bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Biology of Pectin Degradation byEnterobacteriaceae
Authors: Abbott D. Wade , Boraston Alisdair B. 
Published: June 2008

SUMMARYPectin is a structural polysaccharide that is integral for the stability of plant cell walls. During soft rot infection, secreted virulence factors from pectinolytic bacteria such asErwiniaspp. degrade pectin, resulting in characteristic plant cell necrosis and tissue maceration. Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments. This process initiates outside the cell, continues within the periplasmic space, and culminates in the cytoplasm. Although pectin utilization is well understood at the genetic and biochemical levels, an inclusive structural description of pectinases and pectin binding proteins by both extracellular and periplasmic enzymes has been lacking, especially following the recent characterization of several periplasmic components and protein-oligogalacturonide complexes. Here we provide a comprehensive analysis of the protein folds and mechanisms of pectate lyases, polygalacturonases, and carbohydrate esterases and the binding specificities of two periplasmic pectic binding proteins fromEnterobacteriaceae. This review provides a structural understanding of the molecular determinants of pectin utilization and the mechanisms driving catabolite selectivity and flow through the pathway.
Inhibition of Candida albicans extracellular enzyme activity by selected natural substances and their application inCandidainfection
Authors: Yordanov M. , Dimitrova P. , Patkar S. , Saso L. , Ivanovska N. 
Published: June 2008

Extracellular enzymes secreted by Candida albicans are claimed to be virulence factors responsible for penetration of the yeast into host cells. Substances able to inhibit lipolytic and proteinase activities of the fungus might be of therapeutic use in some pathologic conditions caused by C. albicans. In the present work, we have tested the influence of the flavonoid compounds apigenin and kaempferol, the indole alkaloid ibogaine, and the protoberberine alkaloid berberine on the in vitro enzyme activity of C. albicans. The substances showed complex suppressive effects concerning the processes of adherence to epithelial cells, secreted aspartyl proteinase activity, and the rate of cell wall protein glycosylation. Apigenin and kaempferol were administered in systemic C. albicans infection, demonstrating an increased number of survivors by kaempferol. The application of apigenin, kaempferol, ibogaine, and berberine in cutaneous infection suppressed the symptoms and accelerated elimination of the yeast from the site of inoculation.
In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation
Authors: Ikediobi Ogechi N. , Reimers Mark , Durinck Steffen , Blower Paul E. , Futreal Andrew P. , Stratton Michael R. , Weinstein John N. 
Published: June 2008

Abstract
The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. We previously sequenced 24 cancer genes in those cell lines. Eleven of the genes were found to be mutated in three or more of the lines. Using a pharmacogenomic approach, we analyzed the relationship between drug activity and mutations in those 11 genes (APC, RB1, KRAS, NRAS, BRAF, PIK3CA, PTEN, STK11, MADH4, TP53, and CDKN2A). That analysis identified an association between mutation in BRAF and the antiproliferative potential of phenothiazine compounds. Phenothiazines have been used as antipsychotics and as adjunct antiemetics during cancer chemotherapy and more recently have been reported to have anticancer properties. However, to date, the anticancer mechanism of action of phenothiazines has not been elucidated. To follow up on the initial pharmacologic observations in the NCI-60 screen, we did pharmacologic experiments on 11 of the NCI-60 cell lines and, prospectively, on an additional 24 lines. The studies provide evidence that BRAF mutation (codon 600) in melanoma as opposed to RAS mutation is predictive of an increase in sensitivity to phenothiazines as determined by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt assay (Wilcoxon P = 0.007). That pattern of increased sensitivity to phenothiazines based on the presence of codon 600 BRAF mutation may be unique to melanomas, as we do not observe it in a panel of colorectal cancers. The findings reported here have potential implications for the use of phenothiazines in the treatment of V600E BRAF mutant melanoma. [Mol Cancer Ther 2008;7(6):1337–46]
Ceilometer Retrieval of the Boundary Layer Vertical Aerosol Extinction Structure
Authors: Markowicz K. M. , Flatau P. J. , Kardas A. E. , Remiszewska J. , Stelmaszczyk K. , Woeste L. 
Published: June 2008

Abstract
The CT25K ceilometer is a general-purpose cloud height sensor employing lidar technology for detection of clouds. In this paper it is shown that it can also be used to retrieve aerosol optical properties in the boundary layer. The authors present a comparison of the CT25K instrument with the aerosol lidar system and discuss its good overall agreement for both the range-corrected signals and the retrieved extinction coefficient profiles. The CT25K aerosol profiling is mostly limited to the boundary layer, but it is capable of detecting events in the lower atmosphere such as mineral dust events between 1 and 3 km. Assumptions needed for the estimation of the aerosol extinction profiles are discussed. It is shown that, when a significant part of the aerosol layer is in the boundary layer, knowledge of the aerosol optical depth from a sun photometer allows inversion of the lidar signal. In other cases, surface observations of the aerosol optical properties are used. It is demonstrated that additional information from a nephelometer and aethalometer allows definition of the lidar ratio. Extinction retrievals based on spherical and randomly oriented spheroid assumptions are performed. It is shown, by comparison with the field measurements during the United Arab Emirates Unified Aerosol Experiment, that an assumption about specific particle shape is important for the extinction profile inversions. The authors indicate that this limitation of detection is a result of the relatively small sensitivity of this instrument in comparison to more sophisticated aerosol lidars. However, in many cases this does not play a significant role because globally only about 20% of the aerosol optical depth is above the boundary layer.
Intersatellite Temperature Bias: Elimination through Statistical Calibration
Authors: Salby Murry L. , McBride Patrick J. , Callaghan Patrick F. 
Published: June 2008

Abstract
Global cloud imagery (GCI) is constructed from multiple satellite platforms that simultaneously monitor the earth. The GCI overcomes sampling limitations that are inherent to measurements from an individual platform, and provides a continuous and high-resolution description of the global convective pattern. However, it must reconcile inconsistencies in the measurements from different platforms. Escaping operational stages of error detection is a spurious brightening (cooling of brightness temperature), which appears sporadically in the composited imagery and must be removed a posteriori. The spurious brightening is shown to follow from a bias between measurements from polar-orbiting platforms and those from geostationary platforms. The bias is related to the zenith angle dependence of geostationary measurements, which enables its efficient removal. GCI is then composited from satellites in which the zenith angle–dependent bias has been removed a priori. The corrected imagery is shown to be virtually free of the systematic error, leaving a more accurate representation of the global convective pattern.
GOES-R Advanced Baseline Imager Color Product Development
Authors: Hillger Donald W. 
Published: June 2008

Abstract
The current Geostationary Operational Environmental Satellite (GOES) series was inaugurated in 1994 with the launch of GOES-8 and will continue with two more satellites (GOES-O and -P) after the most recent GOES-13 launched in 2006. The next-generation GOES (beginning with GOES-R) will be launched in the 2015 time frame. This new series of satellites will include improved spatial, temporal, spectral, and radiometric resolution. The last two characteristics are manifest by an increased number of spectral bands and increased precision for measurements from those bands. To take advantage of the lead time needed to design, build, and test this new and complex satellite system, work is going into developing image products to be implemented as soon as GOES-R becomes operational.
Preparations for GOES-R image products for applications to various weather events, especially mesoscale events, are well underway. The approach used for these “risk reduction” activities is to apply data from existing operational and experimental satellites (both polar orbiting and geostationary) to create image products that will emulate those to be available from GOES-R as closely as possible. Those image products can either be new products or improvements leveraged on existing operational products. In this article, the new GOES-R Advanced Baseline Imager is briefly reviewed, and the evolutionary development of two qualitative products—one for the detection of fog and stratus, and the other for blowing dust—is presented. Emphasis is on the evolutionary development of these mesoscale products and possible quantitative discrimination among the various image features that are seen.
On Turbulence and Mixing in the Free Atmosphere Inferred from High-Resolution Soundings
Authors: Clayson Carol Anne , Kantha Lakshmi 
Published: June 2008

Abstract
Mixing in the free atmosphere above the planetary boundary layer is of great importance to the fate of trace gases and pollutants. However, direct measurements of the turbulent dissipation rate by in situ probes are very scarce and radar measurements are fraught with uncertainties. In this paper, turbulence scaling concepts, developed over the past decades for application to oceanic mixing, are used to suggest an alternative technique for retrieving turbulence properties in the free atmosphere from high-resolution soundings. This technique enables high-resolution radiosondes, which have become quite standard in the past few years, to be used not only to monitor turbulence in the free atmosphere in near–real time, but also to study its spatiotemporal characteristics from the abundant archives of high-resolution soundings from around the world. Examples from several locations are shown, as well as comparisons with radar-based estimations and a typical Richardson number–based parameterization.
The “BOUSSOLE” Buoy—A New Transparent-to-Swell Taut Mooring Dedicated to Marine Optics: Design, Tests, and Performance at Sea
Authors: Antoine David , Guevel Pierre , Desté Jean-François , Bécu Guislain , Louis Francis , Scott Alec J. , Bardey Philippe 
Published: June 2008

AbstractA new concept of oceanographic data buoy is described, which couples a taut mooring and a “transparent-to-swell” superstructure, and is specifically designed for the collection of radiometric quantities in offshore environments. The design of the thin superstructure addresses two major requirements: stabilizing the instruments in the water column and avoiding shading them. The development of the buoy is described, starting with the theoretical assessment and then describing the various stages of development leading to the latest version of the mooring and buoy. Its performance at sea is also analyzed. This new platform has been deployed in the deep waters (&gt;2400 m) of the northwestern Mediterranean Sea for about 4 yr (since September 2003) and provides a quasi-continuous record of optical properties at this site. The data are used for bio-optics research and for calibration and validation operations of several European and U.S. ocean color satellite missions. The plan is to continue the deployment to build a decadal time series of optical properties. The instrument suite that is installed on this buoy is also briefly described, and sample results are shown to demonstrate the ability of this new system to collect the data at the desired frequency and quality.
Sensitivity of Tropical Rainfall to Banda Sea Diffusivity in the Community Climate System Model
Authors: Jochum Markus , Potemra James 
Published: June 2008

Abstract
Several observational studies suggest that the vertical diffusivity in the Indonesian marginal seas is an order of magnitude larger than in the open ocean and what is used in most ocean general circulation models. The experiments described in this paper show that increasing the background diffusivity in the Banda Sea from the commonly used value of 0.1 cm2 s−1 to the observed value of 1 cm2 s−1 improves the watermass properties there by reproducing the observed thick layer of Banda Sea Water. The resulting reduced sea surface temperatures lead to weaker convection and a redistribution of precipitation, away from the Indonesian seas toward the equatorial Indian and Pacific Oceans. In particular, the boreal summer precipitation maximum of the Indonesian seas shifts northward from the Banda Sea toward Borneo, which reduces a longstanding bias in the simulation of the Austral–Asian Monsoon in the Community Climate System Model. Because of the positive feedback mechanisms inherent in tropical atmosphere dynamics, a reduction in Banda Sea heat loss of only 5% leads locally to a reduction in convection of 20%.
In Situ Calibration of Optode-Based Oxygen Sensors
Authors: Uchida Hiroshi , Kawano Takeshi , Kaneko Ikuo , Fukasawa Masao 
Published: June 2008

Abstract
Eleven optode-based oxygen sensors were used for shipboard hydrographic casts in the North Pacific. Oxygen data from the optode sensors were compared with high-quality oxygen data obtained with discrete water samples, and the performance of the sensors was evaluated. The response of the sensing foil of the optode decreases with increasing ambient pressure, and this pressure effect was found to decrease the response by 3.2% (1000 dbar)−1. A new calibration equation for the optode sensors was proposed. On the basis of oxygen data from water samples, the optode sensors were calibrated so that the reproducibility was less than 1%. High-quality oxygen profiles from the optode were obtained for fast-profiling conductivity–temperature–depth (CTD) observations, by compensating for the temperature-dependent delay in the optode data due to the slow response time of the optode.
Stray Light Correction of the Marine Optical System
Authors: Feinholz Michael E. , Flora Stephanie J. , Yarbrough Mark A. , Lykke Keith R. , Brown Steven W. , Johnson B. Carol , Clark Dennis K. 
Published: June 2008

Abstract
The Marine Optical System is a spectrograph-based sensor used on the Marine Optical Buoy for the vicarious calibration of ocean color satellite sensors. It is also deployed from ships in instruments used to develop bio-optical algorithms that relate the optical properties of the ocean to its biological content. In this work, an algorithm is applied to correct the response of the Marine Optical System for scattered, or improperly imaged, light in the system. The algorithm, based on the measured response of the system to a series of monochromatic excitation sources, reduces the effects of scattered light on the measured source by one to two orders of magnitude. Implications for the vicarious calibration of satellite ocean color sensors and the development of bio-optical algorithms are described. The algorithm is a one-dimensional point spread correction algorithm, generally applicable to nonimaging sensors, but can in principle be extended to higher dimensions for imaging systems.
Changing the priming solution from Ringer’s to Hartmann’s solution is associated with less metabolic acidosis during cardiopulmonary bypass
Authors: Alston RP , Theodosiou C , Sanger K 
Published: June 2008

Background and objective: Previously, it was noted that changing the solutions used for priming and intravascular volume replacement from Hartmann’s to Ringer’s resulted in a more profound metabolic acidosis developing during cardiopulmonary bypass (CPB). The aim of this study was to examine the effects of changing the solutions back to Hartmann’s on metabolic acidosis that develops during CPB in patients undergoing heart surgery. Methods: Two groups of patients were studied sequentially: the first received Ringer’s (n = 63) and the second Hartmann’s solution (n = 66). Arterial blood samples were taken before induction of anaesthesia and towards the end of CPB. Samples were analysed in a blood gas analyser. Results: Hydrogen ion concentration increased from 38 (4) to 41 (7) mm/L in the Ringer’s group, but decreased from 38 (5) to 36 (6) mmol L-1 in the Hartmann’s group. Changes in PaCO2 (0.77, p < 0.001) and volume of fluid administered (r = 0.23, p < 0.01) were significant univariate correlates of change in hydrogen ion concentration, but haemoglobin concentration was not (r < 0.01, p = 0.97). Analysis of variance for repeated measures found significant between subject effects on the change in hydrogen ion concentration during CPB caused by the choice of intravascular solution used (p < 0.001) and PaCO2 (p = 0.001), but not as a result of the volume of solution administered (p > 0.10). Conclusions: Changing the solutions used for priming and intravascular volume replacement from Ringer’s to Hartmann’s was associated with a reduction in metabolic acidosis that developed during CPB.
Insensible water loss from the Jostra Quadrox D oxygenator: an in vitro study
Authors: Lawson DS , Holt D 
Published: June 2008

Extracorporeal membrane oxygenation (ECMO) has been shown to improve outcomes in neonatal patients with respiratory and/or cardiac failure. Insensible water loss is defined as water loss via evaporation from the skin and respiration. Fluid and electrolyte balance are a primary concern and very challenging in the neonatal patient population. Hypernatremia can result from untreated insensible water loss, leading to possible cerebral complications. A new type of fiber used in the Jostra Quadrox D oxygenator has recently been approved for use in the United States of America. This oxygenator uses a polymethylpentene closed hollow-fiber technology and has been approved for six hours of continuous use by the Federal Drug Administration. The closed hollow-fiber technology may be advantageous for extended use due to the fact that it is a true membrane and plasma leakage will not occur across its surface. The Jostra Quadrox D is an adult-sized oxygenator with a surface area of 1.8 M2. The aim of this study is to discover what the insensible water loss will be from the Jostra Quadrox D when used at blood flows which would mimic those used for a neonatal ECMO patient. The median insensible water loss from the Quadrox D oxygenator at a gas flow rate of two liters per minute(LPM) was 4.0 ± 0.2 ml/hour, at five LPM was 9.8 ± 0.4 ml/hour and at 10 LPM was 20.6 ± 0.7 ml/hour. The daily evaporative water loss from the Jostra Quadrox D can be estimated to be 48.0 ± 2.1 ml for each LPM of sweep gas with a normal saline pump flow rate of 500 ml/min.
Neutrophil secondary necrosis is induced by LL-37 derived from cathelicidin
Authors: Zhang Zhifang , Cherryholmes Gregory , Shively John E 
Published: June 2008

AbstractNeutrophils represent the most common granulocyte subtype present in blood. The short half-life of circulating neutrophils is regulated by spontaneous apoptosis, and tissue infiltrating neutrophils die by apoptosis and secondary necrosis. The mechanism of neutrophil apoptosis has been the subject of many studies; however, the mechanism of neutrophil secondary necrosis is less clear. Human cathelicidin cationic peptide 18, proteolytically processed to its active form, LL-37, is secreted by neutrophils and epithelial cells and shown to have effects in addition to bacterial lysis. We demonstrate here that LL-37 affects neutrophil lifespan by the pathway of secondary necrosis, rapidly converting annexin V-positive (AV+), propidium iodide-negative (PI−; apoptotic) cells into PI+ (necrotic) cells with the release of IL-8, IL-1R antagonist, ATP, and intact granules. The effects of LL-37 on apoptotic neutrophils are neither energy-dependent nor affected by pretreatment with G-CSF, GM-CSF, TNF-α, and LPS and are partially inhibited by human serum. Moreover, LL-37 decreases CXCR2 expression of AV−PI− (live) neutrophils, suggesting an effect on the neutrophil response to its chemotactic factors, including IL-8. Thus, the lifespan and inflammatory functions of neutrophils are directly affected by LL-37.
A meta-analysis of the effect of lowering serum levels of GH and IGF-I on mortality in acromegaly
Authors: Holdaway I M , Bolland M J , Gamble G D 
Published: June 2008

ObjectiveFormal studies of acromegaly have found increased mortality associated with the disorder, although reduction of serum levels of GH and IGF-I by treatment appears to improve survival. A meta-analysis of mortality studies in acromegaly has thus been performed to assess the effect of lowering serum GH and IGF-I on survival.Design and methodsMedline was searched for studies under ‘acromegaly’, ‘mortality’ and ‘cause of death’ (1965–2008), and abstracts of recent meetings of the US Endocrine Society were hand searched. Studies were restricted to those presenting mortality data according to serum GH and IGF-I at last follow-up, and with mortality expressed as a standardized mortality ratio (SMR).ResultsPatients with random serum GH <2.5 μg/l following treatment, mostly measured by standard RIA, had mortality close to expected levels (SMR 1.1, 95% confidence interval (CI) 0.9–1.4) compared with an SMR of 1.9 (95% CI 1.5–2.4) for those with final GH >2.5 μg/l. Similarly, a normal serum IGF-I for age and sex at last follow-up after treatment was associated with an SMR of 1.1 (95% CI 0.9–1.4) compared with an SMR of 2.5 (95% CI 1.6–4.0) for those with continued IGF-I elevation. There was a significant trend for reduced mortality in series reporting frequent use of somatostatin analogues and in studies reporting high (>70%) rates of biochemical remission after treatment.ConclusionsClinicians treating acromegalic patients should aim for random serum GH <2.5 μg/l measured by RIA (probably <1 μg/l measured by modern sensitive immunoassay) and normal serum IGF-I values, to restore the elevated mortality of the condition to normal levels.