Semantic based concept differential retrieval & equivalence detection in clinical terms version 3 (Read Codes)

Modern clinical terminologies are required to provide a large corpus of concepts to cover the complexity of medicine. It is well recognised that sufficient scalability is likely to be achieved only with those schemes that can build post-coordinated constructs compositionally. Clinical Terms Version 3 (Read Codes) uses a system of templates to both express the semantic definition (atoms) of concepts and to allow qualification of core concepts with additional detail. This common mechanism for expressing both intrinsic semantic information and additional information allows both pre- and post-coordinated concepts to be retrieved from different perspectives and to detect equivalence between alternative representations of the same concept. The practical application and experience of such an approach is described in relation to a live clinical database (Diabeta). The merits of such an approach are outlined and its relationship to other documented mechanisms outlined.

Telomerase expression in chickens: constitutive activity in somatic tissues and down-regulation in culture

Although human and rodent telomeres have been studied extensively, very little is known about telomere dynamics in other vertebrates. Moreover, our current dependence on mice as a model for human tumorigenesis and aging poses a problem because human and mouse telomere biology is very different. To explore whether chickens might provide a more useful model, we have examined telomerase activity and telomere length in chicken tissues as well as in primary cell cultures. Although chicken telomeres resemble human telomeres in that they are 8-20 kb in length, the distribution of telomerase activity in chickens resembles what is found in mice. Active enzyme is present in germline tissue as well as in a wide range of somatic tissues. Because chicken cells exhibit extremely low rates of spontaneous immortalization, this finding indicates that constitutive telomerase expression does not necessarily lead to an increased immortalization frequency. Finally, we found that telomerase activity is greatly down-regulated when primary cultures are established from chicken embryos. Although this down-regulation explains the telomere loss and replicative senescence that we observed in fibroblast cultures, it raises questions concerning how relevant studies of senescence in primary cell cultures are to aging in whole animals.

Exploring the ontology of surgical procedures in the Read Thesaurus

The Read Thesaurus is a comprehensive user-led clinical vocabulary developed from earlier, and structurally simpler, versions of the Read Codes, with substantial input from United Kingdom health care professionals. A constituent template table underpins a range of functions, including semantic definition of concepts using object-attribute-value triples. Concept representation for surgical procedures has been investigated by a number of groups and a standard European structure has been proposed. Over 50% of the surgical procedures in the Read Thesaurus have been fully characterised using a number of attributes each with a defined concept field. We report progress to date and, based on our large-scale experience, examine the applicability of the European model to a user-defined terminology.

Semantic definition of disorders in version 3 of the Read Codes

The disorder chapter of Version 3 of the Read codes is a rich source of clinically derived terminology. The file structure has been designed to meet a clinical need to support both enumerated and compositional taxonomy. This requirement coupled with the maintenance of multiple classification necessitates a mechanism to identify consistent hierarchical placement and equivalence between concepts. The early work on the semantic definition of the disorder chapter, to support these requirements, is outlined and the attributes that have been found to be important are presented. We also describe different categories of completeness of definition that have been identified, and the scope of those that are likely to remain incompletely characterised.

Lymphopain, a cytotoxic T and natural killer cell-associated cysteine proteinase

Through differential screening of established human leukaemia cell lines, we have identified and molecularly cloned lymphopain, a novel cysteine proteinase of the papain family. Lymphopain exhibits a remarkably restricted cellular pattern of expression, being predominantly expressed in cytotoxic T-lymphocytes and natural killer cells. The human lymphopain locus maps to chromosome 11q13, encodes a polypeptide of 376 amino acids and is conserved in the mouse. Both human and murine forms appear more closely related to protozoan papain-like enzymes than to other mammalian members of the papain family. The cellular distribution of lymphopain expression, together with the functional demonstration of lymphopain-associated proteinase activity in vitro, is suggestive of a role for lymphopain in immune cell-mediated, cell killing.

Regional analgesia in early active labour: combined spinal epidural vs. epidural

We randomly allocated 93 women in early active labour and requesting epidural analgesia to receive either epidural (n = 48) or combined spinal-epidural analgesia (n = 45). For epidural analgesia 15 ml of bupivacaine 0.1% with 75 micrograms of fentanyl were injected into the epidural space. For combined spinal-epidural analgesia 1 ml of bupivacaine 0.25% with 25 micrograms of fentanyl were injected into the subarachnoid space. For both groups subsequent top-ups of 10 ml of bupivacaine 0.1% with fentanyl 20 micrograms were given using a lightweight patient-controlled epidural analgesia (PCEA) pump with a lockout time of 30 min. We assessed analgesia and the degree of motor blockade and found no significant differences in pain or maternal satisfaction scores between the two groups. The time to first top-up was significantly longer in the epidural group than in the CSE group (p = 0.01). The combined spinal-epidural group had significantly greater motor blockade at 30 min than the epidural group (p = 0.01), but there was no difference after this. The PCEA machine failed completely twice and temporarily many times. We conclude that the combined spinal-epidural technique confers no advantages in early active labour. Also, a lightweight PCEA pump needs to be more reliable before we can recommend its use.

A multimodal language region in the ventral visual pathway

Reading words and naming pictures involves the association of visual stimuli with phonological and semantic knowledge. Damage to a region of the brain in the left basal posterior temporal lobe (BA37), which is strategically situated between the visual cortex and the more anterior temporal cortex, leads to reading and naming deficits. Additional evidence implicating this region in linguistic processing comes from functional neuroimaging studies of reading in normal subjects and subjects with developmental dyslexia. Here we test whether the visual component of reading is essential for activation of BA37 by comparing cortical activations elicited by word processing in congenitally blind, late-blind and sighted subjects using functional neuroimaging. Despite the different modalities used (visual and tactile), all groups of subjects showed a common activation of BA37 by words relative to non-word letter-strings. These findings agree with the proposal that BA37 is an association area that integrates converging inputs from many regions. Our study confirms a prediction of theories of brain function that depend on convergence zones; the absence of one input (that is, visual) does not alter the response properties of such a convergence region.

Read Code quality assurance: from simple syntax to semantic stability

As controlled clinical vocabularies assume an increasing role in modern clinical information systems, so the issue of their quality demands greater attention. In order to meet the resulting stringent criteria for completeness and correctness, a quality assurance system comprising a database of more than 500 rules is being developed and applied to the Read Thesaurus. The authors discuss the requirement to apply quality assurance processes to their dynamic editing database in order to ensure the quality of exported products. Sources of errors include human, hardware, and software factors as well as new rules and transactions. The overall quality strategy includes prevention, detection, and correction of errors. The quality assurance process encompasses simple data specification, internal consistency, inspection procedures and, eventually, field testing. The quality assurance system is driven by a small number of tables and UNIX scripts, with "business rules" declared explicitly as Structured Query Language (SQL) statements. Concurrent authorship, client-server technology, and an initial failure to implement robust transaction control have all provided valuable lessons. The feedback loop for error management needs to be short.

Different activation patterns in the visual cortex of late and congenitally blind subjects

A key issue in developmental neuroscience is the role of activity-dependent mechanisms in the epigenetic induction of functional organization in visual cortex. Ocular blindness and ensuing visual deprivation is one of the rare models available for the investigation of experience-dependent cortical reorganization in man. In a PET study we demonstrate that congenitally blind subjects show task-specific activation of extrastriate visual areas and parietal association areas during Braille reading, compared with auditory word processing. In contrast, blind subjects who lost their sight after puberty show additional activation in the primary visual cortex with the same tasks. Studies in blind-raised monkeys show that crossmodal responses in extrastriate areas can be elicited by somatosensory stimulation. This is consistent with the crossmodal extrastriate activations elicited by tactile processing in our congenitally blind subjects. Since primary visual cortex does not show crossmodal responses in primate studies, the differential activation in late and congenitally blind subjects highlights the possibility of reciprocal activation by visual imagery in subjects with early visual experience.

Dual-task results and the lateralization of spatial orientation: artifact of test selection?

An investigation was conducted to identify the degree to which results regarding the lateralization of spatial orientation among men and women are artifacts of test selection. A dual-task design was used to study possible lateralization differences, providing baseline and dual-task measures of spatial-orientation performance, right- and left-hand tapping, and vocalization of "cat, dog, horse." The Guilford-Zimmerman Test (Guilford & Zimmerman, 1953), the Eliot-Price Test (Eliot & Price, 1976), and the Stumpf-Fay Cube Perspectives Test (Stumpf & Fay, 1983) were the three spatial-orientation tests used to investigate possible artifacts of test selection. Twenty-eight right-handed male and 39 right-handed female undergraduates completed random baseline and dual-task sessions. Analyses indicated no significant sex-related differences in spatial-orientation ability for all three tests. Furthermore, there was no evidence of differential lateralization of spatial orientation between the sexes.

Validating clinical terminology structures: integration and cross-validation of Read Thesaurus and GALEN

A European pre-standard and an intermediate representation facilitated exchange of two independently authored compositional knowledge bases: one formal and automatically classified, the other manually classified. The exchange highlights different strengths and weaknesses in each approach, and offers a mechanism for partial, mutual quality assurance.

Clinical administration procedures in the Read Thesaurus: extending the ENV 1828 model to support regional terminology requirements

Documentation of the administrative aspects of clinical practice (fee claims, referrals, visits etc.) is essential and a controlled terminology for the electronic health care record needs to support this requirement. The Read Codes--used in the United Kingdom for over 10 years--include a chapter of administration terms for this purpose. The latest version, the Read Thesaurus, adopts a partially compositional approach to concept representation. We describe an extension of the ENV 1828 surgical procedure scheme developed as a provisional model to represent administrative procedures. Applicable concept fields, semantic links and modifiers are identified and compared. A compositional approach appears to provide a flexible and manageable method of representing administrative procedures, and readily accommodates regional variations.

Updating the Read Codes: user-interactive maintenance of a dynamic clinical vocabulary

The Read Codes are a hierarchically-arranged controlled clinical vocabulary introduced in the early 1980s and now consisting of three maintained versions of differing complexity. The code sets are dynamic, and are updated quarterly in response to requests from users including clinicians in both primary and secondary care, software suppliers, and advice from a network of specialist healthcare professionals. The codes' continual evolution of content, both across and within versions, highlights tensions between different users and uses of coded clinical data. Internal processes, external interactions and new structural features implemented by the NHS Centre for Coding and Classification (NHSCCC) for user interactive maintenance of the Read Codes are described, and over 2000 items of user feedback episodes received over a 15-month period are analysed.

Alcohol removal of the epithelium for excimer laser ablation: outcomes analysis

PURPOSE

To determine whether removing the corneal epithelium by dilute alcohol is equal to other epithelial removal techniques.

SETTING

The Bochner Eye Institute, Toronto, Ontario, Canada.

METHODS

Epithelium was removed using 25% alcohol placed on a circular pledget; the alcohol remained on the cornea for 3 minutes. Irrigation was performed with cold balanced salt solution. The epithelium was then lifted with forceps and removed. Ninety-one eyes having photorefractive keratectomy for low myopia (less than 8.00 diopters) were treated; 41 eyes were followed between 4 and 10 months (mean 6 months). Complications such as haze and loss of best corrected visual acuity (BCVA) were recorded.

RESULTS

All alcohol-treated eyes achieved a BCVA of 20/40 or better, 65.9% had 20/20 and 92.7%, 20/25 or better. There were no complications or adverse effects.

CONCLUSIONS

Epithelial removal using 25% alcohol did not adversely affect the algorithms used with the VISX 20/20 excimer laser, indicating the technique is safe, predictable, and effective. There was no significant loss of BCVA, toxic effects, or stromal hydration.

Genetic divergence among the group B coxsackieviruses

As documented in the preceding discussion, the noncoding regions, and in particular the 5' NTR, of the CVB are tolerant of a substantial degree of nucleotide diversity while still being capable of fulfilling the life cycle requirements for these viruses. While diversity among the CVB is observed in the sequences encoding for the capsid proteins, it tends to involve predominantly those regions coding for amino acids located at the surface of the virus and not those responsible for the structural integrity of the mature virion, i.e., beta-barrels and alpha-helices. It is these capsid surface differences that define the six serotypes of the CVB and subdivide them antigenically into strains. Additionally, these proteins most likely play the major role in determining host and cellular tropism. The most conserved of the CVB proteins and, therefore those with the least diversity in their coding sequences, appear to be the nonstructural proteins. Perhaps, as speculated earlier, it is a conformational requirement imposed by the necessity to interact with host or viral substrates that maintains the high degree of amino acid identity of this group of viral proteins.

Infant acute leukemias show the same biased distribution of ALL1 gene breaks as topoisomerase II related secondary acute leukemias

The ALL1 gene (also called MLL, HRX, or Htrx1) at the cytogenetic band 11q23 is consistently altered by chromosome rearrangements in acute leukemias (ALs) of early infancy, in ALs developed after exposure to topoisomerase (topo) II-inhibitory drugs, and in a small subset of de novo ALs in children and adults. Because exposure to natural or medicinal substances blocking topo II during pregnancy have been proposed as etiological agents for infant leukemia, we have compared the distribution of ALL1 gene breakpoints in infant leukemias with an altered ALL1 gene configuration to those in secondary leukemia associated with prior exposure to topo II targeting drugs and in reference to the major topo consensus binding site in exon 9. ALL1 gene breakpoint distribution was determined by Southern blot hybridization and/or reverse transcription-PCR of the ALL1/AF4 fusion cDNA in 70 patients. Using restriction enzyme analysis, the 8.3-kb ALL1 breakpoint cluster region was divided in a centromeric portion of 3.5 kb (region A) and telomeric portion of a 4.8 kb (region B). ALL1 breakpoint were located in region A in 8 of 28 (28.5%) cases of infant ALs, 16 of 24 (66%) cases of de novo ALs, and 0 of 5 cases of therapy-related (TR) ALs. Conversely, ALL1 breakpoints in region B were detected in 20 of 28 (71.5%) cases of infant AL, 8 of 24 (33%) cases of de novo AL, and 5 of 5 (100%) cases of TR AL (P = 0.002). These results were confirmed by direct sequencing of the ALL1/AF4 fusion transcript in 30 cases (19 infants and 11 child and adult de novo cases). The analysis of ALL1/AF4 junction types showed that children and adults with de novo leukemia had ALL1 breakpoints in intron 6 (9 cases) or intron 7 (2 cases), whereas breakpoints in infant cases were mainly located in intron 8 (14 cases) and less frequently in intron 6 (4 cases) and intron 7 (1 case). The difference in ALL1 breakpoint location between infant and noninfant AL patients with ALL1/AF4 fusion was statistically significant (P = 0.00005). These data demonstrated that infant and TR ALs share a similar biased clustering of ALL1 gene breakpoints, which supports the possibility that topo II inhibitors may also operate in utero and play a crucial role in the etiology of infant leukemia.

Characterisation of the Schizosaccharomyces pombe rad4/cut5 mutant phenotypes: dissection of DNA replication and G2 checkpoint control function

Mutation of the essential Schizosaccharomyces pombe rad4/cut5 gene causes sensitivity to UV and ionising radiation at the permissive temperature whilst at the restrictive temperature cells fail to undergo DNA replication but still attempt mitosis owing to a defective S-phase checkpoint response. Many mutations in genes encoding DNA replication proteins also abolish checkpoint responses, possibly because the replication machinery is a pre-requisite for the generation of the signal. We demonstrate here that rad4/cut5 cells fail to arrest cell division when treated with the replication inhibitor hydroxyurea at the semi-permissive temperature 32 degrees C, but retain essentially normal replicative capacity. This demonstrates that the replication and checkpoint function of the rad4/cut5 gene product can be separated and that the Rad4 protein differs from other replication proteins in being directly involved in generating the S-phase checkpoint signal. Furthermore, we have investigated the checkpoint response or rad4/cut5-deficient cells to gamma-irradiation and UV-mimetic drugs. We find that, at the restrictive temperature, the rad4-/cut5- cells fail to delay mitosis in response to gamma-irradiation whilst retaining a normal checkpoint response to the UV-mimetic drug 4-nitroquinoline-1-oxide. The lack of the gamma-irradiation checkpoint is reminiscent of the deficiency associated with mutation of the human ATM locus, the causative deficiency of the heritable disorder ataxia telangiectasia. The implications of our results for the organisation of distinct checkpoint-response pathways in both fission yeast and mammalian cells are discussed. Moreover the data are consistent with a model in which the generation of the S-Phase checkpoint signal is DNA polymerase epsilon dependent.