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Analysis of codon usage frequency for the combined coding sequences of 52 E. coli genes, taken from the European Molecular Biology Laboratory Nucleotide Sequence Data Library, Release 2, shows that there is a significant positive correlation between the frequency with which a given codon appears on the coding strand and the frequency with which it appears, in phase, on the non-coding strand.
A "code-no code" resuscitation classification was recently instituted at Memorial Sloan Kettering Cancer Center. Physician compliance was voluntary. Of 48 subsequent cardiopulmonary arrests, 7 patients (14.6%) were discharged from hospital. They included 4 of 17 patients (23.5%) previously assigned "code" status and 1 of 27 patients (3%) whose resuscitation status had not been designated. Reluctance on the part of the primary physician to withhold resuscitation was clearly evident in this group, of whom more than half had widespread malignancy. Stage of disease did not influence the 50% rate of successful resuscitations but no patient with metastatic or uncontrolled cancer left hospital. The discharge rate among arrest patients with recently diagnosed or localized cancer was 32%. These observations justify continued efforts to restrict cardiopulmonary resuscitation (CPR) to those with a reasonable prognosis for worthwhile palliation or cure.
The enzymes responsible for replication of the RNA of the single-stranded RNA bacteriophages contain, in addition to one phage-coded polypeptide, three host-coded polypeptides taken from the protein biosynthetic machinery: ribosomal protein S1 and the elongation factors Tu and Ts. While S1 performs a function in RNA replication derived from its protein synthetic function, mRNA binding, the reactions catalysed by the elongation factors in protein synthesis are apparently dispensible for RNA replication. In the replicase, these polypeptides, acting as the EF-Tu . Ts complex, play a fundamental structural role. Replacement of the endogenous EF-Tu with mutant EF-Tu, itself stable, causes the RNA replicase to become unstable. The possibility that EF-Tu . Ts is solely a structural protein in the RNA replicase is suggested by experiments showing that a variety of modifications of the elongation factors can be tolerated without loss of RNA synthetic capacity. In fact, EF-Tu . Ts from distantly related bacterial species can substitute for E. coli EF-Tu . Ts in RNA replicase. Evidence is presented that the high in vitro template specificity of Q beta replicase may be accomplished through modulation of the level of GTP required for initiation of transcription. Different natural and synthetic RNAs require quite different GTP concentrations. Mn2+ ions, which extend the range of templates transcribed by Q beta replicase, lower the requirement for GTP. High ionic strength, which alters the conformation of Q beta replicase such that template specificity is increased, raises the GTP requirement. An additional host coded protein required for in vitro Q beta RNA replication, host factor (HF), interacts specifically with Q beta RNA. This polypeptide acts by allowing Q beta replicase to initiate RNA synthesis with Q beta RNA at reduced GTP concentration.
We tested the hypothesis that pigeons could use a cognitively efficient coding strategy by training them on a conditional discrimination (delayed symbolic matching) in which one alternative was correct following the presentation of one sample (one-to-one), whereas the other alternative was correct following the presentation of any one of four other samples (many-to-one). When retention intervals of different durations were inserted between the offset of the sample and the onset of the choice stimuli, divergent retention functions were found. With increasing retention interval, matching accuracy on trials involving any of the many-to-one samples was increasingly better than matching accuracy on trials involving the one-to-one sample. Furthermore, following this test, pigeons treated a novel sample as if it had been one of the many-to-one samples. The data suggest that rather than learning each of the five sample-comparison associations independently, the pigeons developed a cognitively efficient single-code/default coding strategy.
A purified 15,000-molecular-weight (Mr) Prague strain Rous sarcoma virus gag gene-coded structural protein, p15, was shown to enzymatically cleave the previously described 130,000 Mr feline sarcoma virus-coded polyprotein, Pr130. Cleavage products included proteins ranging in molecular weight from 12,000 to 110,000. The specificity of this cleavage reactivity was indicated by the fact that, under similar conditions, neither purified type C viral structural proteins nor nonviral proteins such as bovine serum albumin were cleaved to significant extents. Moreover, feline leukemia virus Pr65gag was efficiently cleaved, resulting in the generations of proteins of 30,000 (p30), 15,000 (p15), 12,000 (p12), and 10,000 (p10) Mr. Using enzymatically (p15) treated feline sarcoma virus Pr130 as starting material, we were able to purify a major 72,000 Mr cleavage product and to show it to contain the previously described feline sarcoma virus-coded nonstructural component.
A comparison has been made between the coding of the cause of death by (a) the Royal College of General Practitioners (RCGP) during the Oral Contraception Study and (b) the Office of Population Censuses and Surveys (OPCS) or the General Register Office for Scotland (GRO) on death certificates for the same subjects. Broad grouping of the International Classification of Diseases (ICD) showed close agreement between RCGP and OPCS or GRO coding for all deaths which occurred from the start of the Oral Contraception Study in 1968 up to December 1978. Moreover, where discrepancies occurred there were no systematic differences between ever-users of oral contraceptive and non-users. Detailed examinations of discrepancies in the coding of the causes of those deaths included in the RCGP publication of October 1977 shows that our previous estimate of mortality risk associated with oral contraceptives would not be materially altered by the use of death certificate information.
When deciding between different options, individuals are guided by the expected (mean) value of the different outcomes and by the associated degrees of uncertainty. We used functional magnetic resonance imaging to identify brain activations coding the key decision parameters of expected value (magnitude and probability) separately from uncertainty (statistical variance) of monetary rewards. Participants discriminated behaviorally between stimuli associated with different expected values and uncertainty. Stimuli associated with higher expected values elicited monotonically increasing activations in distinct regions of the striatum, irrespective of different combinations of magnitude and probability. Stimuli associated with higher uncertainty (variance) elicited increasing activations in the lateral orbitofrontal cortex. Uncertainty-related activations covaried with individual risk aversion in lateral orbitofrontal regions and risk-seeking in more medial areas. Furthermore, activations in expected value-coding regions in prefrontal cortex covaried differentially with uncertainty depending on risk attitudes of individual participants, suggesting that separate prefrontal regions are involved in risk aversion and seeking. These data demonstrate the distinct coding in key reward structures of the two basic and crucial decision parameters, expected value, and uncertainty.
It is often supposed that the messages sent to the visual cortex by the retinal ganglion cells are encoded by the mean firing rates observed on spike trains generated with a Poisson process. Using an information transmission approach, we evaluate the performances of two such codes, one based on the spike count and the other on the mean interspike interval, and compare the results with a rank order code, where the first ganglion cells to emit a spike are given a maximal weight. Our results show that the rate codes are far from optimal for fast information transmission and that the temporal structure of the spike train can be efficiently used to maximize the information transfer rate under conditions where each cell needs to fire only one spike.
Peripheral sensory activity follows the temporal structure of input signals. Central sensory processing uses also rate coding, and motor outputs appear to be primarily encoded by rate. I propose here a simple, efficient structure, converting temporal coding to rate coding by neuronal phase-locked loops (PLL). The simplest form of a PLL includes a phase detector (that is, a neuronal-plausible version of an ideal coincidence detector) and a controllable local oscillator that are connected in a negative feedback loop. The phase detector compares the firing times of the local oscillator and the input and provides an output whose firing rate is monotonically related to the time difference. The output rate is fed back to the local oscillator and forces it to phase-lock to the input. Every temporal interval at the input is associated with a specific pair of output rate and time difference values; the higher the output rate, the further the local oscillator is driven from its intrinsic frequency. Sequences of input intervals, which by definition encode input information, are thus represented by sequences of firing rates at the PLL's output. The most plausible implementation of PLL circuits is by thalamocortical loops in which populations of thalamic "relay" neurons function as phase detectors that compare the timings of cortical oscillators and sensory signals. The output in this case is encoded by the thalamic population rate. This article presents and analyzes the algorithmic and the implementation levels of the proposed PLL model and describes the implementation of the PLL model to the primate tactile system.
Physician documentation, Current Procedural Terminology (CPT) coding, and compliance with federal billing regulations are essential given the government's significant efforts to address fraud and abuse and the grave financial and legal consequences of noncompliance. Because Medicare guidelines do not focus substantially on psychiatric care, compliance is especially challenging for psychiatrists and psychiatric centers. Four years ago, the University of Texas-Harris County Psychiatric Center formed a medical staff coding committee to assist the center and its psychiatrists in dealing with compliance issues. The committee has evolved into a highly effective and important component of the institution's overall compliance program. The authors discuss the origins, development, and accomplishments of the medical staff coding committee.
In a series of experiments color coding, intensity coding, and decluttering were compared in order to assess their potential benefits for accessing information from electronic map displays. Participants viewed electronic battlefield maps containing 5 classes of information discriminable by color or intensity, or, in the decluttering condition, displayed or removed entirely by a key press. Participants were asked questions requiring them to focus on objects within a class (objects presented at the same color or intensity) or to integrate data between objects in different classes (objects presented at different colors and intensities). The results suggested that the benefits of color and intensity coding appear to be in segregating the visual field rather than calling attention to the objects presented at a certain color or intensity. Interactivity proved to be a disadvantage; the time cost of information retrieval outweighed the time benefits of presenting less information on the display or even allowing map users to customize their displays. Potential applications of this research include a cost-benefit analysis for the use of 3 attentional filtering techniques and an attempt to quantitatively measure map complexity.
In February, the U.S. Food and Drug Administration (FDA) issued its final ruling requiring that all drug and biological products sold to hospitals incorporate bar codes on their labels. The ruling smooths the way for widespread adoption of bar-code-enabled point-of-care (BPOC) systems, which are a valuable tool for reducing medication errors. BPOC systems help ensure that the right medications reach the right patient at the right time by allowing bar codes on a patient's ID wristband to be checked against the medication packaging. But BPOC systems will only become truly effective if medications are widely available in unit-dose packaging. Right now only about a third of all medications are available in this form. Although this situation is likely to improve, hospitals wanting to take advantage of BPOC technology soon may need to do some drug repackaging themselves (or have it done by a third party), along with a lot of other groundwork. Widespread BPOC use may still be several years away, but the time to start preparing is now.
A simple statistical block code in combination with the LZW-based compression utilities gzip and compress has been found to increase by a significant amount the level of compression possible for the proteins encoded in Haemophilus influenzae, the first fully sequenced genome. The method yields an entropy value of 3.665 bits per symbol (bps), which is 0.657 bps below the maximum of 4.322 bps and an improvement of 0.452 bps over the best known to date of 4.118 bps using Matsumoto, Sadakane, and Imai's lza-CTW algorithm. Calculations based on a compact inverse genetic code show that the genome has a maximum entropy of 1.757 bps for the coding regions, with a possibly lower actual entropy. These results hint at the existence of hitherto unexplored redundancies that do not show up in Markov models and are indicative of more internal structure than suspected in both the protein and the genome.
The proportions of glucose phosphate isomerase (GPI-1) allozymes produced by early (Gpi-1sa/Gpi-1sb female X Gpi-1sc/Gpi-1sc male)F1 mouse embryos were analysed by quantitative cellulose acetate electrophoresis. Technical controls showed that this system is extremely sensitive, quantitatively reproducible and quite accurate. Genetic controls established that the Gpi-1sa/Gpi-1sb mothers were homozygous for the Gpi-1tb temporal allele, that produces relatively high GPI-1 activity in the oocyte. The oocyte-coded enzyme lasted until about 5 1/2 days post coitum (p.c.) or shortly thereafter. The maternally derived, embryonic Gpi-1s allele was expressed no earlier than the paternally derived allele. This was first expressed between 2 1/2 and 3 1/2 days p.c. In this cross, most of the transition from oocyte-coded to embryo-coded GPI-1 occurred between 2 1/2 and 5 1/2 days p.c.
Many laboratories use electronic message standards to transmit results to their clients. If all laboratories used the same "universal" set of test identifiers, electronic transmission of results would be greatly simplified. The Logical Observation Identifier Names and Codes (LOINC) database aims to be such a code system, covering at least 98% of the average laboratory's tests. The LOINC database should be of interest to hospitals, clinical laboratories, doctors' offices, state health departments, governmental healthcare providers, third-party payors, organizations involved in clinical trials, and quality assurance and utilization reviewers. The fifth release of the LOINC database, containing codes, names, and synonyms for approximately 6300 test observations, is now available on the Internet for public use. Here we describe the LOINC database, the methods used to produce it, and how it may be obtained.
A method quantifying the randomness of nucleotide sequences is developed, based on the introduction of a standard deviation type of quantity involving locally computed means and a length scale around which is assessed the clustering of nucleotides. It is pointed out that the value taken by this modified standard deviation may distinguish between coding rich and non-coding rich sequences. Moreover, the approach described herein allows the determination of some minimal characteristics of an evolutionary scenario which can account for the origin of the clustering in the nucleotide distribution of the different parts of the genome.
This article discusses the possibilities and pitfalls of constructing a code of ethics for university professors. Professional, educational, legal, and policy questions regarding the goals, format, and content of an academic ethics code are raised and a series of aspirational principles and enforceable standards that might be included in such a document are presented for discussion and debate.
Natural numbers are characterized as being odd or even, prime or non-prime. If the quaternary information units of (DNA or RNA) nucleotide bases are assigned as 0 (for A), 1 (C), 2 (U or T) and 3 (G), then a unique set of amino acid numbers can be obtained by comparing the properties of numbers and coding properties. These numbers are: 0 for "stop" signals, 1 for Trp, 2 for Ile and 3 for Met. For other codons, synonymous quartets follow exclusively the P1 number series (prime numbers of the form 4n + 1); doublets mostly follow the P3 series (primes with quaternary remainder 3). A "one-to-one correspondence" between these numbers and the genetic code is established by considering their combinatorial specificities.