bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery and Characterization of a Distinctive Exo-1,3/1,4-β-Glucanase from the Marine Bacterium
Pseudoalteromonas
sp. Strain BB1
Authors: Nakatani Yoshio , Lamont Iain L. , Cutfield John F. 
Published: August 2010

ABSTRACT

Marine bacteria residing on local red, green, and brown seaweeds were screened for exo-1,3-β-glucanase (ExoP) activity. Of the 90 bacterial species isolated from 32 seaweeds, only one, a
Pseudoalteromonas
sp., was found to display such activity. It was isolated from a
Durvillaea
sp., a brown kelp known to contain significant amounts of the storage polysaccharide laminarin (1,3-β-
d
-glucan with some 1,6-β branching). Four chromatographic steps were utilized to purify the enzyme (ExoP). Chymotryptic digestion provided peptide sequences for primer design and subsequent gene cloning. The
exoP
gene coded for 840 amino acids and was located just 50 bp downstream from a putative lichenase (endo-1,3-1,4-β-glucanase) gene, suggesting possible cotranscription of these genes. Sequence comparisons revealed ExoP to be clustered within a group of bacterial glycosidases with high similarity to a group of glycoside hydrolase (GH3) plant enzymes, of which the barley exo-1,3/1,4-β-glucanase (ExoI) is the best characterized. The major difference between the bacterial and plant proteins is an extra 200- to 220-amino-acid extension at the C terminus of the former. This additional sequence does not correlate with any known functional domain, but ExoP was not active against laminarin when this region was removed. Production of recombinant ExoP allowed substrate specificity studies to be performed. The enzyme was found to possess similar levels of exoglucanase activity against both 1,4-β linkages and 1,3-β linkages, and so ExoP is designated an exo-1,3/1,4-β-exoglucanase, the first such bacterial enzyme to be characterized. This broader specificity could allow the enzyme to assist in digesting both cell wall cellulose and cytoplasmic laminarin.
Coexistence of Pathogens in Host-Seeking and Feeding Ticks within a Single Natural Habitat in Central Germany
Authors: Franke Jan , Fritzsch Julia , Tomaso Herbert , Straube Eberhard , Dorn Wolfram , Hildebrandt Anke 
Published: August 2010

ABSTRACT

The importance of established and emerging tick-borne pathogens in Central and Northern Europe is steadily increasing. In 2007, we collected
Ixodes ricinus
ticks feeding on birds (
n
= 211) and rodents (
n
= 273), as well as host-seeking stages (
n
= 196), in a habitat in central Germany. In order to find out more about their natural transmission cycles, the ticks were tested for the presence of Lyme disease borreliae,
Anaplasma phagocytophilum
, spotted fever group (SFG) rickettsiae,
Francisella tularensis
, and babesiae. Altogether, 20.1% of the 680 ticks examined carried at least one pathogen. Bird-feeding ticks were more frequently infected with
Borrelia
spp. (15.2%) and
A. phagocytophilum
(3.2%) than rodent-feeding ticks (2.6%; 1.1%) or questing ticks (5.1%; 0%).
Babesia
spp. showed higher prevalence rates in ticks parasitizing birds (13.2%) and host-seeking ticks (10.7%), whereas ticks from small mammals were less frequently infected (6.6%). SFG rickettsiae and
F. tularensis
were also found in ticks collected off birds (2.1%; 1.2%), rodents (1.8%; 1.5%), and vegetation (4.1%; 1.6%). Various combinations of coinfections occurred in 10.9% of all positive ticks, indicating interaction of transmission cycles. Our results suggest that birds not only are important reservoirs for several pathogens but also act as vehicles for infected ticks and might therefore play a key role in the dispersal of tick-borne diseases.
Sigma Factor F Does Not Prevent Rifampin Inhibition of RNA Polymerase or Cause Rifampin Tolerance in
Mycobacterium tuberculosis
Authors: Hartkoorn Ruben C. , Sala Claudia , Magnet Sophie J. , Chen Jeffrey M. , Pojer Florence , Cole Stewart T. 
Published: August 2010

ABSTRACT

The tolerance of
Mycobacterium tuberculosis
to antituberculosis drugs is a major reason for the lengthy therapy needed to treat a tuberculosis infection. Rifampin is a potent inhibitor of RNA polymerase (RNAP)
in vivo
but has been shown to be less effective against stationary-phase bacteria. Sigma factor F is associated with bacteria entering stationary phase and has been proposed to impact rifampin activity. Here we investigate whether RNAP containing SigF is more resistant to rifampin inhibition
in vitro
and whether overexpression of
sigF
renders
M. tuberculosis
more tolerant to rifampin. Real-time and radiometric
in vitro
transcription assays revealed that rifampin equally inhibits transcription by RNAP containing sigma factors SigA and SigF, therefore ruling out the hypothesis that SigF may be responsible for increased resistance of the enzyme to rifampin
in vitro
. In addition, overexpression or deletion of
sigF
did not alter rifampin susceptibility in axenic cultures of
M. tuberculosis
, indicating that SigF does not affect rifampin tolerance
in vivo
.
Semantic integrity in large-scale online simulations
Authors: Jha Somesh , Katzenbeisser Stefan , Schallhart Christian , Veith Helmut , Chenney Stephen 
Published: August 2010

As large-scale online simulations such as Second Life and World of Warcraft are gaining economic significance, there is a growing incentive for attacks against such simulation software. We focus on attacks against the semantic integrity of the simulation. This class of attacks exploits the client-server architecture and is specific to online simulations which, for performance reasons, have to delegate the detailed rendering of the simulated world to the clients. Attacks against semantic integrity often compromise the physical laws of the simulated world—enabling the user's simulation persona to fly, walk through walls, or to run faster than anybody else.
We introduce the Secure Semantic Integrity Protocol (SSIP), which enables the simulation provider to audit the client computations. Then we analyze the security and scalability of SSIP. First, we show that under standard cryptographic assumptions SSIP will detect semantic integrity attacks. Second, we analyze the network overhead, and determine the optimum tradeoff between cost of bandwidth and audit frequency for our protocol.
Role of Reactive Oxygen Species in Hyperadrenergic Hypertension
Authors: Gayen Jiaur R. , Zhang Kuixing , RamachandraRao Satish P. , Mahata Manjula , Chen Yuqing , Kim Hyung-Suk , Naviaux Robert K. , Sharma Kumar , Mahata Sushil K. , O’Connor Daniel T. 
Published: August 2010

Background—Oxidative stress, an excessive production of reactive oxygen species (ROS) outstripping antioxidant defense mechanisms, occurs in cardiovascular pathologies, including hypertension. In the present study, we used biochemical, physiological, and pharmacological approaches to explore the role of derangements of catecholamines, ROS, and the endothelium-derived relaxing factor nitric oxide (NO•) in the development of a hyperadrenergic model of hereditary hypertension: targeted ablation (knockout [KO]) of chromogranin A (Chga) in the mouse.Methods and Results—Homozygous (−/−)Chgagene knockout (KO) mice were compared with wild-type (WT, +/+) control mice. In the KO mouse, elevations of systolic and diastolic blood pressure were accompanied by not only elevated catecholamine (norepinephrine and epinephrine) concentrations but also increased ROS (H2O2) and isoprostane (an index of lipid peroxidation), as well as depletion of NO•. Renal transcript analyses implicated changes inNox1/2,Xo/Xdh, andSod1,2mRNAs in ROS elevation by the KO state. KO alterations in blood pressure, catecholamines, H2O2, isoprostane, and NO•could be abrogated or even normalized (rescued) by either sympathetic outflow inhibition (with clonidine) or NADPH oxidase inhibition (with apocynin). In cultured renal podocytes, H2O2production was substantially augmented by epinephrine (probably through β2-adrenergic receptors) and modestly diminished by norepinephrine (probably through α1-adrenergic receptors).Conclusions—ROS appear to play a necessary role in the development of hyperadrenergic hypertension in this model, in a process mechanistically linking elevated blood pressure with catecholamine excess, renal transcriptional responses, ROS elevation, lipid peroxidation, and NO•depletion. Some of the changes appear to be dependent on transcription, whereas others are immediate. The cycle could be disrupted by inhibition of either sympathetic outflow or NADPH oxidase. Because common genetic variation at the humanCHGAlocus alters BP, the results have implications for antihypertensive treatment as well as prevention of target-organ consequences of the disease. The results document novel pathophysiological links between the adrenergic system and oxidative stress and suggest new strategies to probe the role and actions of ROS within this setting.
Determining Longwave Forcing and Feedback Using Infrared Spectra and GNSS Radio Occultation
Authors: Huang Yi , Leroy Stephen S. , Anderson James G. 
Published: August 2010

Abstract
The authors investigate whether combining a data type derived from radio occultation (RO) with the infrared spectral data in an optimal detection method improves the quantification of longwave radiative forcing and feedback. Signals derived from a doubled-CO2 experiment in a theoretical study are used. When the uncertainties in both data types are conservatively estimated, jointly detecting the feedbacks of tropospheric temperature and water vapor, stratospheric temperature, and high-level cloud from the two data types should reduce the mean errors by more than 50%. This improvement is achieved because the RO measurement helps disentangle the radiance signals that are ambiguous in the infrared spectrum. The result signifies the complementary information content in infrared spectral and radio occultation data types, which can be effectively combined in optimal detection to accurately quantify the longwave radiative forcing and feedback. The results herein show that the radiative forcing of CO2 and the longwave radiative feedbacks of tropospheric temperature, tropospheric water vapor, and stratospheric temperature can be accurately quantified from the combined data types, with relative errors in their global mean values being less than 4%, 10%, 15%, and 20%, respectively.
Significance Tests in Climate Science
Authors: Ambaum Maarten H. P. 
Published: August 2010

AbstractA large fraction of papers in the climate literature includes erroneous uses of significance tests. A Bayesian analysis is presented to highlight the meaning of significance tests and why typical misuse occurs. The significance statistic is not a quantitative measure of how confident one can be of the “reality” of a given result. It is concluded that a significance test very rarely provides useful quantitative information.
Estimated Seasonal Cycle of North Atlantic Eighteen Degree Water Volume
Authors: Forget Gaël , Maze Guillaume , Buckley Martha , Marshall John 
Published: August 2010

Abstract
The seasonal cycle in the volume and formation rate of Eighteen Degree Water (EDW) in the North Atlantic is quantified over the 3-yr period from 2004 to 2006. The EDW layer is defined as all waters that have a temperature between 17° and 19°C. The study is facilitated by a synthesis of various observations—principally Argo profiles of temperature and salinity, sea surface temperature, and altimetry—using a general circulation model as an interpolation tool. The winter increase in EDW volume is most pronounced in February, peaking at about 8.6 Svy, where 1 Svy ≈ 3.15 × 1013 m3 corresponding to a 1 Sv (Sv ≡ 106 m3 s−1) flow sustained for one year. This largely reflects winter EDW formation due to air–sea heat fluxes. Over the remainder of the year, newly created EDW is consumed by air–sea heat fluxes and ocean mixing, which roughly contribute ⅔ and ⅓, respectively. The authors estimate a net annual volume increase of 1.4 Svy, averaged over the 3-yr period. It is small compared to the amplitude of the seasonal cycle (8.6 Svy) and annual formation due to air–sea fluxes (4.6 Svy). The overall EDW layer volume thus appears to fluctuate around a stable point during the study period. An estimate of the full EDW volume budget is provided along with an uncertainty estimate of 1.8 Svy, and largely resolves apparent conflicts between previous estimates.
Observational Studies of Atmospheric Aerosols over Bozeman, Montana, Using a Two-Color Lidar, a Water Vapor DIAL, a Solar Radiometer, and a Ground-Based Nephelometer over a 24-h Period
Authors: Repasky Kevin S. , Reagan John A. , Nehrir Amin R. , Hoffman David S. , Thomas Michael J. , Carlsten John L. , Shaw Joseph A. , Shaw Glenn E. 
Published: August 2010

Abstract
Coordinated observational data of atmospheric aerosols were collected over a 24-h period between 2300 mountain daylight time (MDT) on 27 August 2009 and 2300 MDT on 28 August 2009 at Bozeman, Montana (45.66°N, 111.04°W, elevation 1530 m) using a collocated two-color lidar, a diode-laser-based water vapor differential absorption lidar (DIAL), a solar radiometer, and a ground-based nephelometer. The optical properties and spatial distribution of the atmospheric aerosols were inferred from the observational data collected using the collocated instruments as part of a closure experiment under dry conditions with a relative humidity below 60%. The aerosol lidar ratio and aerosol optical depth retrieved at 532 and 1064 nm using the two-color lidar and solar radiometer agreed with one another to within their individual uncertainties while the scattering component of the aerosol extinction measured using the nephelometer matched the scattering component of the aerosol extinction retrieved using the 532-nm channel of the two-color lidar and the single-scatter albedo retrieved using the solar radiometer. Using existing aerosol models developed with Aerosol Robotic Network (AERONET) data, a thin aerosol layer observed over Bozeman was most likely identified as smoke from forest fires burning in California; Washington; British Columbia, Canada; and northwestern Montana. The intrusion of the thin aerosol layer caused a change in the atmospheric radiative forcing by a factor of 1.8 ± 0.5 due to the aerosol direct effect.
Evaluating the Snow Crystal Size Distribution and Density Assumptions within a Single-Moment Microphysics Scheme
Authors: Molthan Andrew L. , Petersen Walter A. , Nesbitt Stephen W. , Hudak David 
Published: August 2010

Abstract
The Canadian CloudSat/Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) Validation Project (C3VP) was a field campaign designed to obtain aircraft, surface, and radar observations of clouds and precipitation in support of improving the simulation of snowfall and cold season precipitation, their microphysical processes represented within forecast models, and radiative properties relevant to remotely sensed retrievals. During the campaign, a midlatitude cyclone tracked along the U.S.–Canadian border on 22 January 2007, producing an extensive area of snowfall. Observations of ice crystals from this event are used to evaluate the assumptions and physical relationships for the snow category within the Goddard six-class, single-moment microphysics scheme, as implemented within the Weather Research and Forecasting (WRF) model.
The WRF model forecast generally reproduced the precipitation and cloud structures sampled by radars and aircraft, permitting a comparison between C3VP observations and model snowfall characteristics. Key snowfall assumptions in the Goddard scheme are an exponential size distribution with fixed intercept and effective bulk density, and the relationship between crystal diameter and terminal velocity. Fixed values for the size distribution intercept and density did not represent the vertical variability of naturally occurring populations of aggregates, and the current diameter and fall speed relationship underestimated terminal velocities for all sizes of crystals.
Does Increased Horizontal Resolution Improve Hurricane Wind Forecasts?
Authors: Davis Christopher , Wang Wei , Dudhia Jimy , Torn Ryan 
Published: August 2010

Abstract
The representation of tropical cyclone track, intensity, and structure in a set of 69 parallel forecasts performed at each of two horizontal grid increments with the Advanced Research Hurricane (AHW) component of the Weather and Research and Forecasting Model (WRF) is evaluated. These forecasts covered 10 Atlantic tropical cyclones: 6 from the 2005 season and 4 from 2007. The forecasts were integrated from identical initial conditions produced by a cycling ensemble Kalman filter. The high-resolution forecasts used moving, storm-centered nests of 4- and 1.33-km grid spacing. The coarse-resolution forecasts consisted of a single 12-km domain (which was identical to the outer domain in the forecasts with nests). Forecasts were evaluated out to 120 h. Novel verification techniques were developed to evaluate forecasts of wind radii and the degree of storm asymmetry. Intensity (maximum wind) and rapid intensification, as well as wind radii, were all predicted more accurately with increased horizontal resolution. These results were deemed to be statistically significant based on the application of bootstrap confidence intervals. No statistically significant differences emerged regarding storm position errors between the two forecasts. Coarse-resolution forecasts tended to overpredict the extent of winds compared to high-resolution forecasts. The asymmetry of gale-force winds was better predicted in the coarser-resolution simulation, but asymmetry of hurricane-force winds was predicted better at high resolution. The skill of the wind radii forecasts decayed gradually over 120 h, suggesting a synoptic-scale control of the predictability of outer winds.
Regulatory impediments jeopardizing the conduct of clinical trials in Europe funded by the National Institutes of Health
Authors: Neaton James D , Babiker Abdel , Bohnhorst Mark , Darbyshire Janet , Denning Eileen , Frishman Arnie , Grarup Jesper , Larson Gregg , Lundgren Jens 
Published: August 2010

Background A number of reports have highlighted problems of conducting publicly funded trials in Europe as a consequence of the European Union (EU) Clinical Trials Directive. The impact of the EU Directive on multi-national trials, which include sites in Europe that are funded by the US National Institutes of Health (NIH) have not been described. Methods Four problems in the conduct of two international HIV treatment trials funded by NIH in the EU are described: (1) conflicting regulations on the continuing review of protocols by Institutional Review Boards/Research Ethics Committees; (2) US regulations requiring Federalwide Assurances for sites which are only partially funded by NIH; (3) EU guidance on the designation of studies as a trial of an investigational medicinal product; and (4) EU guidance on trial sponsorship and the requirements for insurance and indemnification. Following the description of the problems, recommendations for improving global collaborations are made to the US Office of Human Research Protections, to NIH, and to the EU and its Member States. Results A lack of harmonization of regulations at multiple levels caused enrollment in one study to be interrupted for several months and delayed for one year the initiation of another study aimed at obtaining definitive evidence to guide the timing of the initiation of antiretroviral therapy for individuals infected with HIV. The delays and the purchase of insurance resulted in substantial increases in trial costs and caused substantial disruption at clinical sites among staff and study participants. Limitations The problems cited and recommendations made pertain to trials funded by NIH and conducted by sites in the EU. There are many other challenges in the conduct of international research, public and private, that global harmonization would alleviate. Conclusions Disharmony, at multiple levels, in international regulations and guidelines is stifling publicly funded global research. International scientific organizations and government groups should make the documentation and solution of these problems a priority. Clinical Trials 2010; 7: 705—718. http://ctj.sagepub.com
Women’s views and experiences of a patient preference trial in surgery: a qualitative study of the CARPET1 trial
Authors: Jackson Clare J , Dixon-Woods Mary , Eborall Helen , Kenyon Sara , Toozs-Hobson Philip , Tincello Douglas G 
Published: August 2010

Background The randomized controlled trial (RCT) has a well-established role in assessing drug therapies, but its adoption in developing surgical interventions has been slow. Patients’ perspectives on surgical RCTs, especially those including a patient preference option, have received little attention. Purpose To characterize participants’ experiences and views of recruitment to a pilot trial (CARPET1) of two surgical treatments for urinary incontinence and vaginal prolapse that included a patient preference option. Methods Semi-structured qualitative interviews with 16 women who participated in the CARPET1 trial. Data analysis was based on the constant comparative method. Main outcome measures Women’s experiences of taking part in a patient preference trial. Results Women’s motives for participating in CARPET1 focused on the possibility of additional care and, as a secondary motive, the wish to help with research. Most participants expressed a treatment preference rather than accepting randomization. Most were pleased with the information they received, and acknowledged the principle of equipoise, but there was substantial variability in their understanding of aspects of the trial, including randomization. Randomization was considered by women to be appropriate only when both treatments were equally suitable and they had no strong preference. Women suggested that the main influence on their willingness to be randomized was the recruiting clinician’s opinion. Importantly, despite the recruiting clinicians being heavily involved in conception of CARPET1, they did not seem to be in equipoise at the level of the individual patient. Limitations This being a small study it was not possible to interview women who declined trial participation or to observe consultations between surgeons and patients. Conclusions CARPET1 appears to have been more a surgeon preference trial than a patient preference trial. Substantial challenges may remain in conducting RCTs in surgery, particularly where surgeons have preferences about what they perceive as the best option for an individual patient. Clinical Trials 2010; 7: 696—704. http://ctj.sagepub.com