bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Detection of Mutations Associated with First- and Second-Line Drug Resistance Compared with Conventional Drug Susceptibility Testing of Mycobacterium tuberculosis
Authors: Campbell Patricia J. , Morlock Glenn P. , Sikes R. David , Dalton Tracy L. , Metchock Beverly , Starks Angela M. , Hooks Delaina P. , Cowan Lauren S. , Plikaytis Bonnie B. , Posey James E.
Published: February 2011

The emergence of multi- and extensively drug-resistant tuberculosis is a significant impediment to the control of this disease because treatment becomes more complex and costly. Reliable and timely drug susceptibility testing is critical to ensure that patients receive effective treatment and become noninfectious. Molecular methods can provide accurate and rapid drug susceptibility results. We used DNA sequencing to detect resistance to the first-line antituberculosis drugs isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB) and the second-line drugs amikacin (AMK), capreomycin (CAP), kanamycin (KAN), ciprofloxacin (CIP), and ofloxacin (OFX). Nine loci were sequenced:
rpoB
(for resistance to RIF),
katG
and
inhA
(INH),
pncA
(PZA),
embB
(EMB),
gyrA
(CIP and OFX), and
rrs
,
eis
, and
tlyA
(KAN, AMK, and CAP). A total of 314 clinical
Mycobacterium tuberculosis
complex isolates representing a variety of antibiotic resistance patterns, genotypes, and geographical origins were analyzed. The molecular data were compared to the phenotypic data and the accuracy values were calculated. Sensitivity and specificity values for the first-line drug loci were 97.1% and 93.6% for
rpoB
, 85.4% and 100% for
katG
, 16.5% and 100% for
inhA
, 90.6% and 100% for
katG
and
inhA
together, 84.6% and 85.8% for
pncA
, and 78.6% and 93.1% for
embB
. The values for the second-line drugs were also calculated. The size and scope of this study, in numbers of loci and isolates examined, and the phenotypic diversity of those isolates support the use of DNA sequencing to detect drug resistance in the
M. tuberculosis
complex. Further, the results can be used to design diagnostic tests utilizing other mutation detection technologies.
Complementation of
Rickettsia rickettsii
RelA/SpoT Restores a Nonlytic Plaque Phenotype
Authors: Clark Tina R. , Ellison Damon W. , Kleba Betsy , Hackstadt Ted
Published: February 2011

Spotted fever group rickettsiae are known to produce distinct plaque phenotypes. Strains that cause lytic infections in cell culture form clear plaques, while nonlytic strains form opaque plaques in which the cells remain intact. Clear plaques have historically been associated with more-virulent species or strains of spotted fever group rickettsiae. We have selected spontaneous mutant pairs from two independent strains of
Rickettsia rickettsii
, the virulent R strain and the avirulent Iowa strain. A nonlytic variant of
R. rickettsii
R, which typically produces clear plaques, was isolated and stably maintained. A lytic variant of the Iowa strain, which characteristically produces opaque plaques, was also selected and maintained. Genomic resequencing of the variants identified only a single gene disrupted in each strain. In both cases, the mutation was in a gene annotated as
relA
/
spoT
-like. In the Iowa strain, a single mutation introduced a premature stop codon upstream from region encoding the predicted active site of RelA/SpoT and caused the transition to a lytic plaque phenotype. In
R. rickettsii
R, the nonlytic plaque phenotype resulted from a single-nucleotide substitution that shifted a tyrosine residue to histidine near the active site of the enzyme. The intact
relA
/
spoT
gene thus occurred in variants with the nonlytic plaque phenotype. Complementation of the truncated
relA
/
spoT
gene in the Iowa lytic plaque variant restored the nonlytic phenotype. The
relA
/
spoT
mutations did not affect the virulence of either strain in a Guinea pig model of infection; R strain lytic and nonlytic variants both induced fever equally, and the mutation in Iowa to a lytic phenotype did not cause them to become virulent.
Preterm Infants Have Deficient Monocyte and Lymphocyte Cytokine Responses to Group B Streptococcus
Authors: Currie Andrew J. , Curtis Samantha , Strunk Tobias , Riley Karen , Liyanage Khemanganee , Prescott Susan , Doherty Dorota , Simmer Karen , Richmond Peter , Burgner David
Published: February 2011

Group B streptococcus (GBS) is an important cause of early- and late-onset sepsis in the newborn. Preterm infants have markedly increased susceptibility and worse outcomes, but their immunological responses to GBS are poorly defined. We compared mononuclear cell and whole-blood cytokine responses to heat-killed GBS (HKGBS) of preterm infants (gestational age [GA], 26 to 33 weeks), term infants, and healthy adults. We investigated the kinetics and cell source of induced cytokines and quantified HKGBS phagocytosis. HKGBS-induced tumor necrosis factor (TNF) and interleukin 6 (IL-6) secretion was significantly impaired in preterm infants compared to that in term infants and adults. These cytokines were predominantly monocytic in origin, and production was intrinsically linked to HKGBS phagocytosis. Very preterm infants (GA, <30 weeks) had fewer cytokine-producing monocytes, but nonopsonic phagocytosis ability was comparable to that for term infants and adults. Exogenous complement supplementation increased phagocytosis in all groups, as well as the proportion of preterm monocytes producing IL-6, but for very preterm infants, responses were still deficient. Similar defective preterm monocyte responses were observed in fresh whole cord blood stimulated with live GBS. Lymphocyte-associated cytokines were significantly deficient for both preterm and term infants compared to levels for adults. These findings indicate that a subset of preterm monocytes do not respond to GBS, a defect compounded by generalized weaker lymphocyte responses in newborns. Together these deficient responses may increase the susceptibility of preterm infants to GBS infection.
Parity and Placental Infection Affect Antibody Responses againstPlasmodium falciparumduring Pregnancy
Authors: Mayor Alfredo , Rovira-Vallbona Eduard , Machevo Sonia , Bassat Quique , Aguilar Ruth , Quintó Llorenç , Jiménez Alfons , Sigauque Betuel , Dobaño Carlota , Kumar Sanjeev , Singh Bijender , Gupta Puneet , Chauhan Virander S. , Chitnis Chetan E. , Alonso Pedro L. , Menéndez Clara
Published: February 2011

Women are at higher risk ofPlasmodium falciparuminfection when pregnant. The decreasing risk of malaria with subsequent pregnancies is attributed to parity-dependent acquisition of antibodies against placental parasites expressing variant surface antigens, VAR2CSA, that mediate placental sequestration through adhesion to chondroitin sulfate A (CSA). However, modulation of immunity during pregnancy may also contribute to increase the risk of malaria. We compared antibody responses among 30 Mozambican primigravidae and 60 multigravidae at delivery, 40 men, and 40 children. IgG levels were measured against the surface antigens of erythrocytes infected withP. falciparumisolated from 12 pregnant women (4 placental and 8 peripheral blood isolates) and 26 nonpregnant hosts. We also measured IgG levels against merozoite recombinant antigens and total IgG. PlacentalP. falciparuminfection was associated with increased levels of total IgG as well as IgG levels against merozoite antigens and parasite isolates from pregnant and nonpregnant hosts. We therefore stratified comparisons of antibody levels by placental infection. Compared to multigravidae, uninfected primigravidae had lower total IgG as well as lower levels of IgGs against peripheral blood isolates from both pregnant and nonpregnant hosts. These differences were not explained by use of bed nets, season at delivery, neighborhood of residence, or age. Compared to men, infected primigravidae had higher levels of IgGs against isolates from pregnant women and CSA-binding lines but not against other isolates, supporting the concept of a pregnancy-specific development of immunity to these parasite variants. Results of this study show that parity and placental infection can modulate immune responses during pregnancy against malaria parasites.
Toll-Like Receptor 9 Is Required for Full Host Resistance to
Mycobacterium
avium
Infection but Plays No Role in Induction of Th1 Responses
Authors: Carvalho Natália B. , Oliveira Fernanda S. , Durães Fernanda V. , de Almeida Leonardo A. , Flórido Manuela , Prata Luana O. , Caliari Marcelo V. , Appelberg Rui , Oliveira Sérgio C.
Published: February 2011

To investigate the role of Toll-like receptor 9 (TLR9) in innate immunity to
Mycobacterium
avium
, TLR9, TLR2, and MyD88 knockout (KO) mice were infected with this bacterium. Bacterial burdens were higher in the spleens, livers, and lungs of infected TLR9 KO mice than in those of C57BL/6 mice, indicating that TLR9 is required for efficient control of
M
.
avium
infection. However, TLR9 KO or TLR2 KO spleen cells displayed normal
M
.
avium
-induced tumor necrosis factor alpha (TNF-α) and gamma interferon (IFN-γ) responses. This finding was confirmed by determining the number of splenic CD4
+
T cells producing IFN-γ by flow cytometry. Furthermore, TLR2 and MyD88, but not TLR9, played a major role in interleukin-12 and TNF-α production by
M
.
avium
-infected macrophages and dendritic cells (DCs). We also found that major histocompatibility complex class II molecule expression on DCs is regulated by TLR2 and MyD88 signaling but not by TLR9. Finally, lack of TLR9, TLR2, or MyD88 reduced the numbers of macrophages, epithelioid cells, and lymphocytes in
M
.
avium
-induced granulomas but only MyD88 deficiency affected the number of liver granulomas. In summary, our data demonstrated that the involvement of TLR9 in the control of
M
.
avium
infection is not related to the induction of Th1 responses.
The
Neisseria gonorrhoeae
Biofilm Matrix Contains DNA, and an Endogenous Nuclease Controls Its Incorporation
Authors: Steichen Christopher T. , Cho Christine , Shao Jian Q. , Apicella Michael A.
Published: February 2011

Neisseria gonorrhoeae
has been shown to produce biofilms both in experimental flow chambers and in the human host. Our laboratory has shown that extracellular DNA is an essential component of the gonococcal matrix. We have also identified a gene in
N. gonorrhoeae
, which we designated
nuc
. This gene has homology with the staphylococcus-secreted thermonuclease. Our laboratory has characterized
nuc
through phenotypic analysis of a
nuc
deletion mutant. Biofilms grown with this strain are significantly thicker and of greater biomass than the
N. gonorrhoeae
1291 parent strain. Confocal microscopy indicates that the increased size of the mutant biofilms appears to be due to elevated amounts of extracellular DNA in the biofilm matrix. Chromosomal complementation of the
nuc
mutation restored the wild-type biofilm phenotype. In addition, we have cloned and expressed the Nuc protein in
Escherichia coli
, and our data indicate that it has the ability to digest multiple forms of DNA and is a thermonuclease. The ability of Nuc to digest DNA also extends to its ability to disrupt established gonococcal biofilms through degradation of the DNA in the biofilm matrix. Our studies indicate that the
N. gonorrhoeae
biofilm contains DNA and that the Nuc protein appears to play a role in biofilm formation and remodeling.
The current status of bariatric surgery
Authors: Pollard Stephen
Published: February 2011

As the incidence of obesity continues to rise, increasing numbers of patients are undergoing bariatric surgery to address morbid obesity and weight related health issues. Bariatric procedures aim to reduce dietary intake and/or interfere with food absorption and are now in widespread use but with a huge capacity shortfall leading to a degree of rationing of the resource. Such treatment should be regarded as palliative in that it does not cure the underlying disorder, and guidelines have been produced to define which patients should be considered for this type of surgery, which must be undertaken in a multidisciplinary setting. Long term results show this to be a cost-effective intervention with a durable positive impact on cardiac risk factors and in particular type 2 diabetes and obstructive sleep apnoea, together with a reduction in all cause mortality and malignancy and an improvement in quality of life. Systematic data collection has now started in the UK and will assist in defining the best application of the resource.
Republished review: Tourette's syndrome and other tic disorders
Authors: Rickards Hugh
Published: February 2011

Tourette's syndrome is a neuropsychiatric disorder characterised by motor and phonic tics. Although tics are common in children, only about 1% of those affected meet the criteria for Tourette's syndrome, and many are not disabled by it. Associated problems such as attention deficit hyperactivity disorder and obsessive–compulsive disorders can often be more disabling than the tics themselves. People with Tourette's tend to be worst in their teenage years but improve in adulthood. The cause is unknown but there are strong genetic factors. Treatment should be aimed at minimising disability and includes social, psychological and biological approaches.
Development of the England Wildlife Health Strategy – a framework for decision makers
Authors: Hartley M. , Lysons R.
Published: February 2011

Diseases in wildlife have been recognised as having the potential to affect human health, livestock health and species conservation. In order to assess and respond to these potential risks in an effective and a proportionate way, the UK Government initiated development of the Wildlife Health Strategy to provide a framework for decision making. The England Wildlife Health Strategy (EWHS) has been developed through extensive consultation. Discussions and negotiations with government departments, agencies, non‐governmental public bodies and wildlife organisations were held to obtain advice and input on specific and specialised aspects of wildlife health. A series of workshops to investigate the application of innovative science to wildlife health policy contributed further. A formal public consultation was held that proposed a range of actions to implement the strategy. A summary of responses to this consultation was published in October 2007. The EWHS was published in June 2009 and provides a framework for a generic four‐stage approach to wildlife health that can be adopted by decision makers both within and outside government.
Bioremediation of wastewater containing azo dyes through sequential anaerobic–aerobic bioreactor system and its biodiversity
Authors: Dafale Nishant , Wate Satish , Meshram Sudhir , Neti Nageswara Rao
Published: February 2011

Wide range of dyes and dyestuffs used in textile manufacturing are xenobiotic compounds and attract stricter to strict environmental regulations. The ability of microbial consortia to decolorize and metabolize dyes has long been known, and the use of bioremediation based technologies for treating textile wastewater has attracted interest. These dyes are decolorized by microbial consortia but technologies for their complete mineralization are still not developed. The most logical concept for the removal of azo dyes in biological wastewater treatment systems is based on anaerobic treatment, for the reductive decolorization, in combination with aerobic treatment, for the degradation of the by-products (aromatic amines) generated in the anaerobic bioreactor. Several research and review articles were published on anaerobic decolorization; however, research on complete mineralization of dyes through sequential anaerobic–aerobic bioreactors has received greater attention recently. Bioremediation through sequential anaerobic–aerobic bioreactor system has been reviewed in this article with critical appraisal using data generated through our experiments. While reviewing this work, we realized the importance of microbial diversity in a treatment unit to better understand the functional status to enhance the mineralization activity of the bioreactor.
A conceptual framework for understanding, assessing, and mitigating ecological effects of forest roads
Authors: Robinson C. , Duinker P.N. , Beazley K.F.
Published: February 2011

A review of road-ecology literature suggests that impacts of forest roads on species and ecosystems begin during the road construction phase, but persist and accumulate well after a road is no longer in use. Over this time, impacts stemming originally from construction, but then also from the continued physical presence and human use of the road, follow complex multiple pathways ending in diminished species persistence. Yet in practice, road-impact considerations rarely extend beyond short-term issues related to road construction or beyond the spatial extent of the road corridor. Even when the range of potential impacts is recognized, managers rarely have a framework for assessing those impacts. This can be problematic, as informed decisions regarding the long-term, wide-ranging ecological consequences of road placement, design, and use can lessen the degree to which a road modifies the composition, structure, and function of forest ecosystems. This paper presents a conceptual framework for organizing, synthesizing, and applying our growing understanding of how roads affect forest ecosystems. The framework includes two parts: (1) a series of impact-hypothesis diagrams wherein ecological impacts are organized relevant to three phases of road existence: construction, presence and use; and (2) a five-step approach whereby ecological impact and road importance can be evaluated and a decision matrix used to determine appropriate mitigation strategies. Highlights of a case study conducted in southwestern Nova Scotia are presented to illustrate the applicability of the framework.
Conditions controlling atmospheric pollutant deposition via snowpack
Authors: Błaś Marek , Cichała-Kamrowska Katarzyna , Sobik Mieczysław , Polkowska Żaneta , Namieśnik Jacek
Published: February 2011

Solid precipitation represents a potentially important addition to other measures of deposition. However, an accurate estimate of snowfall amount and pollutant loading is not a trivial matter. There are obvious distinctions between regular precipitation collection and snowpack sampling that represent the cumulative chemistry of bulk deposition. The main goal is to show the most important processes and factors that may influence the rate and magnitude of pollutants deposition affected by the snowfall and snow cover: atmospheric pollutant enhancement of snowfall, pollutants deposition at snow cover surface, drifting and blowing snow, formation of the snow cover and its internal changes, as well as pollutants flow through the snowpack. These phenomena lead to continuous changes in the chemistry of the snow cover and the deposition calculated on the basis of pollutants concentrations in daily portions of atmospheric precipitation. The real deposition released from snowpack is strictly related to the number and depth of thaw episodes. If the amount of stored pollutants is large, first portions of ablation water flushing from the snowpack can carry the load of pollutants, and potentially affecting the environment in a detrimental way. Igneous bedrock is especially sensitive to acidic ions because of its low buffering capacity.
Carbon monoxide modeling studies: a review
Authors: Nigam Sudhir , Nigam Rashmi , Kulshrestha Mukul , Mittal Sushil Kumar
Published: February 2011

The use of computational models plays a vital role in the environmental regulatory process. The complex relationship between environmental emissions, the quality of the environment, and human and ecological impacts can be vividly elucidated by modeling process. Among the six criteria, the pollutant carbon monoxide (CO) is given least attention for imperative modeling. The frequent exceedance of CO emissions can be harmful to human health and the environment. Effectively managing of CO critically demands an accurate emissions estimate and an efficient model for forecasting the future status of the CO. Most of the CO forecast models have been developed to describe the temporal and spatial distribution of CO on roadways. Main categories of CO models are deterministic, statistical, hybrid, and neural network in nature. This paper reviews attempts and resources for carrying out CO dispersion modeling studies. The scope and restraint associated with various modeling attempts are also discussed.
Bioretention processes for phosphorus pollution control
Authors: Roy-Poirier Audrey , Champagne Pascale , Filion Yves
Published: February 2011

Phosphorus is a water pollutant of concern around the world as it limits the productivity of most freshwater systems which can undergo eutrophication under high phosphorus inputs. The importance of treating stormwater as part of an integrated phosphorus pollution management plan is now recognized. Bioretention systems are urban stormwater best management practices (BMPs) that rely on terrestrial ecosystem functions to retain storm flows and reduce pollutant loads. Bioretention has shown great potential for stormwater quantity and quality control. However, phosphorus removal has been inconsistent in bioretention systems, with phosphorus leaching observed in some systems. Numerical models can be used to predict the performance of bioretention systems under various conditions and loadings. The aim of this paper is to identify and characterize bioretention phosphorus cycling processes, with a particular focus on process modelling. Both soluble and particulate phosphorus forms are expected in significant proportions in bioretention system inflows. Sorption mechanisms are expected to dominate soluble phosphorus cycling, while particulate phosphorus transport occurs mainly through sedimentation. Vegetative uptake, mineralization, and immobilization are also known to play a role in the cycling of phosphorus; however, data is lacking to assess their importance. There is a need for simple mathematical equations to represent dissolution and precipitation reactions in bioretention systems. More research is also needed to characterize the rates of colloidal capture and mobilization within soils. Finally, approaches used to model phosphorus transport in systems similar to bioretention are not applicable to bioretention system modelling. This reinforces the need for the development of a bioretention phosphorus transport model.
A review on the removal of nitrogen oxides from polluted flow by bioreactors
Authors: Niu Hejingying , Leung D.Y.C.
Published: February 2011

Nitric oxide (NO) and nitrogen dioxide (NO2) are the main pollutants of nitrogen oxides (NOx) released during a combustion process. They induce harmful effects both to the environment and human health, such as the formation of acid rain, an increase of the tropospheric ozone, global warming, etc. Selective catalytic reduction, selective non-catalytic reduction, adsorption and scrubbing (absorption) are the conventional technologies used to control NOxemission from exhaust gas. The bioreactor appears superior to conventional technologies in terms of simplicity and economy in operation, low process energy requirements, and easy treatment of residual products. This paper reviews two biologically-based NOxremoval theories, i.e., nitrification and denitrification. The use of bacteria, fungi and microalgae are discussed and compared. The study indicates that the bioreactor is a promising technology that can be used to control NOxemitted during combustion processes.
Environmental review of geyser basins: resources, scarcity, threats, and benefits
Authors: Barrick Kenneth A.
Published: February 2011

The world’s geysers are known for providing one of nature’s most unusual water spectacles, with most sending water upwards of about 3 m, but a few “grand” or tall geysers erupt to heights of 60 m or more. A geyser basin is a composite resource made up of geysers and hot springs that cluster around a common hydrothermal reservoir, and might also contain other hydrothermal features like fumaroles and mud pots. The world’s remaining geyser basins are exceptionally rare, and are increasingly important recreation, economic, scientific, cultural, spiritual, therapeutic, and national heritage assets. Geyser basins harbor thermophilic microorganisms that contain heat-adapted biomolecules that can be harvested to provide vital components for DNA testing, and other high-temperature industrial processes. However, geysers and other surface hydrothermal features are increasingly vulnerable, and can be quickly and irreversibly damaged. Energy development projects quenched about 249 geysers, or about half of all geysers that were not protected in a national park or reserve. About 100 geysers were driven to extinction in New Zealand, about 46 in Iceland, and about 48 in the USA. Sustaining the world’s remaining geyser basins requires protecting the hydrothermal reservoirs that support them based on an integrated management approach that takes into account the distinctive characteristics of surface hydrothermal features and the benefits that society derives from them. A framework is provided that defines geyser basin resources, the scarcity of the remaining geysers, the environmental threats, and preservation benefits. Multiple case studies of mass geyser extinction are highlighted, including a summary of the landscape changes that can accompany geothermal energy development.
Anaerobic digestion from the viewpoint of microbiological, chemical, and operational aspects — a review
Authors: Amani T. , Nosrati M. , Sreekrishnan T.R.
Published: February 2011

Anaerobic digestion (AD) is intrinsically a sequential complex chemical and biochemical process, and many factors (microbiological, operational, and chemical) can affect its performance. The great complexity of AD may lead to many serious problems (such as instability, long retention times, low efficiency, and high polluted supernatant) that prevent this technique from being widely used and commercialized. The aim of this paper is to review the present knowledge of the AD process in view of its microbiological, operational, and chemical aspects. Different groups of anaerobic microorganisms with specific growth conditions, physiological properties, and metabolic activities are involved in the AD process. Interactions of anaerobic microorganisms are incredibly complicated, and the effective performance of AD strongly depends on the balance of these relationships. The syntrophic interaction of acetogens and methanogens is the most important relationship in AD because acetogenesis and methanogenesis reactions under thermodynamic standard conditions are endergonic and naturally do not occur. Moreover, operational and chemical factors affect the anaerobes in certain ways. It is believed that there are many ambiguous points in AD that are not yet known. Therefore, by controlling and monitoring each of the microbiological, operational, and chemical parameters, AD performance may be enhanced.
Osmotic adjustment and plant adaptation to environmental changes related to drought and salinity
Authors: Chen Hui , Jiang Jian-Guo
Published: February 2011

The salinization and water deficit of soil are widespread environmental problems in limiting plant survival, growth, and productivity. However, some plants could adopt some strategies to resist salinity and drought stresses. Among these strategies, the mechanism of osmotic adjustment could help plants and algae to avoid ion toxicity and maintain water uptake in both stresses by accumulating large quantities of osmolytes. Two types of osmolytes, organic solutes and inorganic ions, play a key role in osmotic adjustment. Different osmolytes and their osmotic adjustment actions are different according to their distribution in different plants. Organic solutes, known as compatible solutes, include amino acids, glycerol, sugars, and other low molecular weight metabolites, serve a function in cells to lower or balance the osmotic potential of intracellular and extracellular ions in resistance to osmotic stresses. Inorganic ions for osmotic adjustment are mainly Na+, K+, Ca2+, and Cl–. Inorganic ions make great contribution in osmotic adjustment by ion transport processes with related ion antiporters and ion channels. The aim of this review is to integrate recent data on the mechanisms of osmotic adjustment by osmolytes in plants and algae, and to illustrate the variety of related molecular mechanisms, to introduce new concepts and techniques into this research field. Genetic manipulation including the application of transgenic techniques in plants provides promising strategies to elevate the tolerance capability of plants under osmotic stress conditions.
Growth and reproduction of vascular plants in polluted environments: a synthesis of existing knowledge
Authors: Zvereva Elena L. , Roitto Marja , Kozlov Mikhail V.
Published: February 2011

Identification of factors explaining diversity in plant responses to industrial pollution is crucial for predicting fates of polluted ecosystems. Meta-analysis based on 203 publications demonstrated that plants growing near point polluters showed similar decreases in characters reflecting growth (–13.1%) and reproduction processes (–8.5%). In herbaceous plants, root growth was reduced, while aboveground biomass did not change, because the decrease in leaf size was compensated by an increase in leaf number. In contrast, woody plants demonstrated no changes in allometry and their growth was reduced to a greater extent than growth of herbaceous plants. Raunkiaer’s classification of life forms appeared the best predictor of species’ responses to pollution. Within woody plants, trees and shrubs, but not dwarf shrubs, showed strong decreases in growth and reproduction. Within herbaceous plants, significant growth reduction was observed only in annuals. Longevity of foliage or plant phylogeny did not explain variation in species’ responses. Adverse effects of pollution were stronger in regions with higher temperature and precipitation, hinting that existing pollution loads may become more harmful for plants as climate changes. Relatively minor explanatory value of the characteristics of individual polluters removes one of the principal obstacles to accounting for the effects of pollution in vegetation models and allows extrapolation of the effects observed near point polluters to both regional and global scales. We conclude that losses in productivity of plant communities due to aerial pollution can be approximately estimated on the basis of the life form spectra and climate.
Biological effects from exposure to electromagnetic radiation emitted by cell tower base stations and other antenna arrays
Authors: Levitt B. Blake , Lai Henry
Published: February 2011

The siting of cellular phone base stations and other cellular infrastructure such as roof-mounted antenna arrays, especially in residential neighborhoods, is a contentious subject in land-use regulation. Local resistance from nearby residents and landowners is often based on fears of adverse health effects despite reassurances from telecommunications service providers that international exposure standards will be followed. Both anecdotal reports and some epidemiology studies have found headaches, skin rashes, sleep disturbances, depression, decreased libido, increased rates of suicide, concentration problems, dizziness, memory changes, increased risk of cancer, tremors, and other neurophysiological effects in populations near base stations. The objective of this paper is to review the existing studies of people living or working near cellular infrastructure and other pertinent studies that could apply to long-term, low-level radiofrequency radiation (RFR) exposures. While specific epidemiological research in this area is sparse and contradictory, and such exposures are difficult to quantify given the increasing background levels of RFR from myriad personal consumer products, some research does exist to warrant caution in infrastructure siting. Further epidemiology research that takes total ambient RFR exposures into consideration is warranted. Symptoms reported today may be classic microwave sickness, first described in 1978. Nonionizing electromagnetic fields are among the fastest growing forms of environmental pollution. Some extrapolations can be made from research other than epidemiology regarding biological effects from exposures at levels far below current exposure guidelines.
Down wood and biodiversity — implications to forest practices
Authors: Bunnell Fred L. , Houde Isabelle
Published: February 2011

Many species require or use down wood (fine and coarse woody debris) as habitat. Where forestry has been practiced for several rotations large proportions of these species are considered threatened. Key attributes determining the suitability of down wood as habitat are decay stage, tree species, and size, specifically diameter. Both quantity and distribution of suitable down wood influence species’ presence and abundance. We present a simple framework describing use of down wood based on broad natural history features, derive predictions from the framework, then test these by review and summary of literature. Our focus is terrestrial vertebrates, particularly in the Pacific Northwest. Species other than vertebrates are addressed to ensure that metrics derived for vertebrates also are appropriate for other organisms. Basic metrics are the same, but appropriate values span a larger range among nonvertebrates. Current evidence suggests that the “extinction debt” apparent for nonvertebrates is approaching for vertebrates. Predictions derived from underlying natural history hold when tested. From that basis we derive broad guidelines for forest planning and practice, and suggest how regional target values can be derived.
APPLICATION OF GENERALIZED FEYNMAN–HELLMANN THEOREM IN QUANTIZATION OF LC CIRCUIT IN THERMO BATH
Authors: FAN HONG-YI , TANG XU-BING
Published: February 2011

For the quantized LC electric circuit, when taking the Joule thermal effect into account, we think that physical observables should be evaluated in the context of ensemble average. We then use the generalized Feynman–Hellmann theorem for ensemble average to calculate them, which seems convenient. Fluctuation of observables in various LC electric circuits in the presence of thermo bath growing with temperature is exhibited.
CHARGE TUNNELING IN DOPED QUANTUM ROD
Authors: JAĆIMOVSKI S. K. , TOŠIĆ B. S. , ŠETRAJČIĆ J. P. , SAJFERT V. D.
Published: February 2011

This work analyzes the Abrikosov's idea that high temperature conductivity is based on resonant tunneling. A rectangular rod was considered and it was shown that high values of transparency coefficient can be produced in it. It is the consequence of the fact that electrons as well as phonons have energy gap within a rectangular rod.
A METHOD FOR CREATING MATERIALS WITH A DESIRED REFRACTION COEFFICIENT
Authors: RAMM A. G.
Published: February 2011

It is proposed to create materials with a desired refraction coefficient in a bounded domain D ⊂ ℝ3 by embedding many small balls with constant refraction coefficients into a given material. The number of small balls per unit volume around every point x ∈ D, i.e., their density distribution, is calculated, as well as the constant refraction coefficients in these balls. Embedding into D small balls with these refraction coefficients according to the calculated density distribution creates in D a material with a desired refraction coefficient.
TRANSPORT PROPERTIES OF Ag-DOPED La0.7Ca0.3MnO3 THIN FILMS ON SILICON SUBSTRATE
Authors: JIANG H. C. , ZHANG W. L. , CAO X. F. , ZHANG W. X. , PENG B.
Published: February 2011

Ag -doped La 0.7 Ca 0.3 MnO 3 (LCMO) films were prepared on silicon substrate by RF magnetron sputtering. The dependences of transport properties on annealing temperature were explored. It is shown that the resistivity of the samples decreases and the metal–insulator transition temperature shifts to higher temperature with the increase in annealing temperature. Two metal–insulator transition temperatures are presented in the R – T plots of Ag -doped LCMO films, which can be explained by the Ag 1+ substitution of La 3+ to form La 1-x Ag x MnO 3 compound. Compared with LCMO thin films, Ag -doping can observably improve the TM-I and decrease the resistivity of the samples.
CRYSTALLINE AgInSe2 FILMS ON GLASS BY LASER ABLATION
Authors: PATHAK DINESH , BEDI R. K. , KAUSHAL AJAY , KAUR DAVINDER
Published: February 2011

Laser ablation has attracted special interest for the formation of thin films compared with other formation technique. A distinctive feature of laser ablation is that it allows high quality and stoichiometry of films of even very complex element material. In this presentation, laser ablation of AgInSe 2 chalcopyrite semiconductor will be discussed in which it is difficult to maintain stoichiometry by conventional method. High Quality AgInSe 2 (AIS) films were grown on Glass substrates by the ultra-high-vacuum pulsed laser deposition technique from the AIS target synthesized from high-purity materials. The X-ray diffraction studies of the films show that films are textured in (112) direction. The substrate temperature appears to influence the properties of films. Increase in substrate temperature results in a more ordered structure. Compositional analysis has been carried out by EDAX. It is observed that compositional stoichiometry is maintained to a greater extent by PLD technique than other traditional methods like thermal evaporation. The optical studies of the films show that the optical band gap is about 1.20 eV.
THE REFLECTIVITY OF THE MIXED CRYSTAL AB1-xCx
Authors: ZHANG XIAOYAN , WANG JINGFENG , FAN GUOLIANG
Published: February 2011

The properties of long wavelength optical phonons in mixed crystals AB 1-x C x is discussed by a model similar to Modified Random Element Isodisplacement (MREI). Using this method we investigate the frequencies, the dielectric functions, and the reflectivity of several mixed crystals. It is found that this model can be applied to the one-mode behavior, the two-mode behavior, and that of the third category. So the model provides a possible way to understand the optical character of the ternary mixed crystal. Based on it, we can discuss other problems similar to electron–phonon interaction and so on.
NUMERICAL UNDERSTANDING OF THE SELF-INDUCED OSCILLATION OF FLOW PAST THE OPEN CAVITY WITH A STORE
Authors: SI HAI-QING , WANG TONG-GUANG
Published: February 2011

The flows around a typical open cavity with a store are numerically simulated in this paper. A fully implicit unfactored method is employed in the solver of RANS equations, where the S-A turbulent model is implemented to calculate the turbulent eddy viscosity. The flow-induced oscillation of the free shear layer around the cavity lip is captured and analyzed. Comparisons for the different cases of the cavity flow are made. The calculated results show that the pressure fluctuation is pertinent to the different positions of the store inside the cavity. The power spectral density (PSD) of the pressure by fast Fourier transformations (FFT) is also displayed in the paper. For the Rossiter's oscillatory mode, the numerical results compare well with the experimental data.
ON THE RELATION BETWEEN ORGANIZATIONS AND LIMIT SETS IN CHEMICAL REACTION SYSTEMS
Authors: PETER STEPHAN , DITTRICH PETER
Published: February 2011

Chemical organization theory has been suggested as a new approach to analyze complex reaction networks. Concerning the long-term behavior of the network dynamics we will study its foundations mathematically. Therefore we consider a chemical reactor containing molecules of different species reacting with each other according to a set of reaction rules. We further assume that the dynamical behavior of the concentration of each species is given by a continuous chemical ordinary differential equation. Abstracting from dedicated concentration values we consider a discrete problem: Which species can appear in the reactor after a long time? We define the limit set abstraction, which contains the subsets of species characterizing the long-term behavior. We prove that all these subsets are closed and that for all bounded limit sets, at least one of them is self-maintaining and thus is an organization. This implies for a chemical ordinary differential equation systems that any attractor that does not touch the state space boundaries (in particular, any periodic attractor) lies within one organization, that is, the set of species with positive concentrations in any state of such an attractor is an organization. This in turn explains why in a deterministic system evolving according to reaction rules one can observe species sets that are closed and self-maintaining, thus organizations.
BOOLEAN NETWORK AND SIMMELIAN TIE IN THE CO-AUTHOR MODEL: A STUDY OF DYNAMICS AND STRUCTURE OF A STRATEGIC ALLIANCE MODEL
Authors: TAMBAYONG LAURENT
Published: February 2011

This article explains a simulation of the Co-Author Model (CAM) applied in strategic alliance setting where firms use and optimize their network resources. To understand its process casualty better, I explain the model's mechanisms in terms of its interactive dynamics and resulting equilibrium structure. Classified as a Boolean network with two inputs, CAM's dynamics cause a biased equilibrium structure that could then be explained by the Simmelian tie and the completion of structure through structural balance. These explanations not only could answer the criticism that a simulation model is merely a toy model without much realism but could also explain and give insights to both substantive theory and methodology development in strategic alliance research. The results include the effect of a third party, the embeddedness of firms in their alliances, and the real-world implications of the "frozen web": a phenomenon drawn parallel to the financial crisis beginning in 2007.
A METHODOLOGY BASED ON MOLECULAR INTERACTIONS AND PATHWAYS TO FIND CANDIDATE GENES ASSOCIATED TO DISEASES: ITS APPLICATION TO SCHIZOPHRENIA AND ALZHEIMER'S DISEASE
Authors: OCHAGAVÍA MARÍA ELENA , MIRANDA JAMILET , NAZÁBAL MARCELO , MARTIN ALEXANDER , NOVOA LIDIA INÉS , BRINGAS RICARDO , FERNÁNDEZ-DE-COSSÍO JORGE , CAMACHO HANLET
Published: February 2011

Experimental techniques for the identification of genes associated with diseases are expensive and have certain limitations. In this scenario, computational methods are useful tools to identify lists of promising genes for further experimental verification. This paper describes a flexible methodology for the in silico prediction of genes associated with diseases combining the use of available tools for gene enrichment analysis, gene network generation and gene prioritization. A set of reference genes, with a known association to a disease, is used as bait to extract candidate genes from molecular interaction networks and enriched pathways. In a second step, prioritization methods are applied to evaluate the similarities between previously selected candidates and the set of reference genes. The top genes obtained by these programs are grouped into a single list sorted by the number of methods that have selected each gene. As a proof of concept, top genes reported a few years ago in SzGene and AlzGene databases were used as references to predict genes associated to schizophrenia and Alzheimer's disease, respectively. In both cases, we were able to predict a statistically significant amount of genes belonging to the updated lists.
THE EFFECT OF In0.1Ga0.9As UNDERLYING LAYER ON THE STRUCTURAL PROPERTIES OF SELF-ASSEMBLED In0.5Ga0.5As QUANTUM DOTS
Authors: ARYANTO DIDIK , OTHAMAN ZULKAFLI , ISMAIL ABD. KHAMIM
Published: February 2011

The effect of a thin In0.1Ga0.9As underlying layer on the structural properties of single layer In0.5Ga0.5As quantum dots (QDs) was investigated using atomic force microscopy (AFM), transmission electron microscopy (TEM) and high-resolution X-ray diffraction (HR-XRD) characterization. The size of dots formed on the surface is uniform but the density increases with the addition of In0.1Ga0.9As underlying between In0.5Ga0.5As QDs and GaAs buffer layer. This is consistent with the TEM characterization. The existence of thin underlying layer has caused the dots to have different crystal orientation as shown in TEM characterization. From the HR-XRD characterization, broad peak of In0.1Ga0.9As underlying layer and QDs has been observed. The wider width of the layer peak than the expected one has been attributed to the strain-relaxation-induced defects. The growth of a thin In0.1Ga0.9As underlying layer in the In0.5Ga0.5As/GaAs structures strongly affects the structural properties, which was also believed to influence the optical properties of QDs.
Matrix Nanodevice-Based Logic Architectures and Associated Functional Mapping Method
Authors: Gaillardon P.-E. , Clermidy F. , O’Connor I. , Liu J. , Amadou M. , Nicolescu G.
Published: February 2011

This article describes a novel computing architecture organization based on nanoscale logic cells. We propose the use of a cluster of matrix arrangements of cells. In order to interconnect such fine-grained logic cells within a matrix, conventional techniques are not suitable due to a large interconnect overhead. Therefore, we propose the use of static and incomplete interconnect topologies to create matrices of cells. We also propose a method to map functions onto such architectures. We then explore the main parameters of the structure (size of matrices and interconnect topologies) and their impact on the main performance metrics (packing efficiency, speed, and fault tolerance). A cluster packing method also allows the evaluation of the number of matrices used by complex functions and the fill factor for various matrix sizes. The analyses show that this approach is particularly suited for matrices of 16 cells interconnected by modified omega networks. We can conclude that this architecture could improve the scalability of traditional FPGAs by a factor of 8.5.
Redundant Residue Number System Code for Fault-Tolerant Hybrid Memories
Authors: Haron Nor Zaidi , Hamdioui Said
Published: February 2011

Hybrid memories are envisioned as one of the alternatives to existing semiconductor memories. Although offering enormous data storage capacity, low power consumption, and reduced fabrication complexity (at least for the memory cell array), such memories are subject to a high degree of intermittent and transient faults leading to reliability issues. This article examines the use of Conventional Redundant Residue Number System (C-RRNS) error correction code, which has been extensively used in digital signal processing and communication, to detect and correct intermittent and transient cluster faults in hybrid memories. It introduces a modified version of C-RRNS, referred to as 6M-RRNS, to realize the aims at lower area overhead and performance penalty. The experimental results show that 6M-RRNS realizes a competitive error correction capability, provides larger data storage capacity, and offers higher decoding performance as compared to C-RRNS and Reed-Solomon (RS) codes. For instance, for 64-bit hybrid memories at 10% fault rate, 6M-RRNS has 98.95% error correction capability, which is 0.35% better than RS and 0.40% less than C-RRNS. Moreover, when considering 1Tbit memory, 6M-RRNS offers 4.35% more data storage capacity than RS and 11.41% more than C-RRNS. Additionally, it decodes up to 5.25 times faster than C-RRNS.
An analysis of object oriented variability implementation mechanisms
Authors: Fazal-e-Amin  , Mahmood Ahmad Kamil , Oxley Alan
Published: February 2011

Software variability is the capacity of software to satisfy variant requirements. Component based software engineering and reuseintense software development, such as software product line engineering, demand software components with high variability. Increased variability influences a component's utility as it can be reused in multiple applications. In this paper a review and analysis of variability implementation mechanisms is presented. It builds on earlier work on software variability by providing an analysis and a synthesis. The purpose of this work is to classify the available variability mechanisms in terms of type, scope, and the artefact to be targeted. Examples to illustrate the points under discussion are given in the form of Java code.