bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of an Orphan Response Regulator Required for the Virulence ofFrancisellaspp. and Transcription of Pathogenicity Island Genes
Authors: Mohapatra Nrusingh P. , Soni Shilpa , Bell Brian L. , Warren Richard , Ernst Robert K. , Muszynski Artur , Carlson Russell W. , Gunn John S.
Published: April 2007

Francisella tularensisis a category A agent of biowarfare/biodefense. Little is known about the regulation of virulence gene expression inFrancisellaspp. Comparatively few regulatory factors exist inFrancisella, including those belonging to two-component systems (TCS). However, orphan members of typical TCS can be identified. To determine if orphan TCS members affectFrancisellagene expression, a gene encoding a product with high similarity to theSalmonellaPmrA response regulator (FTT1557c/FNU0663.2) was deleted inFrancisella novicida(a model organism forF. tularensis). TheF. novicida pmrAmutant was defective in survival/growth within human and murine macrophage cell lines and was 100% defective in virulence in mice at a dose of up to 108CFU. In addition, the mutant strain demonstrated increased susceptibility to antimicrobial peptide killing, but no differences were observed between the lipid A of the mutant and the parental strain, as has been observed withpmrAmutants of other microbes. TheF. novicida pmrAmutant was 100% protective as a single-dose vaccine when challenge was with 106CFU ofF. novicidabut did not protect against type A Schu S4 wild-type challenge. DNA microarray analysis identified 65 genes regulated by PmrA. The majority of these genes were located in the region surroundingpmrAor within theFrancisellapathogenicity island (FPI). These FPI genes are also regulated by MglA, but MglA does not regulatepmrA, nor does PmrA regulate MglA. Thus, the orphan response regulator PmrA is an important factor in controlling virulence inF. novicida, and apmrAmutant strain is an effective vaccine against homologous challenge.
Use of a Genetically Defined Double Mutant Strain of
Bordetella bronchiseptica
Lacking Adenylate Cyclase and Type III Secretion as a Live Vaccine
Authors: Mann Paul , Goebel Elizabeth , Barbarich James , Pilione Mylisa , Kennett Mary , Harvill Eric
Published: April 2007

While most vaccines consisting of killed bacteria induce high serum antibody titers, they do not always confer protection as effective as that induced by infection, particularly against mucosal pathogens.
Bordetella bronchiseptica
is a gram-negative respiratory pathogen that is endemic in many nonhuman mammalian populations and causes substantial disease in a variety of animals. At least 14 different live attenuated vaccines against this pathogen are available for use in a variety of livestock and companion animals. However, there are few published data on the makeup or efficacy of these vaccines. Here we report the use of a genetically engineered double mutant of
B. bronchiseptica
, which lacks adenylate cyclase and type III secretion, as a vaccine candidate. This strain is safe at high doses, even for highly immunocompromised animals, and induces immune responses that are protective against highly divergent
B. bronchiseptica
strains, preventing colonization in the lower respiratory tract and decreasing the bacterial burden in the upper respiratory tract. This novel
B. bronchiseptica
vaccine candidate induces strong local immunity while eliminating damage caused by the two predominant cytotoxic mechanisms.
Fungicidal Monoclonal Antibody C7 Binds to
Candida albicans
Als3
Authors: Brena Sonia , Omaetxebarría Miren J. , Elguezabal Natalia , Cabezas Jonathan , Moragues María D. , Pontón José
Published: April 2007

Monoclonal antibody (MAb) C7 reacted with a >200-kDa component from the
Candida albicans
cell wall identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry as Als3. It also bound the recombinant N terminus of Als3. Binding of MAb C7 to Als3 may explain the biological activities exerted by the MAb on
C. albicans
.
Toll-Like Receptor 2-Dependent NF-κB Activation Is Involved in Nontypeable
Haemophilus influenzae
-Induced Monocyte Chemotactic Protein 1 Up-Regulation in the Spiral Ligament Fibrocytes of the Inner Ear
Authors: Moon Sung K. , Woo Jeong-Im , Lee Haa-Yung , Park Raekil , Shimada Jun , Pan Huiqi , Gellibolian Robert , Lim David J.
Published: April 2007

Inner ear dysfunction secondary to chronic otitis media (OM), including high-frequency sensorineural hearing loss or vertigo, is not uncommon. Although chronic middle ear inflammation is believed to cause inner ear dysfunction by entry of OM pathogen components or cytokines from the middle ear into the inner ear, the underlying mechanisms are not well understood. Previously, we demonstrated that the spiral ligament fibrocyte (SLF) cell line up-regulates monocyte chemotactic protein 1 (MCP-1) expression after treatment with nontypeable
Haemophilus influenzae
(NTHI), one of the most common OM pathogens. We hypothesized that the SLF-derived MCP-1 plays a role in inner ear inflammation secondary to OM that is responsible for hearing loss and dizziness. The purpose of this study was to investigate the signaling pathway involved in NTHI-induced MCP-1 up-regulation in SLFs. Here we show for the first time that NTHI induces MCP-1 up-regulation in the SLFs via Toll-like receptor 2 (TLR2)-dependent activation of NF-κB. TLR2
−/−
- and MyD88
−/−
-derived SLFs revealed involvement of TLR2 and MyD88 in NTHI-induced MCP-1 up-regulation. Studies using chemical inhibitors and dominant-negative constructs demonstrated that it is mediated by the IκKβ-dependent IκBα phosphorylation and NTHI-induced NF-κB nuclear translocation. Furthermore, we demonstrated that the binding of NF-κB to the enhancer region of MCP-1 is involved in this up-regulation. In addition, we have identified a potential NF-κB motif that is responsive and specific to certain NTHI molecules or ligands. Further studies are necessary to reveal specific ligands of NTHI that activate host receptors. These results may provide us with new therapeutic strategies for prevention of inner ear dysfunction secondary to chronic middle ear inflammation.
Mixed Transition Metal Acetylides Connected by Carbon-Rich Bridging Units: On the Way to Heterohexametallic Organometallics
Authors: Lang Heinrich , Packheiser Rico
Published: April 2007

This review describes the synthesis, reaction chemistry, structures and bonding of heterotri- to heterohexametallic complexes with early and late transition metal centres by applying the molecular Tinkertoy approach. The use of π-conjugated carbon-rich multifunctional organic units such as alkynyl-functionalized bipyridine, 1,4-di- and 1,3,5-trisubstituted benzene or phosphane moieties connecting the different metal atoms, is highlighted.
A New Supported Rhodium Catalyst for Selective Hydrogenation of Nitriles to Primary Amines
Authors: Witte Peter T.
Published: April 2007

Nitriles are converted to primary amines with high selectivity using a newly developed alumina-supported rhodium catalyst. The high selectivity is obtained without any additives, which are often used to prevent the formation of higher amines. The catalyst is active under mild conditions in various solvents, which makes it specifically suitable for use in pharmaceutical applications or for other substrates that can react with additives like strong acids or bases.
IT SECURITY IN BIOMEDICAL IMAGING INFORMATICS: THE HIDDEN VULNERABILITY
Authors: CHEE W. S. ADAM
Published: April 2007

The convergence of biomedical instruments and computing platforms has resulted in medical imaging equipment being subjected to the threats of malicious software (Malware) which have traditionally plagued the computing industry.

Vulnerabilities increase several-fold with implementations of Clinical Information Systems like the Picture Archival & Communication Systems (PACS), where computer-based biomedical equipment work hand in glove with computer servers.

With the increasing complexity of modern Malware, proactive monitoring and reviews of known vulnerabilities are no longer sufficient. An institute faced with an IT security attack on their medical networks will still experience extended downtime, performance degradation and increased service costs, even if equipped with an adequate security system and recovery plans.

Biomedical equipment vendors usually need more time than computing vendors to validate the security updates required for vulnerabilities before they can recommend changes for installation to their systems. This includes all system changes, patches, updates, and enhancements. However, the interval between the launch of a new Malware attack and the availability of a solution from the vendor can result in the medical network being compromised and rendered totally crippled.

In view of such new challenges, it is crucial to redesign your medical network and operating procedures to ensure continuous operation with minimum performance degradation even under a Malware attack until the biomedical equipment vendor can provide the software updates to resolve security vulnerabilities.

Such strategic implementation is not only necessary to ensure integrity and confidentiality of patient's data but also to protect the healthcare institute's reputation and business continuity.
LEFT VENTRICULAR FUNCTIONAL INDICES BASED ON LEFT VENTRICULAR ELASTANCES AND SHAPE FACTOR
Authors: ZHONG LIANG , GHISTA DHANJOO N. , NG EDDIE Y.-K. , CHUA TERRANCE S.-J. , LEE CHUEN N. , LIM SOO TEIK , TAN RU SAN , CHUA LEOK POH
Published: April 2007

This study characterizes left ventricular function in terms of passive and active elastances (Ep & Ea) and shape factor index. Both the active elastance and shape factor indices can be employed as contractility indices. The work also demonstrates how Ep and Ea can explain LV pressure dynamics in terms of LV volume dynamics.
Growth hormone regulation of metabolic gene expression in muscle: a microarray study in hypopituitary men
Authors: Sjögren Klara , Leung Kin-Chuen , Kaplan Warren , Gardiner-Garden Margaret , Gibney James , Ho Ken K. Y.
Published: April 2007

Muscle is a target of growth hormone (GH) action and a major contributor to whole body metabolism. Little is known about how GH regulates metabolic processes in muscle or the extent to which muscle contributes to changes in whole body substrate metabolism during GH treatment. To identify GH-responsive genes that regulate substrate metabolism in muscle, we studied six hypopituitary men who underwent whole body metabolic measurement and skeletal muscle biopsies before and after 2 wk of GH treatment (0.5 mg/day). Transcript profiles of four subjects were analyzed using Affymetrix GeneChips. Serum insulin-like growth factor I (IGF-I) and procollagens I and III were measured by RIA. GH increased serum IGF-I and procollagens I and III, enhanced whole body lipid oxidation, reduced carbohydrate oxidation, and stimulated protein synthesis. It induced gene expression of IGF-I and collagens in muscle. GH reduced expression of several enzymes regulating lipid oxidation and energy production. It reduced calpain 3, increased ribosomal protein L38 expression, and displayed mixed effects on genes encoding myofibrillar proteins. It increased expression of circadian gene CLOCK, and reduced that of PERIOD. In summary, GH exerted concordant effects on muscle expression and blood levels of IGF-I and collagens. It induced changes in genes regulating protein metabolism in parallel with a whole body anabolic effect. The discordance between muscle gene expression profiles and metabolic responses suggests that muscle is unlikely to contribute to GH-induced stimulation of whole body energy and lipid metabolism. GH may regulate circadian function in skeletal muscle by modulating circadian gene expression with possible metabolic consequences.
GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR
Authors: Kidd Mark , Nadler Boaz , Mane Shrikant , Eick Geeta , Malfertheiner Maximillian , Champaneria Manish , Pfragner Roswitha , Modlin Irvin
Published: April 2007

Accurate quantitation of target genes depends on correct normalization. Use of genes with variable tissue transcription ( GAPDH) is problematic, particularly in clinical samples, which are derived from different tissue sources. Using a large-scale gene database (Affymetrix U133A) data set of 36 gastrointestinal (GI) tumors and normal tissues, we identified 8 candidate reference genes and established expression levels by real-time RT-PCR in an independent data set ( n = 42). A geometric averaging method (geNorm) identified ALG9, TFCP2, and ZNF410 as the most robustly expressed control genes. Examination of raw CTvalues demonstrated that these genes were tightly correlated between themselves ( R2> 0.86, P < 0.0001), with low variability [coefficient of variation (CV) <12.7%] and high interassay reproducibility ( r = 0.93, P = 0.001). In comparison, the alternative control gene, GAPDH, exhibited the highest variability (CV = 18.1%), was significantly differently expressed between tissue types ( P = 0.05), was poorly correlated with the three reference genes ( R2< 0.4), and was considered the least stable gene. To illustrate the importance of correct normalization, the target gene, MTA1, was significantly overexpressed ( P = 0.0006) in primary GI neuroendocrine tumor (NET) samples (vs. normal GI samples) when normalized by geNormATZbut not when normalized using GAPDH. The geNormATZapproach was, in addition, applicable to adenocarcinomas; MTA1 was overexpressed ( P < 0.04) in malignant colon, pancreas, and breast tumors compared with normal tissues. We provide a robust basis for the establishment of a reference gene set using GeneChip data and provide evidence for the utility of normalizing a malignancy-associated gene ( MTA1) using novel reference genes and the geNorm approach in GI NETs as well as in adenocarcinomas and breast tumors.
Evidence for Microvascular Dysfunction in Hypertrophic Cardiomyopathy
Authors: Petersen Steffen E. , Jerosch-Herold Michael , Hudsmith Lucy E. , Robson Matthew D. , Francis Jane M. , Doll Helen A. , Selvanayagam Joseph B. , Neubauer Stefan , Watkins Hugh
Published: April 2007

Background—

Microvascular dysfunction in hypertrophic cardiomyopathy (HCM) may create an ischemic substrate conducive to sudden death, but it remains unknown whether the extent of hypertrophy is associated with proportionally poorer perfusion reserve. Comparisons between magnitude of hypertrophy, impairment of perfusion reserve, and extent of fibrosis may offer new insights for future clinical risk stratification in HCM but require multiparametric imaging with high spatial and temporal resolution.

Methods and Results—

Degree of hypertrophy, myocardial blood flow at rest and during hyperemia (hMBF), and myocardial fibrosis were assessed with magnetic resonance imaging in 35 HCM patients (9 [26%] male/26 female) and 14 healthy controls (4 [29%] male/10 female), aged 18 to 78 years (mean±SD, 42±14 years) with the use of the American Heart Association left ventricular 16-segment model. Resting MBF was similar in HCM patients and controls. hMBF was lower in HCM patients (1.84±0.89 mL/min per gram) than in healthy controls (3.42±1.76 mL/min per gram, with a difference of −0.95±0.30 [SE] mL/min per gram;
P
<0.001) after adjustment for multiple variables, including end-diastolic segmental wall thickness (
P
<0.001). In HCM patients, hMBF decreased with increasing end-diastolic wall thickness (
P
<0.005) and preferentially in the endocardial layer. The frequency of endocardial hMBF falling below epicardial hMBF rose with wall thickness (
P
=0.045), as did the incidence of fibrosis (
P
<0.001).

Conclusions—

In HCM the vasodilator response is reduced, particularly in the endocardium, and in proportion to the magnitude of hypertrophy. Microvascular dysfunction and subsequent ischemia may be important components of the risk attributable to HCM.
Development of a Ventilatory Classification System in Patients With Heart Failure
Authors: Arena Ross , Myers Jonathan , Abella Joshua , Peberdy Mary Ann , Bensimhon Daniel , Chase Paul , Guazzi Marco
Published: April 2007

Background—

Ventilatory efficiency, commonly assessed by the minute ventilation (V̇
e
)–carbon dioxide production (V̇
co
2
) slope, is a powerful prognostic marker in the heart failure population. The purpose of the present study is to refine the prognostic power of the V̇
e
/V̇
co
2
slope by developing a ventilatory class system that correlates V̇
e
/V̇
co
2
cut points to cardiac-related events.

Methods and Results—

Four hundred forty-eight subjects diagnosed with heart failure were included in this analysis. The V̇
e
/V̇
co
2
slope was determined via cardiopulmonary exercise testing. Subjects were tracked for major cardiac events (mortality, transplantation, or left ventricular assist device implantation) for 2 years after cardiopulmonary exercise testing. There were 81 cardiac-related events (64 deaths, 10 heart transplants, and 7 left ventricular assist device implantations) during the 2-year tracking period. Receiver operating characteristic curve analysis revealed the overall V̇
e
/V̇
co
2
slope classification scheme was significant (area under the curve: 0.78 [95% CI, 0.73 to 0.83],
P
<0.001). On the basis of test sensitivity and specificity, the following ventilatory class system was developed: (1) ventilatory class (VC) I: ≤29; (2) VC II: 30.0 to 35.9; (3) VC III: 36.0 to 44.9; and (4) VC IV: ≥45.0. The numbers of subjects in VCs I through IV were 144, 149, 112, and 43, respectively. Kaplan-Meier analysis revealed event-free survival for subjects in VC I, II, III, and IV was 97.2%, 85.2%, 72.3%, and 44.2%, respectively (log-rank 86.8;
P
<0.001).

Conclusions—

A multiple-level classificatory system based on exercise V̇
e
/V̇
co
2
slope stratifies the burden of risk for the entire spectrum of heart failure severity. Application of this classification is therefore proposed to improve clinical decision making in heart failure.
Long-Term Prognostic Value of Blood Pressure Variability in the General Population
Authors: Mancia Giuseppe , Bombelli Michele , Facchetti Rita , Madotto Fabiana , Corrao Giovanni , Trevano Fosca Quarti , Grassi Guido , Sega Roberto
Published: April 2007

The hypothesis has been advanced that cardiovascular prognosis is related not only to 24-hour mean blood pressure but also to blood pressure variability. Data, however, are inconsistent, and no long-term prognostic study is available. In 2012 individuals randomly selected from the population of Monza (Milan), 24-hour ambulatory blood pressure (Spacelabs 90207) was measured via readings spaced by 20 minutes. Systolic and diastolic blood pressure variability was obtained by calculating the following: (1) the SD of 24-hour, day, and night mean values; (2) the day–night blood pressure difference; and (3) the residual or erratic blood pressure variability (Fourier spectral analysis). Fatal cardiovascular and noncardiovascular events were registered for 148 months. When adjusted for age, sex, 24-hour mean blood pressure, and other risk factors, there was no relationship between the risk of death and 24-hour, day, and night blood pressure SDs. In contrast, the adjusted risk of cardiovascular death was inversely related to day–night diastolic BP difference (β coefficient=−0.040;
P
<0.02) and showed a significant positive relationship with residual diastolic blood pressure variability (β coefficient=0.175;
P
<0.002). Twenty-four–hour mean blood pressure attenuation of nocturnal hypotension and erratic diastolic blood pressure variability all independently predicted the mortality risk, with the erratic variability being the most important factor. Our data show that the relationship of blood pressure to prognosis is complex and that phenomena other than 24-hour mean values are involved. They also provide the first evidence that short-term erratic components of blood pressure variability play a prognostic role, with their increase being accompanied by an increased cardiovascular risk.
Modifications of Arterial Phenotype in Response to Amine Oxidase Inhibition by Semicarbazide
Authors: Mercier Nathalie , El Hadri Khadija , Osborne-Pellegrin Mary , Nehme Johnny , Perret Claudine , Labat Carlos , Regnault Veronique , Lamazière Jean-Marie Daniel , Challande Pascal , Lacolley Patrick , Fève Bruno
Published: April 2007

Semicarbazide-sensitive amine oxidase (SSAO)–deficient mice present no alteration in elastin cross-linking processes and carotid mechanical properties. In contrast, previous studies have shown that SSAO inhibitors induced marked anomalies in arterial structure and function. The aim of the present study was to examine the effect of semicarbazide (SCZ), an efficient SSAO inhibitor, on the arterial phenotype of the carotid artery in relation to modulation of SSAO and lysyl oxidase activities in growing rats. We first show that after 6 weeks of SCZ treatment (100 mg/kg per day), SSAO activity was reduced by 90%, whereas lysyl oxidase activity was only partially inhibited (<60%) in carotid artery, compared with controls. There was significant growth inhibition and no difference in mean arterial pressure but an increase in pulse pressure with a smaller arterial diameter in SCZ-treated rats. SCZ decreased aortic insoluble elastin without a change in total collagen. In addition, extracellular proteins other than insoluble elastin and collagen were increased in SCZ-treated rats. All of the elastic lamellae presented globular masses along their periphery, and focal disorganization was observed in the ascending aorta. Carotid artery mechanical strength was lower in SCZ-treated rats, and the elastic modulus–wall stress curve was shifted leftward compared with controls, indicating increased stiffness. Thus, SCZ modifies arterial geometry and mechanical properties, alters elastic fiber structure, and reduces the content of cross-linked elastin. Because these abnormalities are essentially absent in SSAO-deficient mice, our results suggest that lysyl oxidase inhibition is responsible for the major part of the vascular phenotype of SCZ-treated rats.
David Ibn Shoshan on Spirit and Soul
Authors: Langermann Y. Tzvi
Published: April 2007

David Ibn Shoshan, a Jewish savant and a victim of the Spanish Expulsion of 1492, addresses the question of the status of the human spirit (rūah, rūh, pneuma) in the course of his commentary to Ecclesiastes. Spirit is the substrate of the soul; but as such, is it divine like the soul, so that it too ascends after death? Or is it rather purely material and hence perishable? After reviewing a number of medieval Islamic sources, Ibn Shoshan decides in favor of the view of Ibny Tufayl who, in his "philosophical romance" Hayy Ibn Yaqzān, declares the spirit to be divine. Among the interpretations that Ibn Shoshan rejects is that of "the authors of the Zohar." However, his critique is conducted entirely in a scientific idiom, without any polemical overtones. This is instructive insofar as it illustrates that kabbalists and natural philosophers of the period engaged on the whole in a constructive discourse based upon shared concepts. The texts studied here testifies to the endurance of Andalusian Jewish learning even after the expulsion of 1492. Indeed, perhaps Giordano Bruno mined some of the same sources utilized by Ibn Shoshan.
Zwischen den Stühlen? On the Taxonomic Anxieties of Modern Jewish Philosophy
Authors: Zank Michael
Published: April 2007

As a subfield of Jewish Studies modern Jewish philosophy is haunted by challenges arising from the culturally specific circumstances and original goals pursued by the Jewish philosophers of the past that are no longer immediately accessible. This essay looks at systematic and historical aspects of Jewish philosophy with the aim of determining ways of retrieving the plausibility of a taxonomically problematic field operating at the intersections of philosophy, history, religion, and Judaism.
A Numerical Study of Hurricane Erin (2001). Part II: Shear and the Organization of Eyewall Vertical Motion
Authors: Braun Scott A. , Wu Liguang
Published: April 2007

A high-resolution numerical simulation of Hurricane Erin (2001) is used to examine the organization of vertical motion in the eyewall and how that organization responds to a large and rapid increase in the environmental vertical wind shear and subsequent decrease in shear. During the early intensification period, prior to the onset of significant shear, the upward motion in the eyewall was concentrated in small-scale convective updrafts that formed in association with regions of concentrated vorticity (herein termed mesovortices) with no preferred formation region around the eyewall. Asymmetric flow within the eye was weak. As the shear increased, an azimuthal wavenumber-1 asymmetry in storm structure developed with updrafts tending to occur on the downshear to downshear-left side of the eyewall. Continued intensification of the shear led to increasing wavenumber-1 asymmetry, large vortex tilt, and a change in eyewall structure and vertical motion organization. During this time, the eyewall structure was dominated by a vortex couplet with a cyclonic (anticyclonic) vortex on the downtilt-left (downtilt-right) side of the eyewall and strong asymmetric flow across the eye that led to strong mixing of eyewall vorticity into the eye. Upward motion was concentrated over an azimuthally broader region on the downtilt side of the eyewall, upstream of the cyclonic vortex, where low-level environmental inflow converged with the asymmetric outflow from the eye. As the shear diminished, the vortex tilt and wavenumber-1 asymmetry decreased, while the organization of updrafts trended back toward that seen during the weak shear period. Based upon the results for the Erin case, as well as that for a similar simulation of Hurricane Bonnie (1998), a conceptual model is developed for the organization of vertical motion in the eyewall as a function of the strength of the vertical wind shear. In weak to moderate shear, higher wavenumber asymmetries associated with eyewall mesovortices dominate the wavenumber-1 asymmetry associated with the shear so that convective-scale updrafts form when the mesovortices move into the downtilt side of the eyewall and dissipate on the uptilt side. Under strong shear conditions, the wavenumber-1 asymmetry, characterized by a prominent vortex couplet in the eyewall, dominates the vertical motion organization so that mesoscale ascent (with embedded convection) occurs over an azimuthally broader region on the downtilt side of the eyewall. Further research is needed to determine if these results apply more generally.
Assessment of Physical Parameterizations Using a Global Climate Model with Stretchable Grid and Nudging
Authors: Coindreau O. , Hourdin F. , Haeffelin M. , Mathieu A. , Rio C.
Published: April 2007

The Laboratoire de Météorologie Dynamique atmospheric general circulation model with zooming capability (LMDZ) has been used in a nudged mode to enable comparison of model outputs with routine observations and evaluate the model physical parameterizations. Simulations have been conducted with a stretched grid refined over the vicinity of Paris, France, where observations, collected at the Trappes station (Météo-France) and at the Site Instrumental de Recherche par Télédétection Atmosphérique observatory, are available. For the purpose of evaluation of physical parameterizations, the large-scale component of the modeled circulation is adjusted toward ECMWF analyses outside the zoomed area only, whereas the inside region can evolve freely. A series of sensitivity experiments have been performed with different parameterizations of land surface and boundary layer processes. Compared with previous versions of the LMDZ model, a “thermal plume model,” in association with a constant resistance to evaporation improves agreement with observations. The new parameterization significantly improves the representation of seasonal and diurnal cycles of near-surface meteorology, the day-to-day variability of planetary boundary layer height, and the cloud radiative forcing. This study emphasizes the potential of using a climate model with a nudging and zooming capability to assess model physical parameterizations.
Radar Characteristics of Precipitation Features in the EPIC and TEPPS Regions of the East Pacific
Authors: Cifelli R. , Nesbitt S. W. , Rutledge S. A. , Petersen W. A. , Yuter S.
Published: April 2007

Ship-based radar data are used to compare the structure of precipitation features in two regions of the east Pacific where recent field campaigns were conducted: the East Pacific Investigation of Climate Processes in the Coupled Ocean–Atmosphere System (EPIC-2001; 10°N, 95°W) in September 2001 and the Tropical Eastern Pacific Process Study (TEPPS; 8°N, 125°W) in August 1997. Corresponding July–September 1998–2004 Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) data are also used to provide context for the field campaign data. An objective technique is developed to identify precipitation features in the ship and TRMM PR data and to develop statistics on horizontal and vertical structure and precipitation characteristics. Precipitation features were segregated into mesoscale convective system (MCS) and sub-MCS categories, based on a contiguous area threshold of 1000 km2 (these features were required to have at least one convective pixel), as well as an “other” (NC) category. Comparison of the satellite and field campaign data showed that the two datasets were in good agreement for both regions with respect to MCS features. Specifically, both the satellite and ship radar data showed that approximately 80% of the rainfall volume in both regions was contributed by MCS features, similar to results from other observational datasets. EPIC and TEPPS MCSs had similar area distributions but EPIC MCSs tended to be more vertically developed and rain heavier than their TEPPS counterparts. In contrast to MCSs, smaller features (NCs and sub-MCSs) sampled by the ship radar in both regions showed important differences compared with the PR climatology. In the EPIC field campaign, a large number of small (<100 km2), shallow (radar echo tops below the melting level) NCs and sub-MCSs were sampled. A persistent dry layer above 800 mb during undisturbed periods in EPIC may have been responsible for the high occurrence of these features. Also, during the TEPPS campaign, sub-MCSs were larger and deeper with respect to the TRMM climatology, which may have been due to the higher than average SSTs during 1997–98 when TEPPS was conducted. Despite these differences, it was found that for sizes greater than about 100 km2, EPIC precipitation features had 30-dBZ echos at higher altitudes and also had higher rain rates than similar sized TEPPS features. These results suggest that ice processes play a more important role in rainfall production in EPIC compared with TEPPS.
Atmospheric Circulation Associated with Persistent Generalized Frosts in Central-Southern South America
Authors: Müller Gabriela V. , Berri Guillermo J.
Published: April 2007

This paper describes the large-scale atmospheric circulation associated with persistent generalized frosts (GFs; at least 75% of the stations report frosts) in the east-central region of Argentina known as the Wet Pampa. The GF events are grouped according to their persistence, and NCEP–NCAR reanalysis data are used to create daily composites of mass and wind field anomalies during the 1961–90 winters. The GFs are caused by an anticyclonic anomaly that enters South America, generating southerly wind anomalies and cold air advection that are strengthened by the meridional layout of a cyclonic anomaly over the South Atlantic Ocean. In the case of the more persistent events the wind anomaly grows during the previous days and becomes quasi-stationary. Also, the study identifies at 250 hPa a double train of eastward-moving Rossby waves along the subtropical and subpolar latitudes, respectively, of the Southern Hemisphere. The layout of both wave trains favors the development of an intense southerly wind anomaly in the entire southern cone of the continent. On the other hand, the propagation pattern during the less persistent GFs shows only one arc-shaped Rossby wave train that reaches South America, and then propagates northeastward. Additionally, there is a subtropical jet entrance/confluence over the western side of the continent that induces a secondary meridional circulation whose subsiding branch facilitates the equatorward displacement of the low-level anticyclone, particularly in the case of the less persistent events. In the case of the more persistent GFs the confluence is located farther east and sustains essentially zonal wave train propagation, so that the surface anticyclone is not able to achieve a major equatorward penetration.
Retrieval of Moisture from Simulated GPS Slant-Path Water Vapor Observations Using 3DVAR with Anisotropic Recursive Filters
Authors: Liu Haixia , Xue Ming , Purser R. James , Parrish David F.
Published: April 2007

Anisotropic recursive filters are implemented within a three-dimensional variational data assimilation (3DVAR) framework to efficiently model the effect of flow-dependent background error covariance. The background error covariance is based on an estimated error field and on the idea of Riishøjgaard. In the anisotropic case, the background error pattern can be stretched or flattened in directions oblique to the alignment of the grid coordinates and is constructed by applying, at each point, six recursive filters along six directions corresponding, in general, to a special configuration of oblique lines of the grid. The recursive filters are much more efficient than corresponding explicit filters used in an earlier study and are therefore more suitable for real-time numerical weather prediction. A set of analysis experiments are conducted at a mesoscale resolution to examine the effectiveness of the 3DVAR system in analyzing simulated global positioning system (GPS) slant-path water vapor observations from ground-based GPS receivers and observations from collocated surface stations. It is shown that the analyses produced with recursive filters are at least as good as those with corresponding explicit filters. In some cases, the recursive filters actually perform better. The impact of flow-dependent background errors modeled using the anisotropic recursive filters is also examined. The use of anisotropic filters improves the analysis, especially in terms of finescale structures. The analysis system is found to be effective in the presence of typical observational errors. The sensitivity of isotropic and anisotropic recursive-filter analyses to the decorrelation scales is also examined systematically.
Nonlinear Horizontal Diffusion for GCMs
Authors: Becker Erich , Burkhardt Ulrike
Published: April 2007

The mixing-length-based parameterization of horizontal diffusion, which was originally proposed by Smagorinsky, is revisited. The complete tendencies of horizontal momentum diffusion, the associated frictional heating, and horizontal diffusion of sensible heat in spherical geometry are derived. The formulations are modified for the terrain-following vertical-hybrid-coordinate system in a way that ensures energy and angular momentum conservation at each layer. Test simulations with a simple general circulation model, run at T42 horizontal resolution and for permanent January conditions, confirm the conservation properties and highlight the enhancement of nonlinear horizontal diffusion in areas of high baroclinic activity. The simulated internal variability is dependent on the nature of the horizontal diffusion, with high-frequency variability being enhanced over the northern continents and low-frequency variability being increased (decreased) over the Pacific (Atlantic) Ocean when using nonlinear rather than linear diffusion. Locally reduced horizontal dissipation over Europe is compensated by increased dissipation owing to vertical diffusion, indicating the potential importance of nonlinear horizontal diffusion for gravity wave–resolving simulations. Inspection of the spectral energy reveals that the scheme needs to be modified in order to damp unbalanced ageostrophic motions at the smallest resolved scales more efficiently. A corresponding empirical modification is proposed and proves to work properly.
Close-Range Observations of Tornadoes in Supercells Made with a Dual-Polarization, X-Band, Mobile Doppler Radar
Authors: Bluestein Howard B. , French Michael M. , Tanamachi Robin L. , Frasier Stephen , Hardwick Kery , Junyent Francesc , Pazmany Andrew L.
Published: April 2007

A mobile, dual-polarization, X-band, Doppler radar scanned tornadoes at close range in supercells on 12 and 29 May 2004 in Kansas and Oklahoma, respectively. In the former tornadoes, a visible circular debris ring detected as circular regions of low values of differential reflectivity and the cross-correlation coefficient was distinguished from surrounding spiral bands of precipitation of higher values of differential reflectivity and the cross-correlation coefficient. A curved band of debris was indicated on one side of the tornado in another. In a tornado and/or mesocyclone on 29 May 2004, which was hidden from the view of the storm-intercept team by precipitation, the vortex and its associated “weak-echo hole” were at times relatively wide; however, a debris ring was not evident in either the differential reflectivity field or in the cross-correlation coefficient field, most likely because the radar beam scanned too high above the ground. In this case, differential attenuation made identification of debris using differential reflectivity difficult and it was necessary to use the cross-correlation coefficient to determine that there was no debris cloud. The latter tornado’s parent storm was a high-precipitation (HP) supercell, which also spawned an anticyclonic tornado approximately 10 km away from the cyclonic tornado, along the rear-flank gust front. No debris cloud was detected in this tornado either, also because the radar beam was probably too high.
The Influence of the Andes on Cutoff Lows: A Modeling Study*
Authors: Garreaud RenéD. , Fuenzalida Humberto A.
Published: April 2007

A cutoff low (COL) pressure system that occurred in March 2005 (late austral summer) over the subtropical southeast Pacific is examined by means of numerical simulations using the Weather and Research Forecasting (WRF) model. The episode exhibited typical features of COLs in this region, including its formation from an elongated northwest–southeast extratropical trough and subsequent intensification off the west coast of South America. During the developing stage, the cyclonic circulation did not extend into the lower troposphere and only upper-level, nonprecipitating clouds were observed at and around the system. When the COL reached the continent it produced moderate but unseasonal rainfall along the semiarid western slope of the Andes cordillera [summit level at ∼5000 m above sea level (ASL)] at the same time that the system experienced a rapid decay. The control simulation used full physics, full topography, and a single domain (54-km grid spacing) laterally forced by atmospheric reanalysis. Model results are in general agreement with upper-air, surface, and satellite observations, and allow a detailed description of the three-dimensional structure of the COL, as well as an evaluation of the vorticity and temperature budgets. A quasi-stationary, amplifying warm ridge over the South Pacific appears as the key precursor feature, in agreement with studies elsewhere. Once the COL formed, it drifted eastward mostly driven by vorticity advection induced by its own circulation, and there was close balance between vertical and horizontal temperature advection near its center. The jet streak along the COL’s periphery migrated from upstream of the COL axis, during the developing stage, to downstream later on. Four sensitivity experiments—reducing/removing topography, suppressing hydrometeors, and using an enlarged domain—were performed to assess the influence of the Andes, the importance of latent heat release, and the effect of the boundary conditions. Comparison among the control and sensitivity runs indicates that the COL formation occurs regardless of the presence of the Andes, and COL dissipation is mainly due to latent heat released in the deep clouds that form over the mountainous terrain. Nevertheless, the Andes cordillera delayed the COL demise by blocking the inflow of warm, moist air from the interior of the continent that otherwise would initiate deep convection in the region of ascending motion downstream of the COL.
A Transformed Lagged Ensemble Forecasting Technique for Increasing Ensemble Size
Authors: Lawrence Andrew R. , Hansen James A.
Published: April 2007

An ensemble-based data assimilation approach is used to transform old ensemble forecast perturbations with more recent observations for the purpose of inexpensively increasing ensemble size. The impact of the transformations are propagated forward in time over the ensemble’s forecast period without rerunning any models, and these transformed ensemble forecast perturbations can be combined with the most recent ensemble forecast to sensibly increase forecast ensemble sizes. Because the transform takes place in perturbation space, the transformed perturbations must be centered on the ensemble mean from the most recent forecasts. Thus, the benefit of the approach is in terms of improved ensemble statistics rather than improvements in the mean. Larger ensemble forecasts can be used for numerous purposes, including probabilistic forecasting, targeted observations, and to provide boundary conditions to limited-area models. This transformed lagged ensemble forecasting approach is explored and is shown to give positive results in the context of a simple chaotic model. By incorporating a suitable perturbation inflation factor, the technique was found to generate forecast ensembles whose skill were statistically comparable to those produced by adding nonlinear model integrations. Implications for ensemble forecasts generated by numerical weather prediction models are briefly discussed, including multimodel ensemble forecasting.
A Data Assimilation Case Study Using a Limited-Area Ensemble Kalman Filter
Authors: Dirren Sébastien , Torn Ryan D. , Hakim Gregory J.
Published: April 2007

Ensemble Kalman filter (EnKF) data assimilation experiments are conducted on a limited-area domain over the Pacific Northwest region of the United States, using the Weather Research and Forecasting model. Idealized surface pressure, radiosoundings, and aircraft observations are assimilated every 6 h for a 7-day period in January 2004. The objectives here are to study the performance of the filter in constraining analysis errors with a relatively inhomogeneous, sparse-observation network and to explore the potential for such a network to serve as the basis for a real-time EnKF system dedicated to the Pacific Northwest region of the United States. When only a single observation type is assimilated, results show that the ensemble-mean analysis error and ensemble spread (standard deviation) are significantly reduced compared to a control ensemble without assimilation for both observed and unobserved variables. Analysis errors are smaller than background errors over nearly the entire domain when averaged over the 7-day period. Moreover, comparisons of background errors and observation increments at each assimilation step suggest that the flow-dependent filter corrections are accurate in both scale and amplitude. An illustrative example concerns a misspecified mesoscale 500-hPa short-wave trough moving along the British Columbia coast, which is corrected by surface pressure observations alone. The relative impact of each observation type upon different variables and vertical levels is also discussed.
Latitude–Height Structure of the Atmospheric Angular Momentum Cycle Associated with the Madden–Julian Oscillation
Authors: Egger Joseph , Weickmann Klaus
Published: April 2007

The angular momentum cycle of the Madden–Julian oscillation is analyzed by regressing the zonally averaged axial angular momentum (AAM) budget including fluxes and torques against the first two principal components P1 and P2 of the empirical orthogonal functions (EOFs) of outgoing longwave radiation (OLR). The maximum of P1 coincides with an OLR minimum near 150°E and a shift from anomalously negative AAM to positive AAM in the equatorial troposphere. AAM anomalies of one sign develop first in the upper-equatorial troposphere and then move downward and poleward to the surface of the subtropics within two weeks. During the same time the opposite sign AAM anomaly develops in the upper-equatorial troposphere. The tropical troposphere is warming when P1 approaches its maximum while the stratosphere is cooling. The torques are largest in the subtropics and are linked with the downward and poleward movement of AAM anomalies. The evolution is conveniently summarized using a time–height depiction of the global mean AAM and vertical flux anomaly.
A Modified Approach to Initialize an Idealized Extratropical Cyclone within a Mesoscale Model
Authors: Olson Joseph B. , Colle Brian A.
Published: April 2007

A technique for initializing realistic idealized extratropical cyclones for short-term (0–72 h) numerical simulations is described. The approach modifies select methods from two previous studies to provide more control over the initial cyclone structure. Additional features added to the technique include 1) deformation functions to initialize more realistic low-level fronts, tropopause structure, and enhanced jet maximum at upper levels; 2) a barotropic shear function to help develop different cyclone and frontal geometries; and 3) damping functions to create an isolated baroclinic wave in the horizontal; therefore, the initialized cyclone is not influenced by the domain boundaries for relatively short simulations. Since this procedure allows for control of the initialized cyclone structures, it may be useful for studies of frontal and cyclone interaction with topography and mesoscale predictability. The initialization system produces a variety of basic states and synoptic disturbances, ranging from weak to explosively developing cyclones. Examples are shown to provide some insight on how to adjust selected parameters. The output is compatible with the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model and the Weather Research and Forecasting model. This note describes the procedure as well as presents an example of a landfalling cyclone along the U.S. west coast with and without terrain.
Evaluation of a Technique for Radar Identification of Large Hail across the Upper Midwest and Central Plains of the United States
Authors: Donavon Rodney A. , Jungbluth Karl A.
Published: April 2007

Radar data were analyzed for severe thunderstorms that produced severe hail (>19 mm diameter) across the central and northern plains of the United States during the 2001–04 convective seasons. Results showed a strongly linear relationship between the 50-dBZ echo height and the height of the melting level—so strong that a severe hail warning methodology was successfully deployed at the National Weather Service Warning and Forecast Offices in North Dakota and Iowa. Specifically, for each of 183 severe hailstorms, the 50-dBZ echo height near the hail event time was plotted against the depth of the environmental melting level. Linear regression revealed a coefficient of determination of 0.86, which suggested a strong linear relationship between the 50-dBZ echo height and the melting-level depth for the severe hail producing storms. As the height of the melting level increased, the expected 50-dBZ echo height increased. A severe warning criterion for large hail was based on the 10th percentile from the linear regression, producing a probability of detection of 90% and a false alarm rate of 22%. Additional analysis found that the 50-dBZ echo-height technique performs very well for weakly to moderately sheared thunderstorm environments. However, for strongly sheared, supercell-type environments, signatures such as weak-echo regions and three-body scatter spikes led to more rapid severe thunderstorm detection in many cases.