Analysis of Kenyan isolates of Fusarium solani f. sp. phaseoli from common bean using colony characteristics, pathogenicity and microsatellite DNA

Fusarium solani (Mart) f.sp. phaseoli (Burk) Synd. and Hans., is a plant pathogenic fungus that causes root rot in garden bean (Phaseolus vulgaris L.). To evaluate methods used in classifying strains of thispathogen, 52 Fusarium solani f.sp. phaseoli isolates from infected bean plants grown on different farms in Taita hills of Coast province, Kenya, were cultured and characterized using morphology, pathogenicity and microsatellite DNA. All the isolates showed high variability in aerial mycelial growth, mycelia texture, pigmentation (mycelia colour) when cultured on potato dextrose agar medium, and conidial measurements on Spezieller Nahrstoffarmer agar medium. Colonies were grouped intoluxuriant, moderately luxuriant and scanty on aerial mycelial growth; fluffy and fibrous based on mycelial texture; purple, pink and white based on mycelia colour; aid long, medium and short macroconidial length. All the isolates were pathogenic on GLP-2 (Rosecoco), a susceptible bean variety commonly grown in Kenya. DNA analysis showed that the isolates carried a high genetic diversity(gene diversity = 0.686; mean number of alleles = 9). Neighbour-Joining phylogenetic clusters reconstructed using microsatellite variation showed three major clusters. However, the microsatellitegroupings were independent of the altitude, colony characteristics and virulence of the isolates

Infection of Oesophagostomum columbianum in Small ruminants of the Nigerian Sahel Region and its Economic Importance

Nigerian Veterinary Journal, Vol. 32(3): 2011; 162 - 16

A frailty model for (interval) censored family survival data, applied to the age at onset of non-physical problems

Family survival data can be used to estimate the degree of genetic and environmental contributions to the age at onset of a disease or of a specific event in life. The data can be modeled with a correlated frailty model in which the frailty variable accounts for the degree of kinship within the family. The heritability (degree of heredity) of the age at a specific event in life (or the onset of a disease) is usually defined as the proportion of variance of the survival age that is associated with genetic effects. If the survival age is (interval) censored, heritability as usually defined cannot be estimated. Instead, it is defined as the proportion of variance of the frailty associated with genetic effects. In this paper we describe a correlated frailty model to estimate the heritability and the degree of environmental effects on the age at which individuals contact a social worker for the first time and to test whether there is a difference between the survival functions of this age for twins and non-twins. © 2009 The Author(s)

Ultra-Sensitive Hot-Electron Nanobolometers for Terahertz Astrophysics

The background-limited spectral imaging of the early Universe requires spaceborne terahertz (THz) detectors with the sensitivity 2-3 orders of magnitude better than that of the state-of-the-art bolometers. To realize this sensitivity without sacrificing operating speed, novel detector designs should combine an ultrasmall heat capacity of a sensor with its unique thermal isolation. Quantum effects in thermal transport at nanoscale put strong limitations on the further improvement of traditional membrane-supported bolometers. Here we demonstrate an innovative approach by developing superconducting hot-electron nanobolometers in which the electrons are cooled only due to a weak electron-phonon interaction. At T<0.1K, the electron-phonon thermal conductance in these nanodevices becomes less than one percent of the quantum of thermal conductance. The hot-electron nanobolometers, sufficiently sensitive for registering single THz photons, are very promising for submillimeter astronomy and other applications based on quantum calorimetry and photon counting.Comment: 19 pages, 3 color figure

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.

We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

BACKGROUND: Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. RESULTS: With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. CONCLUSIONS: Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history

Hydrodynamics of R-charged D1-branes

We study the hydrodynamic properties of strongly coupled $SU(N)$ Yang-Mills theory of the D1-brane at finite temperature and at a non-zero density of R-charge in the framework of gauge/gravity duality. The gravity dual description involves a charged black hole solution of an Einstein-Maxwell-dilaton system in 3 dimensions which is obtained by a consistent truncation of the spinning D1-brane in 10 dimensions. We evaluate thermal and electrical conductivity as well as the bulk viscosity as a function of the chemical potential conjugate to the R-charges of the D1-brane. We show that the ratio of bulk viscosity to entropy density is independent of the chemical potential and is equal to $1/4\pi$. The thermal conductivity and bulk viscosity obey a relationship similar to the Wiedemann-Franz law. We show that at the boundary of thermodynamic stability, the charge diffusion mode becomes unstable and the transport coefficients exhibit critical behaviour. Our method for evaluating the transport coefficients relies on expressing the second order differential equations in terms of a first order equation which dictates the radial evolution of the transport coefficient. The radial evolution equations can be solved exactly for the transport coefficients of our interest. We observe that transport coefficients of the D1-brane theory are related to that of the M2-brane by an overall proportionality constant which sets the dimensions.Comment: 57 pages, 12 figure

Mediated behavioural change in human-machine networks: exploring network characteristics, trust and motivation

Human-machine networks pervade much of contemporary life. Network change is the product of structural modifications along with differences in participant be-havior. If we assume that behavioural change in a human-machine network is the result of changing the attitudes of participants in the network, then the question arises whether network structure can affect participant attitude. Taking citizen par-ticipation as an example, engagement with relevant stakeholders reveals trust and motivation to be the major objectives for the network. Using a typology to de-scribe network state based on multiple characteristic or dimensions, we can pre-dict possible behavioural outcomes in the network. However, this has to be medi-ated via attitude change. Motivation for the citizen participation network can only increase in line with enhanced trust. The focus for changing network dynamics, therefore, shifts to the dimensional changes needed to encourage increased trust. It turns out that the coordinated manipulation of multiple dimensions is needed to bring about the desired shift in attitude.Comment: Paper submitted to SocInfo, organised by the Oxford Internet Institute, September 201

Additive and multiplicative hazards modeling for recurrent event data analysis

<p>Abstract</p> <p>Background</p> <p>Sequentially ordered multivariate failure time or recurrent event duration data are commonly observed in biomedical longitudinal studies. In general, standard hazard regression methods cannot be applied because of correlation between recurrent failure times within a subject and induced dependent censoring. Multiplicative and additive hazards models provide the two principal frameworks for studying the association between risk factors and recurrent event durations for the analysis of multivariate failure time data.</p> <p>Methods</p> <p>Using emergency department visits data, we illustrated and compared the additive and multiplicative hazards models for analysis of recurrent event durations under (i) a varying baseline with a common coefficient effect and (ii) a varying baseline with an order-specific coefficient effect.</p> <p>Results</p> <p>The analysis showed that both additive and multiplicative hazards models, with varying baseline and common coefficient effects, gave similar results with regard to covariates selected to remain in the model of our real dataset. The confidence intervals of the multiplicative hazards model were wider than the additive hazards model for each of the recurrent events. In addition, in both models, the confidence interval gets wider as the revisit order increased because the risk set decreased as the order of visit increased.</p> <p>Conclusions</p> <p>Due to the frequency of multiple failure times or recurrent event duration data in clinical and epidemiologic studies, the multiplicative and additive hazards models are widely applicable and present different information. Hence, it seems desirable to use them, not as alternatives to each other, but together as complementary methods, to provide a more comprehensive understanding of data.</p

Long-term follow-up of beryllium sensitized workers from a single employer

<p>Abstract</p> <p>Background</p> <p>Up to 12% of beryllium-exposed American workers would test positive on beryllium lymphocyte proliferation test (BeLPT) screening, but the implications of sensitization remain uncertain.</p> <p>Methods</p> <p>Seventy two current and former employees of a beryllium manufacturer, including 22 with pathologic changes of chronic beryllium disease (CBD), and 50 without, with a confirmed positive test were followed-up for 7.4 +/-3.1 years.</p> <p>Results</p> <p>Beyond predicted effects of aging, flow rates and lung volumes changed little from baseline, while D_LCO dropped 17.4% of predicted on average. Despite this group decline, only 8 subjects (11.1%) demonstrated physiologic or radiologic abnormalities typical of CBD. Other than baseline status, no clinical or laboratory feature distinguished those who clinically manifested CBD at follow-up from those who did not.</p> <p>Conclusions</p> <p>The clinical outlook remains favorable for beryllium-sensitized individuals over the first 5-12 years. However, declines in D_LCO may presage further and more serious clinical manifestations in the future. These conclusions are tempered by the possibility of selection bias and other study limitations.</p