Capacity and coding in digital communications

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Population Dynamics In A Model Closed Ecosystem

For almost any species in any environment, it is nearly impossible to predict its fitness from molecular knowledge. If fitness is not to be a mere tautology, reproducible measurements of the survival and reproduction of populations are needed over many generations. Laboratory microbial ecosystems afford the short time and length scales required for such measurements. Their conventional implementations, batch cultures with period refreshment of growth medium or chemostats with continuous refreshment, have a number of disadvantages, such as the introduction of additional frequencies, selection for surface growth and the distortion of chemical interactions. In closed ecosystems free energy is instead supplied as light, allowing for simpler, replicable protocols and a consistent interpretation of interactions, independent of their mode or timescale. Here, I describe a model closed ecosystem consisting of three singlecelled microbes, Escherichia coli, Chlamydomonas reinhardtii and Tetrahymena thermophila and show that these species can coexist for hundreds of days under closure. Using a custom built in situ fluorescence microscopy set up, the densities of these three species can be measured automatically and noninvasively over months with low classification error and large dynamical range. When kept under identical boundary conditions, these ecosystems reproducibly diverge in composition, with characteristic divergence times of ~20 days for T. thermophila, ~40 days for the other two species, and an approximately linear increase of an aggregate divergence measure over the first ~60 days. For two ecosystems, densities were measured continuously under constant conditions and their dynamics shown to be nonstationary for all three species \u3e100 days after closure. As a consequence, conventional time series methods assuming stationarity are inadequate and wavelet analysis is proposed as an alternative. Species-species interactions are further investigated using oscillations in illumination intensity. Densities of C. reinhardtii and, surprisingly, E. coli respond to modest perturbations of light intensity. Variation of the modulation frequency strongly implicates the circadian clock of C. reinhardtii in its response. The nonlinearity of the E. coli response suggests that it depends on C. reinhardtii density or spatial distribution rather than directly responds to the modulation of illumination. Further improvements in the detection of interactions are proposed

Assessment of a New Healthy Food Policy at Two Food Pantries in Grand Rapids, MI

Background The purpose of food pantries has traditionally been to provide short-term assistance to food insecure individuals, however recent research indicates that food pantries are often used longer periods of time. This increased use indicates a greater importance for food pantries to distribute nutrient-dense foods to food insecure individuals, some who may suffer from chronic disease. Objectives This study measured food pantry client satisfaction pre- and post- implementation of a new healthy food policy at two Grand Rapids, MI food pantries. An additional purpose was to measure the change in food environment and distribution of nutrient-dense foods after implementation of this policy. Subjects Food pantry clients were recruited to complete a survey while waiting to utilize the pantry services. The distribution of foods was determined by completion of a food distribution checklist by pantry volunteers. Methods Pantry clients completed a survey before and after implementation of the new polices. All collection periods lasted one month. Clients completed the pre survey prior to healthy food intervention. Clients then completed the survey at 3 and 6 months post implementation. Pantry volunteers completed the food distribution checklists during the same time periods. Demographic data on the clients was provided by Access of West Michigan. Nutrition Environmental Measurement Survey (NEMS) was used to measure nutrition environment at each pantry at baseline and 6 months post-implementation. Analysis Frequencies were used to describe discrete characteristics. Food distribution checklists were analyzed for percentage change month to month. Results The pre-surveys indicated clients wanted to have more access to fruits and vegetables. The clients noticed the increase in fruits and vegetables after implementation of the healthy food policy. Client satisfaction remained high throughout the implementation of the healthy food policy. NEMS indicated one of the pantries had an increase in the healthy food environment. The food distribution checklist at one pantry showed a greater amount of fruits/vegetables and whole grains were distributed to clients at both 3 and 6 months post-implementation. Conclusion The new healthy food policy improved the nutrition environment and increased the amount of fruits, vegetables and whole grains selected by clients

Contingency and Statistical Laws in Replicate Microbial Closed Ecosystems

SummaryContingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years. We precisely measure the local population density of each species in many CES replicates, started from the same initial conditions and kept under constant light and temperature. The covariation among replicates of the three species densities acquires a stable structure, which could be decomposed into discrete eigenvectors, or “ecomodes.” The largest ecomode dominates population density fluctuations around the replicate-average dynamics. These fluctuations follow simple power laws consistent with a geometric random walk. Thus, variability in ecological dynamics can be studied with CES replicates and described by simple statistical laws

Thermodynamics of RNA/DNA hybridization in high density oligonucleotide microarrays

We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity versus the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091\_at due to annotation problems, i.e. the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.Comment: 11 pages, 16 figures - final version as publishe

Houdbaarheid van tulpebloemen op water

De houdbaarheid van tulpebloemen op water behoort tot een der belangrijkste eigenschappen van het gewas. Onder houdbaarheid wordt hier verstaan: het aantal dagen dat verloopt tussen het moment waarop de bloem op water wordt geplaatst en waarop de eerste tekenen van verval optreden. Uit ervaring is het een ieder wel bekend dat de houdbaarheid bij de verschillende tulpesoorten zeer uiteenloopt. Toenemende concurrentie van andere snijbloemen, vooral ook in de wintermaanden, maakt dat een goede houdbaarheid van steeds groter belang wordt in de handhaving van de concurrentiepositie

Selectieve teelt van tulpen gebaseerd op produktie-analyse

In tulip cultivation many stocks of good producing varieties in course of time showed a decrease in production of large marketable bulbs. Meanwhile the number of small bulbs in these stocks increased. This phenomenon was investigated. It was attributable to three causes: contamination of the stock by either foreign material ('thieves') or mutants originating from the variety itself ('wild'); a wrong temperature treatment of the planting material; differences in production between the several bulb types growing at different places in the mother bulb.The newly produced bulbs were named, after the scale of the mother bulb in whose axil they were formed, as A, B, C, and D for the fleshy scales (from inside to exterior) and H for the dry tunic. The production pattern of all types and grades was studied during three years. Especially the A and H bulbs were superior to the others in productivity. Second were B bulbs, followed by C and D. This productivity was not concerned with weight increase but to growth of the main bulb and offset number, which should not be too high.Based on these results a selection scheme was proposed to eliminate all bulbs inferior in productivity. This scheme was the basis for tulip cultivation with selection in the meantime, so that productivity of the stock stayed maximum.</p