bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Human T-Box Mesodermal Transcription Factor Brachyury Is a Candidate Target for T-Cell–Mediated Cancer Immunotherapy
Authors: Palena Claudia , Polev Dmitry E. , Tsang Kwong Y. , Fernando Romaine I. , Litzinger Mary , Krukovskaya Larisa L. , Baranova Ancha V. , Kozlov Andrei P. , Schlom Jeffrey 
Published: April 2007

AbstractPurpose: Identification of tumor antigens is essential in advancing immune-based therapeutic interventions in cancer. Particularly attractive targets are those molecules that are selectively expressed by malignant cells and that are also essential for tumor progression.Experimental Design and Results: We have used a computer-based differential display analysis tool for mining of expressed sequence tag clusters in the human Unigene database and identified Brachyury as a novel tumor antigen. Brachyury, a member of the T-box transcription factor family, is a key player in mesoderm specification during embryonic development. Moreover, transcription factors that control mesoderm have been implicated in the epithelial-mesenchymal transition (EMT), which has been postulated to be a key step during tumor progression to metastasis. Reverse transcription-PCR analysis validated the in silico predictions and showed Brachyury expression in tumors of the small intestine, stomach, kidney, bladder, uterus, ovary, and testis, as well as in cell lines derived from lung, colon, and prostate carcinomas, but not in the vast majority of the normal tissues tested. An HLA-A0201 epitope of human Brachyury was identified that was able to expand T lymphocytes from blood of cancer patients and normal donors with the ability to lyse Brachyury-expressing tumor cells.Conclusions: To our knowledge, this is the first demonstration that (a) a T-box transcription factor and (b) a molecule implicated in mesodermal development, i.e., EMT, can be a potential target for human T-cell–mediated cancer immunotherapy.
Characterization and Magnetic Resonance Imaging of a Rat Model of Human B-Cell Central Nervous System Lymphoma
Authors: Soussain Carole , Muldoon Leslie L. , Varallyay Csanad , Jahnke Kristoph , DePaula Luciana , Neuwelt Edward A. 
Published: April 2007

Abstract
Purpose: The incidence of primary central nervous system lymphoma (PCNSL) is increasing. Therapeutic approaches remain controversial. An animal model that mimics the clinical situation would be useful for evaluating PCNSL biology and treatment.
Experimental Design: Nude rats received intracerebral (caudate nucleus, n = 49) or intraventricular (n = 4) inoculation of human B-lymphoma cell line MC116. Two to five weeks after tumor inoculation, magnetic resonance imaging (MRI) was done (n = 24), and rat brains were assessed for pathology. Five rats each received whole-brain radiotherapy (WBRT, 20 Gy) or high-dose i.v. methotrexate (3 g/m2).
Results: Intracerebral tumors developed in 84% of evaluable animals with no pretreatment, 79% of rats pretreated with 4 Gy total body irradiation, and 92% of rats pretreated with cyclophosphamide (300 mg/m2). MRI showed abnormal T2 signal and gadolinium enhancement on T1-weighted images, consistent with tumor growth 19 to 24 days after inoculation. Tumor cells staining positively for B-lymphoma markers infiltrated within the inoculated hemisphere, along fiber tracks to the contralateral hemisphere, and along the subarachnoid space and ventricles. Tumors showed reactive gliosis. Intraventricular tumor cell injection resulted in periventricular parenchymal infiltration in both hemispheres. Radiation and methotrexate were effective in vitro, but only WBRT was clearly effective after 1 week in the intracerebral model.
Conclusion: This model closely mimics human PCNSL in terms of imaging, histology, and treatment sensitivity and will be useful for the development of future therapeutic strategies for PCNSL.
Evolution of Low-Level Angular Momentum in the 2 June 1995 Dimmitt, Texas, Tornado Cyclone
Authors: Rasmussen Erik N. , Straka Jerry M. 
Published: April 2007

Abstract
The life cycle of the 2 June 1995 Dimmitt, Texas, tornado cyclone, observed during the Verification of the Origins of Rotation in Tornadoes Experiment (VORTEX), is described. The tornado cyclone here is defined as a significantly axisymmetric flow larger than the visible tornado and characterized by increasing angular momentum with increasing radius. Its life cycle included three phases with somewhat differing evolution of angular momentum, herein called intensifying, transition, and weakening. During the intensifying stage, the funnel and debris cloud gradually increased in size. The azimuthally averaged secondary circulation of the larger-scale tornado cyclone, as determined using high-resolution single-Doppler data obtained by a mobile radar, was primarily inward and upward, consistent with the presence of a wall cloud outside the tornado. The azimuthally averaged angular momentum increased monotonically away from the tornado, so inward advection allowed the angular momentum to increase slowly with time in part of the tornado cyclone. During the transition phase, downdrafts began to occur within the tornado cyclone. The transport of angular momentum by the secondary circulation nearly was offset by eddy flux convergence of angular momentum so that the azimuthally averaged angular momentum tendency was only weakly negative at most radii. The tornado was visually impressive during this stage, featuring a 400-m diameter debris cloud extending to cloud base, while the surrounding wall cloud shrank and eroded. During the weakening phase, the funnel and debris cloud gradually shrank, and the funnel went through a rope stage prior to disappearing. The weakening phase was characterized by extensive downdrafts at all radii outside the tornado, and large-scale near-ground outflow as observed by mobile mesonet systems in a portion of the tornado cyclone. The secondary circulation acted to transport smaller angular momentum downward from aloft, and outward along the ground. All terms of the angular momentum budget became negative throughout most of the low-level (0–800-m AGL) tornado cyclone during the weakening phase. Several hypotheses for this evolution are evaluated, including changes in water loading in the tornado cyclone, cooling of the near-ground air, and the distribution of tangential velocity with height with its concomitant influence on the nonhydrostatic vertical pressure gradient force.
Optimal Perturbations in Quasigeostrophic Turbulence
Authors: DelSole Timothy 
Published: April 2007

Abstract
This paper tests the hypothesis that optimal perturbations in quasigeostrophic turbulence are excited sufficiently strongly and frequently to account for the energy-containing eddies. Optimal perturbations are defined here as singular vectors of the propagator, for the energy norm, corresponding to the equations of motion linearized about the time-mean flow. The initial conditions are drawn from a numerical solution of the nonlinear equations associated with the linear propagator. Experiments confirm that energy is concentrated in the leading evolved singular vectors, and that the average energy in the initial singular vectors is within an order of magnitude of that required to explain the average energy in the evolved singular vectors. Furthermore, only a small number of evolved singular vectors (4 out of 4000) are needed to explain the dominant eddy structure when total energy exceeds a predefined threshold. The initial singular vectors explain only 10% of such events, but this discrepancy was similar to that of the full propagator, suggesting that it arises primarily due to errors in the propagator. In the limit of short lead times, energy conservation can be expressed in terms of suitable singular vectors to constrain the energy distribution of the singular vectors in statistically steady equilibrium. This and other connections between linear optimals and nonlinear dynamics suggests that the positive results found here should carry over to other systems, provided the propagator and initial states are chosen consistently with respect to the nonlinear system.
Turbulent Fluxes in the Hurricane Boundary Layer. Part II: Latent Heat Flux
Authors: Drennan William M. , Zhang Jun A. , French Jeffrey R. , McCormick Cyril , Black Peter G. 
Published: April 2007

Abstract
As part of the recent ONR-sponsored Coupled Boundary Layer Air–Sea Transfer (CBLAST) Departmental Research Initiative, an aircraft was instrumented to carry out direct turbulent flux measurements in the high wind boundary layer of a hurricane. During the 2003 field season flux measurements were made during Hurricanes Fabian and Isabel. Here the first direct measurements of latent heat fluxes measured in the hurricane boundary layer are reported. The previous wind speed range for humidity fluxes and Dalton numbers has been extended by over 50%. Up to 30 m s−1, the highest 10-m winds measured, the Dalton number is not significantly different from the Humidity Exchange over the Sea (HEXOS) result, with no evidence of an increase with wind speed.
Refinements to Ice Particle Mass Dimensional and Terminal Velocity Relationships for Ice Clouds. Part I: Temperature Dependence
Authors: Heymsfield Andrew J. , Bansemer Aaron , Twohy Cynthia H. 
Published: April 2007

Abstract
This two-part study attempts to find appropriate mass dimension and terminal velocity relationships that, when considered together with particle size distributions (PSD), agree with coincident measurements of ice water content (IWC), and with variables related to higher moments such as the mean mass-weighted fall speed. Reliable relationships are required for improving microphysical parameterizations for weather forecast models and developing methods for evaluating them, subjects addressed in detail in Part II of this study.
Here, a range of values from 1.5 to 2.3 is assumed for the exponent b in the mass dimension relationship, m = aDb, where D is the maximum particle dimension, to bound its likely value for sizes above about 100 μm. Measured IWC and size spectra are used to find appropriate values for the coefficient a. It is demonstrated that all values of the exponent b, with appropriate a coefficients, can fit the IWC measurements. Coincident information on particle cross-sectional areas with the m(D) relationships is used to develop general fall velocity relationships of the form Vt = ADB. These assessments use five midlatitude, synoptically generated ice layers, and 10 low-latitude, convectively generated ice cloud layers, spanning the temperature range from −60° to 0°C.
The coefficients a and A and exponent B are represented in terms of the exponent b and are shown to be temperature-dependent for the synoptic clouds and relatively independent of it in the convective clouds, a result of particle mixing through the cloud column. Consistency is found with earlier results and with analytic considerations. It is found that the fall velocity is inversely proportional to the air density to approximately the exponent 0.54, close to values assumed in earlier studies.
Genesis of the Northeast Brazil Upper-Tropospheric Cyclonic Vortex: A Primitive Equation Barotropic Instability Study
Authors: Mishra S. K. , Rao V. Brahmananda , Franchito Sergio H. 
Published: April 2007

Abstract
The primitive equation barotropic unstable linear normal modes are computed using an eigenvalue approach for daily latitudinal profiles of zonal flow in the upper-tropospheric layer of 100–350 hPa before and after formation of cyclonic vortices during January 1993 and November 2001 off the coast of northeast Brazil. The wave kinetic energy equation for u- and υ-motion is presented. Equations are derived to isolate the contribution of divergence and other dynamical processes in the movement and growth of unstable modes. Numerical accuracy and physical nature of unstable modes are tested.
In a short span of 2–3 days, prior to formation of vortices, a progressive and a sharp intensification of the basic flow shear zone and its barotropic instability are seen with time. The horizontal structure, momentum transport, and zonal and meridional scales of the most unstable normalized wave are obtained and compared with the vortex extracted from the 200-hPa observed winds using a bandpass smoother. A close agreement is found between them. It is shown that the zonal and meridional scales of the preferred wave are related to the length scale of the shear zone. The wave is confined to the shear zone and its maximum amplitude is located at the latitude of maximum β − uyy. The role of divergence in the movement and growth of the wave is investigated. The energetics of the unstable wave u- and υ-motion is computed, and it is inferred that the energy source for the growth of wave u- (υ-) motion is the energy conversion (work done by pressure force), which lies in the shear zone.
It is emphasized that a deeper insight regarding the genesis of the cyclonic vortex can be gained on the basis of stability analysis of daily observed zonal flow profiles, which may not be possible using idealized or mean profiles. An explanation for nonmanifestation of the instability in the monthly mean flow is provided.
Refinements to Ice Particle Mass Dimensional and Terminal Velocity Relationships for Ice Clouds. Part II: Evaluation and Parameterizations of Ensemble Ice Particle Sedimentation Velocities
Authors: Heymsfield Andrew J. , van Zadelhoff Gerd-Jan , Donovan David P. , Fabry Frederic , Hogan Robin J. , Illingworth Anthony J. 
Published: April 2007

AbstractThis two-part study addresses the development of reliable estimates of the mass and fall speed of single ice particles and ensembles. Part I of the study reports temperature-dependent coefficients for the mass-dimensional relationship, m = aDb, where D is particle maximum dimension. The fall velocity relationship, Vt = ADB, is developed from observations in synoptic and low-latitude, convectively generated, ice cloud layers, sampled over a wide range of temperatures using an assumed range for the exponent b. Values for a, A, and B were found that were consistent with the measured particle size distributions (PSD) and the ice water content (IWC).To refine the estimates of coefficients a and b to fit both lower and higher moments of the PSD and the associated values for A and B, Part II uses the PSD from Part I plus coincident, vertically pointing Doppler radar returns. The observations and derived coefficients are used to evaluate earlier, single-moment, bulk ice microphysical parameterization schemes as well as to develop improved, statistically based, microphysical relationships. They may be used in cloud and climate models, and to retrieve cloud properties from ground-based Doppler radar and spaceborne, conventional radar returns.
Relating Static Energy to Potential Temperature: A Caution
Authors: DeCaria Alex J. 
Published: April 2007

Abstract
The relationship between dry static energy and potential temperature, cpθ = cpT + gz, is exact for an adiabatic temperature profile, and extremely close to exact for an isothermal profile. Even though it is extremely accurate, its use in atmospheres with nonadiabatic temperature profiles can lead to significant errors when comparing the entropies of isolated atmospheric layers. Use of the relation in this context leads to the incorrect conclusion that an adiabatic temperature profile has greater entropy than an isothermal profile for the same static energy. The relation fails in this application because of the extreme sensitivity of the column-integrated entropy to temperature.
Twentieth-Century Trends in Runoff, Evapotranspiration, and Soil Moisture in the Western United States*
Authors: Hamlet Alan F. , Mote Philip W. , Clark Martyn P. , Lettenmaier Dennis P. 
Published: April 2007

Abstract
A physically based hydrology model is used to produce time series for the period 1916–2003 of evapotranspiration (ET), runoff, and soil moisture (SM) over the western United States from which long-term trends are evaluated. The results show that trends in ET in spring and summer are determined primarily by trends in precipitation and snowmelt that determine water availability. From April to June, ET trends are mostly positive due primarily to earlier snowmelt and earlier emergence of snow-free ground, and secondarily to increasing trends in spring precipitation. From July to September trends in ET are more strongly influenced by precipitation trends, with the exception of areas (most notably California) that receive little summer precipitation and have experienced large changes in snowmelt timing. Trends in the seasonal timing of ET are modest, but during the period 1947–2003 when temperature trends are large, they reflect a shift of ET from midsummer to early summer and late spring. As in other studies, it is found that runoff is occurring earlier in spring, a trend that is related primarily to increasing temperature, and is most apparent during 1947–2003. Trends in the annual runoff ratio, a variable critical to western water management, are determined primarily by trends in cool season precipitation, rather than changes in the timing of runoff or ET. It was found that the signature of temperature-related trends in runoff and SM is strongly keyed to mean midwinter [December–February (DJF)] temperatures. Areas with warmer winter temperatures show increasing trends in the runoff fraction as early as February, and colder areas as late as June. Trends toward earlier spring SM recharge are apparent and increasing trends in SM on 1 April are evident over much of the region. The 1 July SM trends are less affected by snowmelt changes and are controlled more by precipitation trends.
Impact of Desert Dust Radiative Forcing on Sahel Precipitation: Relative Importance of Dust Compared to Sea Surface Temperature Variations, Vegetation Changes, and Greenhouse Gas Warming
Authors: Yoshioka Masaru , Mahowald Natalie M. , Conley Andrew J. , Collins William D. , Fillmore David W. , Zender Charles S. , Coleman Dani B. 
Published: April 2007

Abstract
The role of direct radiative forcing of desert dust aerosol in the change from wet to dry climate observed in the African Sahel region in the last half of the twentieth century is investigated using simulations with an atmospheric general circulation model. The model simulations are conducted either forced by the observed sea surface temperature (SST) or coupled with the interactive SST using the Slab Ocean Model (SOM). The simulation model uses dust that is less absorbing in the solar wavelengths and has larger particle sizes than other simulation studies. As a result, simulations show less shortwave absorption within the atmosphere and larger longwave radiative forcing by dust. Simulations using SOM show reduced precipitation over the intertropical convergence zone (ITCZ) including the Sahel region and increased precipitation south of the ITCZ when dust radiative forcing is included. In SST-forced simulations, on the other hand, significant precipitation changes are restricted to over North Africa. These changes are considered to be due to the cooling of global tropical oceans as well as the cooling of the troposphere over North Africa in response to dust radiative forcing. The model simulation of dust cannot capture the magnitude of the observed increase of desert dust when allowing dust to respond to changes in simulated climate, even including changes in vegetation, similar to previous studies. If the model is forced to capture observed changes in desert dust, the direct radiative forcing by the increase of North African dust can explain up to 30% of the observed precipitation reduction in the Sahel between wet and dry periods. A large part of this effect comes through atmospheric forcing of dust, and dust forcing on the Atlantic Ocean SST appears to have a smaller impact. The changes in the North and South Atlantic SSTs may account for up to 50% of the Sahel precipitation reduction. Vegetation loss in the Sahel region may explain about 10% of the observed drying, but this effect is statistically insignificant because of the small number of years in the simulation. Greenhouse gas warming seems to have an impact to increase Sahel precipitation that is opposite to the observed change. Although the estimated values of impacts are likely to be model dependent, analyses suggest the importance of direct radiative forcing of dust and feedbacks in modulating Sahel precipitation.
Analysis of the Dominant Mode of Convectively Coupled Kelvin Waves in the West African Monsoon
Authors: Mounier Flore , Kiladis George N. , Janicot Serge 
Published: April 2007

Abstract
The dominant mode of convectively coupled Kelvin waves has been detected over the Atlantic and Africa during northern summer by performing composite analyses on observational fields based on an EOF reconstructed convection index over West Africa. Propagating eastward, many waves originate from the Pacific sector, interact with deep convection of the marine ITCZ over the Atlantic and the continental ITCZ over West and central Africa, and then weaken over East Africa and the Indian Ocean. It has been shown that they are able to modulate the life cycle and track of individual westward-propagating convective systems. Their mean kinematic characteristics comprise a wavelength of 8000 km, and a phase speed of 15 m s−1, leading to a period centered on 6 to 7 days. The African Kelvin wave activity displays large seasonal variability, being highest outside of northern summer when the ITCZ is close to the equator, facilitating the interactions between convection and these equatorially trapped waves. The convective and dynamical patterns identified over the Atlantic and Africa show some resemblance to the theoretical equatorially trapped Kelvin wave solution on an equatorial β plane. Most of the flow is in the zonal direction as predicted by theory, and there is a tendency for the dynamical fields to be symmetric about the equator, even though the ITCZ is concentrated well north of the equator at the full development of the African monsoon. In the upper troposphere and the stratosphere, the temperature contours slope sharply eastward with height, as expected from an eastward-moving heat source that forces a dry Kelvin wave response. It is finally shown that the mean impact of African Kelvin waves on rainfall and convection is of the same level as African easterly waves.