bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Hypervirulent
Clostridium difficile
Strains Exhibit Increased Sporulation as Well as Robust Toxin Production
Authors: Merrigan Michelle , Venugopal Anilrudh , Mallozzi Michael , Roxas Bryan , Viswanathan V. K. , Johnson Stuart , Gerding Dale N. , Vedantam Gayatri
Published: July 2010

Toxigenic
Clostridium difficile
strains produce two toxins (TcdA and TcdB) during the stationary phase of growth and are the leading cause of antibiotic-associated diarrhea.
C. difficile
isolates of the molecular type NAP1/027/BI have been associated with severe disease and hospital outbreaks worldwide. It has been suggested that these “hypervirulent” strains produce larger amounts of toxin and that a mutation in a putative negative regulator (TcdC) allows toxin production at all growth phases. To rigorously explore this possibility, we conducted a quantitative examination of the toxin production of multiple hypervirulent and nonhypervirulent
C. difficile
strains. Toxin gene (
tcdA
and
tcdB
) and toxin gene regulator (
tcdR
and
tcdC
) expression was also monitored. To obtain additional correlates for the hypervirulence phenotype, sporulation kinetics and efficiency were measured. In the exponential phase, low basal levels of
tcdA
,
tcdB
, and
tcdR
expression were evident in both hypervirulent and nonhypervirulent strains, but contrary to previous assumptions, toxin levels were below the detectable thresholds. While hypervirulent strains displayed robust toxin production during the stationary phase of growth, the amounts were not significantly different from those of the nonhypervirulent strains tested; further, total toxin amounts were directly proportional to
tcdA
,
tcdB
, and
tcdR
gene expression. Interestingly,
tcdC
expression did not diminish in stationary phase, suggesting that TcdC may have a modulatory rather than a strictly repressive role. Comparative genomic analyses of the closely related nonhypervirulent strains VPI 10463 (the highest toxin producer) and 630 (the lowest toxin producer) revealed polymorphisms in the
tcdR
ribosome binding site and the
tcdR-tcdB
intergenic region, suggesting that a mechanistic basis for increased toxin production in VPI 10463 could be increased TcdR translation and read-through transcription of the
tcdA
and
tcdB
genes. Hypervirulent isolates produced significantly more spores, and did so earlier, than all other isolates. Increased sporulation, potentially in synergy with robust toxin production, may therefore contribute to the widespread disease now associated with hypervirulent
C. difficile
strains.
Antimicrobial Peptides Activate the Rcs Regulon through the Outer Membrane Lipoprotein RcsF
Authors: Farris Carol , Sanowar Sarah , Bader Martin W. , Pfuetzner Richard , Miller Samuel I.
Published: July 2010

Salmonella enterica
species are exposed to envelope stresses due to their environmental and infectious lifestyles. Such stresses include amphipathic cationic antimicrobial peptides (CAMPs), and resistance to these peptides is an important property for microbial virulence for animals. Bacterial mechanisms used to sense and respond to CAMP-induced envelope stress include the RcsFCDB phosphorelay, which contributes to survival from polymyxin B exposure. The Rcs phosphorelay includes two inner membrane (IM) proteins, RcsC and RcsD; the response regulator RcsB; the accessory coregulator RcsA; and an outer membrane bound lipoprotein, RcsF. Transcriptional activation of the Rcs regulon occurred within minutes of exposure to CAMP and during the first detectable signs of CAMP-induced membrane disorder. Rcs transcriptional activation by CAMPs required RcsF and preservation of its two internal disulfide linkages. The rerouting of RcsF to the inner membrane or its synthesis as an unanchored periplasmic protein resulted in constitutive activation of the Rcs regulon and RcsCD-dependent phosphorylation. These findings suggest that RcsFCDB activation in response to CAMP-induced membrane disorder is a result of a change in structure or availability of RcsF to the IM signaling constituents of the Rcs phosphorelay.
Different Roles of DosS and DosT in the Hypoxic Adaptation of Mycobacteria
Authors: Kim Min-Ju , Park Kwang-Jin , Ko In-Jeong , Kim Young Min , Oh Jeong-Il
Published: July 2010

The DosS (DevS) and DosT histidine kinases form a two-component system together with the DosR (DevR) response regulator in
Mycobacterium tuberculosis.
DosS and DosT, which have high sequence similarity to each other over the length of their amino acid sequences, contain two GAF domains (GAF-A and GAF-B) in their N-terminal sensory domains. Complementation tests in conjunction with phylogenetic analysis showed that DevS of
Mycobacterium smegmatis
is more closely related to DosT than DosS. We also demonstrated
in vivo
that DosS and DosT of
M. tuberculosis
play a differential role in hypoxic adaptation. DosT responds to a decrease in oxygen tension more sensitively and strongly than DosS, which might be attributable to their different autooxidation rates. The different responsiveness of DosS and DosT to hypoxia is due to the difference in their GAF-A domains accommodating the hemes. Multiple alignment analysis of the GAF-A domains of mycobacterial DosS (DosT) homologs and subsequent site-directed mutagenesis revealed that just one substitution of E87, D90, H97, L118, or T169 of DosS with the corresponding residue of DosT is sufficient to convert DosS to DosT with regard to the responsiveness to changes in oxygen tension.
Characterization of the Enzymes Encoded by the Anthrose Biosynthetic Operon of
Bacillus anthracis
Authors: Dong Shengli , McPherson Sylvia A. , Wang Yun , Li Mei , Wang Pengfei , Turnbough Charles L. , Pritchard David G.
Published: July 2010

Bacillus anthracis
spores, the etiological agents of anthrax, possess a loosely fitting outer layer called the exosporium that is composed of a basal layer and an external hairlike nap. The filaments of the nap are formed by trimers of the collagenlike glycoprotein BclA. Multiple pentasaccharide and trisaccharide side chains are O linked to BclA. The nonreducing terminal residue of the pentasaccharide side chain is the unusual sugar anthrose. A plausible biosynthetic pathway for anthrose biosynthesis has been proposed, and an
antABCD
operon encoding four putative anthrose biosynthetic enzymes has been identified. In this study, we genetically and biochemically characterized the activities of these enzymes. We also used mutant
B. anthracis
strains to determine the effects on BclA glycosylation of individually inactivating the genes of the anthrose operon. The inactivation of
antA
resulted in the appearance of BclA pentasaccharides containing anthrose analogs possessing shorter side chains linked to the amino group of the sugar. The inactivation of
antB
resulted in BclA being replaced with only trisaccharides, suggesting that the enzyme encoded by the gene is a dTDP-β-
l
-rhamnose α-1,3-
l
-rhamnosyl transferase that attaches the fourth residue of the pentasaccharide side chain. The inactivation of
antC
and
antD
resulted in the disappearance of BclA pentasaccharides and the appearance of a tetrasaccharide lacking anthrose. These phenotypes are entirely consistent with the proposed roles for the
antABCD
-encoded enzymes in anthrose biosynthesis. Purified AntA was then shown to exhibit β-methylcrotonyl-coenzyme A (CoA) hydratase activity, as we predicted. Similarly, we confirmed that purified AntC had aminotransferase activity and that purified AntD displayed
N
-acyltransferase activity.
NADP+Reduction with Reduced Ferredoxin and NADP+Reduction with NADH Are Coupled via an Electron-Bifurcating Enzyme Complex inClostridium kluyveri
Authors: Wang Shuning , Huang Haiyan , Moll Johanna , Thauer Rudolf K.
Published: July 2010

It was recently found that the cytoplasmic butyryl-coenzyme A (butyryl-CoA) dehydrogenase-EtfAB complex fromClostridium kluyvericouples the exergonic reduction of crotonyl-CoA to butyryl-CoA with NADH and the endergonic reduction of ferredoxin with NADH via flavin-based electron bifurcation. We report here on a second cytoplasmic enzyme complex inC. kluyvericapable of energetic coupling via this novel mechanism. It was found that the purified iron-sulfur flavoprotein complex NfnAB couples the exergonic reduction of NADP+with reduced ferredoxin (Fdred) and the endergonic reduction of NADP+with NADH in a reversible reaction: Fdred2−+ NADH + 2 NADP++ H+= Fdox+ NAD++ 2 NADPH. The role of this energy-converting enzyme complex in the ethanol-acetate fermentation ofC. kluyveriis discussed.
A Novel Replicative Enzyme Encoded by the LinearArthrobacterPlasmid pAL1
Authors: Kolkenbrock Stephan , Naumann Bianca , Hippler Michael , Fetzner Susanne
Published: July 2010

The soil bacteriumArthrobacter nitroguajacolicusRü61a contains the linear plasmid pAL1, which codes for the degradation of 2-methylquinoline. Like other linear replicons of actinomycetes, pAL1 is characterized by short terminal inverted-repeat sequences and terminal proteins (TPpAL1) covalently attached to its 5′ ends. TPpAL1, encoded by thepAL1.102gene, interactsin vivowith the protein encoded bypAL1.101.Bioinformatic analysis of the pAL1.101 protein, which comprises 1,707 amino acids, suggested putative zinc finger and topoisomerase-primase domains and part of a superfamily 2 helicase domain in its N-terminal and central regions, respectively. Sequence motifs characteristic of the polymerization domain of family B DNA polymerases are partially conserved in a C-terminal segment. The purified recombinant protein catalyzed the deoxycytidylation of TPpAL1in the presence of single-stranded DNA templates comprising the 3′-terminal sequence (5′-GCAGG-3′), which in pAL1 forms the terminal inverted repeat, but also at templates with 5′-(G/T)CA(GG/GC/CG)-3′ ends. Enzyme assays suggested that the protein exhibits DNA topoisomerase, DNA helicase, and DNA- and protein-primed DNA polymerase activities. The pAL1.101 protein, therefore, may act as a replicase of pAL1.
Bathy Phytochromes in Rhizobial Soil Bacteria
Authors: Rottwinkel Gregor , Oberpichler Inga , Lamparter Tilman
Published: July 2010

Phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. Prototypical phytochromes have a Pr ground state that absorbs in the red spectral range and is converted by light into the Pfr form, which absorbs longer-wavelength, far-red light. Recently, some bacterial phytochromes have been described that undergo dark conversion of Pr to Pfr and thus have a Pfr ground state. We show here that such so-called bathy phytochromes are widely distributed among bacteria that belong to the order
Rhizobiales
. We measured
in vivo
spectral properties and the direction of dark conversion for species which have either one or two phytochrome genes.
Agrobacterium tumefaciens
C58 contains one bathy phytochrome and a second phytochrome which undergoes dark conversion of Pfr to Pr
in vivo
. The related species
Agrobacterium
vitis
S4 contains also one bathy phytochrome and another phytochrome with novel spectral properties.
Rhizobium leguminosarum
3841,
Rhizobium etli
CIAT652, and
Azorhizobium caulinodans
ORS571 contain a single phytochrome of the bathy type, whereas
Xanthobacter autotrophicus
Py2 contains a single phytochrome with dark conversion of Pfr to Pr. We propose that bathy phytochromes are adaptations to the light regime in the soil. Most bacterial phytochromes are light-regulated histidine kinases, some of which have a C-terminal response regulator subunit on the same protein. According to our phylogenetic studies, the group of phytochromes with this domain arrangement has evolved from a bathy phytochrome progenitor.
The Genome Sequence of the Cyanobacterium
Oscillatoria
sp. PCC 6506 Reveals Several Gene Clusters Responsible for the Biosynthesis of Toxins and Secondary Metabolites
Authors: Méjean Annick , Mazmouz Rabia , Mann Stéphane , Calteau Alexandra , Médigue Claudine , Ploux Olivier
Published: July 2010

We report a draft sequence of the genome of
Oscillatoria
sp. PCC 6506, a cyanobacterium that produces anatoxin-a and homoanatoxin-a, two neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of genes responsible for the biosynthesis of these toxins, we have found other clusters of genes likely involved in the biosynthesis of not-yet-identified secondary metabolites.
Left ventricular underfilling and not septal bulging dominates abnormal left ventricular filling hemodynamics in chronic thromboembolic pulmonary hypertension
Authors: Lumens Joost , Blanchard Daniel G. , Arts Theo , Mahmud Ehtisham , Delhaas Tammo
Published: July 2010

Chronic thromboembolic pulmonary hypertension (CTEPH) is associated with abnormal left ventricular (LV) filling hemodynamics [mitral early passive filling wave velocity/late active filling wave velocity ( E/ A) < 1]. Pulmonary endarterectomy (PEA) acutely reduces pulmonary vascular resistance, resulting in an increase of mitral E/ A. The abolishment of leftward septal bulging and an increase in right ventricular (RV) output are thought to be responsible for the increase of mitral E/ A. In this study, we quantified the separate effects of leftward septal bulging and RV output on LV hemodynamics. In 39 CTEPH patients who underwent PEA, transmitral flow velocities and RV hemodynamic data were obtained pre- and postoperatively. A mathematical model describing the mechanics of ventricular interaction was fitted to the preoperative average values of cardiac output (CO; 4.4 l/min), mean pulmonary artery pressure (mPAP; 50 mmHg), mitral E/ A (0.74), and mean left atrial pressure (mLAP; 9.8 mmHg). Starting from this preoperative reference state with leftward septal bulging, PEA was simulated by changing mPAP and CO to average postoperative values (28 mmHg and 5.7 l/min, respectively). Simulated and postoperatively measured data on E/ A (1.27 vs. 1.48), mLAP (12.6 vs. 11.5 mmHg), and septal curvature (both rightward) were consistent. When an exclusive decrease of mPAP was simulated, mitral E/ A increased 26%, mLAP decreased 16%, and septal curvature became rightward. When an exclusive increase of CO was simulated, mitral E/ A increased 53% and mLAP increased 62%, whereas leftward septal bulging persisted. Thus, our simulations suggest that the increase of mitral E/ A with PEA is caused two-thirds by an increase of RV output and one-third by the abolishment of leftward septal bulging.
Angiotensin-(1–7) upregulates cardiac nitric oxide synthase in spontaneously hypertensive rats
Authors: Costa María A. , Lopez Verrilli María A. , Gomez Karina A. , Nakagawa Pablo , Peña Clara , Arranz Cristina , Gironacci Mariela M.
Published: July 2010

It has been shown that angiotensin (ANG)-(1–7) activates nitric oxide synthase (NOS) in isolated ventricular myocytes from normotensive rats. Since many ANG-(1–7) actions are enhanced in situations of increased ANG II activity, as in hypertension, in this study we investigated the in vivo effect of ANG-(1–7) on NOS activity and expression of endothelial (eNOS), neuronal (nNOS), and inducible NOS (iNOS) in ventricles from spontaneously hypertensive rats (SHR). Rats were subjected to a 60-min ANG-(1–7) infusion (0.35 nmol/min); controls received saline. NOS activity was measured using the NADPH diaphorase histochemical method and by the conversion of l-[14C]arginine to citrulline, and NOS phosphorylation and expression were determined using Western blotting. In SHR, ANG-(1–7) infusion diminished mean arterial pressure from 180 ± 9 to 146 ± 9 mmHg ( P < 0.05), and this effect was prevented by nitro-l-arginine methyl ester (l-NAME), a NOS inhibitor. In addition, NOS activity and eNOS phosphorylation were increased by ANG-(1–7) infusion. Ventricular eNOS and nNOS expression were increased 67.4 ± 6.4 and 51 ± 10%, respectively, by ANG-(1–7), whereas iNOS was not changed. In another set of experiments, we evaluated the mechanism by which ANG-(1–7) modifies NOS activity. Isolated ventricle slices preincubated with ANG-(1–7) showed an increase in NOS activity and eNOS phosphorylation, which was blocked by an AT2 and a bradykinin B2 receptor antagonist, but not by the Mas receptor antagonist. Our results show that in rats in a hypertensive state, ANG-(1–7) infusion upregulates cardiac NOS expression and activity through an AT2- and bradykinin-dependent mechanism. In this way ANG-(1–7) may elicit its cardioprotective action and contribute to some of the counterregulatory AT2 receptor effects that oppose the AT1 receptor-mediated effects.
The Manifestation of Stopping Sets and Absorbing Sets as Deviations on the Computation Trees of LDPC Codes
Authors: Psota Eric , Pérez Lance C.
Published: August 2010

The error mechanisms of iterative message‐passing decoders for low‐density parity‐check codes are studied. A tutorial review is given of the various graphical structures, including trapping sets, stopping sets, and absorbing sets that are frequently used to characterize the errors observed in simulations of iterative decoding of low‐density parity‐check codes. The connections between trapping sets and deviations on computation trees are explored in depth using the notion ofproblematictrapping sets in order to bridge the experimental and analytic approaches to these error mechanisms. A new iterative algorithm for finding low‐weight problematic trapping sets is presented and shown to be capable of identifying many trapping sets that are frequently observed during iterative decoding of low‐density parity‐check codes on the additive white Gaussian noise channel. Finally, a new method is given for characterizing the weight of deviations that result from problematic trapping sets.
On the Coverage Extension and Capacity Enhancement of Inband Relay Deployments in LTE‐Advanced Networks
Authors: Bou Saleh Abdallah , Redana Simone , Hämäläinen Jyri , Raaf Bernhard
Published: August 2010

Decode‐and‐forward relaying is a promising enhancement to existing radio access networks and is currently being standardized in 3GPP to be part of the LTE‐Advanced release 10. Two inband operation modes of relay nodes are to be supported, namely Type 1 and Type 1b. Relay nodes promise to offer considerable gain for system capacity or coverage depending on the deployment prioritization. However, the performance of relays, as any other radio access point, significantly depends on the propagation characteristics of the deployment environment. Hence, in this paper, we investigate the performance of Type 1 and Type 1b inband relaying within the LTE‐Advanced framework in different propagation scenarios in terms of both coverage extension capabilities and capacity enhancements. A comparison between Type 1 and Type 1b relay nodes is as well presented to study the effect of the relaying overhead on the system performance in inband relay node deployments. System level simulations show that Type 1 and Type 1b inband relay deployments offer low to very high gains depending on the deployment environment. As well, it is shown that the effect of the relaying overhead is minimal on coverage extension whereas it is more evident on system throughput.
Reproducibility of [11C]Choline-Positron Emission Tomography and Effect of Trastuzumab
Authors: Kenny Laura M. , Contractor Kaiyumars B. , Hinz Rainer , Stebbing Justin , Palmieri Carlo , Jiang Jie , Shousha Sami , Al-Nahhas Adil , Coombes R. Charles , Aboagye Eric O.
Published: August 2010

Purpose: This study sought to evaluate the reproducibility of [11C]choline-positron emission tomography and the effect of trastuzumab in breast cancer.

Experimental Design: Twenty-one patients with newly diagnosed and recurrent breast cancer stage II-IV had a baseline dynamic [11C]choline-PET scan, 10 patients had a second [11C]choline-PET scan to examine reproducibility, and 6 patients had a second scan within a month after trastuzumab. Analysis of [11C]choline uptake was measured as the semiquantitative standardized uptake value at 30 and 60 minutes (SUV30 and SUV60), and quantitatively as the net irreversible retention of the radiotracer at steady-state (Ki) and plasma to tissue exchange at 60 minutes (IRF60min).

Results: Breast tumor lesions in all patients were visualized by [11C]choline PET. The difference in tumor versus normal tissue uptake was significant for SUV30, SUV60, Ki, and IRF60 minutes (Wilcoxon P < 0.0001). At 60 minutes postinjection, 15.1 ± 2.16% of plasma radioactivity was due to unmetabolized [11C]choline radioactivity. [11C]Choline uptake was reproducible in breast tumor lesions (r2 = 0.9 for SUV, 0.9 for Ki, and 0.8 for IRF60). Early responses to trastuzumab measured by [11C]choline-PET were significant in three lesions occurring in two patients who responded clinically.

Conclusions: [11C]Choline-PET uptake variables can be reproducibly assessed. Initial studies show that trastuzumab decreases [11C]choline uptake. Clin Cancer Res; 16(16); 4236–45. ©2010 AACR.
'Progressive Multiculturalism': Minority Women and Cultural Diversity
Authors: Malik Maleiha
Published: July 2010

Recent criticisms of policies which advocate the public accommodation of cultural and religious difference have focused on the fact that 'multiculturalism is bad for women'. Making more explicit the way in which public accommodations of some minority group 'differences' are a requirement of the liberal commitment to individual autonomy and pluralism allows us to develop a version of 'progressive multiculturalism' which also safeguards the autonomy of minority women. This approach integrates two components both of which are important for minority women's autonomy: first, it gives weight to the importance of 'recognition' of cultural and religious difference in the public sphere; and, second, it facilitates full participation by minority women in mainstream political, social and economic processes.
Gender and Its Inter-Sectional Dimension in International Minority Law
Authors: Bantekas Ilias
Published: July 2010

Intersectional gender discrimination in the field of minority law encompasses discrimination not only in respect of one's minority status, but additionally on account of that person being a woman. Such discrimination many times affects female group members only, as in the case of ethnic cleansing through rape, and is thus inapplicable to men. Although the two forms of discrimination (i.e. minority and gender) are not treated as a single act in the relevant international legal documents, the recent practice of United Nations human rights rapporteurs is to identify a unified violation that is gender-specific. This has not yet trickled down to the domestic level, but I argue that a purposive and evolutionary interpretation of the law should move towards recognition of a single violation.
Time Series of Daily Averaged Cloud Fractions over Landfast First-Year Sea Ice from Multiple Data Sources
Authors: Jin Xin , Hanesiak John M. , Barber David G.
Published: July 2010

The time series of daily averaged cloud fractions (CFs) collected from different platforms—two Moderate Resolution Imaging Spectroradiometer (MODIS) instruments on Terra and Aqua satellites, the National Centers for Environmental Prediction (NCEP) model, a Vaisala 25K laser ceilometer, and ground-based manual observations (manobs)—above the winter camp of the Canadian Arctic Shelf Exchange Study (CASES) field experiment are analyzed in this study. Taking the manobs as standard, the authors conclude that 1) the NCEP products considerably underestimated CFs in spring (e.g., from April to May) and 2) the performance of two MODIS products depends on the variation of solar zenith angle (SZA). Aqua MODIS misrepresents the snow-covered surface as clouds with almost randomly distributed CFs during the dark winter [cos(SZA) < 0], leading to the overestimation of CFs in winter while Terra MODIS has good agreement with manobs. When 0.1 < cos(SZA) < 0.4, both MODIS products regularly misrepresent the snow-covered background as clouds, leading to the significant overestimation of CFs in late winter (February) and early spring (March). When cos(SZA) > 0.4, both MODIS products have good performance in detecting cloud masks over snow backgrounds. If the sky is slightly cloudy, surface-based meteorological observers tend to underestimate cloud amounts when there is a lack of light. Comparing the CFs from Terra and manobs, the authors conclude that this bias can be over 10%. Power spectral analysis and wavelet analysis show three results: 1) High clouds more frequently appear in winter than in spring with periods between 8 and 16 days, indicating their close connection with synoptic events. Current NCEP products can predict this periodicity but have a phase lag. 2) Middle and low clouds are more local and are common in mid- and late spring (April and May) with periods between 2 and 4 days. At the CASES winter and spring field site, the periodicity of high clouds is dominant. 3) The time-scale-dependent correlation coefficients (CCs) between both MODIS products, NCEP and manobs, show that with high frequent CF sampling per day, the CCs are stable when the time scale varies between 1 and 4 days: with Terra MODIS and NCEP, the value is about 0.6; with Aqua MODIS, between 0.4 and 0.5. All CCs get smaller when the time scale increases beyond 8 days: with respect to both MODIS products, the CCs get closer with values between 0.3 and 0.4; with respect to NCEP, the CC dramatically decreases from positive values to negative values, indicating the lack of accuracy in current NCEP cloud schemes.
A Quality Assurance System for Canadian Hourly Pressure Data
Authors: Wan Hui , Wang Xiaolan L. , Swail Val R.
Published: July 2010

In this study a comprehensive quality assurance (QA) system, which includes the hydrostatic check combined with a statistical homogeneity test, is designed and applied to hourly pressure records (for 1953–2002) from 761 Canadian stations, to produce a high-quality database of hourly station and sea level pressures for various climate studies. The main principles of the QA system are described in detail, followed by a brief emphasis on the error correction algorithms. The general performance of the QA system and the main problems in the Canadian historical hourly pressure database are discussed and illustrated through various examples. The results show that there are serious systematic errors (i.e., sudden changes in the mean, or mean shifts) in the Canadian hourly pressure database, which are caused either by the use of incorrect station elevation values in the reduction of barometer readings to station or sea level pressure values (e.g., the “50-ft rule” or station relocation without updates to the station elevation), by transposing/swapping station and sea level pressure values, or by mistakes made in the archive data ingestion or data recording/digitization processes (e.g., use of a wrong base number). Random errors also exist and are mainly due to the transposition of two digits or miscoding of one or two digits. These errors must be corrected before the data are used in various climate studies, especially climate change–related studies.
Influence of GPS Precipitable Water Vapor Retrievals on Quantitative Precipitation Forecasting in Southern California
Authors: Marcus Steven , Kim Jinwon , Chin Toshio , Danielson David , Laber Jayme
Published: July 2010

The effects of precipitable water vapor (PWV) retrievals from the Southern California Integrated GPS Network (SCIGN) on quantitative precipitation forecast (QPF) skill are examined over two flood-prone regions of Southern California: Santa Barbara (SB) and Ventura County (VC). Two sets of QPFs are made, one using the initial water vapor field from the NCEP 40-km Eta initial analysis, and another in which the initial Eta water vapor field is modified by incorporating the PWV data from the SCIGN receivers. Lateral boundary data for the QPFs, as well as the hydrostatic component of the GPS zenith delay data, are estimated from the Eta analysis. Case studies of a winter storm on 2 February during the 1997/98 El Niño, and storms leading up to the La Conchita, California, landslide on 10 January 2005, show notably improved QPFs for the first 3–6 h with the addition of GPS PWV data. For a total of 47 winter storm forecasts between February 1998 and January 2005 the average absolute QPF improvement is small; however, QPF improvements exceed 5 mm in several underpredicted rainfall events, with GPS data also improving most cases with overpredicted rainfall. The GPS improvements are most significant (above or near the 2σ level) when the low-level winds off the coast of Southern California are from the southern (SW to SE) quadrant. To extend the useful forecast skill enhancement beyond six hours, however, additional sources of water vapor data over broader areas of the adjacent Pacific Ocean are needed.
The Use of Synthetic Hurricane Tracks in Risk Analysis and Climate Change Damage Assessment
Authors: Hallegatte Stéphane
Published: July 2010

Because of the lack of data on past hurricanes, empirical evaluations of the statistics needed for risk management are very uncertain. An alternative strategy is to use a hurricane model to produce large sets of synthetic hurricane tracks. This method provides, for 11 regions of the U.S. Atlantic and Gulf Coasts, the annual landfall probabilities of hurricanes from each category of the Saffir–Simpson scale. This model can be used to investigate the future of hurricane risks. As a first step, the model is run with a 10% increase in potential intensity. Annual landfall probabilities increase in all regions, especially for the strongest hurricanes. The vulnerability of each U.S. coastal county is then calibrated using data on past hurricanes and their normalized economic losses. Annual hurricane damages increase by +54% in response to a 10% increase in potential intensity, meaning that the average normalized losses caused by hurricanes would increase from approximately $8 billion to about $12 billion per year. These results suggest that hurricane losses are very sensitive to changes in potential intensity and may rise significantly in response to climate change. This paper calls, therefore, for taking into account hurricane damages in the analysis of climate policies, even though other factors like population evolution, economic growth, and preparedness may remain the main drivers of hurricane damages.
Spatial Interpolation of Daily Maximum and Minimum Air Temperature Based on Meteorological Model Analyses and Independent Observations
Authors: DeGaetano Arthur T. , Belcher Brian N.
Published: July 2010

Hourly meteorological forecast model initializations are used to guide the spatial interpolation of daily cooperative network station data in the northeastern United States. The hourly model data are transformed to daily maximum and minimum temperature values and interpolated to the station points after standardization to station elevation based on the model temperature lapse rate. The resulting bias (interpolation − observation) is computed and then interpolated back to the model grids, allowing daily adjustment of the temperature fields based on independent observations. These adjusted data can then be interpolated to the resolution of interest. For testing, the data are interpolated to stations that were withheld during the construction of the bias field. The use of the model initializations as a basis for interpolation improves upon the conventional interpolation of elevation-adjusted station data alone. When inverse-distance-weighted interpolation is used in conjunction with data from a 40-km-model grid, mean annual absolute errors averaged 5% smaller than those from interpolation of station data alone for maximum and minimum temperature, which is a significant decrease. Using data from a 20-km-model grid reduces mean absolute error during June by 10% for maximum temperature and 16% for minimum temperature. Adjustment for elevation based on the model temperature lapse rate improved the interpolation of maximum temperature, but had little effect on minimum temperature. Winter minimum temperature errors were related to snow depth, a feature that likely contributed to the relatively high autocorrelation exhibited by the daily errors.
Surface Energy Components and Land Characteristics of a Rice Paddy
Authors: Tsai Jeng-Lin , Tsuang Ben-Jei , Lu Po-Sheng , Yao Ming-Hwi , Shen Yuan
Published: July 2010

Many meteorological and air-quality models require land characteristics as inputs. A field experiment was conducted to study the surface energy budget of a rice paddy in Taiwan. During the day, the energy balance ratio measured by an eddy covariance (EC) system was found to be 95% after considering the photosynthetic and local advected heat fluxes. The observations by the EC system suggest that the Bowen ratio was about 0.18 during the daytime. The EC system also measured the daytime absorbed carbon dioxide flux. The equivalent photosynthetic energy flux was about 1% of the net solar radiation. A reference table describing the land characteristics of rice paddies for use in meteorological and air-quality models is listed that shows that the albedo and the Bowen ratio measured over rice paddies were lower than those listed in many state-of-the-art models. This study proposes simulating latent heat flux by assigning proper values for canopy resistance rather than by assigning constant values for Bowen ratio or surface moisture availability. The diurnal pattern of the canopy resistance of the rice paddy was found to be “U” shaped. Daytime canopy resistance was observed to be 87 s m−1, and a high canopy resistance (∼900 s m−1) should be assigned during nighttime periods.
Evaluation of Dispersion Forecasts Driven by Atmospheric Model Output at Coarse and Fine Resolution
Authors: Nachamkin Jason E. , Cook John , Frost Mike , Martinez Daniel , Sprung Gary
Published: July 2010

Lagrangian parcel models are often used to predict the fate of airborne hazardous material releases. The atmospheric input for these integrations is typically supplied by surrounding surface and upper-air observations. However, situations may arise in which observations are unavailable and numerical model forecasts may be the only source of atmospheric data. In this study, the quality of the atmospheric forecasts for use in dispersion applications is investigated as a function of the horizontal grid spacing of the atmospheric model. The Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) was used to generate atmospheric forecasts for 14 separate Dipole Pride 26 trials. The simulations consisted of four telescoping one-way nested grids with horizontal spacings of 27, 9, 3, and 1 km, respectively. The 27- and 1-km forecasts were then used as input for dispersion forecasts using the Hazard Prediction Assessment Capability (HPAC) modeling system. The resulting atmospheric and dispersion forecasts were then compared with meteorological and gas-dosage observations collected during Dipole Pride 26. Although the 1-km COAMPS forecasts displayed considerably more detail than those on the 27-km grid, the RMS and bias statistics associated with the atmospheric observations were similar. However, statistics from the HPAC forecasts showed the 1-km atmospheric forcing produced more accurate trajectories than the 27-km output when compared with the dosage measurements.
Estimation and Extrapolation of Climate Normals and Climatic Trends
Authors: Livezey Robert E. , Vinnikov Konstantin Y. , Timofeyeva Marina M. , Tinker Richard , van den Dool Huug M.
Published: July 2010

WMO-recommended 30-yr normals are no longer generally useful for the design, planning, and decision-making purposes for which they were intended. They not only have little relevance to the future climate, but are often unrepresentative of the current climate. The reason for this is rapid global climate change over the last 30 yr that is likely to continue into the future. It is demonstrated that simple empirical alternatives already are available that not only produce reasonably accurate normals for the current climate but also often justify their extrapolation to several years into the future. This result is tied to the condition that recent trends in the climate are approximately linear or have a substantial linear component. This condition is generally satisfied for the U.S. climate-division data. One alternative [the optimal climate normal (OCN)] is multiyear averages that are not fixed at 30 yr like WMO normals are but rather are adapted climate record by climate record based on easily estimated characteristics of the records. The OCN works well except with very strong trends or longer extrapolations with more moderate trends. In these cases least squares linear trend fits to the period since the mid-1970s are viable alternatives. An even better alternative is the use of “hinge fit” normals, based on modeling the time dependence of large-scale climate change. Here, longer records can be exploited to stabilize estimates of modern trends. Related issues are the need to avoid arbitrary trend fitting and to account for trends in studies of ENSO impacts. Given these results, the authors recommend that (a) the WMO and national climate services address new policies for changing climate normals using the results here as a starting point and (b) NOAA initiate a program for improved estimates and forecasts of official U.S. normals, including operational implementation of a simple hybrid system that combines the advantages of both the OCN and the hinge fit.
High-Resolution Numerical Modeling of Thermally Driven Slope Winds in a Valley with Strong Capping
Authors: Catalano Franco , Cenedese Antonio
Published: July 2010

The complete day–night cycle of the circulation over a slope under simplified idealized boundary conditions is investigated by means of large-eddy simulations (LES). The thermal forcing is given with a time-varying law for the surface temperature. A surface layer parameterization based on the Monin–Obukhov similarity theory is used as a wall layer model. The domain geometry is symmetric, having an infinitely long straight valley in the y direction. Since the depth of the katabatic flow in midlatitude climates is limited to 5–30 m, the authors introduced a vertically stretched grid to obtain a finer mesh near the ground. The length scale for the calculation of eddy viscosities is modified to take into account the grid anisotropy. A preintegration of 24 h is made to obtain a capping inversion over the valley. Results show that the model is able to reproduce microscale circulation dynamics driven by thermal forcing over sloping terrain. The diurnal growth of the convective boundary layer leading to the development of the anabatic wind as well as the evolution of the cold pool in the valley during the night and its interaction with the katabatic flow are shown. Waves develop at the interface between the anabatic current and the return flow. During the day, as a combined effect of the geometry and the forcing, a horizontal breeze develops directed from the middle of the valley toward the ridges. The impact of the gravity current on the quiescent atmosphere in the valley generates a weak hydraulic jump during the night.
Application of Dual-Polarization Radar Melting-Layer Detection Algorithm
Authors: Boodoo S. , Hudak D. , Donaldson N. , Leduc M.
Published: July 2010

A polarimetric melting-layer detection algorithm developed for an S-band radar has been modified for use by the King City C-band radar in southern Ontario, Canada. The technique ingests radar scan volume data to determine the melting-layer top and bottom and to diagnose temporal and spatial variations of the melting-layer heights. The thickness of the melting layer is also derived from the algorithm. Detailed case studies of two frontal systems over this region are described, comparing the radar-derived melting-layer height with aircraft measurement of the height of the 0°C isotherm. The analysis demonstrated the ability to detect rapidly changing melting-layer heights during frontal passages in the region. A range of melting-layer heights for a 3-yr period was investigated and produced detections from close to the ground up to about 5.0 km. Comparison of algorithm results to output from a numerical weather prediction model over the 3-yr period showed good agreement. The correlation coefficient of the heights of the 0°C wet-bulb temperature with the radar-derived melting-layer tops was 0.96. The time series of the algorithm output was used to detect frontal passages and showed that the algorithm should be useful for approximately 19 frontal passages per year in this region.
CloudSat Studies of Stratiform Precipitation Systems Observed in the Vicinity of the Southern Great Plains Atmospheric Radiation Measurement Site
Authors: Matrosov Sergey Y.
Published: July 2010

The spaceborne W-band (94 GHz) radar on board the CloudSat polar-orbiting satellite offers new opportunities for retrieving parameters of precipitating cloud systems. CloudSat measurements can resolve the vertical cross sections of such systems. The radar brightband features, which are commonly present when observing stratiform precipitating systems, allow the vertical separation of the ice, mixed, and liquid precipitating hydrometeor layers. In this study, the CloudSat data are used to simultaneously retrieve ice water path (IWP) values for ice layers of precipitating systems using absolute radar reflectivity measurements and mean rainfall rates Rm in the liquid hydrometeor layers using the attenuation-based reflectivity gradient method. The retrievals were performed for precipitating events observed in the vicinity of the Southern Great Plains (SGP) Atmospheric Radiation Measurement Program (ARM) Climate Research Facility. The retrieval results indicated that IWP values in stratiform precipitating systems vary from a few hundreds up to about 10 thousands of grams per meter squared, and the mean rain rates were in a general range between 0.5 and about 12 mm h−1. On average, mean rainfall increases with an increase in ice mass observed above the melting layer; the corresponding mean correlation coefficient is about 0.35, although events with higher correlation as well as those with no appreciable correlation were observed. Horizontal advection, wind shear, and vertical air motions might be some of the reasons for decorrelation between IWP and Rm retrieved for the same vertical atmospheric column. A mean statistical relation between IWP and Rm derived from CloudSat retrievals is in good agreement with the data obtained from multiwavelength ground-based cloud radar measurements at the SGP site.
NARR’s Atmospheric Water Cycle Components. Part I: 20-Year Mean and Annual Interactions
Authors: Ruane Alex C.
Published: July 2010

The North American Regional Reanalysis (NARR) atmospheric water cycle is examined from 1980 to 1999 using a budget approach, with a particular emphasis on annual component interactions and the role of hourly precipitation assimilation. NARR’s summertime atmospheric water cycle and diurnal component interactions are examined in Part II of this study. NARR’s high-resolution reanalysis and precipitation assimilation allow an improved climatology of mean water cycle components over North America, which is very attractive for applications, climate impact assessments, and as a basis for comparison with other products. A 20-yr climatology of precipitation, evaporation, moisture flux convergence, and the residual error term are produced for comparison to observations, other reanalyses and models, and future climate scenarios. Maps of the normalized covariance of annual precipitation with each of the other water cycle components identify regimes of seasonal interaction that form an additional basis for comparison. The annual cycle of assimilated precipitation is compared to high-resolution precipitation products as an example, and points of interest for continuing studies are identified. Analysis of the mean and transient balances reveals a significant effect from NARR’s precipitation assimilation scheme, which is investigated using an estimate of NARR’s underlying model precipitation (before assimilation), generated using the precipitation assimilation increment as a proxy. Biases of the precipitation assimilation scheme are then characterized spatially and temporally to inform the interpretation of NARR applications and comparisons. These model precipitation estimates reveal a more tightly closed atmospheric water cycle with predominantly excessive precipitation, resulting in too vigorous evaporation and moisture flux convergences. The sign and magnitude of evaporation and moisture flux convergence biases are found to be related to the precipitation assimilation correction and are important to consider in applications of NARR output.
Quantifying Drought Risk in a Nonstationary Climate
Authors: Verdon-Kidd Danielle C. , Kiem Anthony S.
Published: July 2010

Water management in Australia has traditionally been carried out on the assumption that the historical record of rainfall, evaporation, streamflow, and recharge is representative of current and future climatic conditions. However, in many circumstances, this does not adequately address the potential risks to supply security for towns, industry, irrigators, and the environment. This is because the Australian climate varies markedly due to natural cycles that operate over periods of several years to several decades. There is also serious concern about how anthropogenic climate change may exacerbate drought risk in the future. In this paper, the frequency and severity of droughts are analyzed during a range of “climate states” (e.g., different phases of the Pacific, Indian, and/or Southern Oceans) to demonstrate that drought risk varies markedly over interannual through to multidecadal time scales. Importantly, by accounting for climate variability and change on multitemporal scales (e.g., interdecadal, multidecadal, and the palaeo scale), it is demonstrated that the risk of failure of current drought management practices may be better assessed and more robust climate adaptation responses developed.
The Hydrology and Hydrometeorology of Flooding in the Delaware River Basin
Authors: Smith James A. , Baeck Mary Lynn , Villarini Gabriele , Krajewski Witold F.
Published: July 2010

Extreme floods in the Delaware River basin are examined through analyses of a sequence of record and near-record floods during September 2004, April 2005, and June 2006. The three flood episodes reflect three principal flood-generating mechanisms in the eastern United States: tropical cyclones (September 2004); late winter–early spring extratropical systems (April 2005); and warm-season convective systems (June 2006). Extreme flooding in the Delaware River basin is the product of heavy rainfall and runoff from high-gradient portions of the watershed. Orographic precipitation mechanisms play a central role in the extreme flood climatology of the Delaware River basin and, more generally, for the eastern United States. Extreme flooding for the 2004–06 events was produced in large measure from forested portions of the watershed. Analyses of flood frequency based on annual flood peak observations from U.S. Geological Survey (USGS) stream gauging stations with “long” records illustrate the striking heterogeneity of flood response over the region, the important role of landfalling tropical cyclones for the upper tail of flood peak distributions, and the prevalence of nonstationarities in flood peak records. Analyses show that changepoints are a more common source of nonstationarity than linear time trends. Regulation by dams and reservoirs plays an important role in determining changepoints, but the downstream effects of reservoirs on flood distributions are limited.