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PubMed2001

Three quantitative approaches to the diagnosis of abdominal pain in children: practical applications of decision theory.

BACKGROUND/PURPOSE: The authors compared 3 quantitative methods for assisting clinicians in the differential diagnosis of abdominal pain in children, where the most common important endpoint is whether the patient has appendicitis. Pretest probability in different age and sex groups were determined to perform Bayesian analysis, binary logistic regression was used to determine which variables were statistically significantly likely to contribute to a diagnosis, and recursive partitioning was used to build decision trees with quantitative endpoints. METHODS: The records of all children (1,208) seen at a large urban emergency department (ED) with a chief complaint of abdominal pain were immediately reviewed retrospectively (24 to 72 hours after the encounter). Attempts were made to contact all the patients' families to determine an accurate final diagnosis. A total of 1,008 (83%) families were contacted. Data were analyzed by calculation of the posttest probability, recursive partitioning, and binary logistic regression. RESULTS: In all groups the most common diagnosis was abdominal pain (ICD-9 Code 789). After this, however, the order of the most common final diagnoses for abdominal pain varied significantly. The entire group had a pretest probability of appendicitis of 0.06. This varied with age and sex from 0.02 in boys 2 to 5 years old to 0.16 in boys older than 12 years. In boys age 5 to 12, recursive partitioning and binary logistic regression agreed on guarding and anorexia as important variables. Guarding and tenderness were important in girls age 5 to 12. In boys age greater than 12, both agreed on guarding and anorexia. Using sensitivities and specificities from the literature, computed tomography improved the posttest probability for the group from.06 to.33; ultrasound improved it from.06 to.48; and barium enema improved it from.06 to.58. CONCLUSIONS: Knowing the pretest probabilities in a specific population allows the physician to evaluate the likely diagnoses first. Other quantitative methods can help judge how much importance a certain criterion should have in the decision making and how much a particular test is likely to influence the probability of a correct diagnosis. It now should be possible to make these sophisticated quantitative methods readily available to clinicians via the computer.

Abdominal Pain↗
PubMedDate not supplied

Nursing classification systems: necessary but not sufficient for representing "what nurses do" for inclusion in computer-based patient record systems.

Our premise is that from the perspective of maximum flexibility of data usage by computer-based record (CPR) systems, existing nursing classification systems are necessary, but not sufficient, for representing important aspects of "what nurses do." In particular, we have focused our attention on those classification systems that represent nurses' clinical activities through the abstraction of activities into categories of nursing interventions. In this theoretical paper, we argue that taxonomic, combinatorial vocabularies capable of coding atomic-level nursing activities are required to effectively capture in a reproducible and reversible manner the clinical decisions and actions of nurses, and that, without such vocabularies and associated grammars, potentially important clinical process data is lost during the encoding process. Existing nursing intervention classification systems do not fulfill these criteria. As background to our argument, we first present an overview of the content, methods, and evaluation criteria used in previous studies whose focus has been to evaluate the effectiveness of existing coding and classification systems. Next, using the Ingenerf typology of taxonomic vocabularies, we categorize the formal type and structure of three existing nursing intervention classification system--Nursing Interventions Classification, Omaha System, and Home Health Care Classification. Third, we use records from home care patients to show examples of lossy data transformation, the loss of potentially significant atomic data, resulting from encoding using each of the three systems. Last, we provide an example of the application of a formal representation methodology (conceptual graphs) which we believe could be used as a model to build the required combinatorial, taxonomic vocabulary for representing nursing interventions.

Abstracting and Indexing↗
PubMed1981

Location of structural domains in protein.

We are surface area measurements based on atomic positions to give a quantitative definition of structural domains in proteins. Segments of the polypeptide chain making a minimum of interactions with the rest of the protein structure are identified on interface area scans, where the area B of the interface between a N-terminal segment of i residues and the complementary C-terminal segment is plotted as a function of i. Domain boundaries appear as minima of B in the scans. The procedure may be iterated to build a hierarchy of subdomains. It detects only continuous domains made of a single stretch of polypeptide chain but may be extended to detect such domains in the presence of discontinuous ones. Domains defined from interface area scans fit very well with globular structural regions identified by inspection of protein models [Wetlaufer, D. B. (1973) Proc. Natl. Acad. Sci U.S.A. 70, 697-701]. They do not in general correspond to the repeated structural units observed in some proteins by superposition studies. In hemoglobin and hen lysozyme, the domains do not correspond to the coding sequences separated by introns in the genes.

Animals↗
PubMed1985

Patterns of expression and organization of cytokeratin intermediate filaments.

Cytokeratins are a large multigene family comprising two polypeptide types, i.e. acidic (type I) and basic (type II) ones, which are distinguished on the basis of immunological, peptide mapping, mRNA hybridization, and primary amino acid sequence data. The acidic (type I) cytokeratins can be subdivided into at least two different subtypes on the basis of their carboxy-terminal sequences. Considerable interspecies conservation of sequences exists, even extending to the 3'-non-coding mRNA regions. Different pairs of type I and II cytokeratins show different resistance to dissociation in urea. Sequence differences of the type I cytokeratins containing functional domains may be an explanation of the observed preference of co-expression with certain type II cytokeratins. The distribution of the different type I and II cytokeratins in normal epithelia and in carcinomas is differentiation related and can be used for cell typing and identification. The cell type-specific expression of cytokeratin polypeptides is recognized at both the protein and the mRNA level. The building block of cytokeratin IFs is a heterotypic tetramer, consisting of two type I and two type II polypeptides arranged in pairs of laterally aligned coiled coils. This principle of tetrameric organization is thought to be generally applicable to IFs.

Amino Acid Sequence↗
PubMedDate not supplied

[Fatal occupational accidents: updating of data from a mortality register].

BACKGROUND: In Italy, almost one thousand deaths due to occupational accidents are usually registered by INAIL each year. Case registration by INAIL has merely administrative purposes and therefore it is necessary to use other sources for case ascertainment in order to better estimate the real number of deaths related to occupational accidents, as shown also by previous papers. OBJECTIVES: Evaluation of the contribution of another data source, namely the Tuscany Regional Mortality Registry, to obtain the correct figure for occupational accident deaths through the use of a place-of-occurrence notation on the death certificate. METHODS: Cases that occurred in residents in Tuscany in 2000-2001 were considered. They were identified from : a) the Tuscany Regional Mortality Registry (RMR) using the E code of the ICD LX code of death, the year and place of occurrence; b) the INAIL archive using the year of event, the type of definition and management. RESULTS: The INAIL source was without doubt the most informative but was only 51% complete, whereas the RMR source, although less informative, was more complete (82.4%) and allowed identification of cases not registered by INAIL, that had occurred for instance in the Armed Forces and in the National Railway Company. However, the vast majority of RMR extra-cases occurred in subjects aged 65+, in agriculture and in the building industry. CONCLUSION: It is currently possible to plan a systematic linkage of the two sources due to the new possibilities that are available: the place-of-occurrence in the death certificate and the availability of individual data in the INAIL source.

Accidents, Occupational↗
PubMed2003

Structure data entry using graphical input: recording symptoms for multiple sclerosis.

Structured Data Entry provides flexible and efficient input to the computer-based patient record. We have utilized the SDE approach to build a prototype interface for recording common symptoms associated with Multiple Sclerosis (MS). The software provides both graphical input and output, to facilitate efficient data entry and monitoring of data. Graphical input is transformed to textual information, which is stored in a database in a hierarchical tree structure. Pain management in MS may be achieved by careful monitoring of the symptom in response to treatment. Pain location is selected on a body image and severity and other attributes represented using a graphical visual analog scale, leading to more convenient input and a less ambiguous coding than is achievable with narrative text alone. This approach could provide an objective means of monitoring the progress of the disease and management of the symptoms. The intuitive interface may also facilitate self-monitoring.

Computer Graphics↗
PubMed2005

Monitoring of symptoms and interventions associated with multiple sclerosis.

We have utilized the Structured Data Entry approach to build a prototype interface for the recording of personalized symptoms associated with Multiple Sclerosis (MS). The software provides both graphical input and output, to facilitate efficient data entry and monitoring. Graphical input is transformed to textual information, which is stored in a database in a hierarchical tree structure. Pain management in MS may be achieved by careful monitoring of the symptom in response to treatment. Pain location is selected on a body image and severity and other attributes represented using a graphical visual analog scale, leading to more convenient input and a less ambiguous coding than is achievable with narrative text alone. The Internet can be used to record and provide access to clinical data, assisting the citizen by providing a healthcare professional partnership approach to care. This approach could provide an objective means of monitoring symptoms and hence provide a more personalized approach to MS management.

Biomedical Technology↗
PubMed2006

Benefits of an external focus of attention: common coding or conscious processing?

We conducted two experiments to assess the effect attentional focus has on learning a complex motor skill and subsequent performance under secondary task loading. Participants in Experiment 1 learnt a golf putting task (300 practice trials) with a single instruction to either focus on their hands (internal focus) or the movement of the putter (external focus). No group differences were evident during learning or retention. Differences between the groups were only apparent under secondary task load; the external group's performance remained robust, while the internal group suffered a drop in performance. Verbal protocols demonstrated that the internal group accumulated significantly more internal knowledge and more task-relevant knowledge in general than the external group. Experiment 2 was designed to establish whether greater internal focus knowledge or greater explicit rule build up in general was responsible for performance breakdown. Two groups were presented with a set of six internal or external rules. Again, no performance differences were found during learning or retention. During the secondary task, both groups experienced performance deterioration. It was concluded that accumulation of explicit rules to guide performance was responsible for the internal group's breakdown in performance under secondary task loading and may be responsible for some of the performance differences reported previously.

Adult↗
PubMed2001

Speech parts as Poisson processes.

This paper presents evidence that six of the seven parts of speech occur in written text as Poisson processes, simple or recurring. The six major parts are nouns, verbs, adjectives, adverbs, prepositions, and conjunctions, with the interjection occurring too infrequently to support a model. The data consist of more than the first 5000 words of works by four major authors coded to label the parts of speech, as well as periods (sentence terminators). Sentence length is measured via the period and found to be normally distributed with no stochastic model identified for its occurrence. The models for all six speech parts but the noun significantly distinguish some pairs of authors and likewise for the joint use of all words types. Any one author is significantly distinguished from any other by at least one word type and sentence length very significantly distinguishes each from all others. The variety of word type use, measured by Shannon entropy, builds to about 90% of its maximum possible value. The rate constants for nouns are close to the fractions of maximum entropy achieved. This finding together with the stochastic models and the relations among them suggest that the noun may be a primitive organizer of written text.

Humans↗
PubMed1999

Monte Carlo-based inverse treatment planning.

A Monte Carlo based inverse treatment planning system (MCI) has been developed which combines arguably the most accurate dose calculation method (Monte Carlo particle transport) with a 'guaranteed' optimization method (simulated annealing). A distribution of photons is specified in the tumour volume; they are transported using an adjoint calculation method to outside the patient surface to build up an intensity distribution. This intensity distribution is used as the initial input into an optimization algorithm. The dose distribution from each beam element from a number of fields is pre-calculated using Monte Carlo transport. Simulated annealing optimization is then used to find the weighting of each beam element, to yield the optimal dose distribution for the given criteria and constraints. MCI plans have been generated in various theoretical phantoms and patient geometries. These plans show conformation of the dose to the target volume and avoidance of critical structures. To verify the code, an experiment was performed on an anthropomorphic phantom.

Algorithms↗
PubMed2003

Rates of pediatric injuries by 3-month intervals for children 0 to 3 years of age.

OBJECTIVE: Mortality and morbidity data on childhood injury are used to construct developmentally appropriate intervention strategies and to guide pediatric anticipatory counseling on injury prevention topics. Effective anticipatory guidance depends on detailed injury data showing how risks change as children develop. Conventional age groupings may be too broad to show the relationship between children's development and their risk of various causes of injury. Previous studies revealed differences in overall rates and specific causes of injury by year of age. However, single year of age rates for children younger than 4 years may not reflect the variations in risk as a result of rapid developmental changes. This study was designed to analyze injury rates for children younger than 4 years by quarter-year intervals to determine more specifically the age period of highest risk for injury and for specific causes. METHODS: We used data from 1996-1998 California hospital discharges and death certificates to identify day of age and external cause of injury (E-code) for children younger than 4 years. The number of California residents for each day of age was estimated from US Census of estimates of California's population by year of age for the midpoints (1996-1998). Rates were calculated by 3-month intervals. We grouped the E-codes into major categories that would be particularly relevant for developmentally related risks of injury specific to young children. The categorization took into account physical, motor, behavioral, and cognitive developmental milestones of children 0 to 3 years. RESULTS: There were a total of 23,173 injuries; 636 resulted in death. The overall annual rate for children aged 0 to 3 years was 371/100,000. Beginning at age 3 to 5 months, the overall rate of injury rapidly increased with increased age, peaking at 15 to 17 months. The mean injury rate calculated for each single year of age did not reflect the variation and the highest rate of injury by quarter year of age for children younger than 1 year, 1 year, and 2 years. The leading major causes of injury in descending order were falls, poisoning, transportation, foreign body, and fires/burns. The overall rate of the major category of falls exceeded poisoning, the second leading cause of injury, by a factor of 2. Age-related differences were detected within each major cause of injury. For children 0 to 12 months of age, there was a different leading cause of specific injury for each 3-month period: other falls from height (0-2 months), battering (3-5 months), falls from furniture (6-8 months), and nonairway foreign body (9-11 months). Hot liquid and vapor injuries were the leading specific causes for children 12 to 17 months. Poisoning by medication was the leading specific cause of injury for all age groups from 18 to 35 months and exceeded poisoning by other substances. Pedestrian injury was the leading specific cause of injury for all age groups from 36 to 47 months. Fall from furniture has the highest rates of specific causes of falls from age 3 to 47 months. Fall from stairs peaked at age 6 to 8 months and 9 to 11 months. Fall from buildings was highest at 24 to 26 months. Poisoning by medication peaked at age 21 to 23 months, but poisoning by other substances peaked at 15 to 17 months. The motor vehicle occupant injury rates were fairly stable over the age span of this study. The pedestrian injury rate increased beginning at age 12 to 14 months and by 15 to 17 months was double that of the motor vehicle occupant. Foreign body had a marked peak at age 9 to 11 months. Both battering and neglect rates were highest among infants 0 to 2 and 3 to 5 months. Bathtub submersions had a narrow peak at age 6 to 11 months. Other submersions peaked at 12 to 14 months and remained high until 33 to 35 months. CONCLUSIONS: We departed from usual groupings of E-codes and devised groupings that would be reflective of age-related developmental characteristics. Differences in rates by narrow age groups for young children can be related to developmental achievements, w can be related to developmental achievements, which place the child at risk for specific causes of injury. We found marked variability in both rates and leading causes of injury by 3-month interval age groupings that were masked by year of age analyses. Children aged 15 to 17 months had the highest overall injury rate before age 15 years. This coincides with developmental achievements such as independent mobility, exploratory behavior, and hand-to-mouth activity. The child is able to access hazards but has not yet developed cognitive hazard awareness and avoidance skills. A remarkable finding was the high rate of battering injury among infants 0 to 5 months, suggesting the need to address potential child maltreatment in the perinatal period. Poisoning was the second major leading cause of injury; more than two thirds were medication. Cultural factors may influence views of medications, storage practices, use of poison control system telephone advice, and risk of toddler poisoning. The pedestrian injury rate doubled between 12 and 14 months and 15 and 17 months and exceeded motor vehicle occupant injury rates for each 3-month interval from 15 to 47 months. Pedestrian injury has not received sufficient attention in general and certainly not in injury prevention counseling for children younger than 4 years. Anticipatory guidance for pedestrian injury should be incorporated before 1 year of age. Effective strategies must be based on the epidemiology of childhood injury. Pediatricians and other pediatric health care providers are in a unique position to render injury prevention services to their patients. Integrating injury prevention messages in the context of developmental assessments of the child is 1 strategy. These data can also be used for complementary childhood injury prevention strategies such as early intervention programs for high-risk families for child abuse and neglect, media and advocacy campaigns, public policies, and environmental and product design.

Accidental Falls↗
PubMed1993

Ordered shotgun sequencing, a strategy for integrated mapping and sequencing of YAC clones.

Ordered shotgun sequencing proposes to organize the mapping and sequencing of YACs with a hierarchical strategy that incorporates a feedback loop. Building on current protocols, a YAC is subcloned into plasmids, plasmid insert ends are sequenced, and the sequences are overlapped to create a partial map. Complete sequencing then starts with plasmids whose end-sequence tracts have overlapped, but to a minimal extent. The next plasmids to be sequenced are again selected for least overlap, striking out progressively to span the YAC with minimal directed gap-filling. Simulations support its feasibility and indicate that during the generation of the complete sequence, the approach facilitates the early choice of regions for selective sequencing, for example, for coding units. The sequencing of plasmids would also require less redundancy, and discriminate repetitive sequences more easily, than random sequencing across larger clones. The overall effort scales with YAC size and can be further reduced by additional mapping information.

Chromosome Mapping↗
PubMed1981

A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins.

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.

Animals↗
PubMed2003

ORCHESTRA: an object-oriented framework for implementing chemical equilibrium models.

This work presents a new object-oriented structure for chemical equilibrium calculations that is used in the modeling framework ORCHESTRA (Objects Representing CHEmical Speciation and TRAnsport). In contrast to standard chemical equilibrium algorithms, such as MINEQL, MINTEQ2A, PHREEQC, and ECOSAT, model equations are not hard-coded in the source code, but instead all equations are defined in text format and read by the ORCHESTRA calculation kernel at run time. This makes model definitions easily accessible and extendible by users. Furthermore, it results in a very compact and efficient calculation kernel that is easy to use as a submodel within mass transport or kinetic models. Finally, the object-oriented structure of the chemical model definitions makes it possible to implement a new object-oriented framework for implementing chemical models. This framework consists of three basic object types, entities, reactions, and phases, that form the building blocks from which other chemical models are composed. The hierarchical approach ensures consistent and compact model definitions and is illustrated here by discussing the implementation of a number of commonly used chemical models such as aqueous complexation, activity correction, precipitation, surface complexation ion exchange, and several more sophisticated adsorption models including electrostatic interactions, NICA, and CD-MUSIC. The ORCHESTRA framework is electronically available from www.macaulay.ac.uk/ORCHESTRA.

Adsorption↗
PubMed2004

Finishing the euchromatic sequence of the human genome.

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

Amino Acid Sequence↗
PubMed2002

Using the American Board of Internal Medicine's "Elements of Professionalism" for undergraduate ethics education.

PURPOSE: To examine the feasibility of using the taxonomy of professional and unprofessional behaviors presented in the American Board of Internal Medicine's (ABIM's) Project Professionalism to categorize ethical issues that undergraduate medical students perceive to be salient. METHOD: Beginning second-year medical students at the University of Washington School of Medicine (n = 120) were asked to respond to three open-ended questions about professional standards of conduct and peer evaluation. Two of the authors read and coded the students' responses according to the ABIM's elements of professionalism (altruism, accountability, excellence, duty, honor and integrity, and respect for others) and the challenges to those elements (abuse of power, arrogance, greed, misrepresentation, impairment, lack of conscientiousness, and conflict of interest). Coding disagreements were solved using review and revision of the category definitions. New categories were created for students' responses that described behaviors or issues that were not captured in the ABIM's categories. RESULTS: A total of 114 students responded. The ABIM's professional code was adapted for students and teachers, making it context- and learning-stage-specific. One new category of challenges, conflicts of conscience, was added, and one category (abuse of power) was expanded to include abuse of power/negotiating power asymmetries. CONCLUSIONS: Using the ABIM's taxonomy to name professional and unprofessional behaviors was particularly useful for examining undergraduate medical students' perceptions of the ethical climate for learning during the first year of medical school, and it holds promise for research into changes in students' perceptions as they move into clinical experiences. Using the framework, students can build a unified professional knowledge-and-skills base.

Behavior↗
PubMed2005

Injuries from slips and trips in construction.

Construction injuries preceded by a slip or trip were documented using data from the building of the Denver International Airport (Denver, Colorado, USA), the largest construction project in the world at the time. Slips and trips occurred at a rate of 5/200,000 h worked accounting for 18% of all injuries and 25% of workers' compensation payments, or more than $10 million. Slips contributed to the vast majority (85%) of same-level falls and over 30% of falls from height, as well as a significant number of musculoskeletal injures sustained after slipping or tripping but without falling. The injury burden would have been under-recognized in analyses of most coded compensation records. In contrast to other types of injuries, the most common contributing factors were environmental in nature including conditions of walking and working surfaces, terrain and weather. Due to the very dynamic nature of construction work, reducing slips and trips will require a focus on environmental and organizational solutions that evolve as the site changes and the construction project evolves.

Accidental Falls↗
PubMed2005

Polymorphisms in the interleukin 17F gene (IL17F) and asthma.

Interleukin17F (IL17F) is a regulatory cytokine for T-cell-mediated immune responses. The gene coding for IL17F (IL17F) is located on chromosome 6p, a genomic region linked to asthma and asthma-related phenotypes in multiple genome scans. IL17F is expressed in lung tissue, in bronchoalveolar lavage fluid from asthmatic subjects, and in activated CD4+ cells. We were thus interested in testing for association between single-nucleotide polymorphisms (SNPs) and haplotypes in IL17F and asthma. To characterize polymorphisms in IL17F, we sequenced this gene in a group of African Americans and a group of European Americans. A total of 50 SNPs (30 not previously reported in a public database (dbSNP build 118)) and two insertions/deletions were detected in IL17F; five of these polymorphisms were genotyped in participants of the Nurses' Health Study. We then tested for association between SNPs and haplotypes in IL17F and physician-diagnosed asthma in subjects with (cases) and without (control subjects) physician-diagnosed asthma. None of the SNPs or haplotypes tested in IL17F were associated with asthma. The polymorphisms identified in this study may be used in future studies of association between IL17F and phenotypes related to immune responses.

Black or African American↗