Analysis of the calving pattern of herds in small-scale dairy systems in central Mexico

This study sets out to find the best calving pattern for small-scale dairy systems in Michoacan State, central Mexico. Two models were built. First, a linear programming model was constructed to optimize calving pattern and herd structure according to metabolizable energy availability. Second, a Markov chain model was built to investigate three reproductive scenarios (good, average and poor) in order to suggest factors that maintain the calving pattern given by the linear programming model. Though it was not possible to maintain the optimal linear programming pattern, the Markov chain model suggested adopting different reproduction strategies according to period of the year that the cow is expected to calve. Comparing different scenarios, the Markov model indicated the effect of calving interval on calving pattern and herd structure.

Estimating numbers of infectious units from serial dilution assays

The paper concerns the design and analysis of serial dilution assays to estimate the infectivity of a sample of tissue when it is assumed that the sample contains a finite number of indivisible infectious units such that a subsample will be infectious if it contains one or more of these units. The aim of the study is to estimate the number of infectious units in the original sample. The standard approach to the analysis of data from such a study is based on the assumption of independence of aliquots both at the same dilution level and at different dilution levels, so that the numbers of infectious units in the aliquots follow independent Poisson distributions. An alternative approach is based on calculation of the expected value of the total number of samples tested that are not infectious. We derive the likelihood for the data on the basis of the discrete number of infectious units, enabling calculation of the maximum likelihood estimate and likelihood-based confidence intervals. We use the exact probabilities that are obtained to compare the maximum likelihood estimate with those given by the other methods in terms of bias and standard error and to compare the coverage of the confidence intervals. We show that the methods have very similar properties and conclude that for practical use the method that is based on the Poisson assumption is to be recommended, since it can be implemented by using standard statistical software. Finally we consider the design of serial dilution assays, concluding that it is important that neither the dilution factor nor the number of samples that remain untested should be too large.

Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge: influences on perception or mobility and host defence responses

Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidopsis of calcium influx and oxidative burst induced by non-saturating concentrations of bacterial MAMPs, used singly and in combination: flagellin peptide (flg22), elongation factor peptide (elf18), peptidoglycan (PGN) and component muropeptides, lipo-oligosaccharide (LOS) and core oligosaccharides. This revealed that some MAMPs have additive (e.g. flg22 with elf18) and even synergistic (flg22 and LOS) effects, whereas others mutually interfere (flg22 with OGA). OGA suppression of flg22-induced defences was not a result of the interference with the binding of flg22 to its receptor flagellin-sensitive 2 (FLS2). MAMPs induce different calcium influx signatures, but these are concentration dependent and unlikely to explain the differential induction of defence genes [pathogenesis-related gene 1 (PR1), plant defensin gene 1.2 (PDF1.2) and phenylalanine ammonia lyase gene 1 (PAL1)] by flg22, elf18 and OGA. The peptide MAMPs are potent elicitors at subnanomolar levels, whereas PGN and LOS at high concentrations induce low and late host responses. This difference might be a result of the restricted access by plant cell walls of MAMPs to their putative cellular receptors. flg22 is restricted by ionic effects, yet rapidly permeates a cell wall matrix, whereas LOS, which forms supramolecular aggregates, is severely constrained, presumably by molecular sieving. Thus, MAMPs can interact with each other, whether directly or indirectly, and with the host wall matrix. These phenomena, which have not been considered in detail previously, are likely to influence the speed, magnitude, versatility and composition of plant defences.

The glycosylation pattern of baculovirus expressed envelope protein E2 affects its ability to prevent infection with bovine viral diarrhoea virus

We have investigated the role of glycosylation of the envelope glycoprotein E2 of bovine viral diarrhoea virus (BVDV), produced in insect cells, in BVDV infection. When amino acids predicated to code for the C-terminal N-linked glycosylation site were mutated the resulting protein was less efficient than wild type protein at preventing infection of susceptible cells with BVDV. In addition, mutational analysis showed that a further two predicted N-terminal N-linked glycosylation sites of E2 are required for efficient production of recombinant protein. (c) 2005 Elsevier B.V. All rights reserved.

Evidence for a reversal with age in the pattern of near-wall blood flow around aortic branches

The changes that occur with age in the distribution of atherosclerotic lesions around arterial branch points challenge accepted theories relating disease to haemodynamic stresses. We investigated whether flow near branch points changes with age in a way that can account for the different lesion distributions. Flow around 20 branches from immature and mature aortas was investigated by examining the length:width ratio and orientation of endothelial nuclei; these properties depend on the magnitude and direction of near-wall flows, respectively. There were significant changes in the pattern of nuclear shape with age, consistent with a reversal in the pattern of shear around branches. In control regions away from branches, there were no such changes. The role of haemodynamic stresses in atherogenesis may require re-evaluation in the light of these results. (C) 2003 Elsevier Ireland Ltd. All rights reserved.

Fracture incidence in relation to the pattern of use of hormone therapy in postmenopausal women

Context: Evidence is limited on the effects of different patterns of use of postmenopausal hormone therapy on fracture incidence and particularly on the effects of ceasing use. Objective: To investigate the effect of different patterns of hormone therapy use on fracture incidence. Design, Setting, and Participants: Prospective study of 138737 postmenopausal women aged 50 to 69 years recruited from the UK general population in 19961998 (the Million Women Study) and followed up for 1.9 to 3.9 years (average, 2.8 years) for fracture incidence. Main Outcome Measure: Adjusted relative risk (RR) for incident fracture (except fracture of the fingers, toes, and ribs) in hormone therapy users compared with never users at baseline. Results: A total of 5197 women (3.7%) reported 1 or more fractures, 79% resulting from falls. Current users of hormone therapy at baseline had a significantly reduced incidence of fracture (RR, 0.62; 95% confidence interval [CI], 0.58-0.66; P<.001). This protection was evident soon after hormone therapy began, and the RR decreased with increasing duration of use (P=.001). Among current users at baseline the RR of fracture did not vary significantly according to whether estrogen-only, estrogen-progestin, or other types of hormones were used (RR [95% CI], 0.64 [0.58-0.71], 0.58 [0.53-0.64], and 0.67 [0.56-0.80], respectively; P=19), nor did it vary significantly according to estrogen dose or estrogen or progestin constituents. The RR associated with current use of hormone therapy did not vary significantly according to 11 personal characteristics of study participants, including their age at menopause, body mass index, and physical activity. Past users of hormone therapy at baseline experienced no significant protection against fractures (RR, 1.07; 95% CI, 0.99-1.15); incidence rates returned to those of never-users within about a year of ceasing use. Conclusions: All types of hormone therapy studied confer substantial protection against fracture while they are used. This protection appears rapidly after use commences and wears off rapidly after use ceases. The older women are, the greater is their absolute reduction in fracture incidence while using hormone therapy.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Evidence for a reversal with age in the pattern of near-wall blood flow around aortic branches

The changes that occur with age in the distribution of atherosclerotic lesions around arterial branch points challenge accepted theories relating disease to haemodynamic stresses. We investigated whether flow near branch points changes with age in a way that can account for the different lesion distributions. Flow around 20 branches from immature and mature aortas was investigated by examining the length:width ratio and orientation of endothelial nuclei; these properties depend on the magnitude and direction of near-wall flows, respectively. There were significant changes in the pattern of nuclear shape with age, consistent with a reversal in the pattern of shear around branches. In control regions away from branches, there were no such changes. The role of haemodynamic stresses in atherogenesis may require re-evaluation in the light of these results.

Analysis of chain and blood group type and branching pattern of sialylated oligosaccharides by negative ion electrospray tandem mass spectrometry

We previously reported sequence determination of neutral oligosaccharides by negative ion electrospray tandem mass spectrometry on a quadrupole-orthogonal time-of-flight instrument with high sensitivity and without the need of derivatization. In the present report, we extend our strategies to sialylated oligosaccharides for analysis of chain and blood group types together with branching patterns. A main feature in the negative ion mass spectrometry approach is the unique double glycosidic cleavage induced by 3-glycosidic substitution, producing characteristic D-type fragments which can be used to distinguish the type 1 and type 2 chains, the blood group related Lewis determinants, 3,6-disubstituted core branching patterns, and to assign the structural details of each of the branches. Twenty mono- and disialylated linear and branched oligosaccharides were used for the investigation, and the sensitivity achieved is in the femtomole range. To demonstrate the efficacy of the strategy, we have determined a novel complex disialylated and monofucosylated tridecasaccharide that is based on the lacto-N-decaose core. The structure and sequence assignment was corroborated by :methylation analysis and H-1 NMR spectroscopy.

Input and output modality effects in immediate serial recall

In immediate recall tasks, visual recency is substantially enhanced when output interference is low (Cowan, Saults, Elliott, & Moreno, 2002; Craik, 1969) whereas auditory recency remains high even under conditions of high output interference. Ibis auditory advantage has been interpreted in terms of auditory resistance to output interference (e.g., Neath & Surprenant, 2003). In this study the auditory-visual difference at low output interference re-emerged when ceiling effects were accounted for, but only with spoken output. With written responding the auditory advantage remained significantly larger with high than with low output interference. These new data suggest that both superior auditory encoding and modality-specific output interference contribute to the classic auditory-visual modality effect.

The relationship between absolute and proportion scores of serial order memory: simulation predictions and empirical data

The capability of a feature model of immediate memory (Nairne, 1990; Neath, 2000) to predict and account for a relationship between absolute and proportion scoring of immediate serial recall when memory load is varied (the list-length effect, LLE) is examined. The model correctly predicts the novel finding of an LLE in immediate serial order memory similar to that observed with free recall and previously assumed to be attributable to the long-term memory component of that procedure (Glanzer, 1972). The usefulness of formal models as predictive tools and the continuity between short-term serial order and longer term item memory are considered.

Memory operations in rapid serial visual presentation

Short-term memory (STM) has often been considered to be a central resource in cognition. This study addresses its role in rapid serial visual presentation (RSVP) tasks tapping into temporal attention-the attentional blink (AB). Various STM operations are tested for their impact on performance and, in particular, on the AB. Memory tasks were found to exert considerable impact on general performance but the size of the AB was more or less immune to manipulations of STM load. Likewise, the AB was unaffected by manipulating the match between items held in STM and targets or temporally close distractors in the RSVP stream. The emerging picture is that STM resources, or their lack, play no role in the AB. Alternative accounts assuming serial consolidation, selection for action, and distractor-induced task-set interference are discussed.

Towards a unifying framework for pattern transformation in swarm systems

This paper identifies the major challenges in the area of pattern formation. The work is also motivated by the need for development of a single framework to surmount these challenges. A framework based on the control of macroscopic parameters is proposed. The issue of transformation of patterns is specifically considered. A definition for transformation and four special cases, namely elementary and geometrical transformations by repositioning all or some robots in the pattern are provided. Two feasible tools for pattern transformation namely, a macroscopic parameter method and a mathematical tool - Moebius transformation also known as the linear fractional transformation are introduced. The realization of the unifying framework considering planning and communication is reported.

Modeling and simulating a mathematical tool for multi-robot pattern transformation

The work reported in this paper is motivated by the need to investigate general methods for pattern transformation. A formal definition for pattern transformation is provided and four special cases namely, elementary and geometric transformation based on repositioning all and some agents in the pattern are introduced. The need for a mathematical tool and simulations for visualizing the behavior of a transformation method is highlighted. A mathematical method based on the Moebius transformation is proposed. The transformation method involves discretization of events for planning paths of individual robots in a pattern. Simulations on a particle physics simulator are used to validate the feasibility of the proposed method.