Pattern-based clustering of daily weigh-in trajectories using dynamic time warping

“Smart”-scales are a new tool for frequent monitoring of weight change as well as weigh-in behavior. These scales give researchers the opportunity to discover patterns in the frequency that individuals weigh themselves over time, and how these patterns are associated with overall weight loss. Our motivating data come from an 18-month behavioral weight loss study of 55 adults classified as overweight or obese who were instructed to weigh themselves daily. Adherence to daily weigh-in routines produces a binary times series for each subject, indicating whether a participant weighed in on a given day. To characterize weigh-in by time-invariant patterns rather than overall adherence, we propose using hierarchical clustering with dynamic time warping (DTW). We perform an extensive simulation study to evaluate the performance of DTW compared to Euclidean and Jaccard distances to recover underlying patterns in adherence time series. In addition, we compare cluster performance using cluster validation indices (CVIs) under the single, average, complete, and Ward linkages and evaluate how internal and external CVIs compare for clustering binary time series. We apply conclusions from the simulation to cluster our real data and summarize observed weigh-in patterns. Our analysis finds that the adherence trajectory pattern is significantly associated with weight loss.     

Increased Phosphorylation of a 26-kD Pollen Protein Is Induced by the Self-Incompatibility Response in Papaver rhoeas

We have investigated whether specific protein phosphorylation events are induced in Papaver rhoeas pollen as a consequence of the self-incompatibility (SI) response. Pollen grown in vitro in the presence of 32P-orthophosphate was challenged with biologically active recombinant S proteins, and pollen proteins were extracted and analyzed. The results provide strong evidence that the increased phosphorylation of a 26-kD protein of pl 6.2, p26, is specifically induced by the SI response. This phosphorylation event occurs in living pollen tubes and was observed specifically when pollen was challenged with S proteins that are incompatible with the S alleles carried by the pollen and not when pollen was challenged with compatible or incompatible heat-denatured S proteins. Further characterization demonstrated that p26 comprises two phosphoproteins, p26.1 and p26.2, that are found in soluble and microsomal fractions, respectively. Increased phosphorylation of p26.1 is implicated in the SI response and appears to be Ca2+ and calmodulin dependent. These data argue for the involvement of a Ca2+-dependent protein kinase requiring calmodulin-like domains, whose activation comprises an intracellular signal mediating the SI response in P. rhoeas pollen.     

Sucrose consumption in mice: Major influence of two genetic Loci affecting peripheral sensory responses

Individual variability in sucrose consumption is prominent in humans and other species. To investigate the genetic contribution to this complex behavior, we conducted behavioral, electrophysiological, and genetic studies, using male progeny of two inbred mouse strains (C57BL/6ByJ [B6] and 129/J [129]) and their F₂ hybrids. Two loci on Chromosome (Chr) 4 were responsible for over 50% of the genetic variability in sucrose intake. These loci apparently modulated intake by altering peripheral neural responses to sucrose. One locus affected the response threshold, whereas the other affected the response magnitude. These findings suggest that the majority of difference in sucrose intake between male B6 and 129 mice is due to polymorphisms of two genes that influence receptor or peripheral nervous system activity. Received: 27 January 1997 / Accepted: 17 March 1997     

Propylthiouracil Tasting: Determination of Underlying Threshold Distributions using Maximum Likelihood

The ability to taste low concentrations of propylthiouracil(PROP) and related bitter compounds is heritable. The currentanalysis determines whether the distribution of PROP taste thresholdsis consistent with an additive or a dominant mode of Mendeliantransmission. To that end, the lowest concentration of PROPdetectable was determined for 1015 subjects and models of bi-or tri-modal distributions of PROP taste thresholds were tested.The model with the greatest likelihood had three distributionsand followed an additive model of PROP taste sensitivity ifthe variances associated with the distributions were assumedto be equal. However, if the taste thresholds were transformedto remove skewness, or if the variances were unequal, then three-or two-distribution models were equally likely. Resolution ofthe mode of inheritance for bitter taste perception awaits additionalfamily studies and the characterization of the molecular basisof taste perception for these bitter compounds. Chem. Senses20: 529–533, 1995.     

DNA sequences of the two homoeologous SLR1 genes of Brassica napus cv Westar

The DNA sequence data reported have been lodged in the Genbank, EMBL and DDBJ databases under the accession numbers Z21609 and Z26914     

The chromosomal locations and linkage relationships of the structural genes for the prolamin storage proteins (secalins) of rye

Summary Rye secalins are a polymorphic mixture of polypeptides which are classified into four major groups. Previous studies have shown that the structural genes for two of the groups (the -secalins and 40K -secalins) are located on the short arm of chromosome 1R and those for a third group (the high molecular weight secalins) on the long arm of the same chromosome. Analysis of F₂ grain from crosses between inbred lines of S. cereale shows that the structural genes for the -secalins (designated Sec 1) and the high molecular weight secalins (designated Sec 3) are loosely linked (40.8 ±3.76% recombination, 57.4 ± 11.30 cM). Analysis of wheat rye addition lines shows that the structural genes for the 75K -secalins are present on chromosome 2R. This locus is provisionally designated Sec 2. These genes are probably derived from those for the 40K -secalins by duplication, divergence and translocation. Analysis of secalin fractions from wild species of rye shows that all contain 75K -secalins, indicating that the duplication and divergence, if not the translocation, occurred before speciation of the genus.     

Optimized extracellular production of alkaline phosphatase by lky mutants of Escherichia coli K12

Summary Periplasmic-leaky (lky) Hfr mutant strains of Escherichia coli K12, grown in low-phosphate Tris medium, excreted alkaline phosphatase (AP) into the extracellular fluid. The lky207 mutation, which proved to induce the highest AP excretion rate, was transferred to an F^- host, carrying a phoS, T mutation allowing constitutive AP biosynthesis. Use of high-phosphate LB-rich medium for growing this F^- lky strain improved cell biomass, extracellular AP activity and excretion specificity in favour of the enzyme. Physiological studies helped us to develop a new culture medium (LB 8.3) giving higher enzyme and excretion yields. LB 8.3 medium also increased cell viability of lky mutants stored at 4° C.Using optimized culture conditions, the highest extracellular enzyme activity produced by lky mutant 706 was reached in the late stationary growth phase and was equal to 1,400 U/ml of culture medium (i.e., 6 times the intracellular AP content of wild-type strain, Ga15, developed in derepressed conditions); AP released into the extracellular fluid corresponded to 34% of total excreted proteins and was equivalent to a purified enzyme preparation.     

The uptake of soil and fertilizer-nitrogen by barley growing under Scottish climatic conditions

Summary Field experiments were carried out using¹⁵N-labelled calcium nitrate, to investigate the relative uptake by barley of fertilizer-N and soil-N. On imperfectly drained till soils uptake of soil-N increased with increasing rate of fertilizer, but remained constant on a brown sand, possibly due to more efficient root exploration in the latter soil. In four out of five seasons, late uptake of soil-derived N was a major feature, and uptake from ploughed soil as compared with uptake from direct-drilled soil was correlated with seasonal rainfall patterns. Significantly higher quantities of both fertilizer- and soil-derived N were taken up by winter barley than by spring barley, reflecting the longer growth period and higher dry matter yield from the former crop.