bluuebunny/crossref_metadata_2025_split huggingface dataset:
MÖBIUS TRANSFORMATIONS OF POLYGONS AND PARTITIONS OF 3-SPACE
Authors: RANDELL RICHARD , SIMON JONATHAN , TOKLE JOSHUA 
Published: November 2008

The image of a polygonal knot K under a spherical inversion of ℝ3 ∪ ∞ is a simple closed curve made of arcs of circles, perhaps some line segments, having the same knot type as the mirror image of K. But suppose we reconnect the vertices of the inverted polygon with straight lines, making a new polygon [Formula: see text]. This may be a different knot type. For example, a certain 7-segment figure-eight knot can be transformed to a figure-eight knot, a trefoil, or an unknot, by selecting different inverting spheres. Which knot types can be obtained from a given original polygon K under this process? We show that for large n, most n-segment knot types cannot be reached from one initial n-segment polygon, using a single inversion or even the whole Möbius group. The number of knot types is bounded by the number of complementary domains of a certain system of round 2-spheres in ℝ3. We show the number of domains is at most polynomial in the number of spheres, and the number of spheres is itself a polynomial function of the number of edges of the original polygon. In the analysis, we obtain an exact formula for the number of complementary domains of any collection of round 2-spheres in ℝ3. On the other hand, the number of knot types that can be represented by n-segment polygons is exponential in n. Our construction can be interpreted as a particular instance of building polygonal knots in non-Euclidean metrics. In particular, start with a list of n vertices in ℝ3 and connect them with arcs of circles instead of line segments: Which knots can be obtained? Our polygonal inversion construction is equivalent to picking one fixed point p ∈ ℝ3 and replacing each edge of K by an arc of the circle determined by p and the endpoints of the edge.
Climate Change over the Equatorial Indo-Pacific in Global Warming*
Authors: Ihara Chie , Kushnir Yochanan , Cane Mark A. , de la Peña Victor H. 
Published: November 2008

AbstractThe response of the equatorial Indian Ocean climate to global warming is investigated using model outputs submitted to the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report. In all of the analyzed climate models, the SSTs in the western equatorial Indian Ocean warm more than the SSTs in the eastern equatorial Indian Ocean under global warming; the mean SST gradient across the equatorial Indian Ocean is anomalously positive to the west in a warmer twenty-first-century climate compared to the twentieth-century climate, and it is dynamically consistent with the anomalous westward zonal wind stress and anomalous positive zonal sea level pressure (SLP) gradient to the east at the equator. This change in the zonal SST gradient in the equatorial Indian Ocean is detected even in the lowest-emission scenario, and the size of the change is not necessarily larger in the higher-emission scenario.With respect to the change over the equatorial Pacific in climate projections, the subsurface central Pacific displays the strongest cooling or weakest warming around the thermocline depth compared to that above and below in all of the climate models, whereas changes in the zonal SST gradient and zonal wind stress around the equator are model dependent and not straightforward.
The Skill of Probabilistic Precipitation Forecasts under Observational Uncertainties within the Generalized Likelihood Uncertainty Estimation Framework for Hydrological Applications
Authors: Pappenberger F. , Ghelli A. , Buizza R. , Bódis K. 
Published: November 2008

Abstract
A methodology for evaluating ensemble forecasts, taking into account observational uncertainties for catchment-based precipitation averages, is introduced. Probability distributions for mean catchment precipitation are derived with the Generalized Likelihood Uncertainty Estimation (GLUE) method. The observation uncertainty includes errors in the measurements, uncertainty as a result of the inhomogeneities in the rain gauge network, and representativeness errors introduced by the interpolation methods. The closeness of the forecast probability distribution to the observed fields is measured using the Brier skill score, rank histograms, relative entropy, and the ratio between the ensemble spread and the error of the ensemble-median forecast (spread–error ratio). Four different methods have been used to interpolate observations on the catchment regions. Results from a 43-day period (20 July–31 August 2002) show little sensitivity to the interpolation method used. The rank histograms and the relative entropy better show the effect of introducing observation uncertainty, although this effect on the Brier skill score and the spread–error ratio is not very large. The case study indicates that overall observation uncertainty should be taken into account when evaluating forecast skill.
A Diagnostic Model for Mixed Layer Depth Estimation with Application to Ocean Station P in the Northeast Pacific
Authors: Thomson Richard E. , Fine Isaac V. 
Published: November 2008

Abstract
This paper presents a simple diagnostic model for estimating mixed layer depth based solely on the one-dimensional heat balance equation, the surface heat flux, and the sea surface temperature. The surface fluxes drive heating or cooling of the upper layer whereas the surface temperature acts as a “thermostat” that regulates the vertical extent of the layer. Daily mixed layer depth estimates from the diagnostic model (and two standard bulk mixed layer models) are compared with depths obtained from oceanic profiles collected during the 1956–80 Canadian Weathership program at Station P and more recent (2001–07) profiles from the vicinity of this station from Argo drifters. Summer mixed layer depths from the diagnostic model agree more closely with observed depths and are less sensitive to heat flux errors than those from bulk models. For the Weathership monitoring period, the root-mean-square difference between modeled and observed monthly mean mixed layer depths is ∼6 m for the diagnostic model and ∼10 m for the bulk models. The diagnostic model is simpler to apply than bulk models and sidesteps the need for wind data and turbulence parameterization required by these models. Mixed layer depths obtained from the diagnostic model using NCEP–NCAR reanalysis data reveal that—contrary to reports for late winter—there has been no significant trend in the summer mixed layer depth in the central northeast Pacific over the past 52 yr.
Differential oxidative stress and DNA damage in rat brain regions and blood following chronic arsenic exposure
Authors: Mishra D , Flora SJS 
Published: November 2008

Chronic arsenic poisoning caused by contaminated drinking water is a wide spread and worldwide problem particularly in India and Bangladesh. One of the possible mechanisms suggested for arsenic toxicity is the generation of reactive oxygen species (ROS). The present study was planned 1) to evaluate if chronic exposure to arsenic leads to oxidative stress in blood and brain – parts of male Wistar rats and 2) to evaluate which brain region of the exposed animals was more sensitive to oxidative injury. Male Wistar rats were exposed to arsenic (50 ppm sodium arsenite in drinking water) for 10 months. The brain was dissected into five major parts, pons medulla, corpus striatum, cortex, hippocampus, and cerebellum. A number of biochemical variables indicative of oxidative stress were studied in blood and different brain regions. Single-strand DNA damage using comet assay was also assessed in lymphocytes. We observed a significant increase in blood and brain ROS levels accompanied by the depletion of GSH/GSSG ratio and glucose-6-phosphate dehydrogenase (G6PD) activity in different brain regions of arsenic-exposed rats. Chronic arsenic exposure also caused significant single-strand DNA damage in lymphocytes as depicted by comet with a tail in arsenic-exposed cells compared with the control cells. On the basis of results, we concluded that the cortex region of the brain was more sensitive to oxidative injury compared with the other regions studied. The present study, thus, leads us to suggest that arsenic induces differential oxidative stress in brain regions with cortex followed by hippocampus and causes single-strand DNA damage in lymphocytes.
Inhibition of carbon tetrachloride–mediated apoptosis and oxidative stress by melatonin in experimental liver fibrosis
Authors: Ogeturk M , Kus I , Pekmez H , Yekeler H , Sahin S , Sarsilmaz M 
Published: November 2008

Melatonin, the principal secretory product of the pineal gland, functions as a potent antioxidant and free radical scavenger. Additionally, the antiapoptotic effect of melatonin has been observed both in vivo and in vitro. The aim of this experimental study was to investigate the protective effects of melatonin against carbon tetrachloride (CCl4)–induced apoptosis and oxidative stress in rat liver. Twenty-four male Wistar rats were divided in three equal groups. Group I was used as control. Rats in group II were injected every other day with CCl4 (0.5 mL/kg BW) for a month, whereas rats in group III were treated every other day with the same dose of CCl4 plus melatonin (25 mg/kg BW). At the end of the experiment, all animals were killed by decapitation and the livers were rapidly removed. Some of the liver tissue specimens were used for determination of malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) levels. The remaining tissue specimens were processed for immunohistochemical assessment, and the percentage rates of apoptotic liver cells stained with immunoreactive Bax were determined. Chronic administration of CCl4 significantly increased liver MDA contents, as an end product of lipid peroxidation, and also significantly decreased SOD and GSH-Px activities, emphasizing the generation of increased oxidative stress. Moreover, it caused an evident increase in apoptotic cells. Melatonin treatment significantly reduced MDA levels and elevated SOD and GSH-Px activities in rats received CCl4 plus melatonin. Furthermore, apoptotic changes caused by CCl4 were considerably decreased in these animals. The results of the present study indicate that melatonin treatment substantially prevents CCl4-induced apoptosis and oxidative damage in the liver. Thus, melatonin may serve as a drug for treating many clinical conditions that arise from inappropriate apoptosis.
JP-8 jet fuel exposure suppresses the immune response to viral infections
Authors: Harris DT , Sakiestewa D , Titone D , He X , Hyde J , Witten M 
Published: November 2008

The US Air Force has implemented the widespread use of JP-8 jet fuel in its operations, although a thorough understanding of its potential effects upon exposed personnel is unclear. Previous work has reported that JP-8 exposure is immunosuppressive. Exposure of mice to JP-8 for 1 h/day resulted in immediate secretion of two immunosuppressive agents, namely, interleukin-10 and prostaglandin E2. Thus, it was of interest to determine if jet fuel exposure might alter the immune response to infectious agents. The Hong Kong influenza model was used for these studies. Mice were exposed to 1000 mg/m3 JP-8 (1 h/day) for 7 days before influenza viral infection. Animals were infected intra-nasally with virus and followed in terms of overall survival as well as immune responses. All surviving animals were killed 14 days after viral infection. In the present study, JP-8 exposure increased the severity of the viral infection by suppressing the anti-viral immune responses. That is, exposure of mice to JP-8 for 1 h/day for 7 days before infection resulted in decreased immune cell viability after exposure and infection, a greater than fourfold decrease in immune proliferative responses to mitogens, as well as an overall loss of CD3+, CD4+, and CD8+ T cells from the lymph nodes, but not the spleens, of infected animals. These changes resulted in decreased survival of the exposed and infected mice, with only 33% of animals surviving as compared with 50% of mice infected but not jet fuel–exposed (and 100% of mice exposed only to JP-8). Thus, short-term, low-concentration JP-8 jet fuel exposures have significant suppressive effects on the immune system which can result in increased severity of viral infections.
Ethyl benzene should be considered ototoxic at occupationally relevant exposure concentrations
Authors: Vyskocil A , Leroux T , Truchon G , Lemay F , Gendron M , Gagnon F , El Majidi N , Viau C 
Published: November 2008

Organic solvents can produce ototoxic effects in both man and experimental animals. The objective of this study was to review the literature on the effects of low-level exposure to ethyl benzene on the auditory system and consider its relevance for the occupational settings. Both human and animal investigations were evaluated only for realistic exposure concentrations based on the permissible exposure limits. In Quebec, the Time-Weighed Average Exposure Value for 8 h (TWAEV) is 100 ppm (434 mg/m3) and the Short-Term Exposure Value for 15 min (STEV) is 125 ppm (543 mg/m3). In humans, the upper limit for considering ototoxicity data relevant to the occupational exposure situation was set at STEV. Animal data were evaluated only for exposure concentrations up to 100 times the TWAEV. In workers, there is no evidence of either ethyl benzene-induced hearing losses or ototoxic interaction after combined exposure to ethyl benzene and noise. In rats, ethyl benzene affects the auditory function mainly in the cochlear mid-frequency range and ototoxic interaction was observed after combined exposure to noise and ethyl benzene. Further studies with sufficient data on the ethyl benzene exposure of workers are necessary to make a definitive conclusion. Given the current evidence from animal studies, we recommend considering ethyl benzene as an ototoxic agent.
Chelation of bismuth by combining desferrioxamine and deferiprone in rats
Authors: Tubafard S , Fatemi SJ 
Published: November 2008

Consumption and production of bismuth compounds are increasing, however, a little information on the toxic effect and also the effective method in removal of bismuth compounds are available. The present research aimed to characterize the potential efficiency of two chelators after bismuth administration for 55 days following two dose levels of 20 and 40 mg/kg body weight daily to male rats. However, we found abnormalities after bismuth administration in clinical signs, such as body weight, kidneys and liver damages, a black line on gums and skin reactions. Furthermore, the hypothesis that the two chelators might be more efficient as combined therapy than as single therapy in removing bismuth from the body was considered. Along this line, two known chelators deferiprone (1, 2-dimethy1-3-hydroxypyride-4-one, L1) and desferrioxamine (DFO) were chosen and tested in the acute rat model. Chelators were given orally (L1) or intraperitoneally (DFO) as a single or combined therapy for the period of a week. Doses of L1 and DFO were 110 mg/kg body weight in experiments. Bismuth and iron concentrations in various tissues were determined by graphite furnace and flame atomic absorption spectrometry, respectively. The combined chelation therapy results show that DFO and L1 are able to remove bismuth ions from the body, whereas iron concentration returned to the normal level and symptoms are also decreased. DFO was more effective than L1 in reducing bismuth concentration in tissues. The efficiency of DFO + L1 is more than DFO or L1 in removing bismuth from organs. Our results are indicative that the design procedure might be useful for preliminary in-vivo testing of the efficiency of chelating agents. Results of combined chelators’ treatment should be confirmed in a different experimental model before extrapolation to other systems. This testing procedure of course does not provide all the relevant answers for efficiency of chelating agents in bismuth toxicity.
Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic leukemia
Authors: de Jonge Robert , Tissing Wim J. E. , Hooijberg Jan Hendrik , Jansen Gerrit , Kaspers Gertjan J. L. , Lindemans Jan , Peters Godefridus J. , Pieters Rob 
Published: November 2008

AbstractPolymorphisms in folate pathway genes may influence the susceptibility to acute lymphoblastic leukemia (ALL). DNA was isolated from 245 pediatric ALL patients (cases) and from 500 blood bank donors (controls). Polymorphisms in methylene-tetrahydrofolate reductase (MTHFR 677C>T, 1298A>C), methionine synthase (MTR 2756A>G), methionine synthase reductase (MTRR 66A>G), methylenetetrahydrofolate dehydrogenase (MTHFD1 1958G>A), nicotinamide N-methyltransferase (NNMT IVS −151C>T), serine hydroxymethyl transferase (SHMT1 1420C>T), thymidylate synthase (TS 2R3R), and the reduced folate carrier (RFC1 80G>A) were detected. In ALL patients, an increased occurrence was observed of the RFC1 80AA variant (odds ratio [OR] = 2.1; 95% confidence interval [CI] = 1.3-3.2; P = .002) and the RFC1 80A allele (OR = 1.5; 95% CI, 1.1-2.1; P = .02). Likewise, the NNMT IVS −151TT genotype showed a 2.2-fold increased ALL risk (OR = 2.2; 95% CI, 1.1-4.6; P = .04). A 1.4-fold reduction in ALL risk was observed for (heterozygous or homozygous) carriers of the TS 2R allele and the MTHFR 677T allele (OR = 0.7; 95% CI, 0.5-1.0; P < .05). Furthermore, interactions between NNMT and MTHFR 677C>T and RFC1 were observed. NNMT IVS −151CC/MTHFR 677CT + TT patients exhibited a 2-fold reduction in ALL risk whereas RFC1 80AA/NNMT IVS −151CT + TT subjects had a 4.2-fold increase in ALL risk (P = .001). For the first time, we associate the RFC1 80G>A and NNMT IVS −151C>T variants to an increased ALL susceptibility.
Zalypsis: a novel marine-derived compound with potent antimyeloma activity that reveals high sensitivity of malignant plasma cells to DNA double-strand breaks
Authors: Ocio Enrique M. , Maiso Patricia , Chen Xi , Garayoa Mercedes , Álvarez-Fernández Stela , San-Segundo Laura , Vilanova David , López-Corral Lucía , Montero Juan C. , Hernández-Iglesias Teresa , de Álava Enrique , Galmarini Carlos , Avilés Pablo , Cuevas Carmen , San-Miguel Jesús F. , Pandiella Atanasio 
Published: November 2008

Abstract
Multiple myeloma (MM) remains incurable, and new drugs with novel mechanisms of action are still needed. In this report, we have analyzed the action of Zalypsis, an alkaloid analogous to certain natural marine compounds, in MM. Zalypsis turned out to be the most potent antimyeloma agent we have tested so far, with IC50 values from picomolar to low nanomolar ranges. It also showed remarkable ex vivo potency in plasma cells from patients and in MM cells in vivo xenografted in mice. Besides the induction of apoptosis and cell cycle arrest, Zalypsis provoked DNA double-strand breaks (DSBs), evidenced by an increase in phospho-histone-H2AX and phospho-CHK2, followed by a striking overexpression of p53 in p53 wild-type cell lines. In addition, in those cell lines in which p53 was mutated, Zalypsis also provoked DSBs and induced cell death, although higher concentrations were required. Immunohistochemical studies in tumors also demonstrated histone-H2AX phosphorylation and p53 overexpression. Gene expression profile studies were concordant with these results, revealing an important deregulation of genes involved in DNA damage response. The potent in vitro and in vivo antimyeloma activity of Zalypsis uncovers the high sensitivity of tumor plasma cells to DSBs and strongly supports the use of this compound in MM patients.
Preferred and avoided codon pairs in three domains of life
Authors: Tats Age , Tenson Tanel , Remm Maido 
Published: November 2008

Abstract

Background
Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons – neighboring nucleotides and neighboring codons – can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserved the codon context preferences in different organisms are. We analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs.

Results
After removing the effects of single codon usage and dipeptide biases we discovered a set of neighboring codons for which avoidances or preferences were conserved in all three domains of life. Such biased codon pairs could be divided into subtypes on the basis of the nucleotide patterns that influence the bias. The most frequently avoided type of codon pair was nnUAnn. We discovered that 95.7% of avoided nnUAnn type patterns contain out-frame UAA or UAG triplets on the sense and/or antisense strand. On average, nnUAnn codon pairs are more frequently avoided in ORFeomes than in genomes. Thus we assume that translational selection plays a major role in the avoidance of these codon pairs. Among the preferred codon pairs, nnGCnn was the major type.

Conclusion
Translational selection shapes codon pair usage in protein coding sequences by rules that are common to all three domains of life. The most frequently avoided codon pairs contain the patterns nnUAnn, nnGGnn, nnGnnC, nnCGCn, GUCCnn, CUCCnn, nnCnnA or UUCGnn. The most frequently preferred codon pairs contain the patterns nnGCnn, nnCAnn or nnUnCn.
Engineering and Applications of fungal laccases for organic synthesis
Authors: Kunamneni Adinarayana , Camarero Susana , García-Burgos Carlos , Plou Francisco J , Ballesteros Antonio , Alcalde Miguel 
Published: November 2008

AbstractLaccases are multi-copper containing oxidases (EC 1.10.3.2), widely distributed in fungi, higher plants and bacteria. Laccase catalyses the oxidation of phenols, polyphenols and anilines by one-electron abstraction, with the concomitant reduction of oxygen to water in a four-electron transfer process. In the presence of small redox mediators, laccase offers a broader repertory of oxidations including non-phenolic substrates. Hence, fungal laccases are considered as ideal green catalysts of great biotechnological impact due to their few requirements (they only require air, and they produce water as the only by-product) and their broad substrate specificity, including direct bioelectrocatalysis.Thus, laccases and/or laccase-mediator systems find potential applications in bioremediation, paper pulp bleaching, finishing of textiles, bio-fuel cells and more. Significantly, laccases can be used in organic synthesis, as they can perform exquisite transformations ranging from the oxidation of functional groups to the heteromolecular coupling for production of new antibiotics derivatives, or the catalysis of key steps in the synthesis of complex natural products. In this review, the application of fungal laccases and their engineering by rational design and directed evolution for organic synthesis purposes are discussed.
High prevalence of HIV infection among homeless and street-involved Aboriginal youth in a Canadian setting
Authors: Marshall Brandon DL , Kerr Thomas , Livingstone Chris , Li Kathy , Montaner Julio SG , Wood Evan 
Published: November 2008

Abstract
Aboriginal people experience a disproportionate burden of HIV infection among the adult population in Canada; however, less is known regarding the prevalence and characteristics of HIV positivity among drug-using and street-involved Aboriginal youth. We examined HIV seroprevalence and risk factors among a cohort of 529 street-involved youth in Vancouver, Canada. At baseline, 15 (2.8%) were HIV positive, of whom 7 (46.7%) were Aboriginal. Aboriginal ethnicity was a significant correlate of HIV infection (odds ratio = 2.87, 95%CI: 1.02 – 8.09). Of the HIV positive participants, 2 (28.6%) Aboriginals and 6 (75.0%) non-Aboriginals reported injection drug use; furthermore, hepatitis C co-infection was significantly less common among Aboriginal participants (p = 0.041). These findings suggest that factors other than injection drug use may promote HIV transmission among street-involved Aboriginal youth, and provide further evidence that culturally appropriate and evidence-based interventions for HIV prevention among Aboriginal young people are urgently required.