Doubly penalized buckley-james method for survival data with high-dimensional covariates.

Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method for the semiparametric accelerated failure time model to relate high-dimensional genomic data to censored survival outcomes, which uses the elastic-net penalty that is a mixture of L1- and L2-norm penalties. Similar to the elastic-net method for a linear regression model with uncensored data, the proposed method performs automatic gene selection and parameter estimation, where highly correlated genes are able to be selected (or removed) together. The two-dimensional tuning parameter is determined by generalized crossvalidation. The proposed method is evaluated by simulations and applied to the Michigan squamous cell lung carcinoma study.     

Modelling the effect of the redox potential and pH of heating media on Listeria monocytogenes heat resistance

Aims:  Study the effect of redox potential and pH of the heating media on Listeria monocytogenes heat resistance and model its action at fixed temperature.
Methods and Results:  The heat resistance of Listeria monocytogenes at 58°C was studied in Brain Heart Infusion broth as a function of pH (from 5·0 to 7·0) and redox potential ( E _h7). The media redox was adjusted with nitrogen gas, potassium ferricyanide and dithiothreitol. A Weibull model was used to fit survival curves. The heat resistance parameter (δ_58°C) was estimated from each inactivation curve. A major effect of pH was observed. Bigelow model was used to describe the effect of redox potential on the apparent L. monocytogenes heat resistance. The highest δ_58°C values have been obtained at pH 7·0 and oxidizing conditions.
Conclusions:  The developed model indicates that the E _h7 has a significant effect and varied depending on the pH of the heating media. The z _redox values, calculated from δ_58°C allowed quantifying the influence of heating media redox potential on L. monocytogenes thermal inactivation.
Significance and Impact of the Study:  The obtained model shows the action of redox potential on L. monocytogenes thermal destruction and might be useful to take into account in food thermal processes.     

Assessing mortality changes from size‐frequency curves

The relationship between the instantaneous mortality rate ( Z ) and the instantaneous change in length‐frequency distribution of organisms per unit of animal size (μ _L ) takes the following form: Z  = μ _L k ( L _∞ −  L ) +  k , where k and L _∞ are coefficients of the von Bertalanffy equation, and L is organism size (length). Z and μ_L change coherently when they are measured for a specific size or age class. Therefore, observations of μ _L can provide information on the relative changes in mortality. This is useful when no precise information about animal growth is available and growth curve is assumed to be invariable. This method was tested on a heavily exploited population of St Peter's fish (mango tilapia) Sarotherodon galilaeus in Lake Kinneret, Israel, where large fluctuations in the size structure of the catch have occurred over the past few years. Analysis of the changes in the length‐frequency distributions showed that the changes in μ _L over multiple years estimated for fully exploited fish reflected the respective changes in Z .     

Age and growth of the striped mullet, Mugil platanus (Actinopterygii, Mugilidae), in a southwestern Atlantic coastal lagoon (37°32'S–57°19'W): a proposal for a life-history model

Species of Mugilidae are an important economic resource supporting several small communities in Argentina and Brazil through fishing. The growth parameters of the von Bertalanffy model, age limit ( t _0.95) and natural mortality ( M ) for the striped mullet ( Mugil platanus ) Günther, 1880, in the Mar Chiquita coastal lagoon (37°32'S–57°19'W) were estimated. These results constitute the first estimated values for the species as: L _∞ (cm) = 563.82; K (years⁻¹) = 0.30; t ₀ (years) = −0.057 (age groups 1–8); t _0.95 = 10.07 years and M  = 0.30. Moreover, a hypothetical model is proposed for the life history of the adult stock of M. platanus from the Mar Chiquita coastal lagoon based on CPUE data, environmental parameters, ovarian maturity stages, gonadosomatic indexes, the allometric growth coefficient b and deposition of hyaline or opaque rings in the otholiths. Mugil platanus is therefore regarded as a species of moderate to rapid growth rate, with a relatively low longevity and a high natural mortality rate, compared to other species of Mugilidae.     

Growth and reproduction of Mesopotamian spiny eel (Mastacembelus mastacembelus Banks & Solander, 1794) in Ataturk Dam Lake (Şanliurfa), Turkey

Age at length, growth and reproduction of 220 Mastacembelus mastacembelus specimens from the Atatürk Dam Lake were studied from July 2005 to July 2006. Total lengths and weights ranged from 7.0 to 85.0 cm and from 6 to 1100 g, respectively. Maximum age was 13 years. The regression model fitted to length and weight data was W  =   0.0228  L ^2.43 for males and W  =   0.0029  L ^2.95 for females. The von Bertalaffy growth equations for males and females were L _t  = 99.2 [1−e^{−0.11 ( t −0.12)}] and L _t  = 69.2 [1−e^{−0.26 ( t −0.35)}], respectively. Males dominated especially at an older age; the overall sex ratio was 1 : 0.63 (M:F). The breeding period was from May to July. Fecundity ranged from 2540 to 24 000 eggs per female.     

Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species

The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes ( N _b  = 70 individuals, σ _e  = 417 m) were similar to those inferred from adult genotypes ( N _b  = 114 individuals, σ _e  = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (σ _c  = 211 m) was ∼twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.     

Selectivity of diamond, square and hexagonal mesh codends for Atlantic horse mackerel Trachurus trachurus, European hake Merluccius merluccius, and greater forkbeard Phycis blennoides in the eastern Mediterranean

Knowledge on selectivity is considered essential for an adequate management of the trawl fishery. This paper compares the selectivity of conventionally used codends of 44 mm diamond mesh, 40 mm square, and hexagonal mesh for Atlantic horse mackerel, European hake and greater forkbeard in the eastern Mediterranean. Data were collected using the covered codend method and analyzed using the logistic equation with the maximum likelihood method. Mean selection curves were analyzed and compared using the between-haul variations model. The mean L ₅₀ v alues of diamond, square and hexagonal mesh codends are 14.7, 15.9 and 17.1 cm total length (TL) for horse mackerel, 10.4, 14.4 and 11.0 cm TL for hake and 12.2, 15.8 and 12.7 cm TL for greater forkbeard, respectively. For horse mackerel, the differences among the codends are statistically significant (P   <   0.05); however, the L ₅₀ values for all three meshes are higher than the minimum landing size (13 cm TL). For hake and greater forkbeard, the L ₅₀ value for the square mesh codend is significantly different from the values for diamond and hexagonal meshes (P   <   0.01), whereas there is no significant difference between diamond and hexagonal meshes (P   >   0.05). Regardless of the mesh shape, L ₅₀ values were substantially lower than the minimum landing size or size at first maturity for hake and greater forkbeard. To enable more effective solutions, research on species-selective trawls is required for the Mediterranean demersal trawl fishery.     

Inheritance of Anthracnose Resistance in the Common Bean Differential Cultivar G 2333 and Identification of a New Molecular Marker Linked to the Co-42 gene

The inheritance of anthracnose resistance of the common bean ( Phaseolus vulgaris L.) differential cultivar G 2333 to Colletotrichum lindemuthianum races 73 and 89 was studied in crosses with the susceptible cultivar Rudá. The segregation ratios of 15 : 1 in the F₂ and 3 : 1 in the backcrosses to Rudá indicate that for each of the races tested there are two independent resistance loci in G 2333. A random amplified polymorphic DNA (RAPD) molecular marker (OPH18_1200C) linked in resistance to race 73 was identified in a BC₃F_2:3 population derived from crosses between Rudá and G 2333. A RAPD molecular marker OPAS13_950C, previously identified as linked to gene Co-4² , was also amplified in this population. Co-segregation analyses showed that these two markers are located at 5.6 (OPH18_1200C) and 11.2 (OPAS13_950C) cM of the Co-4² gene. These markers were not present in BC₁F_2:3 plants resistant to race 89 indicating that this population carries a different resistance gene. DNA amplification of BC₁F_2:3 plants with RAPD molecular marker OPAB_450C, previously identified as linked to gene Co-5 , indicated that this gene is present in this population.     

Sliced inverse regression with regularizations

Summary .   In high-dimensional data analysis, sliced inverse regression (SIR) has proven to be an effective dimension reduction tool and has enjoyed wide applications. The usual SIR, however, cannot work with problems where the number of predictors, p , exceeds the sample size, n , and can suffer when there is high collinearity among the predictors. In addition, the reduced dimensional space consists of linear combinations of all the original predictors and no variable selection is achieved. In this article, we propose a regularized SIR approach based on the least-squares formulation of SIR. The L ₂ regularization is introduced, and an alternating least-squares algorithm is developed, to enable SIR to work with   n < p   and highly correlated predictors. The L ₁ regularization is further introduced to achieve simultaneous reduction estimation and predictor selection. Both simulations and the analysis of a microarray expression data set demonstrate the usefulness of the proposed method.     

Allometric models for non-destructive leaf area estimation in coffee (Coffea arabica and Coffea canephora)

We aimed to evaluate the currently used allometric models, as well as to propose a reliable and accurate model using non-destructive measurements of leaf length (L) and/or width (W), for estimating the area of leaves of eight field-grown coffee cultivars. For model construction, a total of 1563 leaves were randomly selected from different levels of the tree canopies and encompassed the full spectrum of measurable leaf sizes (0.3–263 cm²) for each genotype. Power models better fit coffee leaf area (LA) than linear models. To validate the model, an independent data set of 388 leaves was used. We demonstrated that the currently used allometric models are biased, underestimating the area of a coffee leaf. We developed a single power model     based on two leaf dimensions [LA = 0.6626 (LW)^1.0116; standard errors: β₀ = 0.0064, β₁ = 0.0019; R² = 0.996] with high precision and accuracy, random dispersion pattern of residuals and also unbiased, irrespective of cultivar and leaf size and shape. Even when the L (but not width) alone was used as the single leaf dimension, the power model developed still predicted with good accuracy the LA but at the expense of some loss of precision, as particularly found for 8% of the leaves sampled with length-to-width ratios below 2.0 or above 3.0.     

Borrelia burgdorferi BBB07 interaction with integrin alpha3beta1 stimulates production of pro-inflammatory mediators in primary human chondrocytes

Borrelia burgdorferi , the causative agent of Lyme disease, activates multiple signalling pathways leading to induction of pro-inflammatory mediators at sites of inflammation. Binding of B. burgdorferi to integrin α₃β₁ on human chondrocytes activates signalling leading to release of several pro-inflammatory mediators, but the B. burgdorferi protein that binds integrin α₃β₁ and elicits this response has remained unknown. A search of the B. burgdorferi genome for a canonical integrin binding motif, the RGD (Arg–Gly–Asp) tripeptide, revealed several candidate ligands for integrins. In this study we show that one of these candidates, BBB07, binds to integrin α₃β₁ and inhibits attachment of intact B. burgdorferi to the same integrin. BBB07 is expressed during murine infection as demonstrated by recognition by infected mouse sera. Recombinant purified BBB07 induces pro-inflammatory mediators in primary human chondrocyte cells by interaction with integrin α₃β₁. This interaction is specific, as P66, another integrin ligand of B. burgdorferi , does not activate signalling through α₃β₁. In summary, we have identified a B. burgdorferi protein, BBB07, that interacts with integrin α₃β₁ and stimulates production of pro-inflammatory mediators in primary human chondrocyte cells.     

Effect of herbicide diclofop-methyl on proton extrusion from Lolium multiflorum seedlings differing in resistance and in fungal endophyte (Neotyphodium sp.) infection

Lolium multiflorum (Italian ryegrass), an annual weed invading wheat and barley cropping systems, has evolved resistance to diclofop-methyl (DM) herbicide. Earlier studies on the mode of action of DM in susceptible L. multiflorum and L. rigidum populations have shown that herbicide promotes oxidative stress leading to senescence, a process reversible through the action of auxins. The disruption of cell membrane potential ( E _m ) appears to be correlated with DM phytotoxicity in susceptible populations, suggesting that the continuous H⁺ extrusion from plasmalemma to extracellular space is inhibited. L. multiflorum usually establishes a symbiotic relationship with fungal endophytes of the Neotyphodium genus. This fungus confers to host plants higher survival at sublethal dosages of DM, probably due to the production of auxinic compounds. Our goal was to characterize DM-resistant and DM-susceptible L. multiflorum populations infected (E+) and non-infected (E−) with endophytes, by studying the capacity of H⁺ bumping of plasmalemma of intact roots under DM selection. We correlated the effects of DM on H⁺ disruption with plant survival. DM inhibited acidification markedly more in susceptible than in resistant populations. Continued extrusion of H⁺ by DM-resistant cell membranes was positively related to plant survival and growth. There was no detectable difference in the capacity of bumping H⁺ between DM-susceptible E+ and E− seedlings, even though survival was higher in E+ plants. The basis for the differential response in H⁺ extrusion between resistant and susceptible populations of L. multiflorum is discussed.     

THE CHEMICAL FORM OF DISSOLVED SI TAKEN UP BY MARINE DIATOMS

Results of past studies of the pH-dependent Si uptake kinetics of Phaeodactylum tricornutum Bohlin suggested that the anion SiO(OH)     is the chemical form of dissolved Si taken up by marine diatoms. We determined the chemical form of Si taken up by three other marine diatom species and P. tricornutum by examining the kinetics of Si use under two dramatically different SiO(OH)     :Si(OH)₄ ratios in seawater by varying pH from ≈8 to ≈9.6. Uptake rates were determined using a precise and sensitive ³²Si tracer methodology. The pH-dependent uptake kinetics obtained for all species except P. tricornutum suggest that marine diatoms transport Si(OH)₄. The half-saturation constant (K _m ) varies strongly as a function of pH for all species when the substrate of transport is assumed to be SiO(OH)     . Kinetic curves for Thalassiosira pseudonana (Hustedt) Hasle et Heimdal, Thalassiosira weissflogii (Grunow) G. Fryxell et Hasle, and Cylindrotheca fusiformis Reimann et Lewin have statistically identical values of K _m at each pH when the substrate for transport is assumed to be Si(OH)₄ ( T. pseudonana and T. weissflogii ) or total dissolved silicon ( C. fusiformis ). In contrast, P. tricornutum exhibits unusual biphasic uptake kinetics: uptake conforms to Michaelis–Menten kinetics up to 15 to 25 μM, above which uptake increases linearly. This enigmatic response may have biased conclusions drawn from past experiments using this species. However, based on the consistency of the results for the three other species, a new model of Si transport in marine diatoms is proposed on the basis of the direct formation of a complex between the Si-transport protein and Si(OH)₄.     

Variable selection in penalized model-based clustering via regularization on grouped parameters

Summary .   Penalized model-based clustering has been proposed for high-dimensional but small sample-sized data, such as arising from genomic studies; in particular, it can be used for variable selection. A new regularization scheme is proposed to group together multiple parameters of the same variable across clusters, which is shown both analytically and numerically to be more effective than the conventional L ₁ penalty for variable selection. In addition, we develop a strategy to combine this grouping scheme with grouping structured variables. Simulation studies and applications to microarray gene expression data for cancer subtype discovery demonstrate the advantage of the new proposal over several existing approaches.     

A qRT-PCR-based method for the measurement of rrn operon copy number

Aim:  To develop a convenient and accurate method for estimating the rrn operon copy number ( Y _rrn ) in cells of pure prokaryotic cultures based on quantitative real-time polymerase chain reaction (qRT-PCR).
Methods & Results:  Using Escherichia coli, the Y _rrn of which is known to be 7, as a reference, the rrn concentrations of target species and E. coli in sample solutions were measured based on their respective threshold cycle numbers ( C _t ), whereas the cell concentrations of both species were measured by microscopic counting after staining. The Y _rrn of the target species was then calculated from the initial cell concentrations and the rrn concentrations of the target species and E. coli . Using this method, the Y _rrn values of four species, i.e. Xanthomonas campestris , Staphylococcus aureus , Aeromonas hydrophila and Pseudomonas fluorescens , were estimated as 1·80, 4·73, 8·58 and 5·13, respectively, comparable to their respective known values of 2, 5, 10, and 5, resulting in an average deviation of 8%.
Conclusions:  The whole cell qRT-PCR based methods were convenient, accurate and reproducible in quantification of rrn copy number of prokaryotic cells.
Significance and Impact of the Study:  qTR-PCR is a fast and reliable DNA quantification approach. Compared with previous qTR-PCR based methods measuring rrn copy number, the present method avoided the prerequisite for the information on genome size and GC content of target bacteria or a gene with known copy number, thus should be more widely applicable.     

Resting spore formation of aphid-pathogenic fungus Pandora nouryi depends on the concentration of infective inoculum

Resting spore formation of some aphid-pathogenic Entomophthorales is important for the seasonal pattern of their prevalence and survival but this process is poorly understood. To explore the possible mechanism involved in the process, Pandora nouryi (obligate aphid pathogen) interacted with green peach aphid Myzus persicae on cabbage leaves under favourable conditions. Host nymphs showered with primary conidia of an isolate (LC₅₀: 0.9–6.7 conidia mm⁻² 4–7 days post shower) from air captures in the low-latitude plateau of China produced resting spores (azygospores), primary conidia or both spore types. Surprisingly, the proportion of mycosed cadavers forming resting spores ( P _cfrs ) increased sharply within the concentrations ( C ) of 28–240 conidia mm⁻², retained high levels at 240–1760, but was zero or extremely low at 0.3–16. The P _cfrs – C relationship fit well the logistic equation P _cfrs  = 0.6774/[1 + exp(3.1229–0.0270 C )] ( r ² = 0.975). This clarified for the first time the dependence of in vivo resting spore formation of P. nouryi upon the concentration of infective inoculum. A hypothesis is thus proposed that some sort of biochemical signals may exist in the host–pathogen interaction so that the fungal pathogen perceives the signals for prompt response to forthcoming host-density changes by either producing conidia for infecting available hosts or forming resting spores for surviving host absence in situ .     

NIDA522131, a new radioligand for imaging extrathalamic nicotinic acetylcholine receptors: in vitro and in vivo evaluation

A novel radioligand, 6-chloro-3-((2-( S )-azetidinyl)methoxy)-5-(2-fluoropyridin-4-yl)pyridine (NIDA522131), for imaging extrathalamic nicotinic acetylcholine receptors (nAChRs) was characterized in vitro and in vivo using positron emission tomography. The K_d and T_1/2 of dissociation of NIDA522131 binding measured at 37°C in vitro were 4.9 ± 0.4 pmol/L and 81 ± 5 min, respectively. The patterns of radioactivity distribution in monkey brain in vivo was similar to that of 2-[¹⁸F]fluoro-3-(2( S )-azetidinylmethoxy)pyridine (2FA), a radioligand that has been successfully used in humans, and matched the α₄β₂* nAChRs distribution. Comparison between [¹⁸F]NIDA522131 and 2FA demonstrated better in vivo binding properties of the new radioligand and substantially greater radioactivity accumulation in brain. Consistent with [¹⁸F]NIDA522131 elevated affinity for nAChRs and its increased lipophilicity, both, the total and non-displaceable distribution volumes were substantially higher than those of 2FA. Estimated binding potential values in different brain regions, characterizing the specificity of receptor binding, were 3–4 fold higher for [¹⁸F]NIDA522131 than those of 2FA. Pharmacological evaluation in mice demonstrated a toxicity that was comparable to 2FA and is in agreement with a 2300 fold higher affinity at α₄β₂* versus α₃β₄* nAChRs. These results suggest that [¹⁸F]NIDA522131 is a promising positron emission tomography radioligand for studying extrathalamic nAChR in humans.     

Age, growth and mortality of the Mediterranean amberjack Seriola dumerili (Risso 1810) from the south-eastern Adriatic Sea

The age, growth and mortality of the Mediterranean amberjack Seriola dumerili (Risso 1810) were determined in 298 specimens collected in the south-eastern Adriatic Sea (Donji Molunat Bay) from 17 May to 26 June 1997. The total length ranged from 32.0 to 160.0 cm and weight from 0.5 to 46.5 kg. Ten age classes, ranging from 1° to 10° years were defined by scale readings. Mean total length and weight-at-age data were used to estimate the growth parameters of the von Bertalanffy equation: L _∞=174.6 cm, K =0.190, t ₀=–0.314; W _∞=79.01 kg, K =0.139 and t ₀=–0.746. The length–weight relationship was estimated at: W =0.000123 ×  L ^2.847. The overall sex ratio was 1 : 1.06 in favour of males. Total ( Z ) and natural ( M ) mortality were found to be 0.41 years⁻¹ and 0.30 years^–1, respectively. The exploitation ratio ( E =0.27) indicates that the fishing pressure on the Mediterranean amberjack was low in the investigated region.     

Age-specific survival and fecundity and their effects on the intrinsic rate of increase of Aphelinus gossypii (Hym., Aphelinidae), a parasitoid of Aphis gossypii (Hom., Aphididae)

Abstract: The age-specific survival and fecundity of female adults of the aphidophagous parasitoid, Aphelinus gossypii Timberlake (Hym., Aphelinidae), were determined at a host density of 50 Aphis gossypii Glover (Hom., Aphididae) per leaf of Ageratum houstonianum Mill each day at 25°C. The age-specific mummy production, emergence rate and sex ratio of progeny were calculated. The implication of these results in terms of potential population growth of A. gossypii and related species is discussed. The age-specific survival curve ( l _x ) of females exhibited a Type I pattern, which resulted in little difference between Σ m _x and Σ l _x   m _x . The l _x curve of males exhibited a Type II pattern, and their survival time was much shorter than that of females. Each mated female produced on average 598.9 ± 64.0 aphid mummies, and preyed on 87.9±6.2 aphids. Most of the biological performance parameters were not different significantly between mated and virgin females. The highly female-biased sex ratio of offspring produced by mated females soon after their emergence resulted in a high fecundity rate ( m _x ) during the early reproductive period. Therefore, although the sex ratio of progeny was male-biased during the entire reproductive period, the intrinsic rate of increase estimated using age-specific sex ratios was larger than that estimated using a constant sex ratio of 0.5. These results indicate that the high survival and the adaptation of producing mostly female offspring during the early reproductive period contribute much to the population increase potential of this parasitoid.     

Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua)

DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin (Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size ( N _e ) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and N _e 's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of N _e showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by N _e 's exceeding thousand. Recent fishery-induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of N _e  << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low N _e / N ratios. Our data suggest that very small N _e 's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.