Is there an error correcting code in the base sequence in DNA?

Modern methods of encoding information into digital form include error check digits that are functions of the other information digits. When digital information is transmitted, the values of the error check digits can be computed from the information digits to determine whether the information has been received accurately. These error correcting codes make it possible to detect and correct common errors in transmission. The sequence of bases in DNA is also a digital code consisting of four symbols: A, C, G, and T. Does DNA also contain an error correcting code? Such a code would allow repair enzymes to protect the fidelity of nonreplicating DNA and increase the accuracy of replication. If a linear block error correcting code is present in DNA then some bases would be a linear function of the other bases in each set of bases. We developed an efficient procedure to determine whether such an error correcting code is present in the base sequence. We illustrate the use of this procedure by using it to analyze the lac operon and the gene for cytochrome c. These genes do not appear to contain such a simple error correcting code.     

Coding of the acoustic information in the superior auditory centers

The internal ear may be considered analysing acoustical signals in the frequency domain. This spectral analysis appears in the auditory pathways as a place code, each neuron being activated for a narrow and well defined frequency band. But in addition to this place code, temporal information on the phase and the period of low frequency signals is preserved in the low auditory centers. In the medial geniculate body, the last relay before the cerebral cortex, the place code shows the same properties as in lower centers but with a greater diversity in the response patterns and tuning properties. The tonotopic organization is less precise and, for the pars lateralis, follows the histological lamellar organization of this region. The most lateral laminae are composed of cells responding to low frequencies, the most medial ones of high frequency cells. In the auditory cortex intracellular recordings confirm the importance of an active inhibition underlying the diverse response patterns observed. Persistance of a time code is shown by certain cells presenting responses precisely time-locked to individual clicks in a train for rates ranging from 50 to 1000 Hz. Other cells respond selectively for certain click train frequencies without marking the temporal structure of the stimuli. Thus a temporal and a place code are still both present at the cortical level for this particular kind of signals.     

Cadherins and the formation of neural circuitry in the vertebrate CNS

Cadherins are a family of calcium-dependent morphoregulatory molecules mediating cell-cell adhesion. More than a dozen cadherin subtypes are known to be expressed in the developing and mature CNS. Each of these subtypes shows a restricted and distinct expression pattern that differs from that of the other cadherins. During the formation of fiber tracts and neural circuits, each cadherin is expressed by a subset of neurite fascicles. The differential expression of cadherins provides a molecular code for the high degree of specificity and selectivity in neural circuit formation. This code may be a combinatorial one, since the expression of cadherins shows partial overlap. The expression data and experimental results available at present suggest a role for cadherins in aspects of axon outgrowth, axon navigation, axon fasciculation, axonal target recognition, and, finally, in synaptogenesis. However, the precise role of cadherins in some of these processes and their functional relationship to other molecules involved in neurite outgrowth remains to be experimentally established.     

Empirical correlates of frequently occurring two-point MMPI code types: A replicated study.

Examined whether (a) a relatively small number of 2-point code types could account for a large proportion of MMPI protocols in a psychiatric setting, and (b) reliable behavioral and demographic correlates of these 2-point code types could be identified. MMPI protocols of 588 hospitalized psychiatric patients were randomly divided into 2 subsamples. Within each, the profiles were classified according to 19 frequently occurring 2-point code types (identified in a pilot study), permitting classification of 84% of the 588 profiles. For each subsample, each code type was compared with the remaining Ss on 68 behavioral and demographic variables. Although 300 or more significant differences were found for the comparisons in each subsample, in only 66 instances were the same differences significant in both subsamples. The relevance of these findings to MMPI interpretational practices is discussed. (21 ref.) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains

The universal genetic code is determined by the aminoacylation of tRNAs. In spite of the universality of the code, there are barriers to aminoacylation across taxonomic domains. These barriers are thought to correlate with the co-segregation of sequences of synthetases and tRNAs into distinct taxonomic domains. By contrast, we show here examples of eukaryote-like synthetases that are found in certain prokaryotes. The associated tRNAs have retained their prokaryote-like character in each instance. Thus, co-segregation of domain-specific synthetases and tRNAs does not always occur. Instead, synthetases make adaptations of tRNA-protein contacts to cross taxonomic domains.     

Evaluating and Proposing Models of Predicting IC Debonding Failure

Debonding failure due to intermediate crack-induced (IC) fracture is one of the most dominant failure modes associated with the fiber-reinforced polymer (FRP) bonding technique. To date, extensive efforts have been paid by many researchers worldwide to study the debonding phenomenon for effective applications of FRP composites and rational design of FRP-strengthened structures. Based on these efforts and various relevant field applications, different models and code provisions have been proposed to predict IC debonding failure. Out of all the existing code provisions and models, five typical ones are investigated in the current paper. A comprehensive comparison among these code provisions and models is carried out in order to evaluate their performance and accuracy. Test results of 200 flexural specimens with IC debonding failures collected from the existing literature are used in the current comparison. The effectiveness and accuracy of each model have been evaluated based on these experimental results. Finally, based on a statistical analysis, a simple and more effective model for predicting the load-carrying capacity of FRP-strengthened flexural members due to IC debonding failure is proposed.     

Multiple‐Zone Potential Solution around Wing‐Body Configurations

An existing computer code to solve a supersonic potential equation around three‐dimensional configurations was modified. Using a generalized boundary‐conforming coordinate system, a full potential equation in conservation form was upwind differenced in supersonic direction. Grids were generated in each two‐dimensional cross‐flow plane using the algebraic method. A new topology for grid generation produced appropriate grids around thin wings and wing bodies. Usage of orthogonal grid generation in cross‐flow plane improved results and extended the various cases that can be handled by the code. A zonal flow field solution was obtained using a new method for the implementation of boundary conditions at wing locations on boundaries of each zone. Approximate factorizations were used to solve the resulting equations implicitly. Using these capabilities thin‐wing and wing‐body results are presented that compare well with other results. The capability of running this code on microcomputers makes this program a potentially valuable design tool in primary and middesign stages.     

Kinetics of inclusion precipitation during steel solidification

The precipitation of non-metallic inclusions (complex oxides, sulphides, nitrides …) during steel solidification is analysed using the multiphase equilibrium code CEQCSI and a nucleation and growth model. The CEQCSI code is based in part on the Irsid slag model, and it provides an evaluation of the composition of inclusions formed at equilibrium, as well as guidelines for industrial treatments in order to reach desirable compositions in semi-killed steel grades. The nucleation and growth model can be applied to the formation, during steel solidification, of stoichiometric compounds or liquid oxide inclusions. Two particularities of this kinetic model are that nucleation and growth are treated simultaneously, and they compete in consuming the supersaturation at each moment, and that a mixed controlled growth model transport/interfacial kinetics at the precipitate/liquid steel interface is considered. The predicted size distribution of TiN precipitates formed in two steel grades is in good agreement with the results of laboratory experiments. In the case of liquid oxide precipitation, the first calculations indicate that the composition of inclusions can be significantly different from that of inclusions assumed to precipitate under equilibrium conditions.     

Large-Eddy Simulation of Turbulent Flow over a Fixed Two-Dimensional Dune

Turbulent open-channel flow over a two-dimensional dune is studied using an established large-eddy simulation code. The free surface is approximated as a shear free boundary. Turbulence statistics and instantaneous flow structures are examined. Numerical results from two computational grids agree with each other, and are also in good agreement with recently obtained experimental data. The mean velocity profiles show significant changes along the dune and there is no region that conforms to the standard law-of-the-wall. Profiles of the Reynolds stresses show distinct peaks marking the shear layer that originates from flow separation at the dune crest. Secondary peaks found further from the dune are ascribed to the shear layer over the upstream dune. Details of the separated flow and development of the flow after reattachment are well predicted. Quadrant analysis of the Reynolds shear stress shows that turbulent ejections dominate the near-wall motions. Complex water surface flow structures are visualized.     

Screening for germ-line rearrangements and regulatory mutations in BRCA1 led to the identification of four new deletions

Pogo is a transposable element with short terminal inverted repeats. It contains two open reading frames that are joined by splicing and code for the putative pogo transposase, the sequence of which indicates that it is related to the transposases of members of the Tc1/mariner family as well as proteins that have no known transposase activity including the centromere binding protein CENP-B. We have shown that the N-terminal region of pogo transposase binds in a sequence-specific manner to the ends of pogo and have identified residues essential for this. The results are consistent with a prediction that DNA binding is due to a helix-turn-helix motif within this region. The transposase recognises a 12 bp sequence, two copies of which are present at each end of pogo DNA. The outer two copies occur as inverted repeats 14 nucleotides from each end of the element, and contain a single base mismatch and indicate the inverted repeats of pogo are 26 nucleotides long. The inner copies occur as direct repeats, also with a single mismatch.     

An experimental evaluation of recent electron dosimetry codes of practice

As from the 1 January 1997, the recent IPEMB code of practice for electron dosimetry is the recommended protocol for electron beam dosimetry in the UK, replacing the previous HPA code of practice and its IPSM addendum. New recommendations for electron beam dosimetry have also been formulated recently by the AAPM and the IAEA on the use of parallel-plate ionization chambers in high-energy electron beams. Against this background, the procedures recommended in each of these codes of practice have been followed from intercomparison of the field instrument ionization chamber with a secondary standard through to the determination of absorbed dose at the reference position in the electron beam. Absorbed doses have been determined for a number of electron beam energies ranging from nominal 5 MeV through to 17 MeV, and for four different types of field instrument ionization chamber: an NE2571 graphite walled cylindrical chamber; an NACP parallel-plate chamber; a Markus parallel-plate chamber; and a Roos parallel-plate chamber. The differences in the determination of absorbed dose between the IPEMB protocol and the HPA/IPSM protocol vary from +0.5% to +1.6% at the depth of maximum dose. In addition the IPEMB measured doses are 0.2% larger than those measured following the IAEA code of practice. It may also be stated that the IPEMB measured doses at the depth of maximum dose are up to 1.5%, but generally less than 1.0%, lower than those measured by the AAPM protocol.     

Discrimination of mirror images by young children.

Conducted 3 experiments to investigate the effects of introducing mirror-image configurations into orientation and position discriminations. Ss were 4-8 yr. old children. Results of 2 experiments suggest that the question of mirror images may be irrelevant to the way in which young children differentiate orientation and position; i.e., as many errors were made in successive comparisons of obliques when the obliques were not mirror images as when they were. Similarly when they had to discriminate the positions of dots in squares, Ss confused left with right and up with down as much when the choice squares were asymmetrical as when they were symmetrical. It is suggested that young children adopt a binary match-mismatch code in orientation and position comparisons, which tells them whether lines parallel each other or not and whether objects are in line with each other or not. This code can solve some discriminations but not others. When the code fails, it does so as much with asymmetrical as with symmetrical configurations. (19 ref.) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

MMPI--2 Code-Type Congruence of Injured Workers.

In this study, the authors examined the stability of Minnesota Multiphasic Personality Inventory--2 (J. N. Butcher, W. G. Dahlstrom, J. R. Graham, A. Tellegen, & B. Kaemmer, 1989) code types in a sample of 94 injured workers with a mean test-retest interval of 21.3 months (SD = 14.1). Congruence rates for undefined code types were 34% for high-point codes, 22% for 2-point codes, and 22% for 3-point codes. The data provide tentative evidence suggesting that defined code types are more stable than undefined code types. Cohen's kappa, a statistic that controls for chance agreement, was calculated for each clinical scale for both 2-point and 3-point code types. Only 2 of the 20 kappa coefficients were not significant at the p = .05 level. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Profile classification strategies for the Personality Inventory for Children.

Examined 2 profile classification strategies for use with the 12 clinical scales of the Personality Inventory for Children (PIC): reciprocal 2-point code types and code type factor clusters. The PIC profiles of 556 children, who comprised 6 of the criterion groups used in PIC scale development, and the 6–16 yr old normative sample (n?=?2,390) were classified by each system. Differences in frequencies across criterion groups of all the examined classification categories were significant and conceptually meaningful. Only 12% of the normative profiles had 2 or more PIC clinical scales with T scores greater than 69. Additional study of a heterogeneous sample of 691 child guidance protocols compared code type classification rates using traditional rules with a revised classification system based on previous actuarial study of individual profile scales. The possible interpretive significance of obtained sex and age differences in code type frequencies is discussed, as are proposed efforts to develop optimum code type interpretations. (39 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The area code hypothesis revisited: olfactory receptors and other related transmembrane receptors may function as the last digits in a cell surface code for assembling embryos

Recent evidence emerging from several laboratories, integrated with new data obtained by searching the genome databases, suggests that the area code hypothesis provides a good heuristic model for explaining the remarkable specificity of cell migration and tissue assembly that occurs throughout embryogenesis. The area code hypothesis proposes that cells assemble organisms, including their brains and nervous systems, with the aid of a molecular-addressing code that functions much like the country, area, regional, and local portions of the telephone dialing system. The complexity of the information required to code cells for the construction of entire organisms is so enormous that we assume that the code must make combinatorial use of members of large multigene families. Such a system would reuse the same receptors as molecular digits in various regions of the embryo, thus greatly reducing the total number of genes required. We present the hypothesis that members of the very large families of olfactory receptors and vomeronasal receptors fulfill the criteria proposed for area code molecules and could serve as the last digits in such a code. We discuss our evidence indicating that receptors of these families are expressed in many parts of developing embryos and suggest that they play a key functional role in cell recognition and targeting not only in the olfactory system but also throughout the brain and numerous other organs as they are assembled.     

Implications of the 1992 ethics code for diverse groups.

Previous renditions of the American Psychological Association's (APA's) code of ethics have clearly espoused psychologists' commitment to the ideal of having respect for the dignity and worth of the individual human being. The endorsement of the goal to protect fundamental human rights has always been highlighted in the Preambles of each revision of the code. The current code (APA, 1992) appears to have retreated from prioritizing this humanitarian stance. Ethnic minorities, women, gay men, and lesbians have reason to be apprehensive about the apparent downgrading in importance of psychologists' declaration of respect for the dignity and worth of the individual. All previous codes seemed to have been formulated from a perspective of protecting consumers. The new code appears to be driven by a need to protect psychologists. This article examines the possible impact of the shift in traditional priorities on diverse populations. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Experimental evaluation of binary codes for console display.

"Three binary code schemas were evaluated experimentally in terms of operator coding performance. One of the three code schemas was to be selected for use on a data processing system console display. The criterion for the code evaluation was the operator efficiency measured in terms of speed and accuracy of coding console problems. An independent group of subjects was assigned to each of the three code conditions. One of the three code schemas facilitated a significant time saving of 20-25% as compared to the remaining two code schemas. There were no differences in rate of error between the three code conditions." (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Quantity food production labor time

To facilitate the development and use of production time data in quantity foodservice, Master Standard Data (MSD) were applied to determine the feasibility of developing a standard code for synthesizing and predetermining production times. Observations were made in a 2,000-meal-per-day foodservice system to determine basic activities common to the production of single-item entrées. An MSD Quantity Food Production Code was developed through the use of MSD and verified by stop-watch time study. Three formulas for single-item entrées were analyzed, divided into basic elements of production, from which production time for preparation of 100 portions of each entrée was synthesized. Stop-watch studies were performed on three replications of the production of 100 portions of each item. Differences between synthesized time values determined by applying the MSD and stop-watch technique were within acceptable limits. The MSD Quantity Food Production Code was, therefore, considered valid and reliable. Repeated occurrence of similar elements within production methods indicated that the code could serve as a structural framework for establishing a universal data code applicable to all aspects of quantity food production.     

Unique structure of new serine tRNAs responsible for decoding leucine codon CUG in various Candida species and their putative ancestral tRNA genes

In an asporogenic yeast, Candida cylindracea, codon CUG is not translated as leucine but as serine. On the basis of our recent work on the determination of the genetic code using in vitro translation systems coupled with isolation of the corresponding tRNA molecules, it appears that this non-universal genetic code is unitized not only in C cylindracea but also in various Hemiascomycetes. Here we show that in addition to the species already reported, three pathogenic yeasts, C guilliermondii, C lusitaniae and C tropicalis, have tRNA(Ser)CAG, indicating that this non-universal genetic code (CUG=Ser) also exists in these species. Determination of their primary structures revealed that the uridine conserved at position 33 in usual tRNAs, is replaced by guanosine or cytidine. This suggests that the three-dimensional structures of the anticodon loop of these tRNAs differ from the conventional structure comprising the U turn in this position. Moreover, we succeeded in isolating putative ancestral serine tRNA genes whose sequences are highly homologous to tRNA(Ser)CAG in each case. These tRNA genes all have the anticodon sequence CGA corresponding to the codon UCG, indicating that tRNA(Ser)CAG might have emerged from tRNA(Ser)CGA during evolutionary change of the assignment of codon CUG.