bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric Response to Local Upwelling in the Vicinity of New York–New Jersey Harbor
Authors: Pullen Julie , Holt Teddy , Blumberg Alan F. , Bornstein Robert D. 
Published: August 2007

AbstractMultiply nested urbanized mesoscale model [Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS)] simulations of the New York–New Jersey metropolitan region are conducted for 4–11 July 2004. The simulations differ only in their specification of sea surface temperatures (SSTs) on nest 4 (1.33-km resolution) and nest 5 (0.44-km resolution). The “control SST” simulation (CONTROL-SST) uses an analyzed SST product, whereas the “New York Harbor Observing and Prediction System (NYHOPS) SST” simulation (NYHOPS-SST) uses hourly SSTs from the NYHOPS model hindcast. Upwelling-favorable (southerly) winds preceding the simulation time period and continuing for much of the first 5 days of the simulation generate cold water adjacent to the New Jersey coast and a cold eddy immediately outside of the harbor in the New York Bight. Both features are prominent in NYHOPS-SST but are not pronounced in CONTROL-SST. The upwelled water has a discernible influence on the overlying atmosphere by cooling near-surface air temperatures by approximately 1°–2°C, slowing the near-surface winds by 15%–20%, and reducing the nocturnal urban heat island effect by up to 1.3°C. At two coastal land-based sites and one overwater station, the wind speed mean bias is systematically reduced in NYHOPS-SST. During a wind shift to northwesterly on day 6 (9 July 2004) the comparatively cooler NYHOPS-SSTs impact the atmosphere over an even broader offshore area than was affected in the mean during the previous 5 days. Hence, air temperature evolution measured at the overwater site is better reproduced in NYHOPS-SST. Interaction of the offshore flow with the cool SSTs in NYHOPS-SST induces internal boundary layer (IBL) formation, sustained and deepened by turbulent kinetic energy advected from adjacent land areas; IBL formation did not occur in CONTROL-SST.
Probabilistic Characterization of Atmospheric Transport and Diffusion
Authors: Irwin John S. , Petersen William B. , Howard Steven C. 
Published: August 2007

Abstract
The observed scatter of observations about air quality model predictions stems from a combination of naturally occurring stochastic variations that are impossible for any model to simulate explicitly and variations arising from limitations in knowledge and from imperfect input data. In this paper, historical tracer experiments of atmospheric dispersion were analyzed to develop algorithms to characterize the observed stochastic variability in the ground-level crosswind concentration profile. The algorithms were incorporated into a Lagrangian puff model (“INPUFF”) so that the consequences of variability in the dispersion could be simulated using Monte Carlo methods. The variability in the plume trajectory was investigated in a preliminary sense by tracking the divergence in trajectories from releases adjacent to the actual release location. The variability in the near-centerline concentration values not described by the Gaussian crosswind profile was determined to be on the order of a factor of 2. The variability in the trajectory was determined as likely to be larger than the plume width, even with local wind observations for use in characterizing the transport. Two examples are provided to illustrate how estimates of variability 1) can provide useful information to inform decisions for emergency response and 2) can provide a basis for sound statistical designs for model performance assessments.
Seasonal Simulation of Tropospheric Ozone over the Midwestern and Northeastern United States: An Application of a Coupled Regional Climate and Air Quality Modeling System
Authors: Huang Ho-Chun , Liang Xin-Zhong , Kunkel Kenneth E. , Caughey Michael , Williams Allen 
Published: August 2007

Abstract
The impacts of air pollution on the environment and human health could increase as a result of potential climate change. To assess such possible changes, model simulations of pollutant concentrations need to be performed at climatic (seasonal) rather than episodic (days) time scales, using future climate projections from a general circulation model. Such a modeling system was employed here, consisting of a regional climate model (RCM), an emissions model, and an air quality model. To assess overall model performance with one-way coupling, this system was used to simulate tropospheric ozone concentrations in the midwestern and northeastern United States for summer seasons between 1995 and 2000. The RCM meteorological conditions were driven by the National Centers for Environmental Prediction/Department of Energy global reanalysis (R-2) using the same procedure that integrates future climate model projections. Based on analyses for several urban and rural areas and regional domains, fairly good agreement with observations was found for the diurnal cycle and for several multiday periods of high ozone episodes. Even better agreement occurred between monthly and seasonal mean quantities of observed and model-simulated values. This is consistent with an RCM designed primarily to produce good simulations of monthly and seasonal mean statistics of weather systems.
Observation-Based Assessment of the Impact of Nitrogen Oxides Emissions Reductions on Ozone Air Quality over the Eastern United States
Authors: Gégo Edith , Porter P. Steven , Gilliland Alice , Rao S. Trivikrama 
Published: August 2007

Abstract
Ozone is produced by chemical interactions involving nitrogen oxides (NOx) and volatile organic compounds in the presence of sunlight. At high concentrations, ground-level ozone has been shown to be harmful to human health and to the environment. It has been recognized that ozone is a regional-scale problem and that regionwide control strategies would be needed to improve ozone air quality in the eastern United States. To mitigate interstate transport of ozone and its precursors, the U.S. Environmental Protection Agency issued a regional rule in 1998 known as the “NOx State Implementation Plan (SIP) Call,” requiring 21 states in the eastern United States to reduce their summertime NOx emissions by 30 May 2004. In this paper, the effectiveness of the new emission control measures mandated by the NOx SIP Call is assessed by quantifying the changes that occurred in the daily maximum 8-h ozone concentrations measured at nearly 50 locations, most of which are rural (33 sites of the Clean Air Status and Trend Network and 16 sites of the Air Quality System), over the eastern United States. Given the strong dependence of ozone formation and accumulation on meteorological conditions, the incidence of the latter is first mitigated, and meteorologically adjusted ozone concentrations are extracted using a multiple regression technique. By examining the differences between the cumulative distribution functions of the meteorologically adjusted ozone concentrations, it is shown that ozone concentrations in the eastern United States are now on average 13% less than those prior to the NOx SIP Call. Using back-trajectory analyses, it is also shown that emission controls on the electricity-generating units located in the Ohio River Valley have contributed toward the improvement of ozone air quality in downwind regions, especially east and northeast of the Ohio River Valley.
Colour Doppler Spatial Resolution Performance Testing
Authors: Browne Jacinta E , Brown Ian , Hoskins Peter R , Watson Amanda J , Elliott Alex T 
Published: August 2007

Background: Colour Doppler has become an integral part of many clinical ultrasound investigations, but evaluation of the spatial resolution of colour Doppler scanners remains problematic due to a lack of suitable test phantoms. Methods: The aims of this study were to evaluate two designs of colour Doppler spatial resolution test-phantom to compare their suitability for determining the spatial resolution of five commercially available ultrasound scanners. For the purpose of this study, spatial resolution was defined as the minimum resolvable distance between two channels of flow. Phantom 1 consisted of two diverging flow-channels. Phantom 2 consisted of four pairs of parallel channels with different separations. Results and Discussion: Both designs of phantom highlighted a number of advantages and disadvantages. In principle, phantom 1 allowed the minimal resolvable distance to be identified based on imaging a continuous range of separations, but in practice, the average separation being probed was uncertain, and the minimum separation between vessels of 1 mm was too large to test the resolutions of some of the scanners we studied. Phantom 2 was easier to set up and had a narrower minimum separation of 0.6 mm, but only four nominal separations were tested. Evaluation of five scanners using each prototype phantom suggested typical resolutions of 1·2 mm or lower. Many of the scanners possessed resolutions of approximately 0.6 mm or less, which was the minimum separation we were able to test. The poorest lateral resolution of approximately 1·2 mm was observed for a 13 year old scanner with curvilinear 4 MHz phased array transducer. Conclusion: Construction of the 'perfect' test-object for measuring colour Doppler resolution remains a considerable challenge. Further work will be required to produce acoustically realistic flow phantoms capable of testing the ability of colour Doppler to resolve increasingly narrow flow separations.
Human BSAP and BLIMP1 conform an autoregulatory feedback loop
Authors: Mora-López Francisco , Reales Elena , Brieva José A. , Campos-Caro Antonio 
Published: August 2007

AbstractB-lymphocyte–induced maturation protein-1 (BLIMP1), encoded by the PRDM1 gene, is a transcriptional repressor considered a master regulator that is required and sufficient for plasma cell (PC) differentiation. BLIMP1 represses the PAX5 gene, coding for the B-cell lineage–specific activator protein (BSAP), which is required for B-cell identity and survival. Mutations in PAX5 gene as well as in PRDM1 gene have been recently implicated in lymphomas. In the present study, sequence analysis of PRDM1 gene revealed a binding site for BSAP transcription factor. By analyzing different human cell lines, we have found that a specific nuclear factor for B-cell lines binds to a site on the PRDM1 promoter. Electrophoretic mobility shift assays identified this factor as BSAP, and chromatin immunoprecipitation assays confirmed its binding in vivo to the human PRDM1 promoter. Moreover, by ectopically expressing BSAP, and using a PRDM1 promoter with the BSAP-binding site mutated, we demonstrated that this factor represses the expression of BLIMP1. Therefore, repression of PRDM1 by BSAP reveals an autoregulatory negative-feedback loop that could play a relevant role in controlling human PC differentiation.
TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy
Authors: MessaoudiI Cédric , Boudier Thomas , Sorzano Carlos Oscar Sanchez , Marco Sergio 
Published: August 2007

Abstract

Background
Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.

Results
TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.

Conclusion
The software presented in this work is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.
Portraits of breast cancer progression
Authors: Dalgin Gul S , Alexe Gabriela , Scanfeld Daniel , Tamayo Pablo , Mesirov Jill P , Ganesan Shridar , DeLisi Charles , Bhanot Gyan 
Published: August 2007

AbstractBackgroundClustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based on principal component analysis and ensemble consensus clustering that avoids these problems.ResultsWe illustrate the method on a public microarray dataset from 36 breast cancer patients of whom 31 were diagnosed with at least two of three pathological stages of disease (atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Our method identifies an optimum set of genes and divides the samples into stable clusters which correlate with clinical classification into Luminal, Basal-like and Her2+ subtypes. Our analysis reveals a hierarchical portrait of breast cancer progression and identifies genes and pathways for each stage, grade and subtype. An intriguing observation is that the disease phenotype is distinguishable in ADH and progresses along distinct pathways for each subtype. The genetic signature for disease heterogeneity across subtypes is greater than the heterogeneity of progression from DCIS to IDC within a subtype, suggesting that the disease subtypes have distinct progression pathways.Our method identifies six disease subtype and one normal clusters. The first split separates the normal samples from the cancer samples. Next, the cancer cluster splits into low grade (pathological grades 1 and 2) and high grade (pathological grades 2 and 3) while the normal cluster is unchanged. Further, the low grade cluster splits into two subclusters and the high grade cluster into four. The final six disease clusters are mapped into one Luminal A, three Luminal B, one Basal-like and one Her2+.ConclusionWe confirm that the cancer phenotype can be identified in early stage because the genes altered in this stage progressively alter further as the disease progresses through DCIS into IDC. We identify six subtypes of disease which have distinct genetic signatures and remain separated in the clustering hierarchy. Our findings suggest that the heterogeneity of disease across subtypes is higher than the heterogeneity of the disease progression within a subtype, indicating that the subtypes are in fact distinct diseases.
Establishment and mitotic stability of an extra-chromosomal mammalian replicon
Authors: Stehle Isa M , Postberg Jan , Rupprecht Sina , Cremer Thomas , Jackson Dean A , Lipps Hans J 
Published: August 2007

Abstract

Background
Basic functions of the eukaryotic nucleus, like transcription and replication, are regulated in a hierarchic fashion. It is assumed that epigenetic factors influence the efficiency and precision of these processes. In order to uncouple local and long-range epigenetic features we used an extra-chromosomal replicon to study the requirements for replication and segregation and compared its behavior to that of its integrated counterpart.

Results
The autonomous replicon replicates in all eukaryotic cells and is stably maintained in the absence of selection but, as other extra-chromosomal replicons, its establishment is very inefficient. We now show that following establishment the vector is stably associated with nuclear compartments involved in gene expression and chromosomal domains that replicate at the onset of S-phase. While the vector stays autonomous, its association with these compartments ensures the efficiency of replication and mitotic segregation in proliferating cells.

Conclusion
Using this novel minimal model system we demonstrate that relevant functions of the eukaryotic nucleus are strongly influenced by higher nuclear architecture. Furthermore our findings have relevance for the rational design of episomal vectors to be used for genetic modification of cells: in order to improve such constructs with respect to efficiency elements have to be identified which ensure that such constructs reach regions of the nucleus favorable for replication and transcription.
Analysis of the Rana catesbeiana tadpole tail fin proteome and phosphoproteome during T3-induced apoptosis: identification of a novel type I keratin
Authors: Domanski Dominik , Helbing Caren C 
Published: August 2007

Abstract
Background
Thyroid hormones (THs) are vital in the maintenance of homeostasis and in the control of development. One postembryonic developmental process that is principally regulated by THs is amphibian metamorphosis. This process has been intensively studied at the genomic level yet very little information at the proteomic level exists. In addition, there is increasing evidence that changes in the phosphoproteome influence TH action.

Results
Here we identify components of the proteome and phosphoproteome in the tail fin that changed within 48 h of exposure of premetamorphic Rana catesbeiana tadpoles to 10 nM 3,5,3'-triiodothyronine (T3). To this end, we developed a cell and protein fractionation method combined with two-dimensional gel electrophoresis and phosphoprotein-specific staining. Altered proteins were identified using mass spectrometry (MS). We identified and cloned a novel Rana larval type I keratin, RLK I, which may be a target for caspase-mediated proteolysis upon exposure to T3. In addition, the RLK I transcript is reduced during T3-induced and natural metamorphosis which is consistent with a larval keratin. Furthermore, GILT, a protein involved in the immune system, is changed in phosphorylation state which is linked to its activation. Using a complementary MS technique for the analysis of differentially-expressed proteins, isobaric tags for relative and absolute quantitation (iTRAQ) revealed 15 additional proteins whose levels were altered upon T3 treatment. The success of identifying proteins whose levels changed upon T3 treatment with iTRAQ was enhanced through de novo sequencing of MS data and homology database searching. These proteins are involved in apoptosis, extracellular matrix structure, immune system, metabolism, mechanical function, and oxygen transport.

Conclusion
We have demonstrated the ability to derive proteomics-based information from a model species for postembryonic development for which no genome information is currently available. The present study identifies proteins whose levels and/or phosphorylation states are altered within 48 h of the induction of tadpole tail regression prior to overt remodeling of the tail. In particular, we have identified a novel keratin that is a target for T3-mediated changes in the tail that can serve as an indicator of early response to this hormone.
Detection of "Rickettsia sp. strain Uilenbergi" and "Rickettsia sp. strain Davousti" in Amblyomma tholloni ticks from elephants in Africa
Authors: Matsumoto Kotaro , Parola Philippe , Rolain Jean-Marc , Jeffery Kathryn , Raoult Didier 
Published: August 2007

AbstractBackgroundTo date, 6 tick-borne rickettsiae pathogenic for humans are known to occur in Africa and 4 of them were first identified in ticks before being recognized as human pathogens.ResultsWe examined 33 and 5Amblyomma tholloniticks from African elephants in the Central African Republic and Gabon, respectively, by PCR amplification and sequencing of a part ofgltAandompAgenes of the genusRickettsia. The partial sequences ofgltAandompAgenes detected in tick in Gabon had 99.1% similarity with those ofR. heilongjiangensisand 97.1% with those ofRickettsiasp. HL-93 strain, respectively. The partialgltAandompAgene sequences detected in tick in the Central African Republic were 98.9% and 95.1% similar to those ofRickettsiasp. DnS14 strain andR. massiliae, respectively. Phylogenetic analysis showedRickettsiasp. detected in Gabon clusters withR. japonicaandR. heilongjiangensisin a phylogenetic tree based on the partialgltAandompAgenes. The genotype of theRickettsiasp. detected in the Central African Republic is close to those ofR. massiliaegroup in the phylogenetic tree based on partialgltAgene sequences, and distantly related to other rickettsiae in the tree based on partialompAgene.ConclusionThe degrees of similarity of partialgltAandompAgenes with recognized species indicate the rickettsiae detected in this study may be new species although we could only study the partial sequences of 2 genes regarding the amount of DNA that was available. We propose theRickettsiasp. detected in Gabon be provisionally named "Rickettsia sp. stain Davousti" andRickettsiasp. detected in the Central African Republic be named "Rickettsia sp.strain Uilenbergi".
Optimization of diagnostic imaging use in patients with acute abdominal pain (OPTIMA): Design and rationale
Authors: Laméris Wytze , van Randen Adrienne , Dijkgraaf Marcel GW , Bossuyt Patrick MM , Stoker Jaap , Boermeester Marja A 
Published: August 2007

AbstractBackgroundThe acute abdomen is a frequent entity at the Emergency Department (ED), which usually needs rapid and accurate diagnostic work-up. Diagnostic work-up with imaging can consist of plain X-ray, ultrasonography (US), computed tomography (CT) and even diagnostic laparoscopy. However, no evidence-based guidelines exist in current literature. The actual diagnostic work-up of a patient with acute abdominal pain presenting to the ED varies greatly between hospitals and physicians. The OPTIMA study was designed to provide the evidence base for constructing an optimal diagnostic imaging guideline for patients with acute abdominal pain at the ED.Methods/designThousand consecutive patients with abdominal pain > 2 hours and < 5 days will be enrolled in this multicentre trial. After clinical history, physical and laboratory examination all patients will undergo a diagnostic imaging protocol, consisting of plain X-ray (upright chest and supine abdomen), US and CT. The reference standard will be a post hoc assignment of the final diagnosis by an expert panel. The focus of the analysis will be on the added value of the imaging modalities over history and clinical examination, relative to the incremental costs.DiscussionThis study aims to provide the evidence base for the development of a diagnostic algorithm that can act as a guideline for ED physicians to evaluate patients with acute abdominal pain.