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PubMed2004

Increasing the accuracy of operative coding.

INTRODUCTION: Operative codes provide a readily retrievable record of operative procedures and interventions and are invaluable in performance of clinical audit and research. In most hospitals, coding is performed by coding clerks who depend on legible complete operative notes for coding. In others, coding is by the operator/surgeon. The aim of this audit was to determine the impact of hand-written and typed operative notes on accuracy of coding as well as deciding if the operator is the better coder. METHODS: A total of 200 operations/procedures performed by one surgical firm were randomised, prospectively, into hand-written (HN, 100) and template-based typed (TN, 100) operation notes. Each procedure was coded by the operator/surgeon as well as by the coding clerk. The results were compared for error, incomplete and complete codes. RESULTS: Coding clerks were found to be better coders with 97% of TN and 85% of HN coded completely compared to 48% and 62%, respectively, by operators. There were more incomplete codes for HN compared to TN (15% versus 6% for coders and 62% versus 53% for operators). There were no error codes for both groups. CONCLUSIONS: These results suggest that the quality of coded information is poorer if operation notes are hand-written rather than typed, with template-based mandatory fields in typed notes possibly acting as an aide-memoir in generating complete, accurate notes. In the absence of formal training for clinicians, coding of procedures should probably be left to coding clerks.

Forms and Records Control↗

PubMed1997

[Coding for clinical laboratory information].

The field of clinical laboratory tests is facing an increase in the number of test items as well as a corresponding diversification due to the demands of medical institutions as well as improvements in analytical techniques. To respond to this situation, medical institutions have been promoting systematization of their testing procedures; information exchange among the institutions has likewise expanded with the use of media such as on-line systems and internet. Standardization of interfaces has been proposed to secure a common framework compatible with different types of information. Some embodiments in this country includes; (1) Interface Standards on Clinical Laboratory Information For information exchange, the format and reporting comments used in the media systems were standardized under the sponsorship of The Medical Information System Development Center, with a publication issued on 1993. (2) Standardization of Laboratory Test Code Standardization of codes for information exchange has been established under the sponsorship of The Japan Society of Clinical Pathology (Laboratory Test Coding Committee), through the systematization of laboratory test code used in media systems. A publication entitled "Classification & Coding for Clinical Laboratory Tests (8th edition in 1992, 9th edition in 1994 and supplement in 1996)" has been issued. The system for "Classification & Coding for Clinical Laboratory Tests" is divided into 5 components; (1) analyte code, (2) identification code, (3) specimen code, (4) methodology code, and (5) data classification code. The Laboratory test codes are precisely classified by "(1) analyte code", and then are identified by combination of additional codes such as specimen and methodology codes. In this year, we are making a new easily-used-codes composed of 5 Arabic figures.

Clinical Laboratory Information Systems↗

PubMed2000

Early fixation of an optimal genetic code.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible. Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space. This result is robust to variation in the methods and assumptions of the analysis. Although significantly better codes do exist under some assumptions, they are extremely rare and thus consistent with reports of an adaptive code: previous analyses which suggest otherwise derive from a misleading metric. However, all extant, naturally occurring, secondarily derived, nonstandard genetic codes do appear less adaptive. The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error. Potential criticisms of previous analyses appear to be without substance. That known variants of the standard genetic code appear less adaptive suggests that different evolutionary factors predominated before and after fixation of the canonical code. While the evidence for an adaptive code is clear, the process by which the code achieved this optimization requires further attention.

Amino Acids↗

PubMed2005

Nurses' views on ethical codes: a focus group study.

AIM: This paper reports a study exploring nurses' views on the 'potential' content and functions of an ethical code for nurses in Belgium. The term 'potential' is used, because Belgian nurses do not have experience with an ethical code. BACKGROUND: Ethical codes have been developed to guide nurses' practice and to improve their professional status. Little empirical research, however, has been undertaken to determine nurses' views on the content and functions of these codes. The available quantitative studies merely give some information on nurses' (lack of) knowledge and use of their ethical code. No nursing ethical code currently exists in Belgium. Qualitative research exploring nurses' views, therefore, was needed in order to find out which functions an ethical code could fulfil and what the code's content could be. METHOD: Eight focus groups were conducted with 50 nurses in different healthcare settings in Belgium. Data were generated during 2003. FINDINGS: According to participants, an ethical code could fulfil several functions, including supporting their professional nursing identity (external function) and giving guidelines for nursing practice (internal function). In addition, some aspects of content were mentioned, including nurses' responsibilities in a relational context: particular attention should be paid to the personality of the nurse and to the specificity of nursing as a relational activity. Most agreement was reached on the 'ethical' function of the code, namely guiding nurses' professional moral practice. Regarding disciplinary use and the need for legalization of the ethical code, on the contrary, opinions were divergent. CONCLUSIONS: It is of utmost importance to take into account nurses' views when developing an ethical code for their profession. This study gave a first picture of the views of nurses themselves. These initial findings should be completed with nurses' views on the formulation, dissemination and promotion of the ethical code. Such evidence-based development of an ethical code will probably give more guarantees that the code will meet nurses' expectations and will function optimally.

Adult↗

PubMed2006

Documentation and coding of ED patient encounters: an evaluation of the accuracy of an electronic medical record.

OBJECTIVE: The aim of the study was to describe a paper-based, template-driven and an electronic medical record used for capturing emergency care clinical information and to compare the accuracy of these documentation systems for coding patient encounters using the American Medical Association Current Procedural Terminology-2004 (AMA CPT-2004) evaluation and management codes intended for provider reimbursement. METHODS: A retrospective, cross-sectional study of 4-consecutive-day samples of ED patient encounter records from 2 similar community hospitals was done. For clinical documentation, hospital A uses an electronic medical record, whereas hospital B uses a paper-based template-driven record. Using a simple analytic model, expert coders A and B, respectively, coded the records from hospitals A and B for completeness. First, power analysis determined the acceptability of the patient record sample sizes (1 - beta = .90 at 1% significance level), and the frequency of AMA CPT-2004 primary evaluation and management codes 99281 through 99285 was calculated. Second, the completeness discrepancy rates for hospitals A and B were compared to determine the accuracy of both the paper-based, template-driven record and the electronic medical record in documenting and representing the clinical encounter. Third, interrater reliability between expert coders A and B was calculated to assess the level of agreement between each expert coder in determining the completeness discrepancy rates between hospitals A and B. Finally, the frequency of primary evaluation and management codes was analyzed to determine if there was a statistically significant difference between the paper-based, template-driven record and the electronic medical record representation of the clinical information, and if that difference could be attributable to the differing clinical documentation systems used in hospitals A and B. RESULTS: First, descriptive display demonstrated a difference in the frequency of the primary evaluation and management codes 99283 and 99284 within hospital A (expert coder A assessment, 36.1% vs 39.1%; expert coder B assessment, 36.6% vs 38.7%) and hospital B (expert coder A assessment, 47.8% vs 21.9%; expert coder B assessment, 48.6% vs 21.4%) was noted with the median, primary evaluation, and management code for hospital A of 99284 and the median, primary evaluation, and management code for hospital B of 99283. Second, Fisher exact test compared the completeness discrepancy rates between hospitals A and B as assessed by each expert coder and demonstrated no statistically significant difference in the completeness discrepancy rates (accuracy) between the paper-based, template-driven record and the electronic medical record documentation and coding system when assessed by either expert coder A (P = .370) or expert coder B (P = .819). Third, interrater reliability between expert coders A and B was evaluated using Cohen's kappa statistic. When evaluated both individually and jointly with respect to hospitals A and B, expert coders A and B had a good strength of agreement in their assessments of the accuracy of the documentation and coding system for hospital A (kappa = 0.6200) and hospital B (kappa = 0.6906) as well as for both hospitals evaluated together (kappa = 0.6616). Finally, interhospital differences in the frequency of primary evaluation and management codes were evaluated using Pearson chi(2) test with 3 df. The results for expert coder A (chi(2) = 47.4160; P < .001) and expert coder B (chi(2) = 46.5946; P < .001) recognize that there is a statistically significant degree of difference between hospitals A and B in the frequency distribution of primary evaluation and management codes, probably because of the dispersion of codes 99283 and 99284. CONCLUSIONS: A keystroke-driven, electronic medical record that resides on a knowledge platform that incorporates a clinical structured terminology, administrative coding schemata, AMA CPT-2004 codes and uses object-oriented, open-ended, branching chain clinical algorithms that "force" physician documentation of the clinical elements provides an equally accurate capture and representation of ED clinical encounter data as a paper-based, template-driven documentation system both in terms of the presence or absence of both the medically necessary, discrete data elements and the textual documentation-dependent, medical decision-making elements.

Chi-Square Distribution↗

PubMed2005

Accuracy of coding for possible warfarin complications in hospital discharge abstracts.

BACKGROUND: Hospital discharge abstracts could be used to identify complications of warfarin if coding for bleeding and thromboembolic events are accurate. OBJECTIVES: To measure the accuracy of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9CM) codes for bleeding and thromboembolic diagnoses. SETTING: University affiliated, tertiary care hospital in Ottawa, Canada. PATIENTS: A random sample of patients discharged between September 1999 and September 2000 with an ICD-9-CM code indicating a bleeding or thromboembolic diagnosis. METHODS: Gold-standard coding was determined by a trained chart abstractor using explicit standard diagnostic criteria for bleeding, major bleeding, and acute thromboembolism. The abstractor was blinded to the original coding. We calculated the sensitivity, specificity, positive, and negative predictive values of the original ICD-9CM codes for bleeding or thromboembolism diagnoses. RESULTS: We reviewed 616 medical records. 361 patients (59%) had a code indicating a bleeding diagnosis, 291 patients (47%) had a code indicating a thromboembolic diagnosis and 36 patients (6%) had a code indicating both. According to the gold standard criteria, 352 patients experienced bleeding, 333 experienced major bleeding, and 188 experienced an acute thromboembolism. For bleeding, the ICD-9CM codes had the following sensitivity, specificity, positive and negative predictive values [95% CI]: 93% [90-96], 88% [83-91], 91% [88-94], and 91% [87-94], respectively. For major bleeding, the ICD-9CM codes had the following sensitivity, specificity, positive and negative predictive values: 94% [91-96], 83% [78-87], 87% [83-90], and 92% [88-95], respectively. For thromboembolism, the ICD-9CM codes had the following sensitivity, specificity, positive and negative predictive values: 97% [94-99], 74% [70-79], 62% [57-68], and 98% [96-99], respectively. By selecting a sub-group of ICD-9CM codes for thromboembolism, the positive predictive value increased to 87%. CONCLUSION: In our centre, the discharge abstract could be used to identify and exclude patients hospitalized with a major bleed or thromboembolism. If coding quality for bleeding is similar in other hospitals, these ICD-9-CM diagnostic codes could be used to study population-based warfarin-associated hemorrhagic complications using administrative databases.

Anticoagulants↗

PubMed1998

The use of "diagnostic V codes" in pediatric ophthalmology.

BACKGROUND: Children requiring comprehensive eye examination for signs of familial eye disease or suspected systemic condition are referred to pediatric ophthalmologists. Such examinations may be critical to diagnosis and patient management, yet medically necessary screening examinations are not reimbursed by insurers when the patient is "normal." Faced with this dilemma regularly in a children's hospital practice, we began tracking insurer acceptance of "diagnostic V codes," which are diagnostic codes generally related to symptoms or status conditions rather than to medical states. The authors felt that "diagnostic V codes" might represent a more appropriate and correct code in the circumstance of a medically necessary screening examination found to be normal. METHODS: In July 1995 the use of 11 primary diagnostic V codes and 7 secondary diagnostic V codes was discussed in our faculty meeting and a list was displayed in each examination lane. Acceptance of V codes was then tracked for an 8-month period and analyzed 1 year later to provide a set of closed accounts. RESULTS: The code V71.8, or "observation for other specified, suspected condition" had a 73% acceptance rate by insurers on the basis of 207 examinations. The acceptance rate was not dependent on the use of a secondary code (76% for V71.8 alone vs 71% for secondary code used). Other V codes were infrequently used. CONCLUSIONS: The code V71.8 was an accepted code by insurers in our locality for medically necessary screening examinations found to be normal. The authors feel this high acceptance rate by insurers confirms our impression that V codes are the appropriate and correct codes to use for the medically necessary screening examination found to be normal.

Eye Diseases↗

PubMedDate not supplied

Derivation of emergency medical services dispatch codes associated with low-acuity patients.

OBJECTIVE: To identify emergency medical services (EMS) dispatch codes associated with basic life support (BLS) level of prehospital care, a proxy for low illness acuity. METHODS: This retrospective cohort study was conducted in an urban city with a single advanced life support level EMS provider. The 911 center was certified in using dispatch protocols from Priority Dispatch Corporation (Salt Lake City, UT). Dispatch data on all transported EMS patients from August 2001 to April 2002 were abstracted. The authors prospectively defined a low-acuity patient as one who received BLS-level care and defined a low-acuity dispatch code as one in which at least 90% of coded patients required only BLS care. For each dispatch code or code group, the authors calculated the fraction of patients who received BLS-level care. For each "A"-level (lowest category) dispatch code group, the fraction of patients receiving BLS-level care was also evaluated. RESULTS: A total of 19,332 calls met inclusion criteria and were categorized into 118 dispatch codes or code groups. Twenty-eight codes or code groups with 7,801 patients met the authors' definition of low acuity. Overall, 7,394 patients received only BLS care (94.8%, 95% confidence interval: 94.3%-95.3%). Analysis of "A"-level dispatch code groups found BLS use rates of 52.8% to 99.3%. CONCLUSIONS: Certain dispatch codes are associated with the delivery of BLS-level care, indicating identification of patients likely to be low acuity. These codes are not necessarily "A"-level dispatch codes, which are commonly considered to represent the lowest-acuity patients. Future studies are needed to prospectively validate that these codes do represent low-acuity patients.

Acute Disease↗

PubMed2003

Procedural coding of spinal surgeries (CPT-4 versus ICD-9-CM) and decisions regarding standards: a multicenter study.

STUDY DESIGN: A comparison of procedural coding systems ( [ICD-9-CM] [CPT-4]) applied to lumbar spine surgery patients from six teaching institutions. OBJECTIVE: To compare the detail reflected by coding systems used to describe spinal procedures. SUMMARY OF BACKGROUND DATA: Administrative databases contain ICD-9-CM procedural codes, which are derived from hospital discharge abstracts. These databases are used, in part, to establish health care utilization patterns and set health care policy. Previous studies have demonstrated inaccuracies in ICD diagnosis coding. However, the literature is void of information regarding the accuracy of ICD procedural coding of spine procedures. METHODS: Data were complete in 143 of 150 lumbar spine surgery patients (aged 17-84 years). Surgeons assigned CPT-4 procedural codes. These codes were compared with ICD procedure codes assigned by hospital medical records staff. RESULTS: On average, in four of six hospitals, there were more CPT codes assigned to patient records by the surgeon than ICD codes assigned by hospital medical records staff. Overall, CPT codes reflected a greater level of detail than ICD codes. CONCLUSIONS: These findings illustrate the increased detail of CPT coding over ICD coding in the spinal surgery cases reviewed. The ICD procedural codes contained in administrative databases tend to underrepresent the complexity of the surgical procedures actually performed.

Adolescent↗

PubMed2005

Measuring diagnoses: ICD code accuracy.

OBJECTIVE: To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. DATA SOURCES/STUDY SETTING: The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. STUDY DESIGN/METHODS: We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. PRINCIPLE FINDINGS: Main error sources along the "patient trajectory" include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the "paper trail" include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. CONCLUSIONS: By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways.

Data Collection↗

PubMed2003

Use of Read codes in diabetes management in a south London primary care group: implications for establishing disease registers.

OBJECTIVE: To establish current practice in the use of Read codes for diabetes. DESIGN: Cross sectional study. SETTING: 17 practices in the Battersea primary care group in southwest London. DATA SOURCES: Computerised medical records. MAIN OUTCOME MEASURES: Number of codes in use in all practices; variation in the use of codes between practices; and prevalence of Read code use in diabetic patients. RESULTS: At least 9 separate Read code groupings and 25 individual diabetes codes were in use in the 17 general practices. Only one Read code (C10, diabetes mellitus) and its subcodes was being used in all 17 practices, but its use varied from 14% to 98% of patients with diabetes. The use of other key Read codes for monitoring the care of patients with diabetes also varied widely between practices; for example, < 20% of practices used the code for the location of care. Less than half of patients (45%) with diabetes had their type of diabetes coded, and even fewer (21%) had measures such as the examination of the retina coded. CONCLUSIONS: The use of Read codes for diabetes needs to be standardised and coding levels improved if valid diabetic registers are to be constructed and the quality of care is to be monitored effectively. Until all patients with diabetes have the C10 Read code recorded, clinicians will have to use a wide range of Read codes and prescribing data to ensure that diabetes registers are complete.

Cross-Sectional Studies↗

PubMed2001

Accuracy of external cause of injury codes reported in Washington State hospital discharge records.

OBJECTIVE: To evaluate the accuracy of external cause of injury codes (E codes) reported in computerized hospital discharge records. METHODS: All civilian hospitals in Washington State submit computerized data for each hospital discharge to a file maintained by the Department of Health. In 1996, 32 hospitals accounted for 80% of the injury related discharges in this file; from these hospitals, we sampled 1,260 computerized records for injured patients in a stratified, but random, manner. An expert coder then visited the 32 study hospitals, reviewed the medical records that corresponded to each computerized record, and assigned an E code for that hospitalization. The computerized E code information was compared with codes provided by the expert reviewer. RESULTS: The incidence of hospitalization for injury based upon computerized hospital discharge data was very similar to that based upon chart review: incidence rate ratio 1.0 (95% confidence interval 1.00 to 1.02). Computerized hospital discharge data correctly ranked injuries in regard to both mechanism and intent. Overall agreement on coding was 87% for mechanism of injury, 95% for intent of injury, and 66% for the complete E code. The sensitivity of computerized hospital discharge data for identification of falls, motor vehicle traffic injuries, poisonings, and firearm injuries was 91% or better. The predictive value positive of coding for these four categories of injury ranged from 88% for motor vehicle traffic injuries to 94% for poisonings. The amount of agreement for intent coding ranged from 84% for firearm injuries to 99% for falls. Agreement on coding of the complete E code ranged from 57% for firearm injuries to 72% for poisonings. CONCLUSIONS: Computerized hospital discharge data can be used with confidence to determine how many injuries are treated in a hospital setting and the relative magnitude of various categories of injury. E codes reported in hospital discharge data are a reliable source of information on the types of information most often used for injury related analyses and priority setting. The detail codes (complete E codes) reported in hospital discharge codes are less reliable and must be used with caution.

Forms and Records Control↗

PubMed2000

National Cancer Data Base survey of breast cancer management for patients from low income zip codes.

BACKGROUND: The National Cancer Data Base (NCDB), a joint project of the American College of Surgeons Commission on Cancer and the American Cancer Society, is a cancer management and outcomes data base for health care organizations. It provides a comparative summary of patient care that is used by participating hospitals and communities for self-assessment. The most current (1995-1996) breast cancer data on patients from low income zip codes are described here. METHODS: Since 1989, eight Calls for Data have been issued, yielding a total of 191,714 reports of non-Hispanic white patients with breast cancer for the years analyzed, 1995-1996. A total of 1961 hospital cancer registries have participated in at least one of the Calls for Data. RESULTS: A diverse range of breast cancer cases was reported from a variety of geographic locations and medical care environments. There were general similarities in the treatment of patients from the different income groups; however, some differences were reported. Among patients from lower income zip codes, 60.7% were age 60 years or older, compared with 55.1% from other income zip code groups. The AJCC stage distribution was reported as less favorable for patients from low income zip codes than for other patients. The percentage of patients from low income zip codes diagnosed as Stage 0 or I was 51.2%, compared with 55.9% of patients from the other income zip codes. Of patients from lower income zip codes, 12.1% were reported to have Stage III or IV disease, compared with 10.0% of patients from other income zip codes. Patients from low income zip codes received less tissue-sparing surgery. Of patients from low income zip codes, 14.9% received partial mastectomy with or without radiation or systemic therapy, compared with 18.3% of patients from other income zip codes. The percentage of patients from low income zip codes who received a partial mastectomy with axillary lymph node dissection was 23.3% for patients from other income zip codes, the percentage was 30.5%. Conversely, 49.8% of patients from lower income zip codes received a modified radical mastectomy, compared with 40.5% of patients from other income zip codes. CONCLUSIONS: Further improvements in the early diagnosis and surgical treatment of low income patients can probably be achieved. Programmatic activities that further explain or reduce the apparent nonpreferred treatment of some low income patients should be encouraged.

Adult↗

PubMed1988

Civil Code, 11 December 1987.

Article 162 of this Mexican Code provides, among other things, that "Every person has the right freely, responsibly, and in an informed fashion to determine the number and spacing of his or her children." When a marriage is involved, this right is to be observed by the spouses "in agreement with each other." The civil codes of the following states contain the same provisions: 1) Baja California (Art. 159 of the Civil Code of 28 April 1972 as revised in Decree No. 167 of 31 January 1974); 2) Morelos (Art. 255 of the Civil Code of 26 September 1949 as revised in Decree No. 135 of 29 December 1981); 3) Queretaro (Art. 162 of the Civil Code of 29 December 1950 as revised in the Act of 9 January 1981); 4) San Luis Potosi (Art. 147 of the Civil Code of 24 March 1946 as revised in 13 June 1978); Sinaloa (Art. 162 of the Civil Code of 18 June 1940 as revised in Decree No. 28 of 14 October 1975); 5) Tamaulipas (Art. 146 of the Civil Code of 21 November 1960 as revised in Decree No. 20 of 30 April 1975); 6) Veracruz-Llave (Art. 98 of the Civil Code of 1 September 1932 as revised in the Act of 30 December 1975); and 7) Zacatecas (Art. 253 of the Civil Code of 9 February 1965 as revised in Decree No. 104 of 13 August 1975). The Civil Codes of Puebla and Tlaxcala provide for this right only in the context of marriage with the spouses in agreement. See Art. 317 of the Civil Code of Puebla of 15 April 1985 and Article 52 of the Civil Code of Tlaxcala of 31 August 1976 as revised in Decree No. 23 of 2 April 1984. The Family Code of Hidalgo requires as a formality of marriage a certification that the spouses are aware of methods of controlling fertility, responsible parenthood, and family planning. In addition, Article 22 the Civil Code of the Federal District provides that the legal capacity of natural persons is acquired at birth and lost at death; however, from the moment of conception the individual comes under the protection of the law, which is valid with respect to the individual as far as the effects of this law provides as if the individual were already born.

Abortion, Induced↗

PubMedDate not supplied

On the evolution of redundancy in genetic codes.

We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use very simple assumptions about translation, mutation, and protein fitness to calculate mutation-selection equilibria of codon frequencies and fitness in a large asexual population with a given genetic code. We then compute the fitnesses of altered genetic codes that compete to invade the population by translating its genes with higher fitness. Codes and genes coevolve in a succession of stages, alternating between genetic equilibration and code invasion, from an initial wholly ambiguous coding state to a diversified frozen coding state. Our simulations almost always resulted in partially redundant frozen genetic codes. Also, the range of simulated physicochemical properties among encoded amino acids in frozen codes was always less than maximal. These results did not require the assumption of historical constraints on the number and type of amino acids available to codes nor on the complexity of proteins, stereochemical constraints on the translational apparatus, nor mechanistic constraints on genetic code change. Both the extent and timing of amino-acid diversification in genetic codes were strongly affected by the message mutation rate and strength of missense selection. Our results suggest that various omnipresent phenomena that distribute codons over sites with different selective requirements--such as the persistence of nonsynonymous mutations at equilibrium, the positive selection of the same codon in different types of sites, and translational ambiguity--predispose the evolution of redundancy and of reduced amino acid diversity in genetic codes.

Codon↗

PubMed2001

Optimality of the genetic code with respect to protein stability and amino-acid frequencies.

BACKGROUND: The genetic code is known to be efficient in limiting the effect of mistranslation errors. A misread codon often codes for the same amino acid or one with similar biochemical properties, so the structure and function of the coded protein remain relatively unaltered. Previous studies have attempted to address this question quantitatively, by estimating the fraction of randomly generated codes that do better than the genetic code in respect of overall robustness. We extended these results by investigating the role of amino-acid frequencies in the optimality of the genetic code. RESULTS: We found that taking the amino-acid frequency into account decreases the fraction of random codes that beat the natural code. This effect is particularly pronounced when more refined measures of the amino-acid substitution cost are used than hydrophobicity. To show this, we devised a new cost function by evaluating in silico the change in folding free energy caused by all possible point mutations in a set of protein structures. With this function, which measures protein stability while being unrelated to the code's structure, we estimated that around two random codes in a billion (109) are fitter than the natural code. When alternative codes are restricted to those that interchange biosynthetically related amino acids, the genetic code appears even more optimal. CONCLUSIONS: These results lead us to discuss the role of amino-acid frequencies and other parameters in the genetic code's evolution, in an attempt to propose a tentative picture of primitive life.

Amino Acid Substitution↗

PubMed1994

Drug data coding and analysis in epidemiologic studies.

In epidemiologic studies that collect comprehensive information on medication use, the complexity of dealing with a large number of trade and generic names may limit the utilization of these data bases. This paper shows the specific advantage of using two coding systems, one to maximize efficiency of data entry, and the other to facilitate analysis by organizing the drug ingredients into hierarchical categories. The approach used by two large surveys, one in the USA and one in Italy, is described: the Established Populations for Epidemiologic Studies of the Elderly (EPESE) and the 'Gruppo Italiano di Farmacovigilanza nell' Anziano' (GIFA). To enter the medications into a computerized database, codes matching the drug product names are needed. In the EPESE the prescription and over the counter drug products are coded with the Drug Products Information Coding System (DPICS) and the Iowa Nonprescription Drug Products Information Coding System (INDPICS), respectively. The GIFA study uses the coding system of the Italian Ministry of Health (MINSAN), with a unique numeric code for each drug product available in Italy. To simplify the analytical process the drug entry codes are converted into hierarchical coding systems with unique codes for specific drug ingredients, chemical and therapeutic categories. The EPESE and GIFA drug data are coded with the Iowa Drug Information System (IDIS) ingredient codes, and the Anatomical Therapeutic and chemical (ATC) codes, respectively. Examples are provided that show coding of diuretics in these two studies and demonstrate the analytic advantages of these systems.

Adverse Drug Reaction Reporting Systems↗

PubMed2001

CPT coding by interventional radiologists: accuracy and implications.

PURPOSE: To evaluate the accuracy of Current Procedural Terminology (CPT) coding for interventional radiology services when coding is performed by the operating physician. MATERIALS AND METHODS: Coding data for 1,174 interventional radiology encounters in 736 patients were analyzed for appropriate use of CPT codes. Physician operators initially assigned provisional codes. Formal coding for billing purposes was performed at a later date by one of two experienced interventional radiology physician coders. Initial operator coding errors and associated relative value unit (RVU) impact were analyzed. The coding patterns of experienced physician coders were compared with those of the other interventionalists. RESULTS: Only 82% of encounters were initially coded correctly, with a small net tendency toward undercoding. The overall net RVU impact of errors was only -1.2%, with the effects of undercoding outweighing those of overcoding. More complex cases (> or =4 CPT codes) were much more likely to be coded erroneously than less complex cases (24% vs 14%, P <.001). Experienced physician coders committed significantly fewer errors than other physicians (10% vs 25%, P <.001), but there was a similar minimal net RVU impact of errors (-1.1% vs -1.4%, P =.198). CONCLUSION: Although initial physician coding errors for interventional radiology procedures are common, the net RVU impact is minimal. The accuracy of experienced physician coders is significantly higher than that for other interventionalists. Because of the regulatory consequences of coding inaccuracies, practices should establish quality improvement systems to minimize errors and use the skills of experienced individuals in their coding processes.

Forms and Records Control↗