Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons

Metagenome from refinery wastewater treatment plant running under nitrogen stress was analyzed for mining of novel aromatic hydrocarbon-degrading bacteria. The sequence data were assembled using metaspade followed by binning using the Metabat tool to assemble genome; where coverage and depth were calculated using bowtie and samtools. The analysis picked a novel genome belonging to family Bradyrhizobiaceae, identified based on 16S rDNA gene which was supported by CheckM and Kraken analysis. Using RAST, the assembled genome showed the capabilities for nitrogen fixation with the utilization of multiple hydrocarbon substrates with 14 different types of oxygenases as mapped by Minpath. An additional genetic feature like genes for stress and resistance towards heavy metals and antibiotic suggested that the genome has gone through the rigorous process of adaptation. If such bacteria could be cultivated then it will open the broad window of bioremediation strategies under nitrogen stress environment.     

Feasibility of oral rabies vaccination campaigns of young foxes (<Emphasis Type="Italic">Vulpes vulpes</Emphasis>) against rabies in summer

Oral vaccination of foxes (Vulpes vulpes) against rabies has been shown to be highly effective. Several baiting strategies to increase vaccination coverage of the target population have been developed. For example, to increase the vaccination coverage of the young fox population before dispersal an additional summer vaccination campaign has been suggested. The effectiveness of such a campaign was evaluated using field data on home range size and shape of young foxes and a simulation model for aerial bait distribution. The results indicated that the limited ranging behaviour of the young fox population during the summer months severely reduced bait accessibility and consequently such an additional vaccination campaign would be very cost-ineffective.     

Finite element analysis of an additional implant for intramedullary nailing]

In the surgical treatment of fractured femurs, the fracture is bridged by a medullary nail fixed in the bone with interlocking screws. Failure of bone substance in the region of the interlocking screws is the most common complication in the treatment of osteoporotic bone. With the aim of preventing this complication, an additional implant was developed. A finite element analysis of an ideal bone/implant system was carried out to investigate the role of the additional implant. Three defined finite element models were generated, and the associated stress situations compared. The first model is a standard fixation without the additional implant. In the second model, the additional implant is integrated within the bone/implant system. The third model uses a modified form of the additional implant. The results show that both additional implants reduce the stresses occurring, both in the bone substance and at the screws. The modified form of the additional implant proved to be the most favorable version. In the case of the original additional implant, the negative effect of the sharp edges of the thread was demonstrable.     

Using calibration weighting to adjust for nonresponse under a plausible model

When we estimate the population total for a survey variableor variables, calibration forces the weighted estimates of certaincovariates to match known or alternatively estimated populationtotals called benchmarks. Calibration can be used to correctfor sample-survey nonresponse, or for coverage error resultingfrom frame undercoverage or unit duplication. The quasi-randomizationtheory supporting its use in nonresponse adjustment treats responseas an additional phase of random sampling. The functional formof a quasi-random response model is assumed to be known, itsparameter values estimated implicitly through the creation ofcalibration weights. Unfortunately, calibration depends uponknown benchmark totals while the covariates in a plausible modelfor survey response may not be the benchmark covariates. Moreover,it may be prudent to keep the number of covariates in a responsemodel small. We use calibration to adjust for nonresponse whenthe benchmark model and covariates may differ, provided thenumber of the former is at least as great as that of the latter.We discuss the estimation of a total for a vector of surveyvariables that do not include the benchmark covariates, butthat may include some of the model covariates. We show how tomeasure both the additional asymptotic variance due to the nonresponsein a calibration-weighted estimator and the full asymptoticvariance of the estimator itself. All variances are determinedwith respect to the randomization mechanism used to select thesample, the response model generating the subset of sample respondents,or both. Data from the U.S. National Agricultural StatisticalService's 2002 Census of Agriculture and simulations are usedto illustrate alternative adjustments for nonresponse. The paperconcludes with some remarks about adjustment for coverage error.     

A Simulation model for the arrowhead scale (Hemiptera: Diaspididae) population dynamics on citrus trees in relation to pest-management programs

1. A mathematical model was constructed describing population dynamics of the arrowhead scale, Unaspis yanonensis Kuwana. The population occurrence patterns simulated by the model from 1971 to 1976 were relatively consistent with the actual findings in the field.
2. The effects of control tactics for this pest were examined on the basis of the model.
3. Effective timing of insecticide (petroleum oil and organophosphorous insecticide) application was indicated to be 40 days after the initial appearance of 1st-instar nymphs in both the 1st and 2nd generations of the host.
4. The number of overwintering adult females in May of the next year (i.e., the starting point of the next year's population) decreased linearly with the increment in the degree of insecticide coverage. The pest populations were expected to be kept to low densities by petroleum oil sprays alone for the 1st generation when overall, complete coverage was accomplished.
5. Examination of the effects of two introduced parasitoids, Aphytis yanonensis and Coccobius fulvus, showed that they were able to control the scale population by themselves when more than 70% parasitism was achieved. When petroleum oil was applied to overwintering adults (termed winter petroleum oil) at the degree of coverage of 0.8, host populations were reduced by ca. 60% parasitism. When the winter petroleum oil was combined either with additional petroleum oil 40 days after the initial appearance of 1st-instar nymphs of the 1st generation or with an organophosphorous insecticide 40 days after the initial appearance of 1st-instar nymphs of the 2nd generation (degree of coverage=0.8 in each case), 40% parasitism led the reduction of the pest population.
6. The most desirable control program was considered to be one in which winter petroleum oil was used every year and additional petroleum oil or an organophosphorous insecticide was also used in those years when host density was high.

     

Elimination of African Onchocerciasis: Modeling the Impact of Increasing the Frequency of Ivermectin Mass Treatment

The African Programme for Onchocerciasis Control (APOC) is currently shifting its focus from morbidity control to elimination of infection. To enhance the likelihood of elimination and speed up its achievement, programs may consider to increase the frequency of ivermectin mass treatment from annual to 6-monthly or even higher. In a computer simulation study, we examined the potential impact of increasing the mass treatment frequency for different settings. With the ONCHOSIM model, we simulated 92,610 scenarios pertaining to different assumptions about transmission conditions, history of mass treatment, the future mass treatment strategy, and ivermectin efficacy. Simulation results were used to determine the minimum remaining program duration and number of treatment rounds required to achieve 99% probability of elimination. Doubling the frequency of treatment from yearly to 6-monthly or 3-monthly was predicted to reduce remaining program duration by about 40% or 60%, respectively. These reductions come at a cost of additional treatment rounds, especially in case of 3-monthly mass treatment. Also, aforementioned reductions are highly dependent on maintained coverage, and could be completely nullified if coverage of mass treatment were to fall in the future. In low coverage settings, increasing treatment coverage is almost just as effective as increasing treatment frequency. We conclude that 6-monthly mass treatment may only be worth the effort in situations where annual treatment is expected to take a long time to achieve elimination in spite of good treatment coverage, e.g. because of unfavorable transmission conditions or because mass treatment started recently.     

Simultaneous confidence intervals for a success probability and intraclass correlation,with an application to screening mammography

This paper provides asymptotic simultaneous confidence intervals for a success probability and intraclass correlation of the beta‐binomial model, based on the maximum likelihood estimator approach. The coverage probabilities of those intervals are evaluated. An application to screening mammography is presented as an example. The individual and simultaneous confidence intervals for sensitivity and specificity and the corresponding intraclass correlations are investigated. Two additional examples using influenza data and sex ratio data among sibships are also considered, where the individual and simultaneous confidence intervals are provided.     

Terrestrial mosses as bioindicators of SO2 pollution stress

Summary The turf structure of terrestrial mosses was analysed in the understory of white spruce associations along two SO₂ stress gradients associated with a single SO₂ source. Changes in coverage, turf depth, biomass and percent living moss were followed. SO₂ stress initially caused changes in turf structure in the vertical plane (green turf depth, percentage and biomass) whereas changes in the horizontal plane (coverage) were most noticeable in areas of severe stress. The Index of Atmospheric Purity (IAP) reflected SO₂ stress only in these latter areas. Intrusion of weeds and increased prominence of subordinate species occurred in lightly stressed areas, but these perturbations were not reflected by the IAP. The effect of Q _i, frequency, and coverage factors in the IAP are discussed and the criteria of the Index of Community Vigor are proposed.     

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

Molecular dynamics simulations of an amphipathic helix embedded in a lipid bilayer indicate that it will induce substantial positive curvature (e.g., a tube of diameter 20 nm at 16% surface coverage). The induction is twice that of a continuum model prediction that only considers the shape of the inclusion. The discrepancy is explained in terms of the additional presence of specific interactions described only by the molecular model. The conclusion that molecular shape alone is insufficient to quantitatively model curvature is supported by contrasting molecular and continuum models of lipids with large and small headgroups (choline and ethanolamine, respectively), and of the removal of a lipid tail (modeling a lyso-lipid). For the molecular model, curvature propensity is analyzed by computing the derivative of the free energy with respect to bending. The continuum model predicts that the inclusion will soften the bilayer near the headgroup region, an effect that may weaken curvature induction. The all-atom predictions are consistent with experimental observations of the degree of tubulation by amphipathic helices and variation of the free energy of binding to liposomes.     

Influenza vaccination in the elderly: 2. The economics of sending reminder letters

Reminder letters and follow-up telephone calls were used to increase influenza vaccination acceptance by 273 well elderly registered at an urban community health centre. The net effect of the reminder letters was to increase overall coverage to 43%, from 17% in the previous year. Follow-up telephone calls to patients who had not responded to the letters increased coverage to only 55%. Calculation of costs per additional vaccination given revealed that the use of reminder letters alone was much more cost-effective than follow-up telephone calls in increasing coverage. However, with the current fee-for-service reimbursement by medical care insurance in Ontario, neither means of improving vaccination coverage would result in net practice earnings. The implications for an effective and efficient annual influenza program in Canada are discussed.     

Vaccine coverage: recent trends and future prospects.

OBJECTIVE--To assess the feasibility of achieving the target of 95% coverage for the childhood immunisation schedule by 1995 and to determine the influence of sociodemographic factors and information systems on recent trends. DESIGN--Analyses of trends in quarterly vaccination data for diphtheria, pertussis, and measles in health districts between February 1988 and February 1991. SETTING--District health authorities in England and Wales, and health and social services boards in Northern Ireland. SUBJECTS--Cohorts of children whose youngest member had reached the target age of 18 months for receiving the third doses of diphtheria and pertussis vaccines and 2 years for receiving measles vaccine. RESULTS--Predicted coverage levels for mid-1995 were in excess of 95% for diphtheria, pertussis, and measles vaccines. In the 118 districts that continuously reported between February 1988 and February 1991 the increase in coverage was 6% for diphtheria and 13% for pertussis and measles vaccines. 1991 coverage depended primarily on 1988 coverage. The additional effects of deprivation, change in computer system, and child population size achieved at most only marginal statistical significance. CONCLUSIONS--The government''s target of 95% coverage by 1995 is realistic, although projections should be viewed with caution. Several national vaccination initiatives are likely to have contributed to the recent steady increase in coverage. Updating and validation exercises are likely to improve recorded coverage.     

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

Molecular dynamics simulations of an amphipathic helix embedded in a lipid bilayer indicate that it will induce substantial positive curvature (e.g., a tube of diameter 20 nm at 16% surface coverage). The induction is twice that of a continuum model prediction that only considers the shape of the inclusion. The discrepancy is explained in terms of the additional presence of specific interactions described only by the molecular model. The conclusion that molecular shape alone is insufficient to quantitatively model curvature is supported by contrasting molecular and continuum models of lipids with large and small headgroups (choline and ethanolamine, respectively), and of the removal of a lipid tail (modeling a lyso-lipid). For the molecular model, curvature propensity is analyzed by computing the derivative of the free energy with respect to bending. The continuum model predicts that the inclusion will soften the bilayer near the headgroup region, an effect that may weaken curvature induction. The all-atom predictions are consistent with experimental observations of the degree of tubulation by amphipathic helices and variation of the free energy of binding to liposomes.     

The Impact of Vaccination and Antiviral Therapy on Hepatitis B and Hepatitis D Epidemiology

The major cause of liver cancer around the globe is hepatitis B virus (HBV), which also contributes to a large number of deaths due to liver failure alone. Hepatitis delta virus (HDV) is as potentially alarming as HBV since life threatening cases are 10 times more likely with HBV-HDV dual infection compared to HBV monoinfection. So far, there is no established effective treatment against HDV and the only preventive action suggested by the World Health Organization is to introduce HBV vaccination for children immediately after birth (newborns) and thus reduce the available pool for HDV infection. Here the main objective is to understand the complex dynamics of HBV-HDV infection in a human population that can inform public health policy makers on the level of different preventive measures required to eliminate HBV and HDV infections. Model simulations suggest that HBV vertical transmission and HBV vaccination rates for newborns are instrumental in determining HBV and HDV prevalence. A decrease in HBV prevalence is observed as vaccination coverage increases and it is possible to eradicate both HBV and HDV using high vaccination coverage of ≥80% in the long term. We further found that HDV presence results in lower HBV prevalence. An application of our model to China revealed that vaccinating every newborn in China will further prevent 1.69 million new infections by 2028 as compared to the current 90% vaccination coverage. Although, higher vaccination coverage of newborns should eliminate both HBV and HDV over a long time period, any short term strategy to eradicate HDV must include additional preventive measures such as HBV adult vaccination. Implementation of HBV adult vaccination programs at a rate of 10% per year over 15 years will further prevent 39 thousand new HDV infections in China by 2028 as compared to HBV vaccination programs solely for newborns.     

基于大气辐射校正的广州市植被覆盖度遥感估算

植被覆盖度是描述生态系统的基本参数,也是进行生态系统健康与安全评价的重要生态参数.基于1990、1995、2000和2005年4个时相的TM遥感数据源,以广州市为研究区域,运用减少大气辐射影响的植被指数计算模型,通过非监督分类及图像空间模型运算,修正了大气辐射校正参数,建立了植被覆盖度与校正植被指数的模型,估算了不同时期内广州市的植被覆盖度.结果显示,广州市植被覆盖度在1990—2000年的10年内持续下降,从2000年开始呈上升趋势,符合广州市的经济发展与环境建设实际.所建立的模型适合于区域植被覆盖度动态变化研究,且在植被覆盖度的动态变化特征研究方面有较大优势,其结果适于进行城市生态环境质量与动态评价.     

Efficient spatial coverage by a robot swarm based on an ant foraging model and the Lévy distribution

This work proposes a control law for efficient area coverage and pop-up threat detection by a robot swarm inspired by the dynamical behavior of ant colonies foraging for food. In the first part, performance metrics that evaluate area coverage in terms of characteristics such as rate, completeness and frequency of coverage are developed. Next, the Keller–Segel model for chemotaxis is adapted to develop a virtual-pheromone-based method of area coverage. Sensitivity analyses with respect to the model parameters such as rate of pheromone diffusion, rate of pheromone evaporation, and white noise intensity then identify and establish noise intensity as the most influential parameter in the context of efficient area coverage and establish trends between these different parameters which can be generalized to other pheromone-based systems. In addition, the analyses yield optimal values for the model parameters with respect to the proposed performance metrics. A finite resolution of model parameter values were tested to determine the optimal one. In the second part of the work, the control framework is expanded to investigate the efficacy of non-Brownian search strategies characterized by Lévy flight, a non-Brownian stochastic process which takes variable path lengths from a power-law distribution. It is shown that a control law that incorporates a combination of gradient following and Lévy flight provides superior area coverage and pop-up threat detection by the swarm. The results highlight both the potential benefits of robot swarm design inspired by social insect behavior as well as the interesting possibilities suggested by considerations of non-Brownian noise.     

Efficient manipulation of nanoparticle-bound DNA via restriction endonuclease

As a programmable biopolymer, DNA has shown great potential in the fabrication and construction of nanometer-scale assemblies and devices. In this report, we described a strategy for efficient manipulation of gold nanoparticle-bound DNA using restriction endonuclease. The digestion efficiency of this restriction enzyme was studied by varying the surface coverage of stabilizer, the size of nanoparticles, as well as the distance between the nanoparticle surface and the enzyme-cutting site of particle-bound DNA. We found that the surface coverage of stabilizer is crucial for achieving high digestion efficiency. In addition, this stabilizer surface coverage can be tailored by varying the ion strength of the system. Based on the results of polyacrylamide gel electrophoresis and fluorescent study, a high digestion efficiency of 90+% for particle-bound DNA was achieved for the first time. This restriction enzyme manipulation can be considered as an additional level of control of the particle-bound DNA and is expected to be applied to manipulate more complicated nanostructures assembled by DNA.     

Eggshell Appearance Does Not Signal Maternal Corticosterone Exposure in Japanese Quail: An Experimental Study with Brown-Spotted Eggs

Reproduction is a critical period for birds as they have to cope with many stressful events. One consequence of an acute exposure to stress is the release of corticosterone, the avian stress hormone. Prolonged stress can have negative impacts on the immune system, resulting in, for example, increased oxidative stress. Through maternal effects, females are known to modulate their investment in eggs content according to their own physiological condition. Less is known about maternal investment in eggshells, especially in pigments. The two main eggshell pigments may possess opposite antioxidant properties: protoporphyrin (brown) is a pro-oxidant, whereas biliverdin (blue-green) is an antioxidant. In Japanese quail, we know that the deposition of both pigments is related to female body condition. Thus, a chronic stress response may be reflected in eggshell coloration. Using female Japanese quails that lay brown-spotted eggs, we explored whether physiological exposure to corticosterone induces a change in female basal stress and antioxidant factors, and eggshell pigment concentration, spectrophotometric reflectance, and maculation coverage. We supplemented adult females over a 2 week period with either peanut oil (control) or corticosterone (treatment). We collected pre- and post-supplementation eggs and analysed the effect of corticosterone treatment on female physiology and eggshell appearance parameters. Except for corticosterone-fed birds which laid eggs with brighter spots, supplementation had no significant effect on female physiology or eggshell pigment concentration, reflectance and maculation. The change in eggshell spot brightness was not detected by a photoreceptor noise-limited color opponent model of avian visual perception. Our data confirms that eggshell reflectance in spotted eggs varies over the laying sequence, and spot reflectance may be a key factor that is affected by females CORT exposure, even if the changes are not detected by an avian visual model.     

Sustaining Fragile Gains: The Need to Maintain Coverage with Long-Lasting Insecticidal Nets for Malaria Control and Likely Implications of Not Doing So

Global commitment to malaria control has greatly increased over the last decade. Long-lasting insecticidal nets (LLINs) have become a core intervention of national malaria control strategies and over 450 million nets were distributed in sub-Saharan Africa between 2008 and 2012. Despite the impressive gains made as a result of increased investment in to malaria control, such gains remain fragile. Existing funding commitments for LLINs in the pipeline to 2016 were collated for 40 sub-Saharan African countries. The population-based model NetCALC was used to estimate the potential LLIN coverage achievable with these commitments and identify remaining gaps, and the Lives Saved Tool (LiST) was used to estimate likely consequences for mortality impact if these gaps remain unfilled. Overall, countries calculated a total need of 806 million LLINs for 2013-16. Current funding commitments meet just over half of this need, leaving approximately 374 million LLINs unfunded, most of which are needed to maintain coverage in 2015 and 2016. An estimated additional 938,500 child lives (uncertainty range: 559,400–1,364,200) could be saved from 2013 through 2016 with existing funding (relative to 2009 LLIN coverage taken as the ‘baseline’ for this analysis); if the funding gap were closed this would increase to 1,180,500 lives saved (uncertainty range: 707,000–1,718,900). Overall, the funding gap equates to approximately 242,000 avoidable malaria-attributable deaths amongst under-fives. Substantial additional resources will need to be mobilized to meet the full LLIN need of sub-Saharan countries to maintain universal coverage. Unless these resources are mobilized, the impressive gains made to date will not be sustained and tens of thousands of avoidable child deaths will occur.     

Determining the repertoire of immunodominant proteins via whole-genome amplification of intracellular pathogens

Culturing many obligate intracellular bacteria is difficult or impossible. However, these organisms have numerous adaptations allowing for infection persistence and immune system evasion, making them some of the most interesting to study. Recent advancements in genome sequencing, pyrosequencing and Phi29 amplification, have allowed for examination of whole-genome sequences of intracellular bacteria without culture. We have applied both techniques to the model obligate intracellular pathogen Anaplasma marginale and the human pathogen Anaplasma phagocytophilum, in order to examine the ability of phi29 amplification to determine the sequence of genes allowing for immune system evasion and long-term persistence in the host. When compared to traditional pyrosequencing, phi29-mediated genome amplification had similar genome coverage, with no additional gaps in coverage. Additionally, all msp2 functional pseudogenes from two strains of A. marginale were detected and extracted from the phi29-amplified genomes, highlighting its utility in determining the full complement of genes involved in immune evasion.     

干旱区荒漠稀疏植被覆盖度提取及尺度扩展效应

选择线性混合像元分解模型、亚像元模型、最大三波段梯度差法模型以及修正的三波段梯度差法的2个变异模型来提取植被覆盖度,结合地面实测数据,探讨了提取干旱区荒漠稀疏植被覆盖度信息的适宜模型,并以简单平均法模拟了不同尺度的覆盖度影像,通过尺度上推检验了模型在MODIS尺度上的反演效应.结果表明：线性混合像元分解模型反演覆盖度的精度高于其他模型,适于稀疏植被地区,但端元的正确选取较难,从而影响其运用;亚像元分解模型是一个通用模型,植被分类图越精细,通过亚像元分解模型得到的覆盖度精度越高,但这也同时意味着该模型需要测定大量的输入参数;最大三波段梯度差法的算法简单、易于操作,其在农田等中高植被覆盖区及裸土区的预测值与实测值接近,但对干旱区稀疏植被的估计精度偏低;修正后的三波段最大梯度差法模型在稀疏植被覆盖区的预测值与实测值基本一致,在不同尺度上反演的覆盖度信息与实测值的一致性较好.该方法可有效提取干旱区低覆盖度植被信息.