Extensions of discrete triangular distributions and boundary bias in kernel estimation for discrete functions

Asymmetric discrete triangular distributions are introduced in order to extend the symmetric ones serving for discrete associated kernels in the nonparametric estimation for discrete functions. The extension from one to two orders around the mode provides a large family of discrete distributions having a finite support. Establishing a bridge between Dirac and discrete uniform distributions, some different shapes are also obtained and their properties are investigated. In particular, the mean and variance are pointed out. Applications to discrete kernel estimators are given with a solution to a boundary bias problem. (C) 2010 Elsevier B.V. All rights reserved.

Bias-corrected Pearson estimating functions for Taylor`s power law applied to benthic macrofauna data

Estimation of Taylor`s power law for species abundance data may be performed by linear regression of the log empirical variances on the log means, but this method suffers from a problem of bias for sparse data. We show that the bias may be reduced by using a bias-corrected Pearson estimating function. Furthermore, we investigate a more general regression model allowing for site-specific covariates. This method may be efficiently implemented using a Newton scoring algorithm, with standard errors calculated from the inverse Godambe information matrix. The method is applied to a set of biomass data for benthic macrofauna from two Danish estuaries. (C) 2011 Elsevier B.V. All rights reserved.

Selection bias in gene extraction on the basis of microarray gene-expression data

In the context of cancer diagnosis and treatment, we consider the problem of constructing an accurate prediction rule on the basis of a relatively small number of tumor tissue samples of known type containing the expression data on very many (possibly thousands) genes. Recently, results have been presented in the literature suggesting that it is possible to construct a prediction rule from only a few genes such that it has a negligible prediction error rate. However, in these results the test error or the leave-one-out cross-validated error is calculated without allowance for the selection bias. There is no allowance because the rule is either tested on tissue samples that were used in the first instance to select the genes being used in the rule or because the cross-validation of the rule is not external to the selection process; that is, gene selection is not performed in training the rule at each stage of the cross-validation process. We describe how in practice the selection bias can be assessed and corrected for by either performing a cross-validation or applying the bootstrap external to the selection process. We recommend using 10-fold rather than leave-one-out cross-validation, and concerning the bootstrap, we suggest using the so-called. 632+ bootstrap error estimate designed to handle overfitted prediction rules. Using two published data sets, we demonstrate that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.

PCR bias toward the wild-type k-ras and p53 sequences: Implications for PCR detection of mutations and cancer diagnosis

PCR-based cancer diagnosis requires detection of rare mutations in k-ras, p53 or other genes. The assumption has been that mutant and wild-type sequences amplify with near equal efficiency, so that they are eventually present in proportions representative of the starting material. Work factor IX suggests that this assumption is invalid for one case of near-sequence identity To test the generality of this phenomenon and its relevance to cancer diagnosis, primers distant from point mutations in p53 and k-ras were used to amplify, wild-type and mutant sequences from these genes. A substantial bias against PCR amplification of mutants was observed for two regions of the p53 gene and one region of k-ras. For kras and p53, bias was observed when the wild-type and mutant sequences were amplified separately or when mixed in equal proportions before PCR. Bias was present with proofreading and non-proofreading polymerases. Mutant and wild-type segments of the factor V cystic fibrosis transmembrane conductance regulator and prothrombin genes were amplified and did not exhibit PCR bias. Therefore, the assumption of equal PCR efficiency for point mutant and wild-type sequences is invalid in several systems. Quantitative or diagnostic PCR will require validation for each locus, and enrichment strategies may be needed to optimize detection of mutants.

The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: Fivefold tandem repetition of a coding region

We sequenced across all of the gene boundaries in the mitochondrial genome of the cattle tick, Boophilus microplus, to determine the arrangement of its genes. The mtDNA of B. microplus has a coding region, composed of tRNA(Glu) and 60 bp of the 3' end of ND1, that is repeated five times. Boophilus microplus is the first coelomate animal known to have more than two copies of a coding sequence. The mitochondrial genome of B, microplus has other unusual features, including (1) reduced T arms in tRNAs, (2) an AT bias in codon use, (3) two control regions that have evolved in concert, (4) three gene rearrangements, and (5) a stem-loop between tRNA(Gln) and tRNA(Phe). The short T arms and small control regions (CRs) of B. microplus and other ticks suggest strong selection for small genomes. Imprecise termination of replication beyond its origin, which can account for the evolution of tandem repeats of coding regions in other mitochondrial genomes, cannot explain the evolution of the fivefold repeated sequence in the mitochondrial genome of B. microplus. Instead, slipped-strand mispairing or recombination are the most plausible explanations for the evolution of these tandem repeats.

Mothers' mental illness and child behavior problems: Cause-effect association or observation bias

Objective: A number, of studies have consistently found that a mother's mental health (particularly her level of depression) is a strong predictor of mental health problems experienced by her child(ren). However, the validity of this finding is in doubt because the majority of these studies have relied on maternal reports as indicators of children's behavior. Method: This prospective, longitudinal study examines data an the mental health of the mother from prior to the birth of her child to when the child reaches 14 years of age. Child behavior is measured at 14 years of age using reports from mother and child. Mother and child responses are compared to provide an indication of the possible magnitude of maternal observation bias in the reporting of child behavior problems. Results: Anxious and/or depressed mothers tend to report more cases of child behavior problems than do their mentally healthy counterparts or children themselves. Differences between mothers and youths In reporting behavior problems appear to be related to the mothers' mental health. Conclusions: Current maternal mental health impairment appears to have a substantial effect on the reporting of child behavior problems by the mother, thereby raising questions about the validity of reports of child behavior by persons who are currently emotionally distressed.

Investigation of threat-related attentional bias in anxious children using the startle eyeblink modification paradigm

We used the startle eyeblink modification paradigm to investigate whether clinically anxious children, like high trait-anxious adults, display a bias in favour of threat words compared to neutral words. The present study included 16 clinically anxious children whose diagnostic status was determined using the parent version of a semistructured diagnostic interview as part of a larger childhood anxiety study. The children were presented with threat and neutral words fur 6 s each. A startle-eliciting auditory stimulus - a 100 dBA burst of white noise of 50 ms duration - was presented during the words at lead intervals of 60, 120, 240, or 3500 ms and during intertrial intervals. The overall pattern of startle eyeblink modification indicated inhibition at the 120 and 240 ms lead intervals and facilitation at the 3500 ms lead interval. startle-latency shortening during threat words at the :60 ms lead interval was larger than at other intervals, whereas there was no difference during neutral words. This result reflects an anxiety-related bias in favour of threat words occurring at a very early - and possibly preattentive stage - of information processing.

Size-based predation by kookaburras (Dacelo novaeguineae) on lizards (Eulamprus tympanum : Scincidae): what determines prey vulnerability?

Lizards and birds are both popular model organisms in behavioural ecology, but the interactions between them have attracted little study. Given the putative importance of birds as predators of diurnal Lizards, it is of considerable interest to know which traits (of lizards as well as birds) influence the outcome of a predatory attempt. We studied predation by giant terrestrial kingfishers (kookaburras, Dacelo novaeguineae: Alcedinidae) on heliothermic diurnal lizards (highland water skinks, Eulamprus tympanum: Scincidae), with particular reference to the role of prey (lizard) size. Our approach was twofold: to gather direct evidence (sizes of lizards consumed in the field, compared to those available) and indirect evidence rite-related shifts in lizard behaviour). We quantified the size structure of a natural population of skinks (determined by an extensive mark-recapture program), and compared it to the sizes of wild lizards taken by kookaburras (determined by analysis of prey remains left at the birds' nests,. Kookaburras showed size-based predation: they preyed mainly on small and medium-sized rather than large lizards in the field. However, the mechanism producing this bias remains elusive. It is not due to any distinctive behavioural attributes (locomotor ability, activity level, habitat usage) of the lizards of the size class disproportionately taken by the kookaburras. The greater vulnerability of subadult lizards may reflect subtle ontogenetic shifts in ecological and behavioural traits, but our data suggest that great caution is needed in inferring patterns of vulnerability to predation from indirect measures based on either the prey or the predator alone. Instead, we need direct observations on the interaction between the two.

Stereotypic explanatory bias: Implicit stereotyping as a predictor of discrimination

Two experiments examined whether a measure of implicit stereotyping based on the tendency to explain Black stereotype-incongruent events more often than Black stereotype-congruent events (Stereotypic Explanatory Bias or SEB) is predictive of behavior toward a partner in an interracial interaction. In Experiment I SEB predicted White males' choice to ask stereotypic questions of a Black female (but not a White male or White female) in an interview. In Experiment 2 the type of explanation (internal or external attribution) made for stereotype-inconsistency was examined. Results showed that White participants who made internal attributions for Black stereotype-incongruent behavior were rated more positively and those who made external attributions were rated more negatively by a Black male confederate. These results point to the potential of implicit stereotyping as an important predictor of behavior in an interracial interaction. (C) 2002 Elsevier Science (USA). All rights reserved.

Dissolved organic carbon in rainwater from areas heavily impacted by sugar cane burning

This work reports on rainwater dissolved organic carbon (DOC) from Ribeirao Preto (RP) and Araraquara over a period of 3 years. The economies of these two cities, located in Sao Paulo state (Brazil), are based on agriculture and related industries, and the region is strongly impacted by the burning of sugar cane foliage before harvesting. Highest DOC concentrations were obtained when air masses traversed sugar cane fields burned on the same day as the rain event. Significant increases in the DOC volume weighted means (VWM) during the harvest period, for both sites, and a good linear correlation (r=0.83) between DOC and K (a biomass burning marker) suggest that regional scale organic carbon emissions prevail over long-range transport. The DOC VWMs and standard deviations were 272 +/- 22 mu mol L-1 (n=193) and 338 +/- 40 mu mol L-1 (n=80) for RP and Araraquara, respectively, values which are at least two times higher than those reported for other regions influenced by biomass burning, such as the Amazon. These high DOC levels are discussed in terms of agricultural activities, particularly the large usage of biogenic fuels in Brazil, as well as the analytical method used in this work, which includes volatile organic carbon when reporting DOC values. Taking into account rainfall volume, estimated annual rainwater DOC fluxes for RP (4.8 g C m(-2) yr(-1)) and Araraquara (5.4 g C m(-2) yr(-1)) were close to that previously found for the Amazon region (4.8 g C m(-2) yr(-1)). This work also discusses whether previous calculations of the global rainwater carbon flux may have been underestimated, since they did not consider large inputs from biomass combustion sources, and suffered from a possible analytical bias. (c) 2008 Elsevier Ltd. All rights reserved.

Spatial bias and temporal lag in tactile space perception

Constructing a veridical spatial map by touch poses at least two problems for a perceptual system. First, as the hand is moved through space, the locations of features may be displaced if there is an uncorrected lag between the moment the hand encounters a feature and the time that feature is encoded on a spatial map. Second, due to the sequential nature of the process, some form of memory, which itself may be subject to spatial distortions, is required for integration of spatial samples. We investigated these issues using a task involving active haptic exploration with a stylus swept back and forth in the horizontal plane at the wrist. Remembered locations of tactile targets were shifted towards the medial axis of the forearm, suggesting a central tendency in haptic spatial memory, while evidence for a displacement of perceived locations in the direction of sweep motion was consistent with processing delays.

Commercialisation of agriculture in Kenya: Case study of urban bias on food availability in farm households

This study investigates the effect of cash cropping on food availability and examines the determinants of the proportion of income allocated for food expenditures in the Nyeri district in Kenya. Using a Tobit model, the results suggest that in general food expenditure allocations suffer due to cash cropping in Kenya as the lump-sum income flows from this may be used for purchases other than food. Food expenditure also suffers when remittances are irregular. On the other hand, earnings from outside employment for married women living with husbands are positively associated with food expenditure allocations. Amounts of non-cash food output as well as ownership of livestock are negatively associated with food expenditure allocations. These findings indicate that lump sum income may not lead to improved welfare of women and children. Thus, there may be social reasons for increasing non-cash food production especially by women, instead of over emphasizing cash cropping as now seems to be so in public policy.

Dengue virus binding to human leukocyte cell lines: receptor usage differs between cell types and virus strains

Monocyte macrophages (M phi) are thought to be the principal target cells for the dengue viruses (DV), the cause of dengue fever and hemorrhagic fever. Cell attachment is mediated by the virus envelope (E) protein, but the host-cell receptors remain elusive. Currently, candidate receptor molecules include proteins, Fc receptors, glycosaminoglycans (GAGs) and lipopolysaccharide binding CD14-associated molecules. Here, we show that in addition to M phi, cells of the T- and B-cell lineages, and including cells lacking GAGs, can bind and become infected with DV. The level of virus binding varied widely between cell lines and, notably, between virus strains within a DV serotype. The latter difference may be ascribable to one or more amino acid differences in domain II of the E protein. Heparin had no significant effect on DV binding, while heparinase treatment of cells in all cases increased DV binding, further supporting the contention that GAGs are not required for DV binding and infection of human cells. In contrast to a recent report, we found that lipopolysaccharide (LPS) had either no effect or enhanced DV binding to, and infection of various human leukocyte cell lines, while in all virus-cell combinations, depletion of Ca2+/Mg2+ enhanced DV binding. This argues against involvement of beta (2) integrins in virus-host cell interactions, a conclusion in accord with the demonstration of three virus binding membrane proteins of < 75 kDa. Collectively, the results of this study question the purported exclusive importance of the E protein domain III in DV binding to host cells and point to a far more complex interaction between various target cells and, notably, individual DV strains. (C) 2001 Elsevier Science B.V. All rights reserved.