bluuebunny/crossref_metadata_2025 huggingface dataset:
Biodegradation of groundwater pollutants by a combined culture ofMycobacterium vaccaeand aRhodococcussp.
Authors: Fairlee Jason R. , Burback Brian L. , Perry Jerome J.
Published: February 2010

The catabolism of selected groundwater pollutants by a combined culture of Mycobacterium vaccae and a Rhodococcus sp. (strain R-22) was investigated. The M. vaccae – R-22 combined culture was five times more effective in mineralizing benzene than either organism alone. Mycobacterium vaccae oxidized benzene to phenol, and R-22 catabolized the phenol to cellular components and CO2. Benzene did not support growth of M. vaccae, R-22, or the combined culture. Optimization of ratios of the two species indicated that the maximum mineralization of benzene occurred at an initial ratio of 75% M. vaccae to 25% R-22. Cell fractionation of the combined culture after mineralization of [U-14C]benzene indicated that 10% of the benzene carbon was incorporated into cell material, and of this 45% was present in protein and 20% in nucleic acids. This suggested that minimally one species could utilize the products of benzene as a nutrient source. The M. vaccae – R-22 combined culture catabolized ethylbenzene and chlorobenzene without the accumulation of phenolic intermediates, which are inhibitory to M. vaccae's ability to degrade the parent compounds. This study demonstrates that defined mixed cultures may be useful in studying the effects of environmental pollutant degradation on microbial ecosystems and mineralization of these pollutants by the ecosystem.Key words: biodegradation, groundwater pollutant, Mycobacterium vaccae, Rhodococcus sp.
Detection and enumeration of Erwinia carotovora subsp. atroseptica using spiral plating and immunofluorescence colony staining
Authors: Schober B. M. , Vuurde J. W. L. van
Published: February 2010

Immunofluorescence colony staining (IFC) and a new technique using spiral plating combined with IFC were evaluated for the soft-rot pathogen Erwinia carotovora subsp. atroseptica in witloof chicory. Target bacteria could be detected in platings at various dilutions of plant washings. Brilliance of the stained colonies of E. carotovora subsp. atroseptica was high. Spiral plating, used for both the plating of the bacteria and for the delivery of the conjugated antiserum, had a positive effect on the reduction of the background compared with the staining of the bacteria. The combination of spiral plating and IFC proved to be a functional tool for the quantification of target and nontarget bacteria and the isolation of target bacteria as pure culture from IFC-positive colonies. The method uses less conjugated antiserum than traditional IFC and produces results with very small variation within replications. The recovery of the bacteria in both pure culture and plant washing is significantly higher than the recovery using crystal violet pectate medium.Key words: soft rot, witloof chicory, detection, Erwinia carotovora subsp. atroseptica.
Characteristics of stationary-phase variation affecting virulence in Xanthomonas oryzae pv. oryzae
Authors: Rajeshwari R. , Yashitola J. , Sonti R. V. , Reddy A. P. K.
Published: February 2010

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight, a serious disease of rice. Spontaneous loss of virulence in X. oryzae pv. oryzae is associated with mutants that produce reduced levels of extracellular polysaccharide. Evidence is presented that these mutants accumulate in long-term stationary phase cultures but are not obtained from exponentially growing cultures. A number of independent spv (stationary-phase variation) mutants have been isolated and characterized. These mutants differ from each other with respect to the stability of the mutant phenotype, extent of loss of virulence, ability to outcompete wild type cells in stationary-phase cocultures, and hypersensitivity to hydrogen peroxide.Key words: stationary-phase variation, spontaneous loss of virulence, Xanthomonas oryzae.
Tyrosine is involved in protection from oxidative stress inSaccharomyces cerevisiae
Authors: Lupo Sandra , Aranda Cristina , Olivera Hiram , Riego Lina , González Alicia , Miranda-Ham Lourdes , Servin Luis
Published: February 2010

The phenotypic characterization of a Saccharomyces cerevisiae mutant unable to grow under agitated conditions is presented here. When this strain was incubated under aerobic conditions, it did not grow and the viability of the culture decreased. The loss in viability was prevented by the addition of antioxidants or chelating agents to the medium, indicating that this mutant was unable to withstand the oxidative stress generated by aerobic metabolism. This strain was complemented with plasmids from a yeast genomic library. The transformants that were obtained carried plasmids harbouring the TYR1 gene, which codes for one of the enzymes involved in tyrosine biosynthesis. A monogenic S. cerevisiae tyr1 mutant obtained from the Yeast Genetic Stock Center showed higher sensitivity to hydrogen peroxide than a TYR1 strain. This sensitivity was reverted when this strain was complemented with the TYR1 gene. Considering these results, we propose that tyrosine plays a role in the protection against oxidative stress.Key words: oxidative stress, amino acid biosynthesis, reactive oxygen intermediates, nitrogen metabolism.
Structural and physiological determinants of resistance ofAeromonas salmonicidato reactive radicals
Authors: Garduño Rafael A. , Kuzyk Michael A. , Kay William W.
Published: February 2010

The facultative intracellular pathogen Aeromonas salmonicida survives and replicates in macrophages, a virulence trait presumed to be associated with its ability to resist reactive radicals. The mechanisms used by A. salmonicida to resist reactive radicals in vitro were shown to have both structural and physiological determinants. The sensitivity of A. salmonicida to exogenous H2O2, superoxide, and nitrogen radicals, as well as endogenous oxygen radicals, differed depending on growth conditions, cell surface structure, and preexposure to sublethal doses of radicals. Whereas sensitivities to exogenous oxygen radicals did not correlate with basal levels of catalase or Fe-superoxide dismutase, under similar culture conditions S-layer positive cells were more resistant to oxygen radicals than S-layer mutants. S-layer mutants recovered resistance when physically reconstituted with S-layer sheets. Hemin-coated S-layers, while protective against nitrogen radicals, sensitized A. salmonicida to H2O2. Sublethal concentrations of H2O2or superoxide induced a highly protective response characterized by de novo synthesis of both catalase and Mn-superoxide dismutase. It is proposed that for A. salmonicida the constitutive S-layer provides a first line of defense and the inducible catalase and Mn-superoxide dismutase provide a powerful second line of defense against macrophage-mediated killing via reactive oxygen species.Key words: Aeromonas salmonicida, oxygen radicals, nitrogen radicals, oxidative stress, S-layers.
Development and implementation of a loosely coupled, multi-site, networked and replicated electronic medical record in Haiti
Authors: Lober William B. , Wagner Stephen , Quiles Christina
Published: February 2010

Since 2005, we have been developing and implementing an electronic medical record (EMR) that supports both individual and population health care for HIV-infected patients in Haiti. The need to support countrywide monitoring and evaluation drove early architectural decisions to support linking systems under conditions of network uncertainty. Despite numerous challenges including frequent power outages and inadequate Internet access and support, the system (iSanté) is currently implemented in 55 clinic sites nationwide, tracks over 41,000 patients, and synchronizes patient data between in-country sites and the central site databases on a daily basis.
Evolutionary Search for Globally Optimal Stable Multicycles in Complex Systems with Inventory Couplings
Authors: Skowron M. , Styczeń K.
Published: February 2010

This note is devoted to multiperiodically operated complex system with inventory couplings transferring waste products from some subsystems as useful components to other subsystems. The flexibility of the inventory couplings is used to force each of the subsystems with its own period and to exploit its particular dynamic properties. This enhances the performance of the complex system endowed with many recycling loops, which reduce the amount of waste products endangering the natural environment. The subsystems are characterized by generalized populations composed of the individuals (the cycles), each of them encompasses its period, its initial state, its local control, and its inventory interaction. An evolutionary optimization algorithm employing such generalized populations coordinated on the basis of the inventory interaction constraints is developed. It includes the stability requirements imposed on the cyclic control processes connected with particular subsystems. The algorithm proposed is applied to the global multiperiodic optimization of some interconnected chemical production processes.
Dispersal Kernel Determines Symmetry of Spread and Geographical Range for an Insect
Authors: Holland Jeffrey D.
Published: January 2010

The distance from a source patch that dispersing insects reach depends on the number of dispersers, or random draws from a probability density function called a dispersal kernel, and the shape of that kernel. This can cause asymmetrical dispersal between habitat patches that produce different numbers of dispersers. Spatial distributions based on these dynamics can explain several ecological patterns including megapopulations and geographic range boundaries. I hypothesized that a locally extirpated longhorned beetle, the sugar maple borer, has a new geographical range shaped primarily by probabilistic dispersal distances. I used data on occurrence from Ontario, Canada to construct a model of geographical range in Indiana, USA based on maximum dispersal distance scaled by habitat area. This model predicted the new range boundary within 500 m very accurately. This beetle may be an ideal organism for exploring spatial dynamics driven by dispersal.
Some Sufficient Conditions for Fixed Points of Multivalued Nonexpansive Mappings
Authors: Zuo Zhanfei , Cui Yunan
Published: January 2010

We show some sufficient conditions on a Banach space "Equation missing" concerning the generalized James constant, the generalized Jordan-von Neumann constant, the generalized Zbagănu constant, the coefficient "Equation missing", the weakly convergent sequence coefficient WCS("Equation missing"), and the coefficient of weak orthogonality, which imply the existence of fixed points for multivalued nonexpansive mappings. These fixed point theorems improve some previous results in the recent papers.
Collision and Stable Regions around Bodies with Simple Geometric Shape
Authors: Silva A. A. , Winter O. C. , Prado A. F. B. A.
Published: January 2010

We show the expressions of the gravitational potential of homogeneous bodies with well‐defined simple geometric shapes to study the phase space of trajectories around these bodies. The potentials of the rectangular and triangular plates are presented. With these expressions we study the phase space of trajectories of a point of mass around the plates, using the Poincaré surface of section technique. We determined the location and the size of the stable and collision regions in the phase space, and the identification of some resonances. This work is the first and an important step for others studies, considering 3D bodies. The study of the behavior of a point of mass orbiting around these plates (2D), near their corners, can be used as a parameter to understand the influence of the gravitational potential when the particle is close to an irregular surface, such as large craters and ridges.
Activation of TLR4-Mediated NFB Signaling in Hemorrhagic Brain in Rats
Authors: Teng Weiyu , Wang Lishu , Xue Weishuang , Guan Chao
Published: January 2010

Inflammation and immunity play a crucial role in the pathogenesis of Intracerebral hemorrhage (ICH). Toll-like receptor 4- (TLR4-) mediated nuclear factor kappa-B (NFB) signaling plays critical roles in the activation and regulation of inflammatory responses in injured brain. However, the involvement of TLR4-mediated NFB signaling in the pathogenesis of ICH remains unknown. The present study was to evaluate the temporal profile of the expression of TLR4 and the activation of TLR4-mediated NFB signaling in brain tissues of Wistar rats after ICH. TLR4 mRNA and protein, the phosphorylation of inhibitors of kappa B (p-IB), and the activity of NFB were examined in hemorrhagic cerebral tissue by Rt-PCR, Western blots, immunohistochemistry staining, and EMSA. Compared with saline control, the TLR4 mRNA and protein significantly increased starting at 6 hours after ICH, peaked on the 3rd day after ICH, and then decreased but still maintained at a higher level on the 7th day after ICH (). The level of p-IB and the activity of NFB also increased in the brain after ICH compared with saline control. The present study firstly suggests that TLR4-mediated NFB signaling participates in the pathogenesis of ICH, which may become a therapeutic target for ICH-induced brain damage.
Single-Machine Scheduling Problems with a Sum-of-Processing-Time-Based Learning Function
Authors: Zhang Xingong , Yan Guangle
Published: January 2010

Recently, learning scheduling problems have received increasing
attention. However, the majority of the research assume that the
actual job processing time is a function of its position. This paper
deals with the single-machine scheduling problem with a
sum-of-processing-time-based learning effect. By the effect of
sum-of-processing-time-based learning, we mean that the processing
time of a job is defined by total normal processing time of jobs in
front of it in the sequence. We show that the single-machine
makespan problem remains polynomially solvable under the proposed
model. We show that the total completion time minimization problem
for a≥1 remains polynomially solvable under the proposed
model. For the case of 0<a<1, we show that an optimal schedule of
the total completion time minimization problem is V-shaped with respect to normal job processing times.
Colorectal Carcinoma: Local Tumor Staging and Assessment of Lymph Node Metastasis by High‐Resolution MR Imaging in Surgical Specimens
Authors: Yamada Ichiro , Yoshino Norio , Tetsumura Akemi , Okabe Satoshi , Enomoto Masayuki , Sugihara Kenichi , Kumagai Jiro , Shibuya Hitoshi
Published: January 2010

Purpose. To assess the accuracy of high‐resolution MR imaging as a means of evaluating mural invasion and lymph node metastasis by colorectal carcinoma in surgical specimens. Materials and Methods. High‐resolution T1‐weighted and T2‐weighted MR images were obtained in 92 surgical specimens containing 96 colorectal carcinomas. Results. T2‐weighted MR images clearly depicted the normal colorectal wall as consisting of seven layers. In 90 (94%) of the 96 carcinomas the depth of mural invasion depicted by MR imaging correlated well with the histopathologic stage. Nodal signal intensity on T2‐weighted images (93%) and nodal border contour (93%) were more accurate than nodal size (89%) as indicators of lymph node metastasis, and MR imaging provided the highest accuracy (94%–96%) when they were combined. Conclusion. High‐resolution MR imaging is a very accurate method for evaluating both mural invasion and lymph node metastasis by colorectal carcinoma in surgical specimens.
A Pattern Analysis of Gene Conversion Literature
Authors: Lawson Mark J. , Jiao Jian , Fan Weiguo , Zhang Liqing
Published: January 2010

Gene conversion is an important biological process that involves the transfer of genetic (sequence) information from one gene to another. This can have a variety of effects on an organism, both short-term and long-term and both positive and detrimental. In an effort to better understand this process, we searched through over 3,000 abstracts that contain research on gene conversions, tagging the important data and performing an analysis on what we extract. Through this we established trends that give a better insight into gene conversion research and genetic research in general. Our results show the importance of the process and the importance of continuing gene conversion research.
Correlation between Group B Streptococcal Genotypes, Their Antimicrobial Resistance Profiles, and Virulence Genes among Pregnant Women in Lebanon
Authors: Hannoun Antoine , Shehab Marwa , Khairallah Marie-Therese , Sabra Ahmad , Abi-Rached Roland , Bazi Tony , Yunis Khalid A. , Araj George F. , Matar Ghassan M.
Published: February 2010

The antimicrobial susceptibility profiles of 76Streptococcus agalactiae(Group B Streptococci [GBS]) isolates from vaginal specimens of pregnant women near term were correlated to their genotypes generated by Random Amplified Polymorphic DNA analysis and their virulence factors encoding genescylE, lmb, scpB, rib, andbcaby PCR. Based on the distribution of the susceptibility patterns, six profiles were generated. RAPD analysis detected 7 clusters of genotypes. ThecylEgene was present in 99% of the isolates, thelmbin 96%,scpBin 94.7%,ribin 33%, andbcain 56.5% of isolates. The isolates demonstrated a significant correlation between antimicrobial resistance and genotype clusters denoting the distribution of particular clones with different antimicrobial resistance profiles, entailing the practice of caution in therapeutic options. All virulence factors encoding genes were detected in all seven genotypic clusters withribandbcanot coexisting in the same genome.
Distributed Arithmetic for Efficient Base‐Band Processing in Real‐Time GNSS Software Receivers
Authors: Waelchli Grégoire , Baracchi-Frei Marcel , Botteron Cyril , Farine Pierre-André
Published: January 2010

The growing market of GNSS capable mobile devices is driving the interest of GNSS software solutions, as they can share many system resources (processor, memory), reducing both the size and the cost of their integration. Indeed, with the increasing performance of modern processors, it becomes now feasible to implement in software a multichannel GNSS receiver operating in real time. However, a major issue with this approach is the large computing resources required for the base‐band processing, in particular for the correlation operations. Therefore, new algorithms need to be developed in order to reduce the overall complexity of the receiver architecture. Towards that aim, this paper first introduces the challenges of the software implementation of a GPS receiver, with a main focus given to the base‐band processing and correlation operations. It then describes the already existing solutions and, from this, introduces a new algorithm based on distributed arithmetic.
Molecular Modulation of Intestinal Epithelial Barrier: Contribution of Microbiota
Authors: Sharma Renu , Young Christopher , Neu Josef
Published: January 2010

The daunting task required of the gut-barrier to prevent luminal pathogens and harmful substances from entering into the internal milieu and yet promoting digestion and absorption of nutrients requires an exquisite degree of coordination between the different architectural units of this barrier. The complex integration and execution of these functions are superbly carried out by the intestinal mucosal (IM) surface. Exposed to trillions of luminal microbes, the IM averts threats by signaling to the innate immune system, through pattern recognition receptors (PRR), to respond to the commensal bacteria by developing tolerance (hyporesponsiveness) towards them. This system also acts by protecting against pathogens by elaborating and releasing protective peptides, cytokines, chemokines, and phagocytic cells. The IM is constantly sampling luminal contents and making molecular adjustments at its frontier. This article describes the topography of the IM and the mechanisms of molecular adjustments that protect the internal milieu, and also describes the role of the microbiota in achieving this goal.
Foehn-Like Winds and Elevated Fire Danger Conditions in Southeastern Australia
Authors: Sharples Jason J. , Mills Graham A. , McRae Richard H. D. , Weber Rodney O.
Published: February 2010

Bushfires in southeastern Australia are a serious environmental problem, and consistently cause loss of life and damage to property and other assets. Understanding synoptic processes that can lead to dangerous fire weather conditions throughout the region is therefore an important undertaking aimed at improving community safety, protection of assets, and fire suppression tactics and strategies. In southeastern Australia severe fire weather is often associated with dry cool changes or coastally modified cold fronts. Less well known, however, are synoptic events that can occur in connection with the topography of the region, such as cross-mountain flows and foehn-like winds, which can also lead to abrupt changes in fire weather variables that ultimately result in locally elevated fire danger. This paper focuses on foehn-like occurrences over the southeastern mainland, which are characterized by warm, dry winds on the lee side of the Australian Alps. The characteristics of a number of foehn-like occurrences are analyzed based on observational data and the predictions of a numerical weather model. The analyses confirm the existence of a foehn effect over parts of southeastern Australia and suggest that its occurrence is primarily due to the partial orographic blocking of relatively moist low-level air and the subsidence of drier upper-level air in the lee of the mountains. The regions prone to foehn occurrence, the influence of the foehn on fire weather variables, and the connection between the foehn and mountain waves are also discussed.
Decadal Prediction in the Pacific Region
Authors: Meehl Gerald A. , Hu Aixue , Tebaldi Claudia
Published: February 2010

A “perfect model” configuration with a global coupled climate model 30-member ensemble is used to address decadal prediction of Pacific SSTs. All model data are low-pass filtered to focus on the low-frequency decadal component. The first three EOFs in the twentieth-century simulation, representing nearly 80% of the total variance, are used as the basis for early twenty-first-century predictions. The first two EOFs represent the forced trend and the interdecadal Pacific oscillation (IPO), respectively, as noted in previous studies, and the third has elements of both trend and IPO patterns. The perfect model reference simulation, the target for the prediction, is taken as the experiment that ran continuously from the twentieth to twenty-first century using anthropogenic and natural forcings for the twentieth century and the A1B scenario for the twenty-first century. The other 29 members use a perturbation in the atmosphere at year 2000 and are run until 2061. Since the IPO has been recognized as a dominant contributor to decadal variability in the Pacific, information late in the twentieth century and early in the twenty-first century is used to select a subset of ensemble members that are more skillful in tracking the time evolution of the IPO (EOF2) in relation to a notional start date of 2010. Predictions for the 19-yr period centered on the year 2020 use that subset of ensemble members to construct Pacific SST patterns based on the predicted evolution of the first three EOFs. Compared to the perfect model reference simulation, the predictions show some skill for Pacific SST predictions with anomaly pattern correlations greater than +0.5. An application of the Pacific SST prediction is made to precipitation over North America and Australia. Even though there are additional far-field influences on Pacific SSTs and North American and Australian precipitation involving the Atlantic multidecadal oscillation (AMO) in the Atlantic, and Indian Ocean and South Asian monsoon variability, there is qualitative skill for the pattern of predicted precipitation over North America and Australia using predicted Pacific SSTs. This exercise shows that, in the presence of a large forced trend like that in the large ensemble, much of Pacific region decadal predictability about 20 years into the future arises from increasing greenhouse gases.
Relative Contributions of the Indian Ocean and Local SST Anomalies to the Maintenance of the Western North Pacific Anomalous Anticyclone during the El Niño Decaying Summer*
Authors: Wu Bo , Li Tim , Zhou Tianjun
Published: February 2010

To investigate the relative role of the cold SST anomaly (SSTA) in the western North Pacific (WNP) or Indian Ocean basin mode (IOBM) in maintaining an anomalous anticyclone over the western North Pacific (WNPAC) during the El Niño decaying summer, a suite of numerical experiments is performed using an atmospheric general circulation model, ECHAM4. In sensitive experiments, the El Niño composite SSTA is specified in either the WNP or the tropical Indian Ocean, while the climatological SST is specified elsewhere. The results indicate that the WNPAC is maintained by the combined effects of the local forcing of the negative SSTA in the WNP and the remote forcing from the IOBM. The former (latter) contribution gradually weakens (enhances) from June to August. The negative SSTA in the WNP is crucial for the maintenance of the WNPAC in early summer. However, because of a negative air–sea feedback, the negative SSTA gradually decays, as does the local forcing effect. Enhanced local convection associated with the IOBM stimulates atmospheric Kelvin waves over the equatorial western Pacific. The impact of the Kelvin waves on the WNP circulation depends on the formation of the climatological WNP monsoon trough, which does not fully establish until late summer. Therefore, the IOBM plays a crucial role in late summer via the Kelvin wave induced anticyclonic shear and boundary layer divergence.
Time Zone Dependence of Diurnal Cycle Errors in Surface Temperature Analyses
Authors: Zou X. , Qin Z-K.
Published: February 2010

Surface temperatures from both the NCEP analysis and ECMWF Re-Analysis (ERA-Interim) in January 2008 over the Africa–Eurasian region were compared with surface station measurements to study analysis errors in the diurnal cycle, with data sampled at 3-h time intervals. The results show the dominance of the diurnal cycle in surface temperature analyses and the significance of the time zone dependence of diurnal cycle errors in global analyses. While a distinct diurnal cycle of surface temperature is evidenced in all three datasets, with a nearly constant thermal response of about 2 h in surface station data, the thermal response in the two global analyses varies with longitude. A smaller error in analysis is found in time zones where the observed maximum temperatures (Tmax) occurred close to a global analysis time (e.g., 0000, 0600, 1200, or 1800 UTC). The thermal response errors in surface temperature analyses increase linearly with the difference between the observed diurnal peak time and the analysis time closest to the peak time. Large similarities between the results obtained using both NCEP and ERA-Interim analyses give confidence in the significance of these results. The results are potentially useful for forecast verification, surface data assimilation, and climate research.
A Comparison of Labour Market Responses to the Global Downturn
Authors: Holland Dawn , Kirby Simon , Whitworth Rachel
Published: February 2010

The global economic downturn has led to a crisis in labour markets, with an estimated 15.2 million job losses across the OECD economies, equivalent to a rise in the OECD unemployment rate from 5.5 to 8.9 per cent. Initially, the rise in unemployment appeared lower than expected. In Holland, Kirby and Whitworth (2009) we demonstrated a simple rule of thumb between output growth and the unemployment rate in the OECD as a whole, based on Okun's approach. Using a dataset that spans the period 1988–2008, regression analysis suggests that on average a 1 per cent decline in output is associated with a rise of 0.6 percentage points in the unemployment rate across the OECD economies. Between the first quarter of 2008 and the first quarter of 2009, output in the OECD economies declined by 4.8 per cent. The unemployment rate rose by 1.9 points over this period, as compared to 2.9 per cent given by the rule of thumb. However, the labour market tends to lag production. While most of the major economies started to grow again in the second or third quarters of 2009, OECD unemployment continued to rise into the final quarter of the year, with a cumulative increase in the OECD unemployment rate of 3.4 percentage points — even higher than that suggested by our rule of thumb.
Fiscal and Financial Responses to the Economic Downturn
Authors: Barrell Ray , Holland Dawn
Published: February 2010

The financial crisis that started in the summer of 2007 and worsened in the autumn of 2008 has involved a repricing of risk and a reduction in the level of potential output in the OECD of between 3 and 5 per cent. In addition it has caused a major recession, leaving output gaps in the UK, the US and the Euro Area currently standing at 3 to 5 per cent of potential GDP despite active policy responses. We show that monetary policy (and especially quantitative easing) has increased output growth in the US and the UK by half a per cent in 2009, and will do the same in 2010Q1. Fiscal policy is also shown to have been effective, but we argue that more could have been done if unfounded worries about excess borrowing had not arisen.
Assessing non-response bias in pediatric palliative care research
Authors: Knapp Caprice A , Madden Vanessa L , Curtis Charlotte , Sloyer Phyllis J , Shenkman Elizabeth A
Published: February 2010

National experts have recognized a need for increased research in pediatric palliative care. However, when conducting research it is important to use rigorous methods, report significant and non-significant findings, and include information on responders and non-responders. Most studies do not present information on non-responders, yet this is critical as the results many not be generalizable if there are inherent differences between the two groups. Using survey data from parents whose children with life-limiting illnesses were enrolled in Florida’s publicly funded pediatric palliative care program called Partners in Care: Together for Kids; this study investigates whether non-response bias exists, and if so, what characteristics are associated with non-response. Bivariate and multivariate analyses were conducted to determine whether individual characteristics differed between responders and non-responders. Throughout our analyses, we conducted the analyses using different ways in which ‘non-response’ can be defined. Our results suggest that regardless of how non-response is defined, Black, non-Hispanic parents were less likely to participate than White non-Hispanic parents. However, we also found that of the Black, non-Hispanic parents who did not participate, their primary reason for doing so was that they had non-working or disconnected phone numbers. Only 3% of the Black, non-Hispanic parents who did not participate flatly refused. Information from this study can be used to design interventions aimed at increasing minority participation in pediatric palliative care research.
Effect of Obesity on Breast Cancer Development
Authors: Cleary M. P. , Grossmann M. E. , Ray A.
Published: February 2010

In recent years, obesity has been identified as a risk factor for the development of breast cancer in postmenopausal women, and it has been associated with a poor outcome. Many factors appear to be important in the mechanism of this increased risk, including estrogen, estrogen receptors, and the adipokines leptin and adiponectin. Estrogen, a potent mitogen for mammary cells, has long been implicated in the development of mammary tumors. Because adipose-associated aromatase activity increases the conversion of androgen to estrogen, mammary adipose tissue is thought to be an important source of local estrogen production. Leptin, which increases in the circulation in proportion to body fat stores, has been demonstrated in vitro to promote breast cancer cell growth. Animal models have also identified leptin as an important factor for the development of mammary tumors. In contrast to leptin, serum adiponectin concentrations are inversely related to body fat stores, and the addition of adiponectin to human breast cancer cells reduces cell proliferation and enhances apoptosis. This review explores the relationship between these factors and the development of mammary cancer in humans and mouse models.
A Neural Marker of Costly Punishment Behavior
Authors: Knoch Daria , Gianotti Lorena R.R. , Baumgartner Thomas , Fehr Ernst
Published: February 2010

Human readiness to incur personal costs to punish norm violators is a key force in the maintenance of social norms. The willingness to punish is, however, characterized by vast individual heterogeneity that is poorly understood. In fact, this heterogeneity has so far defied explanations in terms of individual-level demographic or psychological variables. Here, we use resting electroencephalography, a stable measure of individual differences in cortical activity, to show that a highly specific neural marker—baseline cortical activity in the right prefrontal cortex—predicts individuals’ punishment behavior. The analysis of task-independent individual variation in cortical baseline activity provides a new window into the neurobiology of decision making by bringing dispositional neural markers to the forefront of the analysis.
Identification of putative innate immune related genes from a cell line of the mosquito Aedes albopictus following bacterial challenge
Authors: Dixit Rajnikant , Patole Millind S. , Shouche Yogesh S.
Published: February 2010

We report identification of putative innate immune related genes from a cell line of the mosquito Aedes albopictus challenged with heat-killed bacteria. Using a subtractive hybridization and sequencing approach, we analyzed a total 309 expressed sequence tags (ESTs) which clustered in 40 contigs. Thirty-five percent of genes yielded homology to known immune genes corresponding to antimicrobial peptides (AMPs), pathogen-associated molecular patterns, protease and immune signaling cascades. Interestingly, most of the genes have not been previously described from this mosquito and thus represent a class of novel immune genes. Further, 25% sequences did not match to any known species in the non-redundant databases, appear to be specific to the mosquito A. albopictus and merit further study.
Polish clayey raw materials for the production of ceramic tiles
Authors: Wyszomirski P. , Galos K.
Published: February 2010

Development of the Polish ceramic industry over the last ten years has resulted in a sharp increase in demand for basic raw materials, especially for ceramic clays – both white- and light-firing as well as red-firing varieties. Polish sources of white-firing clays are rather scarce. Their production is based on Santonian sandy-clayey sediments of the North-Sudetic Trough (Lower Silesia, SW Poland). Light-firing varieties occur mainly in Lower Jurassic sediments on the northern margin of the Holy Cross Mountains (central Poland). Red-firing well-sintering clays of Triassic age are known in the northern margin of the Holy Cross Mountains as well as in the Cracow-Silesian Monocline.

The white-firing Santonian clays contain mainly highly-ordered kaolinite (~50%) and quartz (~30%) with minor amounts of illite. Their grain-size median ranges between 1.9 and 2.5 μm. They show moderate plasticity (bending strength after drying at 1.7–1.9 MPa) and weak sinterability (water absorption after firing ~12%), but greater lightness after firing (L parameter ~86%). The light-firing Jurassic clays are kaolinitic-illitic in character, with a variable content of quartz. Kaolinite is represented by the low-ordered variety. The grain-size median is also variable, ranging between 1.1 and 3.4 μm. They show good plasticity (bending strength after drying 2.6–2.8 MPa), good or very good sinterability (water absorption after firing <6%) but moderate lightness (L ~79%).

Triassic red clays are highly polymineralic, with illite, kaolinite, smectite, chlorite and mixed-layered minerals occurring in variable amounts. Their specific features are: large hematite content (5–12%), commonly small CaO content (<0.5 wt.%) and an extremely small organic matter content (⩽0.1 wt.%). Their grain-size median usually varies between 2 and 3 mm. Using such clays, sintered ceramics (e.g. stoneware tiles) are obtained after firing in the temperature range 1150–1200ºC.
Inactivation of LEF1 in T-cell acute lymphoblastic leukemia
Authors: Gutierrez Alejandro , Sanda Takaomi , Ma Wenxue , Zhang Jianhua , Grebliunaite Ruta , Dahlberg Suzanne , Neuberg Donna , Protopopov Alexei , Winter Stuart S. , Larson Richard S. , Borowitz Michael J. , Silverman Lewis B. , Chin Lynda , Hunger Stephen P. , Jamieson Catriona , Sallan Stephen E. , Look A. Thomas
Published: February 2010

To further unravel the molecular pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL), we performed high-resolution array comparative genomic hybridization on diagnostic specimens from 47 children with T-ALL and identified monoallelic or biallelic LEF1 microdeletions in 11% (5 of 47) of these primary samples. An additional 7% (3 of 44) of the cases harbored nonsynonymous sequence alterations of LEF1, 2 of which produced premature stop codons. Gene expression microarrays showed increased expression of MYC and MYC targets in cases with LEF1 inactivation, as well as differentiation arrest at an early cortical stage of thymocyte development characterized by expression of CD1B, CD1E, and CD8, with absent CD34 expression. LEF1 inactivation was associated with a younger age at the time of T-ALL diagnosis, as well as activating NOTCH1 mutations, biallelic INK4a/ARF deletions, and PTEN loss-of-function mutations or activating mutations of PI3K or AKT genes. These cases generally lacked overexpression of the TAL1, HOX11, HOX11L2, or the HOXA cluster genes, which have been used to define separate molecular pathways leading to T-ALL. Our findings suggest that LEF1 inactivation is an important step in the molecular pathogenesis of T-ALL in a subset of young children.
Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola
Authors: Zhou Yong-Li , Xu Mei-Rong , Zhao Ming-Fu , Xie Xue-Wen , Zhu Ling-Hua , Fu Bin-Ying , Li Zhi-Kang
Published: February 2010

Background

Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown.

Results

A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation.

Conclusions

In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.
Heads or tails: L1 insertion-associated 5' homopolymeric sequences
Authors: Meyer Thomas J , Srikanta Deepa , Conlin Erin M , Batzer Mark A
Published: February 2010

Background

L1s are one of the most successful autonomous mobile elements in primate genomes. These elements comprise as much as 17% of primate genomes with the majority of insertions occurring via target primed reverse transcription (TPRT). Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications.

Results

We report on loci with sequence architecture consistent with variants of the twin priming mechanism and introduce dual priming, a mechanism that could generate similar sequence characteristics. These insertions take the form of truncated L1s with hallmarks of classical TPRT insertions but having a poly(T) simple repeat at the 5' end of the insertion. We identified loci using computational analyses of the human, chimpanzee, orangutan, rhesus macaque and marmoset genomes. Insertion site characteristics for all putative loci were experimentally verified.

Conclusions

The 39 loci that passed our computational and experimental screens probably represent inversion-deletion events which resulted in a 5' inverted poly(A) tail. Based on our observations of these loci and their local sequence properties, we conclude that they most probably represent twin priming events with unusually short non-inverted portions. We postulate that dual priming could, theoretically, produce the same patterns. The resulting homopolymeric stretches associated with these insertion events may promote genomic instability and create potential target sites for future retrotransposition events.
High-order finite-difference simulations of marine CSEM surveys using a correspondence principle for wave and diffusion fields
Authors: Mittet Rune
Published: February 2010

The computer time required to solve a typical 3D marine controlled-source electromagnetic surveying (CSEM) simulation can be reduced by more than one order of magnitude by transforming low-frequency Maxwell equations in the quasi-static or diffusive limit to a hyperbolic set of partial differential equations that give a representation of electromagnetic fields in a fictitious wave domain. The dispersion and stability analysis can be made equivalent to that of other types of wave simulation problems such as seismic acoustic and elastic modeling. Second-order to eighth-order spatial derivative operators are implemented for flexibility. Fourth-order and sixth-order methods are the most numerically efficient implementations for this particular scheme. An implementation with high-order operators requires that both electric and magnetic fields are extrapolated simultaneously into the air layer. The stability condition given for high-order staggered-derivative operators here should be equally valid for seismic-wave simulation. The bandwidth of recovered fields in the diffusive domain is independent of the bandwidth of the fields in the fictitious wave domain. The fields in the fictitious wave domain do not represent observable fields. Propagation paths and interaction/reflection amplitudes are not altered by the transform from the fictitious wave domain to the diffusive frequency domain; however, the transform contains an exponential decay factor that damps down late arrivals in the fictitious wave domain. The propagation paths that contribute most to the diffusive domain fields are airwave (shallow water) plus typically postcritical events such as refracted and guided waves. The transform from the diffusive frequency domain to the fictitious wave domain is an ill-posed problem. The transform is nonunique. This gives a large degree of freedom in postulating temporal waveforms for boundary conditions in the fictitious wave domain that reproduce correct diffusive frequency-domain fields.
Fresnel-zone binning: Fresnel-zone shape with offset and velocity function
Authors: Monk David J.
Published: February 2010

The concept of the Fresnel zone has been explored by many workers; most commonly, their work has involved examining the Fresnel zone in the limiting case of zero offset and constant velocity. I have examined the shape of the Fresnel zone for nonzero offset and in the situation of constant velocity gradient. Finite-offset Fresnel zones are not circular but are elliptical and may be many times larger than their zero-offset equivalents. My derivation takes a largely geometric approach, and I suggest a useful approximation for the dimension of the Fresnel zone parallel to the shot-receiver azimuth. The presence of a velocity gradient (velocity increasing with depth) in the subsurface leads to an expansion of the Fresnel zone to an area that is far larger than may be determined through a more usual straight-ray determination.
Randomized Study of Lapatinib Alone or in Combination With Trastuzumab in Women With ErbB2-Positive, Trastuzumab-Refractory Metastatic Breast Cancer
Authors: Blackwell Kimberly L. , Burstein Harold J. , Storniolo Anna Maria , Rugo Hope , Sledge George , Koehler Maria , Ellis Catherine , Casey Michelle , Vukelja Svetislava , Bischoff Joachim , Baselga Jose , O'Shaughnessy Joyce
Published: February 2010

Purpose

Preclinical studies in ErbB2-positive cell lines demonstrated a synergistic interaction between lapatinib and trastuzumab, suggesting that dual blockade is more effective than a single agent alone. EGF104900 compared the activity of lapatinib alone or in combination with trastuzumab in patients with ErbB2-positive, trastuzumab-refractory metastatic breast cancer (MBC).

Patients and Methods

Patients with ErbB2-positive MBC who experienced progression on prior trastuzumab-containing regimens were randomly assigned to receive either lapatinib alone or in combination with trastuzumab. The primary end point was progression-free survival (PFS). Secondary efficacy end points included overall response rate (ORR), clinical benefit rate (CBR; complete response, partial response, and stable disease for ≥ 24 weeks), and overall survival (OS).

Results

In the intent-to-treat population (N = 296) who received a median of three prior trastuzumab-containing regimens, the combination of lapatinib with trastuzumab was superior to lapatinib alone for PFS (hazard ratio [HR] = 0.73; 95% CI, 0.57 to 0.93; P = .008) and CBR (24.7% in the combination arm v 12.4% in the monotherapy arm; P = .01). A trend for improved OS in the combination arm was observed (HR = 0.75; 95% CI, 0.53 to 1.07; P = .106). There was no difference in ORR (10.3% in the combination arm v 6.9% in the monotherapy arm; P = .46). The most frequent adverse events were diarrhea, rash, nausea, and fatigue; diarrhea was higher in the combination arm (P = .03). The incidence of symptomatic and asymptomatic cardiac events was low (combination therapy = 2% and 3.4%; monotherapy = 0.7% and 1.4%, respectively).

Conclusion

Despite disease progression on prior trastuzumab-based therapy, lapatinib in combination with trastuzumab significantly improved PFS and CBR versus lapatinib alone, thus offering a chemotherapy-free option with an acceptable safety profile to patients with ErbB2-positive MBC.