bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Field Study of Reflectivity and Z–R Relations Using Vertically Pointing Radars and Disdrometers
Authors: Tokay Ali , Hartmann Peter , Battaglia Alessandro , Gage Kenneth S. , Clark Wallace L. , Williams Christopher R. 
Published: January 2009

Abstract
Observations from a 16-month field study using two vertically pointing radars and a disdrometer at Wallops Island are analyzed to examine the consistency of the multi-instrument observations with respect to reflectivity and Z–R relations. The vertically pointing radars were operated at S and K bands and had a very good agreement in reflectivity at a gate centered on 175 and 177 m above ground level over a variety of storms. This agreement occurred even though the sampling volumes were of different size and even though the S band measured the reflectivity factor directly, whereas the K-band radar deduced it from attenuated K-band measurements. Indeed, the radar agreement in reflectivity at the collocated range gates was superior to that between the disdrometer and either radar. This is attributed in large part to the spatial separation of the disdrometer and radar sample volumes, although the lesser agreement observed in a prior collocated disdrometer–disdrometer comparison suggests the larger size of the radar sample volumes as well as the better overlap also play a role. Vertical variations in the observations were examined with the aid of the two radar profilers. As expected, the agreement between the disdrometer reflectivity and the reflectivity seen in the vertically pointing radars decreased with height. The effect of these vertical variations on determinations of Z–R relation coefficients was then examined, using a number of different methods for finding the best-fitting coefficients. The coefficient of the Z–R relation derived from paired disdrometer rain rate and radar reflectivity decreased with height, while the exponent of the Z–R relation increased with height. The coefficient and exponent of the Z–R relations also showed sensitivity to the choice of derivation method [linear and nonlinear least squares, fixed exponent, minimizing the root-mean-square difference (RMSD), and probability matching]. The influence of the time lag between the radar and disdrometer measurements was explored by examining the RMSD in reflectivity for paired measurements between 0- and 4-min lag. The no-lag conditions had the lowest RMSD up to 400 m, while 1-min lag gave the lowest RMSD at higher heights. The coefficient and exponent of the Z–R relations, on the other hand, did not have a significant change between no-lag- and 1-min-lag-based pairs.
Construction of the Remote Sensing Systems V3.2 Atmospheric Temperature Records from the MSU and AMSU Microwave Sounders
Authors: Mears Carl A. , Wentz Frank J. 
Published: January 2009

Abstract
Measurements made by microwave sounding instruments provide a multidecadal record of atmospheric temperature change. Measurements began in late 1978 with the launch of the first Microwave Sounding Unit (MSU) and continue to the present. In 1998, the first of the follow-on series of instruments—the Advanced Microwave Sounding Units (AMSUs)—was launched. To continue the atmospheric temperature record past 2004, when measurements from the last MSU instrument degraded in quality, AMSU and MSU measurements must be intercalibrated and combined to extend the atmospheric temperature data records. Calibration methods are described for three MSU–AMSU channels that measure the temperature of thick layers of the atmosphere centered in the middle troposphere, near the tropopause, and in the lower stratosphere. Some features of the resulting datasets are briefly summarized.
Computationally Efficient Methods of Collocating Satellite, Aircraft, and Ground Observations
Authors: Nagle Frederick W. , Holz Robert E. 
Published: January 2009

Abstract
The usefulness of measurements from satellite-borne instruments is enhanced if these measurements can be compared to measurements from other instruments mounted aboard the same or different satellite, with measurements from aircraft, or with ground measurements. The process of associating measurements from disparate instruments and platforms is referred to as collocation. In a few cases, two instruments mounted aboard the same spacecraft have been engineered to function in tandem, but commonly this is not the case. The collocation process may then become an awkward geometric problem of finding which of many observations within one dataset corresponds to an observation in another set, possibly from another platform. This paper presents methods that can be applied to a wide range of satellite, aircraft, and surface measurements that allow for efficient collocation with measurements having varying spatial and temporal sampling. Examples of applying the methods are presented that highlight the benefits of efficient collocation. This includes identifying the occurrence of simultaneous nadir observations (SNOs); collocation of sounder, imager, and active remotely sensed measurements on the NASA Earth Observation System (EOS); and collocation of the polar orbiting imager, sounder, and microwave measurements with geostationary observations. It is possible, using an inexpensive laptop computer, to collocate Moderate Resolution Imaging Spectroradiometer (MODIS) imager observations from the Aqua satellite with geostationary observations rapidly enough to deal with these measurements in real time, making either dataset, enhanced by the other, a potentially operational product. A “tool kit” is suggested consisting of computer procedures useful in collocation.
Development and Forcing of the Rear Inflow Jet in a Rapidly Developing and Decaying Squall Line during BAMEX
Authors: Grim Joseph A. , Rauber Robert M. , McFarquhar Greg M. , Jewett Brian F. , Jorgensen David P. 
Published: January 2009

Abstract
This study examines the development, structure, and forcing of the rear inflow jet (RIJ) through the life cycle of a small, short-lived squall line over north-central Kansas on 29 June 2003. The analyses were developed from airborne quad-Doppler tail radar data from the NOAA and NRL P-3 aircraft, obtained over a 2-h period encompassing the formation, development, and decay of the squall line during the Bow Echo and Mesoscale Convective Vortex Experiment (BAMEX). The strengthening of the system-relative rear inflow to 17 m s−1 was concurrent with the formation of a bow echo, an increased dynamic pressure gradient beneath the rearward-tilted updraft, and two counterrotating vortices at either end of the bow. The later weakening of the RIJ to 8 m s−1 was concurrent with the weakening of the bow, a decreased dynamic pressure gradient at midlevels behind the bow, and the weakening and spreading of the vortices. In a modeling study, Weisman quantified the forcing mechanisms responsible for the development of an RIJ. This present study is the first to quantitatively analyze these mechanisms using observational data. The forcing for the horizontal rear inflow was analyzed at different stages of system evolution by evaluating the contributions of four forcing mechanisms: 1) the horizontal pressure gradient resulting from the vertical buoyancy distribution (δPB), 2) the dynamic pressure gradient induced by the circulation between the vortices (δPV), 3) the dynamic irrotational pressure gradient (δPI), and 4) the background synoptic-scale dynamic pressure gradient (δPS). During the formative stage of the bow, δPI was the strongest forcing mechanism, contributing 50% to the rear inflow. However, during the mature and weakening stages, δPI switched signs and opposed the rear inflow while the combination of δPB and δPV accounted for at least 70% of the rear inflow. The δPS forced 4%–25% of the rear inflow throughout the system evolution.
Analysis of chloroethane toxicity and carcinogenicity including a comparison with bromoethane
Authors: Holder JW 
Published: January 2009

Chloroethane (CE) gas carcinogenicity is analyzed and determined from a National Toxicology Program (NTP) bioassay where an inhalation concentration of 15,000 ppm CE gas in air produced the highest incidence of an uncommon-to-rare tumor ever observed by the NTP. Persistently inhaled CE produces endometrial cancers in female mice. The first-tumor-corrected uterine endometrial incidence (I) in B6C3F1 mice is 90%, but no significant tumors occurred in F344 rats. The endometrial cancers dispersed by 1) migrating locally to the adjacent myometrium, 2) then migrating to the bloodstream by intravasation, 3) entering 17 distal organs by extravasation and adapting to the new tissue environment. Distal cancers retained sufficient endometrial cell features to be recognized at each metastatic site. CE produced one of the highest metastasis rates ever observed by NTP of 79%. Comparing CE with bromoethane (BE), a structural analogue, it was found that BE too produced rare murine endometrial cancers yielding the second highest NTP incidence rate of I = 58% with a similar high malignancy rate of 56%. Because of the historical rarity of endometrial tumors in the B6C3F1 mouse, both of these SAR haloethanes seem to be evoking a strong, related carcinogenic potential in B6C3F1 mice, but not in F344 rats. The question of whether humans are similar to mice or to rats is addressed here and in Gargas, et al., 2008. The powerful carcinogenesis caused by these halohydrocarbons may have been caused by excessive and metabolically unresolved acetaldehyde (AC) which is directly generated by Cyp2E1 in the oxidative elimination of CE. With >95% AC metabolic production, as predicted from pharmacokinetic (PK) studies depending on CE exposure, AC is the main elimination intermediate. AC is a known animal carcinogen and a strongly suspected human carcinogen. Also, CE causes incipient decreases of tissue essential glutathione pools [GSH] by Phase II conjugation metabolic elimination of CE (and BE), by glutantione transferase (GST), in most organs (except brain) exposed to high circulating CE and it metabolites. In three laboratories, an excessive stress reaction of hyperkinesis was observed only during 15,000 ppm gas exposure but not when the exposure ceased or when exposure was presented at 150 ppm. Test rodents other than the female mice did not exhibit a pattern of visible stress nor did they have a carcinogenic response to CE gas. Unremitting stress has been documented to contribute a feedback to the hypothalamus which stimulates the hypothalamic-pituitary-axis (HPA), which in turn, induces the adrenal glands. Because estrus and estrogen and progesterone levels were unaltered by CE gas, the adrenal over stimulation, causing high steroid output, may be the penultimate step in this extraordinary carcinogenic response. High adrenal production of corticosteroids could adversely promote endometrial cells to cancers in mice − a mechanism that has already been observed in humans.
Deleterious effects induced by oxidative stress in liver nuclei from rats receiving an alcohol-containing liquid diet
Authors: Díaz Gómez MI , Fanelli SL , Delgado de Layño AMA , Bietto FM , Castro JA , Castro GD 
Published: January 2009

Highly purified rat-liver nuclei were previously shown to have nuclear ethanol (EtOH) metabolizing system able to bioactivate alcohol to acetaldehyde and 1-hydroxyethyl radicals. These reactive metabolites were able to covalently bind to nuclear proteins and lipids potentially being able to provoke oxidative stress of nuclear components. In this study, the above-mentioned possibility was explored. Sprague Dawley male rats (125–150 g) were fed a standard Lieber and De Carli liquid diet for 28 days. Controls were pair-fed with a diet, in which EtOH was isocalorically replaced with carbohydrate. The presence of a chlorzoxazone hydroxylase activity inducible by the repetitive EtOH drinking further suggested the presence of CYP2E1 in the highly purified nuclei. Nuclei from EtOH-drinking rats evidenced significantly increased susceptibility to a t-butyl hydroperoxide challenge as detected by chemiluminescence emission, increased formation of protein carbonyls, and decreased content of protein sulfhydryls. In contrast, no significant changes in the nuclear lipid hydroperoxides formation or even decreases in the 8-oxo-7,8-dihydro-2-deoxyguanosine were observed. No significant differences were observed in different parameters of the alkaline Comet assay. In immunohistochemical studies performed, no expression of p53 was observed in the livers of the animals under the experimental conditions tested. Since nuclear proteins and lipids are known to play a role in cell growth, differentiation, repair and signaling, their alterations by either oxidative stress, or by covalent binding might be of relevance to liver tumor promotion.
Endogenous lipid pneumonia in rats after subacute exposure to CdCl2
Authors: Molina AM , Raya AI , Carrasco L , Blanco A , Monterde JG , Rueda A , Moyano R 
Published: January 2009

The objective of this report was to study lung cellular lesions in Wistar rats after subacute oral exposition to CdCl2. The experimental groups were exposed to CdCl2, through their drinking water in a concentration of 1 g/L, continuously for a period of 9 days. Histologically, all the exposed animals showed the incidence of interstitial pneumonia; hyperplasia of type II pneumocytes and Clara cells; the presence of foamy macrophages; and lesions linked to the existence of endogenous lipid pneumonia. Endogenous lipid pneumonia after CdCl2 exposure has not been previously described; and in its pathogenesis, hyperplasia of type II pneumocytes and Clara cells activation could play an important role.
Influence of alpha lipoic acid on antioxidant status in D-galactosamine-induced hepatic injury
Authors: Shanmugarajan TS , Sivaraman D , Somasundaram I , Arunsundar M , Krishnakumar E , Balaji R , Ravichandiran V 
Published: January 2009

D-Galactosamine (GalN)-induced liver injury is associated with reactive oxygen species and oxidative stress. In the present study, we evaluated the effect of alpha lipoic acid (ALA) supplementation on acute GalN-induced oxidative liver injury. Hepatotoxicity induced by single intraperitoneal injection of GalN (500 mg/kg body wt) was evident from increase in lipid peroxidation and serum marker enzymes (asparate transaminase, alanine transaminase, alkaline phosphatase, and lactate dehydrogenase). The decreased activities of enzymic antioxidants (superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase) as well as glutathione levels were the salient features observed in GalN-induced hepatotoxicity. Pretreatment with ALA (50 mg/kg body weight for 7 days) significantly precluded these changes and prevents the hepatic injury. Hence, this study clearly exemplified that ALA might be a suitable candidate against GalN-induced cellular abnormalities.
Selective testing for thrombophilia in patients with first venous thrombosis: results from a retrospective family cohort study on absolute thrombotic risk for currently known thrombophilic defects in 2479 relatives
Authors: Lijfering Willem M. , Brouwer Jan-Leendert P. , Veeger Nic J. G. M. , Bank Ivan , Coppens Michiel , Middeldorp Saskia , Hamulyák Karly , Prins Martin H. , Büller Harry R. , van der Meer Jan 
Published: January 2009

Abstract
Thrombophilia screening is controversial. In a retrospective family cohort, where probands had thrombosis and a thrombophilic defect, 2479 relatives were tested for thrombophilia. In antithrombin-, protein C–, and protein S–deficient relatives, annual incidences of venous thrombosis were 1.77% (95% CI, 1.14-2.60), 1.52% (95% CI, 1.06-2.11), and 1.90% (95% CI, 1.32-2.64), respectively, at a median age of 29 years and a positive family history of more than 20% symptomatic relatives. In relatives with factor V (FV) Leiden, prothrombin 20210G>A, or high FVIII levels, these were 0.49% (95% CI, 0.39-0.60), 0.34% (95% CI, 0.22-0.49), and 0.49% (95% CI, 0.41-0.51), respectively. High FIX, FXI, and TAFI, and hyperhomocysteinemia were not independent risk factors. Annual incidence of major bleeding in antithrombin-, protein C–, or protein S–deficient relatives on anticoagulants was 0.29% (95% CI, 0.03-1.04). Cumulative recurrence rates in relatives with antithrombin, protein C, or protein S deficiency were 19% at 2 years, 40% at 5 years, and 55% at 10 years. In relatives with FV Leiden, prothrombin 20210G>A, or high levels FVIII, these were 7%, 11%, and 25%, respectively. Considering its clinical implications, thrombophilia testing should address hereditary deficiencies of antithrombin, protein C, and protein S in patients with first venous thrombosis at young age and/or a strong family history of venous thrombosis.
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data
Authors: Martin-Requena Victoria , Muñoz-Merida Antonio , Claros M Gonzalo , Trelles Oswaldo 
Published: January 2009

AbstractBackgroundNowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way.ResultsPreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures – double scan and Supervised Lowess-, a complete set of graphical representations – MA plot, RG plot, QQ plot, PP plot, PN plot – and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled.ConclusionPreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.
Conservation in the face of diversity: multistrain analysis of an intracellular bacterium
Authors: Dark Michael J , Herndon David R , Kappmeyer Lowell S , Gonzales Mikel P , Nordeen Elizabeth , Palmer Guy H , Knowles Donald P , Brayton Kelly A 
Published: January 2009

AbstractBackgroundWith the recent completion of numerous sequenced bacterial genomes, notable advances have been made in understanding the level of conservation between various species. However, relatively little is known about the genomic diversity among strains. We determined the complete genome sequence of the Florida strain ofAnaplasma marginale, and near complete (>96%) sequences for an additional three strains, for comparative analysis with the previously fully sequenced St. Maries strain genome.ResultsThese comparisons revealed thatA. marginalehas a closed-core genome with few highly plastic regions, which include themsp2andmsp3genes, as well as theaaaplocus. Comparison of the Florida and St. Maries genome sequences found that SNPs comprise 0.8% of the longer Florida genome, with 33.5% of the total SNPs between all five strains present in at least two strains and 3.0% of SNPs present in all strains except Florida. Comparison of genomes from three strains ofMycobacterium tuberculosis, Bacillus anthracis, andNessieria meningiditis, as well as fourChlamydophila pneumoniaestrains found that 98.8%–100% of SNPs are unique to each strain, suggestingA. marginale, with 76.0%, has an intermediate level of strain-specific SNPs. Comparison of genomes from other organisms revealed variation in diversity that did not segregate with the environmental niche the bacterium occupies, ranging from 0.00% to 8.00% of the larger pairwise-compared genome.ConclusionAnalysis of multipleA. marginalestrains suggests intracellular bacteria have more variable SNP retention rates than previously reported, and may have closed-core genomes in response to the host organism environment and/or reductive evolution.
Genic regions of a large salamander genome contain long introns and novel genes
Authors: Smith Jeramiah J , Putta Srikrishna , Zhu Wei , Pao Gerald M , Verma Inder M , Hunter Tony , Bryant Susan V , Gardiner David M , Harkins Timothy T , Voss S Randal 
Published: January 2009

Abstract

Background
The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp) were isolated and sequenced to characterize the structure of genic regions.

Results
Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86%) of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases!

Conclusion
This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.