bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multimodel Assessment of RKW Theory’s Relevance to Squall-Line Characteristics
Authors: Bryan George H. , Knievel Jason C. , Parker Matthew D. 
Published: October 2006

Abstract
The authors evaluate whether the structure and intensity of simulated squall lines can be explained by “RKW theory,” which most specifically addresses how density currents evolve in sheared environments. In contrast to earlier studies, this study compares output from four numerical models, rather than from just one. All of the authors’ simulations support the qualitative application of RKW theory, whereby squall-line structure is primarily governed by two effects: the intensity of the squall line’s surface-based cold pool, and the low- to midlevel environmental vertical wind shear. The simulations using newly developed models generally support the theory’s quantitative application, whereby an optimal state for system structure also optimizes system intensity. However, there are significant systematic differences between the newer numerical models and the older model that was originally used to develop RKW theory. Two systematic differences are analyzed in detail, and causes for these differences are proposed.
Structure, Growth Rates, and Tangent Linear Accuracy of Adjoint Sensitivities with Respect to Horizontal and Vertical Resolution
Authors: Ancell Brian C. , Mass Clifford F. 
Published: October 2006

Abstract
In this paper, the variation of adjoint sensitivities as horizontal and vertical resolutions are changed is investigated. The fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) and its adjoint are used with consistent physics to generate adjoint sensitivities over a 24-h period. The sensitivities are generated with respect to a response function defined as the lowest sigma level perturbation pressure over a region of northwestern Oregon. It is found that the scale, magnitude, and structure of sensitivity with respect to initial temperature varies significantly as grid spacing is decreased from 216 to 24 km. As found in other adjoint studies at relatively coarse resolution, low-level, upshear-tilted, subsynoptic-scale sensitivities were apparent, with the wavelike sensitivity pattern decreasing significantly in scale and spatial extent with increased horizontal resolution. It is also found that perturbation growth rates depend on horizontal resolution, with the adjoint sensitivities predicting larger changes in the response function with increased horizontal resolution. Relatively little change in sensitivity structure and growth rates occurred when the vertical resolution was varied from 10 to 50 vertical levels. It is shown that a majority of the predicted change in the response function comes from the very small proportion of the domain occupied by sensitive regions. Last, the accuracy of the tangent linear approximation is examined, and it is found that for perturbations made in sensitive regions, the tangent linear approximation degrades at finer grid spacing. The implications of these results are discussed for methodologies utilizing adjoint sensitivities, such as four-dimensional variational data assimilation and targeted observations strategies.
Cluster Analysis for Verification of Precipitation Fields
Authors: Marzban Caren , Sandgathe Scott 
Published: October 2006

Abstract
A statistical method referred to as cluster analysis is employed to identify features in forecast and observation fields. These features qualify as natural candidates for events or objects in terms of which verification can be performed. The methodology is introduced and illustrated on synthetic and real quantitative precipitation data. First, it is shown that the method correctly identifies clusters that are in agreement with what most experts might interpret as features or objects in the field. Then, it is shown that the verification of the forecasts can be performed within an event-based framework, with the events identified as the clusters. The number of clusters in a field is interpreted as a measure of scale, and the final “product” of the methodology is an “error surface” representing the error in the forecasts as a function of the number of clusters in the forecast and observation fields. This allows for the examination of forecast error as a function of scale.
A Climatology of Synoptic Conditions Associated with Significant Tornadoes across the Southern Appalachian Region
Authors: Gaffin David M. , Parker Stephen S. 
Published: October 2006

Abstract
A 54-yr climatology (1950–2003) of synoptic conditions associated with significant (F2 or greater) tornado events in the southern Appalachian region was compiled to 1) investigate the observed relative minimum of tornadoes in the Great Tennessee Valley, 2) test a hypothesis concerning northwest versus southwest 500-hPa flow events across the Great Tennessee Valley and Cumberland Plateau, 3) examine common operational forecasting techniques often used with synoptic-scale data to determine potentially tornadic environments, and 4) compare the patterns associated with significant, outbreak, and weak tornado events. Individual surface and upper-air charts along with composite charts closest to the time of significant tornado occurrences were used in this investigation. It was found that significant tornado events that occurred with prefrontal troughs (the most common surface boundary in the study) produced significant tornadoes almost exclusively over the Cumberland Plateau and southern Appalachian Mountains, with very few prefrontal trough events producing significant tornadoes in the Great Tennessee Valley of eastern Tennessee. Only four northwest 500-hPa flow events (which produced significant tornadoes almost exclusively in the southern Appalachian Mountains and during the summer) were found in this study, which refuted the initial hypothesis that northwest 500-hPa flow may produce tornadoes mainly in the Great Tennessee Valley with southwest 500-hPa flow producing tornadoes mainly across the Cumberland Plateau. Most significant tornado events in this study were associated with southwest 500-hPa flow ahead of a neutral-tilted trough, which revealed that the particular tilt of a 500-hPa trough does not necessarily enhance the formation of significant tornadoes in the southern Appalachian region. However, outbreak events (with five or more significant tornadoes) in the southern Appalachian region were typically associated with positive-tilted troughs. At 300 or 250 hPa, the southern Appalachian region was frequently located on the right side of a jet streak, with an even split between the entrance and exit regions. This finding indicated that significant tornado events in the southern Appalachian region did not necessarily favor the right-entrance or left-exit regions of a jet streak where rising motion is expected to be most intense (with straight jet streaks). A comparison of the composites of weak, significant, and outbreak tornado events revealed that wind dynamics were more important than instability in the distinction between weak and significant tornado events across the southern Appalachian region.
Cytotoxic CD4+ T cells use granulysin to kill Cryptococcus neoformans, and activation of this pathway is defective in HIV patients
Authors: Zheng Chun Fu , Ma Ling Ling , Jones Gareth J. , Gill M. John , Krensky Alan M. , Kubes Paul , Mody Christopher H. 
Published: October 2006

AbstractAn important mechanism of host defense to Cryptococcus neoformans involves the direct microbicidal activity of lymphocytes. The importance of CD4+ T cells is illustrated by the incidence of this infection in the acquired immunodeficiency syndrome (AIDS) patients; however, the relative activity of microbicidal CD4+ T cells compared with CD8+ T cells and natural killer (NK) cells has not been established. Further, although NK cells and CD8+ T cells use perforin or granulysin, respectively, to kill C neoformans, the effector molecule used by CD4+ T cells is not known. Experiments demonstrated that IL-2–activated peripheral blood lymphocytes from healthy adults acquire anticryptococcal activity, and surprisingly, that CD4+ T cells had the most profound effect on this activity. Using SrCl2induced degranulation and siRNA knockdown, granulysin was shown to be the effector molecule. Although activation by anti–CD3 + IL-2 resulted in the additional expression of perforin, this did not improve the anticryptococcal activity. Cryptococcal killing by CD4+ T cells was defective in human immunodeficiency virus (HIV)–infected patients due to dysregulated granulysin and perforin production in response to IL-2 or anti–CD3 + IL-2. In conclusion, CD4+ T cells are the major subset of cells responsible for killing C neoformans in peripheral blood. These cells use granulysin as the effector molecule, and priming is dysregulated in HIV-infected patients, which results in defective microbicidal activity.
Contribution of Toll-like receptors to the innate immune response to Gram-negative and Gram-positive bacteria
Authors: Elson Greg , Dunn-Siegrist Irène , Daubeuf Bruno , Pugin Jérome 
Published: October 2006

AbstractInnate recognition of bacteria is a key step in the activation of inflammation and coagulation, and it is dependent on pathogen-associated molecular pattern (PAMP) ligation to Toll-like receptors (TLRs) and CD14. The dominant receptors activated when cells encounter a whole bacterium, which express several PAMPs, are poorly defined. Herein, we have stimulated various human cells with prototypic Gram-negative and Gram-positive bacteria. Receptor-dependent responses to whole bacteria were assessed using both TLR-transfected cells and specific monoclonal antibodies against TLRs, MD-2, and CD14. Enterobacteria-activated leukocytes and endothelial cells in a TLR4/MD-2–dependent manner, most likely via lipopolysaccharide (LPS). TLR2 activation was observed with a high bacterial inoculum, and in epithelial cells expressing TLR2 but not TLR4. Pseudomonas aeruginosa stimulated cells by both TLR2 and TLR4/MD-2. Gram-positive bacteria activated cells only at high concentrations, in a partially TLR2-dependent but TLR4/MD-2–independent manner. Either TLR or CD14 neutralization blocked activation to all bacterial strains tested with the exception of some Gram-positive strains in whole blood in which partial inhibition was noted. This study identifies dominant TLRs involved in responses to whole bacteria. It also validates the concept that host cell activation by bacterial pathogens can be therapeutically reduced by anti-TLR4, -TLR2, and -CD14 mAbs.
Shear flow–dependent integration of apical and subendothelial chemokines in T-cell transmigration: implications for locomotion and the multistep paradigm
Authors: Schreiber Taylor H. , Shinder Vera , Cain Derek W. , Alon Ronen , Sackstein Robert 
Published: October 2006

AbstractLymphocyte extravasation requires that emigrating cells process chemoattractant signals, typically mediated by chemokines, encountered on endothelial surface (apical) and subendothelial (basal) compartments. These signals are delivered under conditions of hemodynamic shear, a fundamental feature of all physiologic leukocyte–endothelial interactions. To analyze lymphocyte responsiveness to spatially distributed chemokines and their effects on transendothelial migration (TEM) under hydrodynamic shear, we constructed a transwell-based flow assay. We observed that the inflammatory chemokine CCL5 (RANTES) induces negligible human T-cell migration across inflamed human umbilical vascular endothelial cells (HUVECs) when displayed alone in the subendothelial compartment under static or hemodynamic shear conditions or when combined with apical CXCL12 (SDF-1α) under static conditions. However, under shear stress, T cells encountering apically presented CXCL12 were primed to undergo robust LFA-1–dependent TEM toward subendothelial CCL5. Notably, locomotive T cells arriving at endothelial junctions were retained and extended pseudopodia into and through the junctions, thereby increasing sensitivity to subendothelial CCL5. These findings provide the first evidence that lymphocytes integrate, conditional to shear forces, permissive apical chemokine deposits, and integrin engagement signals, resulting in morphologic changes and amplified chemotaxis to an otherwise weak subendothelial chemokine signal.
Expoldb: ex pression linked pol ymorphism d atab ase with inbuilt tools for analysis of expression and simple repeats
Authors: Sharma Vineet K , Sharma Anu , Kumar Naveen , Khandelwal Mamta , Mandapati Kiran Kumar , Horn-Saban Shirley , Strichman-Almashanu Liora , Lancet Doron , Brahmachari Samir K , Ramachandran Srinivasan 
Published: October 2006

Abstract

Background
Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is associating genome wide transcription patterns with potential cis modifiers of gene expression.

Description
EXPOLDB, a novel Database, is a new effort addressing this need by providing information on gene expression levels variability across individuals, as well as the presence and features of potentially polymorphic (TG/CA)n repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)n repeats. One of the unique features of this database is the display of expression data for 5 pairs of monozygotic twins, which allows identification of genes whose variability in expression, are influenced by non-genetic factors including environment. In addition to queries by gene name, EXPOLDB allows for queries by a pathway name. Users can also upload their list of HGNC (HUGO (The Human Genome Organisation) Gene Nomenclature Committee) symbols for interrogating expression patterns. The online application 'SimRep' can be used to find simple repeats in a given nucleotide sequence. To help illustrate primary applications, case examples of Housekeeping genes and the RUNX gene family, as well as one example of glycolytic pathway genes are provided.

Conclusion
The uniqueness of EXPOLDB is in facilitating the association of genome wide transcription variations with the presence and type of polymorphic repeats while offering the feature for identifying genes whose expression variability are influenced by non genetic factors including environment. In addition, the database allows comprehensive querying including functional information on biochemical pathways of the human genes.
EXPOLDB can be accessed at http://expoldb.igib.res.in/expol
A New Methodology for Adjustment of Iron Scattering Cross Sections Using Time-of-Flight Spectroscopy
Authors: Wenner MT , Haghighat A , Grimes SS , Massey TN , Carlson AD , Adams JM 
Published: October 2006

Abstract
Monte Carlo analysis of a time-of-flight experiment was performed to investigate the iron scattering cross section. Experimental data were utilized to build a Monte Carlo source for simulation of a time-of-flight (ToF) experiment with a spherical iron shell, different source spectra, and different angular beam source alignments. For this study, two pointwise cross section libraries, ENDF/B-VI and JEFF 3.0 are examined. Comparison of calculation and experimental results indicates differences that are larger than experimental and calculation errors. To reduce the observed discrepancy, pointwise data in the ENDF/B-VI iron scattering cross section file were adjusted at a few energy intervals using a utility code developed for this purpose. Adjusted cross sections resulted in closer agreement of calculated results with the experimental Time-of-Flight data. Multigroup cross sections were generated with the adjusted cross sections and results indicate pressure vessel fluence may be underestimated.
Prediction of the Shape of the K
J Ductile-to-Brittle Transition Temperature Curve for Ferritic Pressure Vessel Steels Using the Material's Resistance to Crack Extension K
J versus Δa Curve
Authors: Wardle G , Geary W 
Published: October 2006

Abstract
Fracture toughness (KJ (cleavage)) measurements made within the ductile-to-brittle transition region for ferritic pressure vessel steels are not always described by the shape of the Master Curve currently given in ASTM Standard E 1921. The objective of this paper is to show how the shape of the transition toughness curve may be related to the shape of the material's resistance to crack extension curve (KJR) once the crack tip starts to blunt and ductile crack extension precedes cleavage failure. Using an empirical relationship between the mean ductile crack extension (Δa) prior to the onset of cleavage failure and temperature (Δa=λ exp(ϕT)), then the relationship between KJ and T may simply be given by KJ=KA+α[λ exp(ϕT)]β, where KA, α, and β are simply the coefficients to an offset power law to KJ versus Δa data given by KJR=KA+α(Δa)β. For specimens of different sizes, a reference temperature TK may be defined for a given reference level of Δa or equivalent KJ. Unique curves may be defined for materials with differing crack extension resistance curves through plots of KJ versus (T−TΔa(ref)) or (T−TK(ref)). The generalized form of the transition curve may be given by KJ=KA+α{Δa(ref) exp[ϕ(T−TΔa(ref) &gt;β or KJ=KA+(K(ref)−KA){exp[ϕ(T−TK(ref) &gt;β. Experimentally, ϕ has been estimated as approximately 0.08 for nuclear pressure vessel materials such as A533B/A508. Using a specific situation wherein the value of KA=30MPa√m,K(ref)=100MPa√m, and β=0.25 then, for a B=25-mm specimen, within experimental scatter this provides an almost exact match to the Master Curve given by KJ=30+70 exp[0.019(T−TK100)]. The predictions of transition curve shape using the material's resistance to crack extension curve are believed to be complementary to the Master Curve method, and may describe the shape of the transition curve when there is ductile crack extension prior to cleavage failure. Further work is recommended to investigate the relationship between the predicted ductile-to-brittle transition curve and the Master Curve for probabilities of cleavage failure post-initiation.
Molecular Analysis of LEFTY-Expressing Cells in Early Human Embryoid Bodies
Authors: Dvash Tamar , Sharon Nadav , Yanuka Ofra , Benvenisty Nissim 
Published: October 2006

Abstract
Human ESCs (HESCs) are self-renewing pluripotent cell lines that are derived from the inner cell mass of blastocyst-stage embryos. These cells can produce terminally differentiated cells representing the three embryonic germ layers. We thus hypothesized that during the course of in vitro differentiation of HESCs, progenitor-like cells are transiently formed. We demonstrated that LEFTY proteins, which are known to play a major role during mouse gastrulation, are transiently expressed during HESC differentiation. Moreover, LEFTY proteins seemed to be exclusively expressed by a certain population of cells in the early human embryoid bodies that does not overlap with the population expressing the ESC marker OCT4. We also showed that LEFTY expression is regulated at the cellular transcription level by molecular labeling of LEFTY-positive cells. A DNA microarray analysis of LEFTY-overexpressing cells revealed a signature of cell surface markers such as CADHERIN 2 and 11. Expression of LEFTY controlled by NODAL appears to have a substantial role in mesodermal origin cell population establishment, since inhibition of NODAL activity downregulated expression not only of LEFTY A and LEFTY B but also of BRACHYURY, an early mesodermal marker. In addition, other mesodermal lineage-related genes were downregulated, and this was accompanied by an upregulation in ectoderm-related genes. We propose that during the initial step of HESC differentiation, mesoderm progenitor-like cells appear via activation of the NODAL pathway. Our analysis suggests that in vitro differentiation of HESCs can model early events in human development.
Platelet GPIIb/IIIa antagonist, XV459, in heparin‐induced thrombocytopenia
Authors: Mousa Shaker A. , Ahmad Sarfraz 
Published: October 2006

AbstractHeparin‐induced thrombocytopenia (HIT) is a serious, immune‐related complication of heparin therapy. One of the most severe manifestations of HIT is the development of thromboembolic events, which is based on platelet activation and aggregation caused by HIT‐associated antibodies. Therapeutic options for patients with HIT are limited despite advancement toward the development of alternative (nonheparin) anticoagulants, such as direct thrombin inhibitors and indirect anti‐factor Xa agents. Platelet GPIIb/IIIa receptor antagonists have been shown to be the final common pathway for platelet aggregation regardless of the use of activator or anticoagulant. In this study, the ability of a novel platelet GPIIb/IIIa antagonist, a free acid form of roxifiban (XV459), to block platelet activation/aggregation in response to highly characterized heparin‐PF4 antibody‐positive plasma/heparin was examined using light transmittance aggregometry, serotonin release, and125I‐fibrinogen binding assays to human platelets. XV459 at 20 nM maximally inhibited (P< 0.001) the platelet‐activation/aggregation responses as mediated by the HIT antibody‐positive plasma (in the presence of therapeutic heparin concentrations). Compared with controls, both HIT antibodies/heparin and TEAC (a mixture of thrombin [0.1 IU/ml], epinephrine [1 μg/ml], arachidonate [0.1 mM], and collagen [10 μg/ml]) resulted in significantly higher levels of fibrinogen binding to human platelets (5–7‐fold increase;P< 0.001). Concentration‐dependent profiles of XV459 on the mean percent inhibition of125I‐fibrinogen binding in the presence of HIT antibodies and TEAC were achieved (∼50% inhibition at 10 nM XV459). The platelet GPIIb/IIIa receptor antagonist (XV459) might be of potential benefit in the management of thrombotic thrombocytopenia produced by heparin and/or related glycosaminoglycans. Am. J. Hematol., 2006. © 2006 Wiley‐Liss, Inc.
Wasserstoffperoxid‐Synthese: Perspektiven jenseits des Anthrachinon‐Verfahrens
Authors: Campos‐Martin Jose M. , Blanco‐Brieva Gema , Fierro Jose L. G. 
Published: October 2006

AbstractWasserstoffperoxid (H2O2) wird in vielen Industriezweigen eingesetzt, vor allem in der chemischen Industrie und im Umweltschutz. Das einzige Abbauprodukt bei seiner Verwendung als Oxidationsmittel ist Wasser, weshalb es eine große Rolle bei umweltfreundlichen Verfahren in der chemischen Industrie spielt. Die großtechnische Synthese von Wasserstoffperoxid erfolgt im Anthrachinon(AO)‐Prozess, der selbst aber kaum als ein “grünes” Verfahren angesehen werden kann. Er umfasst die schrittweise Hydrierung und Oxidation eines in einem Gemisch organischer Lösungsmittel gelösten Alkylanthrachinons mit anschließender Abtrennung des Wasserstoffperoxids durch Flüssig‐flüssig‐Extraktion. Der AO‐Prozess ist ein mehrstufiges Verfahren mit beträchtlichem Energieverbrauch und Abfallaufkommen, was sich auf seine Umweltverträglichkeit und die Produktionskosten negativ auswirkt. Transport, Lagerung und Handhabung von H2O2 als Industriechemikalie sind mit Sicherheitsproblemen und erheblichen Kosten verbunden. Aus diesen Gründen werden neue, umweltfreundlichere Methoden zur Herstellung von Wasserstoffperoxid erforscht. Dieser Aufsatz beschäftigt sich insbesondere mit der direkten Synthese von Wasserstoffperoxid aus O2 und H2 mithilfe von Katalysatoren sowie den bei der Bildung und Zersetzung von Wasserstoffperoxid wirksamen Faktoren.
Zur Stereochemie tertiärer cis‐2,6‐Diphenyl‐piperidinole
Authors: Ebersberg J. , Haller R. 
Published: October 2006

AbstractTertiäre cis‐2,6‐Diphenyl‐3‐methyl‐piperidinole‐(4) werden durch Umsetzung von Piperidonen mit Grignard‐Reagenzien oder Phenyllithium erhalten; dabei wird die Alkyl(Aryl‐) Gruppe an C‐4 bevorzugt in cis‐Stellung zu den Substituenten an C‐2 und C‐6 eingeführt. Die Konfiguration und Konformation dieser heterocyclischen Ketone und Alkohole wird an Hand der 1H–NMR‐Spektren untersucht.