The estimation of statistical parameters for local alignment score distributions

The distribution of optimal local alignment scores of random sequences plays a vital role in evaluating the statistical significance of sequence alignments. These scores can be well described by an extreme-value distribution. The distribution’s parameters depend upon the scoring system employed and the random letter frequencies; in general they cannot be derived analytically, but must be estimated by curve fitting. For obtaining accurate parameter estimates, a form of the recently described ‘island’ method has several advantages. We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects.

Impacts fonctionnels du traumatisme craniocérébral léger sur la vision et l'équilibre postural chez l'adulte

Le traumatisme craniocérébral léger (TCCL) a des effets complexes sur plusieurs fonctions cérébrales, dont l’évaluation et le suivi peuvent être difficiles. Les problèmes visuels et les troubles de l’équilibre font partie des plaintes fréquemment rencontrées après un TCCL. En outre, ces problèmes peuvent continuer à affecter les personnes ayant eu un TCCL longtemps après la phase aiguë du traumatisme. Cependant, les évaluations cliniques conventionnelles de la vision et de l’équilibre ne permettent pas, la plupart du temps, d’objectiver ces symptômes, surtout lorsqu’ils s’installent durablement. De plus, il n’existe pas, à notre connaissance, d’étude longitudinale ayant étudié les déficits visuels perceptifs, en tant que tels, ni les troubles de l’équilibre secondaires à un TCCL, chez l’adulte. L’objectif de ce projet était donc de déterminer la nature et la durée des effets d’un tel traumatisme sur la perception visuelle et sur la stabilité posturale, en évaluant des adultes TCCL et contrôles sur une période d’un an. Les mêmes sujets, exactement, ont participé aux deux expériences, qui ont été menées les mêmes jours pour chacun des sujets. L’impact du TCCL sur la perception visuelle de réseaux sinusoïdaux définis par des attributs de premier et de second ordre a d’abord été étudié. Quinze adultes diagnostiqués TCCL ont été évalués 15 jours, 3 mois et 12 mois après leur traumatisme. Quinze adultes contrôles appariés ont été évalués à des périodes identiques. Des temps de réaction (TR) de détection de clignotement et de discrimination de direction de mouvement ont été mesurés. Les niveaux de contraste des stimuli de premier et de second ordre ont été ajustés pour qu’ils aient une visibilité comparable, et les moyennes, médianes, écarts-types (ET) et écarts interquartiles (EIQ) des TR correspondant aux bonnes réponses ont été calculés. Le niveau de symptômes a également été évalué pour le comparer aux données de TR. De façon générale, les TR des TCCL étaient plus longs et plus variables (plus grands ET et EIQ) que ceux des contrôles. De plus, les TR des TCCL étaient plus courts pour les stimuli de premier ordre que pour ceux de second ordre, et plus variables pour les stimuli de premier ordre que pour ceux de second ordre, dans la condition de discrimination de mouvement. Ces observations se sont répétées au cours des trois sessions. Le niveau de symptômes des TCCL était supérieur à celui des participants contrôles, et malgré une amélioration, cet écart est resté significatif sur la période d’un an qui a suivi le traumatisme. La seconde expérience, elle, était destinée à évaluer l’impact du TCCL sur le contrôle postural. Pour cela, nous avons mesuré l’amplitude d’oscillation posturale dans l’axe antéropostérieur et l’instabilité posturale (au moyen de la vitesse quadratique moyenne (VQM) des oscillations posturales) en position debout, les pieds joints, sur une surface ferme, dans cinq conditions différentes : les yeux fermés, et dans un tunnel virtuel tridimensionnel soit statique, soit oscillant de façon sinusoïdale dans la direction antéropostérieure à trois vitesses différentes. Des mesures d’équilibre dérivées de tests cliniques, le Bruininks-Oseretsky Test of Motor Proficiency 2nd edition (BOT-2) et le Balance Error Scoring System (BESS) ont également été utilisées. Les participants diagnostiqués TCCL présentaient une plus grande instabilité posturale (une plus grande VQM des oscillations posturales) que les participants contrôles 2 semaines et 3 mois après le traumatisme, toutes conditions confondues. Ces troubles de l’équilibre secondaires au TCCL n’étaient plus présents un an après le traumatisme. Ces résultats suggèrent également que les déficits affectant les processus d’intégration visuelle mis en évidence dans la première expérience ont pu contribuer aux troubles de l’équilibre secondaires au TCCL. L’amplitude d’oscillation posturale dans l’axe antéropostérieur de même que les mesures dérivées des tests cliniques d’évaluation de l’équilibre (BOT-2 et BESS) ne se sont pas révélées être des mesures sensibles pour quantifier le déficit postural chez les sujets TCCL. L’association des mesures de TR à la perception des propriétés spécifiques des stimuli s’est révélée être à la fois une méthode de mesure particulièrement sensible aux anomalies visuomotrices secondaires à un TCCL, et un outil précis d’investigation des mécanismes sous-jacents à ces anomalies qui surviennent lorsque le cerveau est exposé à un traumatisme léger. De la même façon, les mesures d’instabilité posturale se sont révélées suffisamment sensibles pour permettre de mesurer les troubles de l’équilibre secondaires à un TCCL. Ainsi, le développement de tests de dépistage basés sur ces résultats et destinés à l’évaluation du TCCL dès ses premières étapes apparaît particulièrement intéressant. Il semble également primordial d’examiner les relations entre de tels déficits et la réalisation d’activités de la vie quotidienne, telles que les activités scolaires, professionnelles ou sportives, pour déterminer les impacts fonctionnels que peuvent avoir ces troubles des fonctions visuomotrice et du contrôle de l’équilibre.

Under the Bridge: Utilizing Covered Liminal Spaces for Sanctioned Homeless Encampments in the City of Seattle

Thesis (Master's)--University of Washington, 2016-06

Adherence to a Bronchiolitis Clinical Pathway is Associated with Decreased Length of Stay and Costs

Thesis (Master's)--University of Washington, 2016-06

Deep dermal burn injury results in scarless wound healing in the ovine fetus

Early to mid-term fetuses heal cutaneous incisional wounds without scars; however, fetal response to burn injury has not been ascertained. We present a fetal model of thermal injury and subsequent analysis of fetal and lamb response to burn injury. A reproducible deep dermal burn injury was created in the fetus by application of water at 66 degrees C for 7 seconds, and at 82 degrees C for 10 seconds to the lamb. Macroscopically, the area of fetal scald was undetectable from day 7 post injury, while all lamb scalds were readily identified and eventually healed with scarring. Using a five-point histopathology scoring system for alteration in tissue morphology, differences were detected between control and scalded skin at all stages in lamb postburn, but no difference was detected in the fetal model after day 7. There were also large differences in content of alpha-smooth muscle actin and transforming growth factor-beta 1 between control and scalded lamb and these differences were statistically significant at day 14 (P < 0.01). This novel model of fetal and lamb response to deep dermal injury indicates that the fetus heals a deep burn injury in a scarless fashion. Further elucidation of this specific fetal process of burn injury repair may lead to improved outcome for patients with burn injury.

The reliability and validity of the Therapeutic activity index

Purpose To assess the psychometric properties of the Simplified Therapeutic Intervention Scoring System (TISS 28) scale. Materials and Methods A prospective observational design was used. Patients were recruited from a medical-surgical intensive care unit (ICU) and 4 rehabilitation wards of 2 university-affiliated hospitals in Hong Kong. Results Data necessary for the calculation of the TISS 28, the Therapeutic Intervention Scoring System (TISS 76), and severity of illness scoring system (Simplified Acute Physiology Score [SAPS II]) were recorded for each patient during the first 24 hours after his/her admission to an ICU. A significant positive correlation was found between the TISS 76 and the TISS 28 scores as well as the TISS 28 and the SAPS II scores. There was a significant difference between the TISS 28 scores among ICU patients and patients in rehabilitation wards. A significant correlation was found between the TISS 28 scores of the first and second set of TISS 28 scores. Conclusions Although the findings supported the validity and reliability of the TISS 28, there were limitations of the TISS 28 in measuring nursing workload in ICUs. Hence, continued amendment and validation of the TISS 28 on larger samples in different ICUs would be required so as to provide clinical nurses with a valid and reliable assessment of nursing workload.

A Test of Performance of Breast MRI Interpretation in a Multicentre Screening Study

Objectives: The aim of this study was to assess the consistency and performance of radiologists interpreting breast magnetic resonance imaging (MRI) examinations. Materials and Methods: Two test sets of eight cases comprising cancers, benign disease, technical problems and parenchymal enhancement were prepared from two manufacturers' equipment (X and Y) and reported by 15 radiologists using the recording form and scoring system of the UK MRI breast screening study [(MAgnetic Resonance Imaging in Breast Screening (MARIBS)]. Variations in assessments of morphology, kinetic scores and diagnosis were measured by assessing intraobserver and interobserver variability and agreement. The sensitivity and specificity of reporting performances was determined using receiver operating characteristic (ROC) curve analysis. Results: Intraobserver variation was seen in 13 (27.7%) of 47 of the radiologists' conclusions (four technical and seven pathological differences). Substantial interobserver variation was observed in the scores recorded for morphology, pattern of enhancement, quantification of enhancement and washout pattern. The overall sensitivity of breast MRI was high [88.6%, 95% confidence interval (CI) 77.4-94.7%], combined with a specificity of 69.2% (95% CI 60.5-76.7%). The sensitivities were similar for the two test sets (P=.3), but the specificity was significantly higher for the Manufacturer X dataset (P

The effect of an algorithm-based sedation guideline on the duration of mechanical ventilation in an Australian intensive care unit

To examine the effect of an algorithm-based sedation guideline developed in a North American intensive care unit (ICU) on the duration of mechanical ventilation of patients in an Australian ICU. The intervention was tested in a pre-intervention, post-intervention comparative investigation in a 14-bed adult intensive care unit. Adult mechanically ventilated patients were selected consecutively (n =322) The pre-intervention and post-intervention groups were similar except for a higher number of patients with a neurological diagnosis in the pre-intervention group. An algorithm-based sedation guideline including a sedation scale was introduced using a multifaceted implementation strategy. The median duration of ventilation was 5.6 days in the post-intervention group, compared with 4.8 days for the pre-intervention group (P = 0.99). The length of stay was 8.2 days in the post-intervention group versus 7.1 days in the pre-intervention group (P = 0.04). There were no statistically significant differences for the other secondary outcomes, including the score on the Experience of Treatment in ICU 7 item questionnaire, number of tracheostomies and number of self-extubations. Records of compliance to recording the sedation score during both phases revealed that patients were slightly more deeply sedated when the guideline was used. The use of the algorithm-based sedation guideline did not reduce duration of mechanical ventilation in the setting of this study.

Morphology of breast cancer as a means of triage of patients for BRCA1 genetic testing

Background: Women who have germline mutations in the BRCA1 gene are at substantially increased lifetime risk of developing breast and ovarian cancer but are otherwise normal. Currently. early age of onset of cancer and a strong family history are relied upon as the chief clues as to who should be offered genetic testing. Certain morphologic and immunohistochemical features are overrepresented in BRCA1-associated breast cancers but these differences have not been incorporated into the current selection criteria for genetic testing. Design: Each of the 4 pathologists studied 30 known cases of BRCA1- and BRCA2-associated breast cancer from kConFab families. After reviewing the literature, we agreed on a semiquantitative scoring system for estimating the chances of presence of an underlying BRCA1 mutation, based on the number of the reported prototypic features present. After a time lag of 12 months, we each examined a series of 62 deidentified cases of breast cancer, inclusive of cases of BRCA1-associated breast cancer and controls. The controls included cases of BRCA2-associated breast cancer and sporadic cases. Results: Our predictions had a sensitivity of 92%, specificity of 86%, positive predictive value of 61%, and negative predictive value of 98%. For comparison the sensitivity of currently used selection criteria are in the range of 25% to 30%. Conclusion: The inclusion of morphologic and immunohistochemical features of breast cancers in algorithms to predict the likelihood of presence of germline mutations in the BRCA1 gene improves the accuracy of the selection process.

The development of a new measure of quality of life for children with congenital cardiac disease

The purpose of the study was to develop a questionnaire measuring health-related R1 quality of life for children and adolescents with congenital heart disease, the ConQol, that would have both clinical and research applications. We describe here the process of construction of a questionnaire, the piloting and the development of a weighted scoring system, and data on the psychometric performance of the measure in a sample of 640 children and young people recruited via 6 regional centres for paediatric cardiology from across the United Kingdom. The ConQol has two versions, one designed for children aged from 8 to 11 years, and the other for young people aged from 12 to 16 years. Initial findings suggest that it is a valid and reliable instrument, is acceptable to respondents, and is simple to administer in both a research and clinical context.

Process improvement within a HR division at a UK police force

A structured approach to process improvement is described in the context of the human resources division of a UK police force. The approach combines a number of established techniques of process improvement such as the balanced scorecard and process mapping with a scoring system developed to prioritise processes for improvement. The methodology described presents one way of ensuring the correct processes are identified and redesigned at an operational level in such a way as to support the organisation's strategic aims. In addition, a performance measurement system is utilised to attempt to ensure that the changes implemented do actually achieve the desired effect over time. The case demonstrates the need to choose and in some cases develop in-house tools and techniques dependent on the context of the process improvement effort.

Ecological studies on:(a) the use of colonisation samplers in relation to biological surveillance of river water quality (b) the requirements of freshwater gastropoda

Some of the factors affecting colonisation of a colonisation sampler, the Standard Aufwuchs Unit (S. Auf. U.) were investigated, namely immersion period, whether anchored on the bottom or suspended, and the influence of riffles. It was concluded that a four-week immersion period was best. S. Auf. U. anchored on the bottom collected both more taxa and individuals than suspended ones. Fewer taxa but more individuals colonised S. Auf. U. in the potamon zone compared to the rhithron zone with a consequent reduction in the values of pollution indexes and diversity. It was concluded that a completely different scoring system was necessary for lowland rivers. Macroinvertebrates colonising S. Auf. U. in simulated streams, lowland rivers and the R. Churnet reflected water quality. A variety of pollution and diversity indexes were applied to results from lowland river sites. Instead of these, it was recommended that an abbreviated species - relative abundance list be used to summarise biological data for use in lowland river surveillance. An intensive study of gastropod populations was made in simulated streams. Lynnaea peregra increased in abundance whereas Potamopyrgas jenkinsi decreased with increasing sewage effluent concentration. No clear-cut differences in reproduction were observed. The presence/absence of eight gastropod taxa was compared with concentrations of various pollutants in lowland rivers. On the basis of all field work it appeared that ammonia, nitrite, copper and zinc were the toxicants most likely to be detrimental to gastropods and that P. jenkinsi and Theodoxus fluviatilis were the least tolerant taxa. 96h acute toxicity tests of P. jenkinsi using ammonia and copper were carried out in a flow-through system after a variety of static range finding tests. P. jenkinsi was intolerant to both toxicants compared to reports on other taxa and the results suggested that these toxicants would affect distribution of this species in the field.

Developing a model for consumer product safety evaluation

Safety enforcement practitioners within Europe and marketers, designers or manufacturers of consumer products need to determine compliance with the legal test of "reasonable safety" for consumer goods, to reduce the "risks" of injury to the minimum. To enable freedom of movement of products, a method for safety appraisal is required for use as an "expert" system of hazard analysis by non-experts in safety testing of consumer goods for implementation consistently throughout Europe. Safety testing approaches and the concept of risk assessment and hazard analysis are reviewed in developing a model for appraising consumer product safety which seeks to integrate the human factors contribution of risk assessment, hazard perception, and information processing. The model develops a system of hazard identification, hazard analysis and risk assessment which can be applied to a wide range of consumer products through use of a series of systematic checklists and matrices and applies alternative numerical and graphical methods for calculating a final product safety risk assessment score. It is then applied in its pilot form by selected "volunteer" Trading Standards Departments to a sample of consumer products. A series of questionnaires is used to select participating Trading Standards Departments, to explore the contribution of potential subjective influences, to establish views regarding the usability and reliability of the model and any preferences for the risk assessment scoring system used. The outcome of the two stage hazard analysis and risk assessment process is considered to determine consistency in results of hazard analysis, final decisions regarding the safety of the sample product and to determine any correlation in the decisions made using the model and alternative scoring methods of risk assessment. The research also identifies a number of opportunities for future work, and indicates a number of areas where further work has already begun.

Large scale organisational intervention to improve patient safety in four UK hospitals:mixed method evaluation

Objectives: To conduct an independent evaluation of the first phase of the Health Foundation's Safer Patients Initiative (SPI), and to identify the net additional effect of SPI and any differences in changes in participating and non-participating NHS hospitals. Design: Mixed method evaluation involving five substudies, before and after design. Setting: NHS hospitals in United Kingdom. Participants: Four hospitals (one in each country in the UK) participating in the first phase of the SPI (SPI1); 18 control hospitals. Intervention: The SPI1 was a compound (multicomponent) organisational intervention delivered over 18 months that focused on improving the reliability of specific frontline care processes in designated clinical specialties and promoting organisational and cultural change. Results: Senior staff members were knowledgeable and enthusiastic about SPI1. There was a small (0.08 points on a 5 point scale) but significant (P<0.01) effect in favour of the SPI1 hospitals in one of 11 dimensions of the staff questionnaire (organisational climate). Qualitative evidence showed only modest penetration of SPI1 at medical ward level. Although SPI1 was designed to engage staff from the bottom up, it did not usually feel like this to those working on the wards, and questions about legitimacy of some aspects of SPI1 were raised. Of the five components to identify patients at risk of deterioration - monitoring of vital signs (14 items); routine tests (three items); evidence based standards specific to certain diseases (three items); prescribing errors (multiple items from the British National Formulary); and medical history taking (11 items) - there was little net difference between control and SPI1 hospitals, except in relation to quality of monitoring of acute medical patients, which improved on average over time across all hospitals. Recording of respiratory rate increased to a greater degree in SPI1 than in control hospitals; in the second six hours after admission recording increased from 40% (93) to 69% (165) in control hospitals and from 37% (141) to 78% (296) in SPI1 hospitals (odds ratio for "difference in difference" 2.1, 99% confidence interval 1.0 to 4.3; P=0.008). Use of a formal scoring system for patients with pneumonia also increased over time (from 2% (102) to 23% (111) in control hospitals and from 2% (170) to 9% (189) in SPI1 hospitals), which favoured controls and was not significant (0.3, 0.02 to 3.4; P=0.173). There were no improvements in the proportion of prescription errors and no effects that could be attributed to SPI1 in non-targeted generic areas (such as enhanced safety culture). On some measures, the lack of effect could be because compliance was already high at baseline (such as use of steroids in over 85% of cases where indicated), but even when there was more room for improvement (such as in quality of medical history taking), there was no significant additional net effect of SPI1. There were no changes over time or between control and SPI1 hospitals in errors or rates of adverse events in patients in medical wards. Mortality increased from 11% (27) to 16% (39) among controls and decreased from17%(63) to13%(49) among SPI1 hospitals, but the risk adjusted difference was not significant (0.5, 0.2 to 1.4; P=0.085). Poor care was a contributing factor in four of the 178 deaths identified by review of case notes. The survey of patients showed no significant differences apart from an increase in perception of cleanliness in favour of SPI1 hospitals. Conclusions The introduction of SPI1 was associated with improvements in one of the types of clinical process studied (monitoring of vital signs) and one measure of staff perceptions of organisational climate. There was no additional effect of SPI1 on other targeted issues nor on other measures of generic organisational strengthening.

Are Complications Associated With the Repiphysis(®) Expandable Distal Femoral Prosthesis Acceptable for Its Continued Use?

BACKGROUND: Reconstruction of the distal femur after resection for malignant bone tumors in skeletally immature children is challenging. The use of megaprostheses has become increasingly popular in this patient group since the introduction of custom-made, expandable devices that do not require surgery for lengthening, such as the Repiphysis(®) Limb Salvage System. Early reports on the device were positive but more recently, a high complication rate and associated bone loss have been reported. QUESTIONS/PURPOSES: We asked: (1) what are the clinical outcomes using the Musculoskeletal Tumor Society (MSTS) scoring system after 5-year minimum followup in patients treated with this prosthesis at one center; (2) what are the problems and complications associated with the lengthening procedures of this implant; and (3) what are the specific concerns associated with revision of this implant? METHODS: At our institute, between 2002 and 2007, the Repiphysis(®) expandable prosthesis was implanted in 15 children (mean age, 8 years; range, 6-11 years) after distal femoral resection for malignant bone tumors. During this time, the general indication for use of this implant was resection of the distal femur for localized malignant bone tumors in pediatric patients. Alternative techniques used for this indication were modular prosthetic reconstruction, massive (osteoarticular or intercalary) allograft reconstruction, or rotationplasty. Age and tumor extension were the main factors to decide on the surgical indication. Of the 15 patients who had this prosthesis implanted during reconstruction surgery, five died with the implant in situ or underwent amputation before 5 years followup and the remaining 10 were evaluated at a minimum of 5 years (mean, 104 months; range, 78-140 months). No patients were lost to followup. These 10 patients were long-term survivors and underwent the lengthening program. They were included in our study analysis. The first seven lengthening procedures were attempted in an outpatient setting; however, owing to pain and burning sensations experienced by the patients, the procedures failed to achieve the desired lengthening. Therefore, other procedures were performed with the patients under general anesthesia. We reviewed clinical data at index surgery for all 15 patients. We further analyzed the lengthening procedures, implant survival, radiographic and functional results, for the 10 long-term survivors. Functional results were assessed according to the MSTS scoring system. Complications were classified according to the International Society of Limb Salvage (ISOLS) classification system. RESULTS: Nine of the 10 survivors underwent revision of the implant for mechanical failure. They had a mean MSTS score of 64% (range, 47%-87%) before revision surgery. At final followup the 10 long-term surviving patients had an average MSTS score of 81% (range, 53%-97%). In total, we obtained an average lengthening of 39 mm per patient (range, 17-67 mm). Exact expansion of the implant was unpredictable and difficult to control. Nine of 10 of the long-term surviving patients underwent revision surgery of the prosthesis-eight for implant breakage and one for stem loosening. At revision surgery, six patients had another type of expandable prosthesis implanted and three had an adult-type megaprosthesis implanted. In five cases, segmental bone grafts were used during revision surgery to compensate for loss of bone stock. CONCLUSIONS: We could not comfortably expand the Repiphysis(®) prosthesis in an outpatient setting because of pain experienced by the patients during the lengthening procedures. Furthermore, use of the prosthesis was associated with frequent failures related to implant breakage and stem loosening. Revisions of these procedures were complex and difficult. We no longer use this prosthesis and caution others against the use of this particular prosthesis design. LEVEL OF EVIDENCE: Level IV, therapeutic study.