Does timing and sequencing of transitions to adulthood make a difference? Stress, smoking, and physical activity among young Australian women

The major changes of the transition to adulthood are argued to be stressful, and health-related behaviors such as smoking and physical activity may be adopted, consolidated, or abandoned at this time. On the other hand, research has suggested that the normative transitions of emerging adulthood, although involving considerable change, may be associated with low stress because they are perceived as both positive and normal at this life stage. This article examines relations between the timing and sequencing of life transitions and stress and health-related behaviors, focusing on the transition to young adulthood among Australian women. A total of 853 women aged 22 to 27 provided information about the timing and sequencing of 6 life transitions: moving out of home, stopping full-time education, starting full-time work, having the first live-in relationship, marriage, and motherhood-and stress, smoking, and physical activity. Most had moved out of home, stopped full-time education, and started full-time work, but only 14% had undertaken all 6 transitions. Overall, 70% of participants had made transitions in order Overall, the findings suggest that the relations between timing and sequencing of transitions, and indicators of health, are moderate for smoking, but small for stress and for physical activity. These effects remained after controlling for socioeconomic status of the participants' families of origin. Matching current social norms for the timing and sequencing of life changes may be of less importance for women's well-being than is commonly believed. Although the significant relations between early or out of order transitions and smoking are of concern, the smaller relations with stress and with sedentariness suggest that such transitions may have limited negative consequences, and support the view that individuals are active in choosing the life path that is appropriate for them and their circumstances.

The Pineapple EST sequencing and microarray project

We have initiated an EST sequencing project to survey a range of expressed sequences from green fruit, yellow fruit, roots, and root-knot nematode infected root/gall tissues. In total, 5681 edited EST sequences were retrieved. Clone redundancy was high in the fruit libraries, with the combined fruit 1548 clone sequences clustering into just 634 contigs comprising 191 consensus sequences and 443 singletons. Half of all fruit EST clone sequences clustered within approximately 14 and 9% of contigs from green unripe and yellow ripe libraries respectively, indicating that a small subset of genes dominates the majority of the transcriptome. The root and root/gall libraries had lower levels of redundancy than the fruit libraries. Half of the root/gall ESTs clustered within approximately 40% of all contigs, indicating the roots possess a more complex transcriptome. Contig assembly and cluster analysis revealed major differences in the abundant gene sequences expressed between the unripe green and the ripe yellow fruit tissues, or gene sequences expressed between the weeks 1-4 and weeks 5-10 nematode infected gall vascular cylinder libraries.

Retrotransposon expression profiling: Unveiling the hidden SINE transcriptome through Next-Generation Sequencing data analysis

Of the ~1.7 million SINE elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which SINE transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq datasets and unique SINE DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual SINE elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci and ~1100 MIR loci corresponding to detectable transcripts, with ~120 and ~60 respectively Alu and MIR loci expressed in at least three cell lines. In vitro transcription of selected SINEs did not reflect their in vivo expression properties, and required the native 5’-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for SINEs nested within Pol II-transcribed genes raising the possibility of an underlying mechanism for Pol II gene regulation by SINE transcriptional units. Moreover the application of our bioinformatic pipeline to both RNA-seq data of cells subjected to an in vitro pro-oncogenic stimulus and of in vivo matched tumor and non-tumor samples allowed us to detect increased Alu RNA expression as well as the source loci of such deregulation. The ability to investigate SINE transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant SINE RNAs and the assessment of SINE expression alteration under pathological conditions.

A hybrid genetic algorithm for sequencing PCB component placement

A chip shooter machine for electronic components assembly has a movable feeder carrier holding components, a movable X-Y table carrying a printed circuit board (PCB), and a rotary turret having multiple assembly heads. This paper presents a hybrid genetic algorithm to optimize the sequence of component placements for a chip shooter machine. The objective of the problem is to minimize the total traveling distance of the X-Y table or the board. The genetic algorithm developed in the paper hybridizes the nearest neighbor heuristic, and an iterated swap procedure, which is a new improved heuristic. We have compared the performance of the hybrid genetic algorithm with that of the approach proposed by other researchers and have demonstrated our algorithm is superior in terms of the distance traveled by the X-Y table or the board.

A hybrid genetic algorithm for component sequencing and feeder arrangement

This paper presents a hybrid genetic algorithm to optimize the sequence of component placements on a printed circuit board and the arrangement of component types to feeders simultaneously for a pick-and-place machine with multiple stationary feeders, a fixed board table and a movable placement head. The objective of the problem is to minimize the total travelling distance, or the travelling time, of the placement head. The genetic algorithm developed in the paper hybrisizes different search heuristics including the nearest neighbor heuristic, the 2-opt heuristic, and an iterated swap procedure, which is a new improving heuristic. Compared with the results obtained by other researchers, the performance of the hybrid genetic algorithm is superior to others in terms of the distance travelled by the placement head.

Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing:identification of novel zinc finger proteins.

We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.

Sequencing Jobs with Uncertain Processing Times and Minimizing the Weighted Total Flow Time

We consider an uncertain version of the scheduling problem to sequence set of jobs J on a single machine with minimizing the weighted total flow time, provided that processing time of a job can take on any real value from the given closed interval. It is assumed that job processing time is unknown random variable before the actual occurrence of this time, where probability distribution of such a variable between the given lower and upper bounds is unknown before scheduling. We develop the dominance relations on a set of jobs J. The necessary and sufficient conditions for a job domination may be tested in polynomial time of the number n = |J| of jobs. If there is no a domination within some subset of set J, heuristic procedure to minimize the weighted total flow time is used for sequencing the jobs from such a subset. The computational experiments for randomly generated single-machine scheduling problems with n ≤ 700 show that the developed dominance relations are quite helpful in minimizing the weighted total flow time of n jobs with uncertain processing times.

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.

Operation sequencing optimization for five-axis prismatic parts using a particle swarm optimization approach

Operation sequencing is one of the crucial tasks in process planning. However, it is an intractable process to identify an optimized operation sequence with minimal machining cost in a vast search space constrained by manufacturing conditions. Also, the information represented by current process plan models for three-axis machining is not sufficient for five-axis machining owing to the two extra degrees of freedom and the difficulty of set-up planning. In this paper, a representation of process plans for five-axis machining is proposed, and the complicated operation sequencing process is modelled as a combinatorial optimization problem. A modern evolutionary algorithm, i.e. the particle swarm optimization (PSO) algorithm, has been employed and modified to solve it effectively. Initial process plan solutions are formed and encoded into particles of the PSO algorithm. The particles 'fly' intelligently in the search space to achieve the best sequence according to the optimization strategies of the PSO algorithm. Meanwhile, to explore the search space comprehensively and to avoid being trapped into local optima, several new operators have been developed to improve the particle movements to form a modified PSO algorithm. A case study used to verify the performance of the modified PSO algorithm shows that the developed PSO can generate satisfactory results in optimizing the process planning problem. © IMechE 2009.