells isolated from the peritoneal cavity reenter this compartment more efficiently compared with splenic follicular B cells. Moreover, when kept in the peritoneal cavity splenic follicular B cells gain such increased capability to reenter this compartment. These altered migratory capacities are reflected by an up-regulation of the chemokine receptors CXCR4 and CXCR5 and β7 integrin by the peritoneum-experienced splenic B cells, among which CXCR5 is instrumental in directing B cells into the peritoneal cavity. Moreover, intraperitoneal transfer of plasma blasts favors their migration into the small intestine presumably before class switch recombination occurs, demonstrating that a reconfigured transient migration pattern is not restricted to naive cells. In conclusion, these data demonstrate a hitherto unrecognized role for tissue-specific cues, altering the migratory capacity of B1, naive B2, as well as antigen-experienced B2 cells.
msmsEval: tandem mass spectral quality assignment for high-throughput proteomics
Authors: Wong Jason WH , Sullivan Matthew J , Cartwright Hugh M , Cagney Gerard
Published: February 2007

Background

In proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for these programs have become prohibitive, particularly in searches for modified proteins. Recently, methods to limit the number of spectra to be searched based on spectral quality have been proposed by different research groups, but rankings of spectral quality have thus far been based on arbitrary cut-off values. In this work, we develop a more readily interpretable spectral quality statistic by providing probability values for the likelihood that spectra will be identifiable.

Results

We describe an application, msmsEval, that builds on previous work by statistically modeling the spectral quality discriminant function using a Gaussian mixture model. This allows a researcher to filter spectra based on the probability that a spectrum will ultimately be identified by database searching. We show that spectra that are predicted by msmsEval to be of high quality, yet remain unidentified in standard database searches, are candidates for more intensive search strategies. Using a well studied public dataset we also show that a high proportion (83.9%) of the spectra predicted by msmsEval to be of high quality but that elude standard search strategies, are in fact interpretable.

Conclusion

msmsEval will be useful for high-throughput proteomics projects and is freely available for download fromhttp://proteomics.ucd.ie/msmseval. Supports Windows, Mac OS X and Linux/Unix operating systems.
PASSIM – an open source software system for managing information in biomedical studies
Authors: Viksna Juris , Celms Edgars , Opmanis Martins , Podnieks Karlis , Rucevskis Peteris , Zarins Andris , Barrett Amy , Neogi Sudeshna Guha , Krestyaninova Maria , McCarthy Mark I , Brazma Alvis , Sarkans Ugis
Published: February 2007

Background

One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management.

Results

We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project.

Conclusion

The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
Authors: He Ji , Dai Xinbin , Zhao Xuechun
Published: February 2007

Background

BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming.

Results

Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration.

Conclusion

PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.
The role of laterally transferred genes in adaptive evolution
Authors: Marri Pradeep Reddy , Hao Weilong , Golding G Brian
Published: February 2007

Background

Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.

Methods

A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny.

Results

The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role.

Conclusion

The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8 – 14% of their genomes by LGT and some of these genes may have a role in adaptation.