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PubMed2005

Modelling novice clinical reasoning for a computerized decision support system.

AIM: The aim of this paper is to introduce the theoretical framework that directs the project. BACKGROUND: The Novice Computer Decision Support (N-CODES) Project is developing a point-of-care system to assist novice acute care nurses while making clinical judgements. Unlike prior approaches, N-CODES is guided by a theoretical understanding of nurses' decision-making processes, including the manner by which novices develop this skill. FRAMEWORK: Assumptions within information processing theory guided the clinical decision-making framework. The framework is composed of a clinical decision-making model and a second embedded model depicting the clinical reasoning development of novice nurses. MODELS: The model is developed within a pluralistic perspective synthesizing theoretical and empirical knowledge on clinical decision-making and the development of novice reasoning skills. A visual representation of experienced nurse decision-making is presented. A central element is the nurse's use of pre-encounter data and working knowledge. A second model integrates empirical data on the developing clinical reasoning of the novice. This knowledge is loosely scattered through 25 years of literature. The intersection of these models provides a novel perspective on the way novices begin to identify working knowledge patterns and develop a sense of saliency. CONCLUSIONS: Previous attempts to build comprehensive clinical decision support systems have disregarded important theoretical considerations hindering the success of these projects. Grounding a Decision Support System in a theoretical model of novice nurse decision-making will strengthen the utility and acceptance of the Decision Support System. Additionally, a conceptualization of novice nurse development is an asset to nurse educators, managers and scientists interested in improving clinical decision-making.

Clinical Competence↗
PubMed1998

Combined use of FLUKA and MCNP-4A for the Monte Carlo simulation of the dosimetry of 10B neutron capture enhancement of fast neutron irradiations.

Boron neutron capture enhancement (BNCE) of the fast neutron irradiations use thermal neutrons produced in depth of the tissues to generate neutron capture reactions on 10B within tumor cells. The dose enhancement is correlated to the 10B concentration and to thermal neutron flux measured in the depth of the tissues, and in this paper we demonstrate the feasibility of Monte Carlo simulation to study the dosimetry of BNCE. The charged particle FLUKA code has been used to calculate the primary neutron yield from the beryllium target, while MCNP-4A has been used for the transport of these neutrons in the geometry of the Biomedical Cyclotron of Nice. The fast neutron spectrum and dose deposition, the thermal flux and thermal neutron spectrum in depth of a Plexiglas phantom has been calculated. The thermal neutron flux has been compared with experimental results determined with calibrated thermoluminescent dosimeters (TLD-600 and TLD-700, respectively, doped with 6Li or 7Li). The theoretical results were in good agreement with the experimental results: the thermal neutron flux was calculated at 10.3 X 10(6) n/cm2 s1 and measured at 9.42 X 10(6) n/cm2 s1 at 4 cm depth of the phantom and with a 10 cm X 10 cm irradiation field. For fast neutron dose deposition the calculated and experimental curves have the same slope but different shape: only the experimental curve shows a maximum at 2.27 cm depth corresponding to the build-up. The difference is due to the Monte Carlo simulation which does not follow the secondary particles. Finally, a dose enhancement of, respectively, 4.6% and 10.4% are found for 10 cm X 10 cm or 20 cm X 20 cm fields, provided that 100 micrograms/g of 10B is loaded in the tissues. It is anticipated that this calculation method may be used to improve BNCE of fast neutron irradiations through collimation modifications.

Biophysical Phenomena↗
PubMed2004

How many samples are needed to build a classifier: a general sequential approach.

MOTIVATION: The standard paradigm for a classifier design is to obtain a sample of feature-label pairs and then to apply a classification rule to derive a classifier from the sample data. Typically in laboratory situations the sample size is limited by cost, time or availability of sample material. Thus, an investigator may wish to consider a sequential approach in which there is a sufficient number of patients to train a classifier in order to make a sound decision for diagnosis while at the same time keeping the number of patients as small as possible to make the studies affordable. RESULTS: A sequential classification procedure is studied via the martingale central limit theorem. It updates the classification rule at each step and provides stopping criteria to ensure with a certain confidence that at stopping a future subject will have misclassification probability smaller than a predetermined threshold. Simulation studies and applications to microarray data analysis are provided. The procedure possesses several attractive properties: (1) it updates the classification rule sequentially and thus does not rely on distributions of primary measurements from other studies; (2) it assesses the stopping criteria at each sequential step and thus can substantially reduce cost via early stopping; and (3) it is not restricted to any particular classification rule and therefore applies to any parametric or non-parametric method, including feature selection or extraction. AVAILABILITY: R-code for the sequential stopping rule is available at http://stat.tamu.edu/~wfu/microarray/sequential/R-code.html

Algorithms↗
PubMed2004

[A quantitative and qualitative study on effective information flow for infectious disease control in welfare facilities for the elderly].

OBJECTIVES: To clarify factors associated with effective information tranges among staff of welfare facilities for the elderly, and to propose measures for an appropriate information flow system in welfare facilities and public health centers, communication channels and methods, and encouraging factors and barriers were investigated in terms of a printed medium on the control and management of scabies infections. METHODS: A self-administered questionnaire survey and an interview survey were conducted with the staff of welfare facilities for the elderly where "Control and management manual of scabies infection" had been distributed by the Tama-Tachikawa Public Health Center in Tokyo. A self-administered questionnaire was sent to managers and chief practitioners of 66 facilities. Respondents were obtained from 66 managers and chief practitioners (response rate: 84.8%), and 831 practitioners (response rate: 53.1%). The questionnaire consisted of 20 items for managers and 18 items for chief practitioners, including experience of scabies epidemics in facilities, training experience for the use of "Control and management manual of scabies infection," measures for information gathering, and current information flow within the facility. A semi-structured interview survey was conducted with the manager and/or chief practitioner and practitioners in five facilities. The number of respondents was 10. The interview questions included job description, scabies control measures, dissemination of the manual to the staff, use of the manual, flows of health-related information, and factors associated with information flows. Summarized codes were extracted from the transcriptions from tape recording and were categorized repeatedly according to similarity. RESULTS: In the questionnaire survey, differences of Community information flow by types of facilities and professional backgrounds were found. Variation was detected in measures for information gathering and focuses in information management between managers/chief practitioners and practitioners. Practitioners wanted opportunities for information exchange while managers/chief practitioners mainly focused on prioritization of information collected. In addition, many respondents felt that information networks outside the facilities were poorly organized. From the interview survey, three major categories were extracted, that is, 'Information flow system,' 'Personal qualification,' and 'Factors related to the information flow system.' As factors related to the information flow system, the following 7 subcategories were extracted. 1. Interest in information; 2. Working style and workload; 3. Information networks outside the facility; 4. Information management in the facility; 5. Environment for information sharing; 6. Budget for the information system; and 7. Interpersonal communication. CONCLUSIONS: For an effective information system, welfare facilities for the elderly should work on staff training, building their own information flow systems and improving the environment for information sharing and networking with specialized agencies, such as public health centers. At the same time, public health centers should support networking, interpersonal two-way communication and training of welfare-facility workers.

Aged↗
PubMed2004

Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards.

Phylogenetic studies incorporating multiple loci, and multiple genomes, are becoming increasingly common. Coincident with this trend in genetic sampling, model-based likelihood techniques including Bayesian phylogenetic methods continue to gain popularity. Few studies, however, have examined model fit and sensitivity to such potentially heterogeneous data partitions within combined data analyses using empirical data. Here we investigate the relative model fit and sensitivity of Bayesian phylogenetic methods when alternative site-specific partitions of among-site rate variation (with and without autocorrelated rates) are considered. Our primary goal in choosing a best-fit model was to employ the simplest model that was a good fit to the data while optimizing topology and/or Bayesian posterior probabilities. Thus, we were not interested in complex models that did not practically affect our interpretation of the topology under study. We applied these alternative models to a four-gene data set including one protein-coding nuclear gene (c-mos), one protein-coding mitochondrial gene (ND4), and two mitochondrial rRNA genes (12S and 16S) for the diverse yet poorly known lizard family Gymnophthalmidae. Our results suggest that the best-fit model partitioned among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions. We found this model yielded identical topologies to those from analyses based on the GTR+I+G model, but significantly changed posterior probability estimates of clade support. This partitioned model also produced more precise (less variable) estimates of posterior probabilities across generations of long Bayesian runs, compared to runs employing a GTR+I+G model estimated for the combined data. We use this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae. We then reevaluate the higher-level taxonomic arrangement of the Gymnophthalmidae. Based on our findings, we discuss the utility of nontraditional parameters for modeling among-site rate variation and the implications and future directions for complex model building and testing.

Animals↗
PubMed2000

A theoretical design of a flattening filter to improve field uniformity of a superficial therapeutic X-ray beam.

A Monte Carlo model has been developed using the MCNP code to aid the design of a flattening filter, to improve field uniformity of a superficial x-ray machine. The machine is operating at 90 kV and filtered with a 1.1 mm aluminium filter. In the theoretical simulation the original flat filter was replaced by a varying thickness filter to improve the uniformity across field sizes 20, 5 and 2 cm diameter as well as hardening the beam. Simulation results showed that flatness of the beam profile was improved for the 20 cm field size from +/- 7.3% to +/- 1.1% across the anode/cathode direction and from +/- 7.7% to +/- 3.2% in the anode/cathode direction. For the 5 cm field size the improvement was from +/- 4.6% to +/- 3.1% and from +/- 5.5% to +/- 3.4%, and for the 2 cm field size from +/- 3.1% to +/- 2.4% and from +/- 10.2% to +/- 9.5%, in the same directions, respectively. Beam quality simulations were made and the original half-value layer was reduced from 2.21 +/- 0.09 mm aluminium to 2.04 +/- 0.09 mm aluminium. The study demonstrated that it was possible to build a filter capable of flattening the beam profile for different sized applicators without significantly changing the penetrating ability of the beam.

Aluminum↗
PubMed1987

Cloning of DNA fragments complementary to tobacco nitrate reductase mRNA and encoding epitopes common to the nitrate reductases from higher plants.

Messenger RNAs encoding the nitrate reductase apoenzyme from tobacco can be translated in a cell-free system. Poly(A)+ mRNA fractions from the 23-32 S area of a sucrose gradient were used to build a cDNA library in the expression vector gt11 with an efficiency of cloning of approximately 10(4) recombinants/ng mRNA. Recombinant clones were screened with a rabbit polyclonal antibody directed against the corn nitrate reductase, which cross reacts specifically with the nitrate reductases from dicotyledons. Among 240000 recombinant plaques, eight clones were isolated containing inserts of sizes ranging from 1.6 kb to 2.1 kb and sharing sequence homologies. Seven of these clones contained a common internal 1.6 kb EcoRI fragment. The identity of these clones was confirmed as follows. A fusion protein of 170 kDa inducible by IPTG and recognized by the rabbit nitrate reductase antibody was expressed by a lysogen derived from one of the recombinants. The antibodies binding the fused protein were eluted and shown to be inhibitory to the catalytic activity of tobacco nitrate reductase. Two monoclonal antibodies directed against nitrate reductase were also able to bind the hybrid protein. The 1.6 kb EcoRI fragment was sequenced by the method of Sanger. The open reading frame corresponding to a translational fusion with the -galactosidase coding sequence of the vector shared strong homology at the amino acid level with the heme-binding domain of proteins of the cytochrome b5 superfamily and with human erythrocyte cytochrome b5 reductase. When the 1.6 kb EcoRI fragment was used as a probe for Northern blot experiments a signal corresponding to a 3.5 kb RNA was detected in tobacco and in Nicotiana plumbaginifolia mRNA preparations but no cross-hybridization with corn mRNAs was detected. The probe hybridized with low copy number sequences in genomic blots of tobacco DNA.

Amino Acid Sequence↗
PubMed2005

Prediction error estimation: a comparison of resampling methods.

MOTIVATION: In genomic studies, thousands of features are collected on relatively few samples. One of the goals of these studies is to build classifiers to predict the outcome of future observations. There are three inherent steps to this process: feature selection, model selection and prediction assessment. With a focus on prediction assessment, we compare several methods for estimating the 'true' prediction error of a prediction model in the presence of feature selection. RESULTS: For small studies where features are selected from thousands of candidates, the resubstitution and simple split-sample estimates are seriously biased. In these small samples, leave-one-out cross-validation (LOOCV), 10-fold cross-validation (CV) and the .632+ bootstrap have the smallest bias for diagonal discriminant analysis, nearest neighbor and classification trees. LOOCV and 10-fold CV have the smallest bias for linear discriminant analysis. Additionally, LOOCV, 5- and 10-fold CV, and the .632+ bootstrap have the lowest mean square error. The .632+ bootstrap is quite biased in small sample sizes with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase. SUPPLEMENTARY INFORMATION: A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://linus.nci.nih.gov/brb/TechReport.htm).

Algorithms↗
PubMed2000

Enhancing the expressiveness of structured reporting systems.

The overall goal of this research is to build a structured reporting system that reduces the cost, delays, and inconvenience associated with conventional dictation and speech recognition systems. We have implemented such a structured reporting system for radiology that replaces current dictation and transcription processes by allowing radiologists and other imaging professionals to select imaging findings from a medical lexicon. The system uses an imaging-specific information model, called a "description set,' to organize selected terms in a relational database. Unique features of the knowledge representation that enhance its expressiveness include its ability to codify uncertainty about an imaging observation and to represent explicitly the logical relationships among imaging findings. In addition, the system does not require the user to fill in "blanks' in a static text template. Instead, it allows entry of terms in arbitrary order and uses automated text-generation techniques to create a text report that referring physicians are accustomed to receiving. In parallel, the system also produces a multimedia report that the referring physician can use as a quick reference. Unlike the results of conventional dictation or speech recognition, each finding is coded in a relational database for later information processing. Thus, the structured report database can be used to index images by content, to provide real-time decision support, to enhance radiologists' performance, to conduct exploratory clinical research, and to transmit imaging report data to computer-based patient record systems.

Abstracting and Indexing↗
PubMedDate not supplied

Reducing the frequency of errors in medicine using information technology.

BACKGROUND: Increasing data suggest that error in medicine is frequent and results in substantial harm. The recent Institute of Medicine report (LT Kohn, JM Corrigan, MS Donaldson, eds: To Err Is Human: Building a Safer Health System. Washington, DC: National Academy Press, 1999) described the magnitude of the problem, and the public interest in this issue, which was already large, has grown. GOAL: The goal of this white paper is to describe how the frequency and consequences of errors in medical care can be reduced (although in some instances they are potentiated) by the use of information technology in the provision of care, and to make general and specific recommendations regarding error reduction through the use of information technology. RESULTS: General recommendations are to implement clinical decision support judiciously; to consider consequent actions when designing systems; to test existing systems to ensure they actually catch errors that injure patients; to promote adoption of standards for data and systems; to develop systems that communicate with each other; to use systems in new ways; to measure and prevent adverse consequences; to make existing quality structures meaningful; and to improve regulation and remove disincentives for vendors to provide clinical decision support. Specific recommendations are to implement provider order entry systems, especially computerized prescribing; to implement bar-coding for medications, blood, devices, and patients; and to utilize modern electronic systems to communicate key pieces of asynchronous data such as markedly abnormal laboratory values. CONCLUSIONS: Appropriate increases in the use of information technology in health care- especially the introduction of clinical decision support and better linkages in and among systems, resulting in process simplification-could result in substantial improvement in patient safety.

Decision Support Systems, Clinical↗
PubMed1997

[Cost analysis for DRG and PRG in the treatment of acute myocardial infarction in hospitalized patients].

The cost of diagnostic and therapeutic procedures in patients with acute myocardial infarction (AMI) during hospitalization was determined using both the Diagnosis Related Group (DRG) and Process Related Group (PRG) systems. This cost-analysis system was planned and performed to estimate the cost of medical and non-medical staff involved in patient care, as well as commensurate costs. Over a three-month period, 45 patients discharged with a diagnosis of AMI, equivalent to 410 code ICD-9-CM, were enrolled in the study. The collected data were then processed and the cost for each DRG was derived. The mean cost borne for each patient with AMI was 5,864,345 Italian lire with a maximum of 17,138,300 lire for DRG 112 and a minimum of 3,332,329 lire for DRG 123. Our data suggest that in patients with AMI, there is profound discrepancy between the current DRG reimbursements and "real" cost, for example in DRG 112 (a discrepancy equivalent to 166%). The cost difference is essentially related to different procedures involved in medical care and, therefore, it follows that the overall cost of patient with AMI is primarily related to PRG cost and is largely independent of other components. These results prove that therapeutic strategies are very important in determining the cost for each DRG and that the cost for each DRG can change in relation to the PRG performed and to the progression of illness. The utilization of DRG and PRG systems appears to be an essential tool that can be used to build a system in which not only efficiency but also quality of care are evaluated.

Budgets↗
PubMed2001

The phylogenetic analysis of variable-length sequence data: elongation factor-1alpha introns in European populations of the parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae).

Elongation factor-1alpha (EF-1alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using congruence as a criterion for assessing a range of methods for aligning such variable-length EF-1alpha intron sequences. These methods included distance- and parsimony-based multiple-alignment programs (CLUSTAL W and MALIGN), direct optimization (POY), and two "by eye" alignment strategies. Furthermore, with one method (CLUSTAL W) we explored in detail the robustness of results to changes in the gap cost parameters. Phenetic-based alignments ("by eye" and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more demanding, methods. In general, all of our alignment and tree-building strategies recovered the same basic topological structure, which means that an underlying phylogenetic signal remained regardless of the strategy chosen. However, several relationships between clades were sensitive both to alignment and to tree-building protocol. Further alignments, considering only sequences belonging to the same group, allowed us to infer a range of phylogenetic relationships that were highly robust to tree-building protocol. By comparing these topologies with those obtained by varying the CLUSTAL parameters, we generated the distribution area of congruence and taxonomic compatibility. Finally, we present the first robust estimate of the European Pauesia phylogeny by using two EF-1alpha introns and 38 taxa (plus 3 outgroups). This estimate conflicts markedly with the traditional subgeneric classification. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.

Animals↗
PubMedDate not supplied

Cause of death reporting systems in India: a performance analysis.

BACKGROUND: Reliable statistics on the causes of death in the population are essential for setting priorities in the health sector. Most cause of death reporting systems in developed countries rely on medical certification of the cause of death according to the International Classification of Death (ICD-10), and have achieved near-total coverage. Developing countries such as India, where adequate medical facilities are not available, depend on lay reporting of the cause of death in rural areas, using a sample registration system. The use of the cause of death statistics in India is questioned in view of the poor coverage, and poor compliance with guidelines for cause of death reporting, coding and classification. METHODS: A brief description of the reporting system in India is followed by the characteristics of a usable cause of death reporting system. We identified 9 criteria based on a review of the literature and our own assessment of the problem. The performance of the cause of death reporting system for rural and urban areas of India was examined against each of the 9 criteria. We offer a subjective rating on a three-category rating scale consisting of (i) satisfactory, (ii) tolerable, and (iii) poor. RESULTS: The major factors affecting the use of the cause of death statistics in India are: (i) poor coverage; (ii) high incidence of unclassifiable deaths; (iii) long delay and irregular publication of statistics; and (iv) lack of systematic screening. CONCLUSIONS: We recommend the following steps to improve the usability of cause of death statistics in India. Introducing periodical reviews jointly by the Departments of Health and Municipal Administration to identify non-reporting municipalities, sample units, and further identification of non-reporting health care institutions sustained over a period of, say, five years will raise coverage substantially. The other measures include: (i) training programmes to build up cause of death report writing skills among physicians; (ii) compilation and publication of cause of death statistics at the state level; (iii) sponsored research on the cause of death reporting structure and its implications for policy-making; and (iv) computerization of filling, tabulation and flow of cause of death statistics at the municipality and the state levels. To reduce the unusually high level of unclassifiable deaths, the Registration of Births and Deaths Act should be amended to ensure that hospitals and health care institutions maintain medical records. For accurate cause of death data from rural areas, we recommend that the performance of the sample registration survey-cause of death (SRS-COD) component be evaluated according to the above criteria.

Adolescent↗
PubMed2026

Toward life with a 19-amino acid alphabet through generative artificial intelligence design.

Because all known living organisms are made from at least 20 canonical amino acids, the feasibility of life using a more simplified alphabet remains unclear. In this work, we leveraged computational design and synthetic biology to explore building a cell from a 19-amino acid alphabet. Initial analyses suggested that isoleucine (Ile) may be dispensable, which we confirmed by directly replacing Ile residues in essential proteins in Escherichia coli. Critically, protein language models and structure-based models were necessary to redesign functional Ile-less proteins in most cases. We systematically replaced all 382 Ile residues from the ribosome and combined 21 redesigned subunits at a native genomic locus to produce a viable, evolutionarily stable cell. This work provides a roadmap to create the first 19-amino acid organism since early evolution.

Escherichia coli↗
PubMed1984

Unrelated business income tax: an update.

To meet spiraling costs, tax-exempt hospitals increasingly are operating businesses unrelated to direct patient care. Knowing which activities may be open to challenge by the Internal Revenue Service (IRS) is essential to avoid the unrelated business income (UBI) tax. Three criteria must be met for an activity to be taxable as UBI: It must constitute a trade or business; It must be regularly carried on; and It must be unrelated to the organization's exempt purpose. The Internal Revenue Code and IRS rulings clearly exclude the following areas from UBI taxation: Activities performed by unpaid volunteers (e.g., hospital auxiliaries' fund-raising dinners and bazaars and the operation of thrift stores); Operations conducted for the convenience of the organization's members, students, patients, or employees (e.g., gift shops, cafeterias, coffee shops, parking lots, lounges, vending machines, pharmaceutical sales to inpatients and emergency room outpatients, and research activities for students' benefit; The sale of merchandise that has been received by gift (e.g., flea markets, baked goods sales, book sales, and rummage sales); Investment income such as dividends, interest, annuities, royalties, certain rents, and capital gains from the sale of investment assets; Gifts or contributions made directly to the facility; and Bingo games that are conducted commercially. Areas which may be subject to UBI taxation, or in which there have been controversial or contradictory court rulings, include: Pharmaceutical sales to the public or private physicians' patients; and Laboratory services provided to private physicians for treating their patients. IRS private letter rulings, though not precedential, have excluded from UBI taxation the x-ray income from a hospital's branch facility and rental income from property leased for use as a clinic or medical office building that is substantially related to the hospital's exempt functions. Private letter rulings have subjected to UBI taxation the income for a professional standards review organization's private review activities and debt-financed income from property that is not substantially related to the organization's exempt purpose.

Commerce↗
PubMed1983

High resolution structural studies of Cro repressor protein and implications for DNA recognition.

Cro repressor is a small dimeric protein that binds to specific sites on the DNA of bacteriophage lambda. The structure of Cro has been determined and suggests that the protein binds to its sequence-specific sites with a pair of two-fold related alpha-helices of the protein located within successive major grooves of the DNA. From the known three-dimensional structure of the repressor, model building and energy refinement have been used to develop a detailed model for the presumed complex between Cro and DNA. Recognition of specific DNA binding sites appears to occur via multiple hydrogen bonds between amino acid side chains of the protein and base pair atoms exposed within the major groove of DNA. The Cro:DNA model is consistent with the calculated electrostatic potential energy surface of the protein. From a series of amino acid sequence and gene sequence comparisons, it appears that a number of other DNA-binding proteins have an alpha-helical DNA-binding region similar to that seen in Cro. The apparent sequence homology includes not only DNA-binding proteins from different bacteriophages, but also gene-regulatory proteins from bacteria and yeast. It has also been found that the conformations of part of the presumed DNA-binding regions of Cro repressor, lambda repressor and CAP gene activator proteins are strikingly similar. Taken together, these results strongly suggest that a two-helical structural unit occurs in the DNA-binding region of many proteins that regulate gene expression. However, the results to date do not suggest that there is a simple one-to-one recognition code between amino acids and bases. Crystals have been obtained of complexes of Cro with six-base-pair and nine-basepair DNA oligomers, and X-ray analysis of these co-crystals is in progress.

Amino Acid Sequence↗
PubMed1999

A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base.

The expressed human genome is being sequenced and analyzed by disparate groups producing disparate data. The majority of the identified coding portion is in the form of expressed sequence tags (ESTs). The need to discover exonic representation and expression forms of full-length cDNAs for each human gene is frustrated by the partial and variable quality nature of this data delivery. A highly redundant human EST data set has been processed into integrated and unified expressed transcript indices that consist of hierarchically organized human transcript consensi reflecting gene expression forms and genetic polymorphism within an index class. The expression index and its intermediate outputs include cleaned transcript sequence, expression, and alignment information and a higher fidelity subset, SANIGENE. The STACK_PACK clustering system has been applied to dbEST release 121598 (GenBank version 110). Sixty-four percent of 1,313, 103 Homo sapiens ESTs are condensed into 143,885 tissue level multiple sequence clusters; linking through clone-ID annotations produces 68,701 total assemblies, such that 81% of the original input set is captured in a STACK multiple sequence or linked cluster. Indexing of alignments by substituent EST accession allows browsing of the data structure and its cross-links to UniGene. STACK metaclusters consolidate a greater number of ESTs by a factor of 1. 86 with respect to the corresponding UniGene build. Fidelity comparison with genome reference sequence AC004106 demonstrates consensus expression clusters that reflect significantly lower spurious repeat sequence content and capture alternate splicing within a whole body index cluster and three STACK v.2.3 tissue-level clusters. Statistics of a staggered release whole body index build of STACK v.2.0 are presented.

Algorithms↗
PubMed2003

The ethics of theatre nurse practice under the microscope.

Perioperative practice is a multidisciplinary environment. In some theatres, student nurse allocations are at last becoming longer, although some theatres still only get a brief visit from student nurses who wish to watch an operation all the way through. Furthermore, practically all operating departments have trainee operating department practitioners (tODPs). Diploma and degree level tODPs are now beginning to produce higher academic levels of coursework and many warrant recognition. We should remember that these 'learners' are potentially the theatre practitioners of the future and we should encourage them, not only within the perioperative environment but also towards their academic achievements. Qualified nurses and operating department practitioners (ODPs) now have access to various multi-disciplinary post-registration/gradate courses, which not only build upon theoretical knowledge, but also enhance practical skills. Individuals work long and hard to achieve high level academic pieces of coursework. Unfortunately after courses finish many assignments are packed away, collect dust and get forgotten, instead of the authors being brave enough to submit them for consideration for publication. This new series offers all practitioners the chance to share with others their work within this speciality. Whether you are a nurse or an ODP undertaking, or having recently completed a course, tODP or student nurse (but preferably a member of NATN) the possibility to share your experiences or coursework with other perioperative practitioners is available to you in these articles. It has always been so, but this new series is dedicated to you all and to the hard work you put into your coursework.

Codes of Ethics↗