Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.     

A rationale for the TEI recommendations for feature-structure markup

In this paper, we concentrate on justifying the decisions we made in developing the TEI recommendations for feature structure markup. The first four sections of this paper present the justification for the recommended treatment of feature structures, of features and their values, and of combinations of features or values and of alternations and negations of features and their values. Section 5 departs briefly from the linguistic focus to argue that the markup scheme developed for feature structures is in fact a general-purpose mechanism that can be used for a wide range of applications. Section 6 describes an auxiliary document called a feature system declaration that is used to document and validate a system of feature-structure markup. The seventh and final section illustrates the use of the recommended markup scheme with two examples, lexical tagging and interlinear text analysis.Terry Langendoen is Professor and Head of the Department of Linguistics at The University of Arizona. He was Chair of the TEI Committee on Analysis and Interpretation. He received his PhD in Linguistics from the Massachusetts Institute of Technology in 1964, and held teaching positions at The Ohio State University and the City University of New York (Brooklyn College and the Graduate Center) before moving to Arizona in 1988. He is author, co-author, or co-editor of six books in linguistics, and of numerous articles.Gary Simons is Director of the Academic Computing Department of the Summer Institute of Linguistics, Dallas, TX. He served on the TEI Committee on Analysis and Interpretation. He received his PhD in Linguistics (with minor emphasis in Computer Science) from Cornell University in 1979. Before taking up his current position in 1984, he spent five years in the Solomon Islands doing field work with SIL. He is author, co-author, or co-editor of eight books in the fields of linguistics and linguistic computing.The initial feature-structure recommendations were formulated by the Analysis and Interpretation Committee at a meeting in Tucson, Arizona in March 1990, following suggestions by Mitch Marcus and Beatrice Santorini. The authors received valuable help in the further revision and refinement of the recommendations from Steven Zepp.     

Epinephrine doses delivered from auto-injectors stored at excessively high temperatures

Context: Prompt injection of epinephrine (adrenaline) from epinephrine auto-injectors (EAIs) is the primary treatment for anaphylaxis in out-of-hospital settings. Storage of EAIs at room temperature (25?°C) is advised; however, storage at excessively high temperatures sometimes occurs. To our knowledge, there are no previous publications on the doses of epinephrine ejected from EAIs after storage at such temperatures.

Objective: We examined the epinephrine doses delivered from activated EAIs stored constantly or cyclically at 70?°C.

Methods: Twenty-five in-date EAIs were stored constantly or cyclically at 70?°C (excessive heat) or 25?°C (controls) for 5?d or 10?d. EAIs were activated and the epinephrine doses in the ejected solutions were measured using HPLC-UV. The enantiomeric purity of epinephrine was also measured by HPLC-UV.

Results: Control EAIs ejected a volume of 0.300?±?0.006?mL containing 103.7?±?3.3% of labeled dose (LD). After 5?d or 10?d of constant storage at 70?°C and activation at 70?°C, EAIs ejected a volume of 0.367?±?0.008?mL containing 96.8?±?3.8% LD and 0.373?±?0.007?mL containing 77.7?±?3.3% LD, respectively. After 5?d of cyclic storage at 70?°C and cooling to 25?°C before activation, EAIs ejected a volume of 0.311?±?0.008?mL containing 87.2?±?1.9% LD. Under the experimental conditions of this study, the resultant chromatographic peaks of epinephrine solutions from all EAIs represented only the pure l-enantiomer of epinephrine.

Conclusion: EAIs should be stored under recommended conditions of the manufacturer. EAIs stored at excessively high temperatures cannot be used to treat humans while still hot, and when cooled, cannot be relied on to deliver the labeled epinephrine dose in anaphylaxis.     

Lipid domain structure of the plasma membrane revealed by patching of membrane components

Lateral assemblies of glycolipids and cholesterol, "rafts," have been implicated to play a role in cellular processes like membrane sorting, signal transduction, and cell adhesion. We studied the structure of raft domains in the plasma membrane of non-polarized cells. Overexpressed plasma membrane markers were evenly distributed in the plasma membrane. We compared the patching behavior of pairs of raft markers (defined by insolubility in Triton X-100) with pairs of raft/non-raft markers. For this purpose we cross-linked glycosyl-phosphatidylinositol (GPI)-anchored proteins placental alkaline phosphatase (PLAP), Thy-1, influenza virus hemagglutinin (HA), and the raft lipid ganglioside GM1 using antibodies and/or cholera toxin. The patches of these raft markers overlapped extensively in BHK cells as well as in Jurkat T-lymphoma cells. Importantly, patches of GPI-anchored PLAP accumulated src-like protein tyrosine kinase fyn, which is thought to be anchored in the cytoplasmic leaflet of raft domains. In contrast patched raft components and patches of transferrin receptor as a non-raft marker were sharply separated. Taken together, our data strongly suggest that coalescence of cross-linked raft elements is mediated by their common lipid environments, whereas separation of raft and non-raft patches is caused by the immiscibility of different lipid phases. This view is supported by the finding that cholesterol depletion abrogated segregation. Our results are consistent with the view that raft domains in the plasma membrane of non-polarized cells are normally small and highly dispersed but that raft size can be modulated by oligomerization of raft components.     

alt.metadata.health: Ontological Context for Data Use and Integration

Increasingly powerful computers and increased emphasis on evidence based decision making are creating a demand for merging and integrating data from different sources into a single data set. The demand for data is outstripping our ability to ensure data integrity, and sometimes analysis is performed on data that are not appropriate for the purposes they are used for. Here we describe problems that arise when data from different sources are merged, and we suggest that one way to add context to data so that users can make informed decisions about their ontological context is through ontology-based metadata. Examples of the problem are taken from health data with emphasis on difficulties in standardizing Emergency Room wait times. We describe eight fields that can be used to capture contextual metadata. These fields are captured using ethnographic methods from users and database stewards who frequently understand precisely how context and institutional usage have shaped interpretation of semantic fields. We argue that attaching a portable archive of ontological context to travel with data—based on information from users and developers—is a means of ensuring that data are integrated and compared in multiple contexts with greater integrity and more robust results.

Limiting optimal discounted-cost control of a class of time-varying stochastic systems

We consider a class of time-varying -valued control models, and with possibly unbounded costs. The processes evolve according to the system equation x_n+1=G_n(x_n,a_n)+ξ_n ( ), where {ξ_n} are i.i.d. random vectors and {G_n} a sequence of known functions converging to some function G_∞. Under suitable hypotheses, we show the existence of an α-discount optimal policy for the limiting system x_n+1=G_∞(x_n,a_n)+ξ_n.     

Nanoparticle‐embedded polymer‐dispersed liquid crystal for paper‐like displays

Abstract— A polymer‐dispersed liquid‐crystal (PDLC) matrix template embedded with nano/microparticles can be backfilled/infiltrated with a dye‐doped liquid crystal for a paper‐like reflective display. In this way, a desirable degree of diffusion can be realized to reduce the viewing‐angle dependency of a gain reflector and metallic glare without changing other electro‐optical properties.     

Flight deck disturbance management: a simulator study of diagnosis and recovery from breakdowns in pilot-automation coordination

OBJECTIVE: To examine operator strategies for diagnosing and recovering from errors and disturbances as well as the impact of automation design and time pressure on these processes. BACKGROUND: Considerable efforts have been directed at error prevention through training and design. However, because errors cannot be eliminated completely, their detection, diagnosis, and recovery must also be supported. Research has focused almost exclusively on error detection. Little is known about error diagnosis and recovery, especially in the context of event-driven tasks and domains. METHOD: With a confederate pilot, 12 airline pilots flew a 1-hr simulator scenario that involved three challenging automation-related tasks and events that were likely to produce erroneous actions or assessments. Behavioral data were compared with a canonical path to examine pilots' error and disturbance management strategies. Debriefings were conducted to probe pilots' system knowledge. RESULTS: Pilots seldom followed the canonical path to cope with the scenario events. Detection of a disturbance was often delayed. Diagnostic episodes were rare because of pilots' knowledge gaps and time criticality. In many cases, generic inefficient recovery strategies were observed, and pilots relied on high levels of automation to manage the consequences of an error. CONCLUSION: Our findings describe and explain the nature and shortcomings of pilots' error management activities. They highlight the need for improved automation training and design to achieve more timely detection, accurate explanation, and effective recovery from errors and disturbances. APPLICATION: Our findings can inform the design of tools and techniques that support disturbance management in various complex, event-driven environments.     

Stability ball versus office chair: comparison of muscle activation and lumbar spine posture during prolonged sitting

OBJECTIVE: The objective of the study was to evaluate the differences between sitting on a stability ball and in an office chair in terms of trunk muscle activation and lumbar spine posture. BACKGROUND: Stability balls have become increasingly popular as an alternative to office chairs to help reduce the prevalence of low back pain; however, little research has been conducted on their use as office chairs. METHODS: The 14 participants (7 men, 7 women) were required to sit on both a stability ball and an office chair for 1 hour each while performing various computer workstation tasks throughout the sitting periods. The activation of eight muscles and lumbar spine posture were measured and analyzed. RESULTS: Increased muscle activation in thoracic erector spinae (p = .0352), decreased pelvic tilt (p = .0114), and increased perceived discomfort (p < .0001) while sitting on the stability ball were observed. CONCLUSIONS: The small changes in biological responses when sitting on a stability ball as compared with an office chair, combined with the increased reported discomfort while on the ball, suggests its use for prolonged sitting may not be advantageous. APPLICATION: Prolonged sitting on a stability ball does not greatly alter the manner in which an individual sits, yet it appears to increase the level of discomfort. Therefore, it is important to fully explore a new chair design and consult scientific research before implementing its use.