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PubMed1996

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.

The relative performances of four strategies for aligning a large number of protein sequences were assessed by referring to corresponding structural alignments of 54 independent families. Multiple sequence alignment of a family was constructed by a given method from the sequences of known structures and their homologues, and the subset consisting of the sequences of known structures was extracted from the whole alignment and compared with the structural counterpart in a residue-to-residue fashion. Gap-opening and -extension penalties were optimized for each family and method. Each of the four multiple alignment methods gave significantly more accurate alignments than the conventional pairwise method. In addition, a clear difference in performance was detected among three of the four multiple alignment methods examined. The currently most popular progressive method ranked worst among the four, and the randomized iterative strategy that optimizes the sum-of-pairs score ranked next worst. The two best-performing strategies, one of which was newly developed, both pursue an optimal weighted sum-of-pairs score, where the pair weights were introduced to correct for uneven representations of subgroups in a family. The new method uses doubly nested iterations to make alignment, phylogenetic tree and pair weights mutually consistent. Most importantly, the improvement in accuracy of alignments obtained by these iterative methods over pairwise or progressive method tends to increase with decreasing average sequence identity, implying that iterative refinement is more effective for the generally difficult alignment of remotely related sequences. Four well-known amino acid substitution matrices were also tested in combination with the various methods. However, the effects of substitution matrices were found to be minor in the framework of multiple alignment, and the same order of relative performance of the alignment methods was observed with any of the matrices.

Algorithms↗

PubMed2006

Relationships between community characteristics and municipal smoke-free bylaw status and strength.

BACKGROUND: Municipal smoke-free spaces bylaws are a common population-level intervention to address the prominent health risks associated with exposure to second-hand smoke. In Canada, bylaw prevalence is increasing, but inequities in level of protection across communities remain as bylaws vary from place to place. Little is known about the role of place in this policy disparity. To address this gap, this study examined associations between community characteristics and municipal smoke-free spaces policy outcomes to elucidate how ecological conditions are associated with bylaw status and strength. METHOD: Smoke-free public place and workplace bylaws were obtained from all municipalities with a population of >or=5000 in the provinces of Alberta (N=78) and Ontario (N=245), Canada. Bylaws were assigned a strength score (ranging 0-100) rating the degree of bylaw comprehensiveness, restrictiveness and enforcement provisions. These data were then linked to socio-demographic data from the Canadian Census (1996) and the Canadian Community Health Survey Cycle 1.1 (2000/2001). Logistic and multiple linear regression analyses were used to develop models for municipal bylaw status and strength using community factors including: socio-demographics, municipality type, health region smoking rates, and provincial tobacco control environment. CONCLUSIONS: Study findings suggest that community characteristics play a key role in the status and strength of municipal smoke-free bylaws. As smoking bans continue to emerge world-wide under the Framework Convention on Tobacco Control, knowledge about conditions that promote policy success will be critical for those in need of immediate information to maximize policy-making in their own settings. Use of community profiles that consider socio-demographics along with broader contextual factors can aid decision-makers, public health advocates, and researchers in identifying similar jurisdictions with a successful smoke-free spaces policy and communicating with them about their policy-making experiences. Knowledge about the conditions associated with municipal policy-development may be translated to other jurisdictions where information is sparse, or evidence is newly emerging.

Alberta↗

PubMed2004

The hidden error of mismanaged pain: a systems approach.

Undertreatment of pain resulting in physiological, psychosocial, and economic consequences continues despite targeted improvement approaches. Starck et al. propose a systems framework for study of pain management errors. This secondary analysis examined pain outcomes of hospitalized inpatients to determine factors predicting adequate pain management. Data were collected from 964 hospitalized adult patients in the southwestern United States. The American Pain Society Patient Outcome Questionnaire and a demographic and chart audit form were used to collect data. The Pain Management Index (PMI) was computed for all participants. Results revealed that 30% of patients were undertreated for pain, with 67.5% reporting severe worst pain ratings (7 on a 0-10 scale). Non-whites, the elderly, and women had significantly higher pain ratings and higher proportions of negative PMI scores. Logistic regression predicted adequate pain management based on analgesic rating, ethnicity, age, and educational level with 0.89 accuracy. The study findings support conceptualizing mismanagement of pain as a medical error. An intervention model describes the use of a systems approach to identify high risk patients and ensure effective pain management practices for all.

Adult↗

PubMed1993

Symposium: Dream research methodology: The quest for dream sources.

Within a Human Information Processing (HIP) framework, dreaming can be subdivided into three main components: Input, Processing and Output. Until recently, only the Output has been extensively studied due to its relatively easy accessibility in the form of dream reports. Much less is known about the other two components. A method is presented by which one can get information on the nature of the input component to dream processing. In this method the subjects are requested to identify the memory sources of their dreams, collected upon experimental awakenings. The materials thus obtained are then classified into categories derived from Tulving's distinction between Episodic and Semantic memory. Several aspects, including interviewing and scoring procedures, had to be specified in order to use the method, which was applied in a series of studies. The aim was to clarify the similarities as well as the differences between REM and NREM dreams. The main results give further support to the hypothesis of the existence of a unique dream production system that operates at different levels of engagement during the various sleep phases.

Journal Article↗

PubMed2006

Worries and concerns of patients with multiple sclerosis: development of an assessment scale.

This study examined the nature of worry in adult patients with multiple sclerosis (MS) in the UK. A measure of worry in MS was developed and the relationship between worry and standard scale measures of anxiety and depression was examined. Thirty-nine patients with MS and 40 controls completed the new worry scale (WQMS) that was psychometrically evaluated, together with the Penn State Worry Questionnaire (PSWQ), the Hospital Anxiety and Depression Scale (HAD) and a previously developed scale to assess self-efficacy in MS (SESMS). The scores for both anxiety (t = 2.34; P < 0.05) and depression (t = 5.52; P <0.01) were higher in MS patients than controls, as was the new scale for worry--the WQMS. A factor analysis (explaining 65.73% of the variance) suggests that the worries of patients may be dichotomized into those concerned with the physical effects of the disease and those relating to the impact on social interaction, family relationships and daily activity in the home and/or work. Worry in patients with MS was associated with a decreased sense of being able to produce positive activities or effect positive outcomes (low self-efficacy). The questionnaire provides a framework for investigation in clinic of specific concerns and level of worry they engender.

Adult↗

PubMed1980

Relationship of reinforcement by student clinicians and peers to accuracy of imitated grammatical constructions during language training.

Percentages of correctly imitated grammatical constructions were examined within a framework of reinforcement theory. Four small treatment groups, each of 4 language-delayed children, were repeatedly observed interacting with different student-clinicians. The Therapy Reinforcement Schedule was used to obtain frequency counts of verbal and non-verbal reinforcements so that within each language group the students could be objectively divided into those who frequently and infrequently were reinforcing, and the children into those for whom peer-reinforcement was high or low. The resulting 4 groups were compared for proportions of accurately imitated constructions with a repeated-measures analysis of variance design (student-clinicians' reinforcement x peers' reinforcement x trials). Correctly scored imitations increased significantly over trials. In addition, children interacting with frequently reinforcing students received higher imitation scores than those with infrequently rewarding ones. Significant main effects of reinforcement by the peer group were not observed, although a reliable interaction of student-clinicians' reinforcement x peers' reinforcement was present. Regression analyses indicated the importance of certain types of reinforcements in predicting accuracy of imitation.

Child, Preschool↗

PubMed1993

Effectiveness of thymostimulin and study of lymphocyte-dependent antibacterial activity in children with recurrent respiratory infections.

Recurrent respiratory infections (RRI) consist of more relapsing acute respiratory infections than the ones expected for the age [> 6 acute respiratory tract infections (RTI) per year if age is > 3 years, and > 8 acute RTI per year if age is < 3 years]. Concerning the pathogenesis of RRI, several investigations report the important role of environmental factors, early socialization and immunological dysfunctions, such as lymphocyte subpopulations alterations, IgG subclass deficiency and phagocytosis and/or opsonization deficit during acute infections. In this framework, we have studied the lymphocyte-dependent antibacterial activity (ABA) among 121 children affected by RRI. Results show a statistically significant alteration of this function in 38 children (31.4%): 19 of them exhibited an absent ABA (group 1), while in the others same function was reduced (group 2). A bovine thymic extract, thymostimulin, was administered to both groups by intramuscular injections (1 mg/kg) for a 3 month cycle. At the end of therapy we observed a statistical significant rise of ABA only in group 1 and among children aged > 3 years. Among the same patients, 33 children (86.8%) improved in terms of reduction of clinical score and better results were seen among children aged > 3 years. These data emphasize the beneficial role of thymostimulin in RRI-affected children, suggesting a transient immaturity of the immune system as one of the possible pathogenetic factor.

Adjuvants, Immunologic↗

PubMedDate not supplied

[Analysis of 94 dexamethasone tests in a population of patients manifesting depressive symptomatology within the framework of a manic-depressive psychosis or other psychotic state].

The authors report a study of 94 dexamethasone-suppression-tests conducted in a group of 29 patients with either a manic-depressive psychosis (n = 14) or a depressive symptomatology associated or not with a chronic psychotic disorder. 1 mg of dexamethasone was given orally at 11 p.m. and plasma cortisol levels were determined the following day at 4 p.m. The same day, a MADS was calculated. These tests were repeated every month for each patient independently of the clinical state. 9 patients received between 4 and 11 tests. A non suppression (cortisol plasma levels greater than or equal to 140 nmol/l) was observed in 27% of the tests. A comparable percentage was obtained in the whole group of patients and in the manic-depressive psychosis group. A good correlation appeared between plasma cortisol level at 4 p.m. and score for MADS. The study of the validity of the test shows a sensibility of 50% and a specificity of 85%. These results are similar with those presented in the literature.

Adult↗

PubMed1987

Cognitive antecedents of coronary heart disease.

The purpose was to explore cognitive antecedents of CHD proneness in an attempt to avoid some of the problems besetting research focused on type A. The theoretical framework was the cognitive orientation theory by Kreitler and Kreitler which shows how cognitive contents, primarily beliefs about goals, norms, the self and reality guide human behavior and enable its prediction and change. The hypotheses referred to endorsement of beliefs orienting towards CHD-involved behaviors, inconsistencies among belief types and the relation of the beliefs to risk factors in CHD patients as compared to the controls. A self-administered questionnaire was constructed assessing endorsement of four belief types. Subjects were 92 males under 60: 44 with CHD, and two control groups: 28 orthopedic patients without CHD, and 20 healthy subjects. Results showed that CHD individuals scored higher than the controls on the overall beliefs measure, beliefs about norms and about self, had higher inconsistency scores, and had more correlations between belief measures and risk factors (e.g. blood pressure, cholesterol). Discussion centered on suggesting a definition of CHD-proneness as consisting of a sustained externally-maintained tension-producing cognitive-motivational conflict, and on the psychometric and practical implications of the findings.

Adult↗

PubMed2004

The Wheezing Illnesses Study Leidsche Rijn (WHISTLER): rationale and design.

The Wheezing Illnesses Study Leidsche Rijn (WHISTLER) was initiated in December 2001 as a single-centre prospective birth cohort study and will include a population-based sample of at least 2000 healthy newborns. The aims of WHISTLER are to investigate determinants for wheezing illnesses (including neonatal lung function, viral infections, asthma-susceptibility genes and endotoxin exposure) and to derive a comprehensive risk score, that is appropriate for use in primary health care and allows for efficient planning of early preventive strategies. Baseline examination includes a questionnaire evaluating known risk factors for wheezing illnesses; anthropometric measurements; measurements of infant and parental lung function; and sampling of infant and parental DNA. Participants will be followed for respiratory events using data from a daily respiratory symptom questionnaire; visits to the general practitioner (primary health care visits, drugs prescriptions and hospital referral); viral sampling during wheezing episodes; and house dust sampling. Based on actual neonatal care practice and embedded in a larger epidemiological study, the Utrecht Health Project, WHISTLER will provide an unique framework to address issues in childhood respiratory disease that are currently insufficiently understood. In particular, WHISTLER will provide a well-balanced view on the prognostic power of neonatal lung function and genetic and environmental factors (including viral infections and endotoxin exposure) to predict wheezing illnesses from birth to young adulthood and beyond. In the scope of prevention, WHISTLER is expected to support the design of solid based prevention measures to reduce respiratory morbidity, mortality and associated costs, and to improve quality of life.

Dust↗

PubMed2001

An exploration of the relationships between uncertainty, psychological distress and type of coping strategy among Chinese men after cardiac catheterization.

The experience of cardiac catheterization (CC) has included feelings of uncertainty, stress, fear and anxiety in many patients. However, conflicting findings from previous research have been reported. Chinese patients who undergo CC may experience psychological distress in a different way to other cultures as a result of traditional beliefs. Moreover, little research examining the impact of CC among Hong Kong Chinese has been carried out. Therefore, the aim of the study was to explore relationships between uncertainty, psychological distress and coping strategy in Chinese men after CC, using Mishel's model of uncertainty in illness as a framework. A convenience sample of 27 men hospitalized for cardiac catheterization participated in this study using a descriptive, correlational research design. Ethical approval was obtained from the Ethics Committee of the Medical Faculty at the Chinese University of Hong Kong and from the Executive Committee of the hospital. Participation was on a voluntary basis with patient confidentiality assured. Self-report questionnaires included Chinese versions of Mishel's Uncertainty in Illness Scale (MUIS), the Profile of Mood States (POMS), the State-Trait Anxiety Inventory (STAI) and the Chinese Coping Scale (CCS) for data collection. Data were analysed using the Statistical Package for Social Sciences. High mean scores for uncertainty (mean=101.4, SD=11.49) and variables measuring psychological distress (mood disturbance mean=36.6, SD=33.6, state-anxiety mean=39.1, SD=8.95, trait-anxiety mean=43.7, SD=8.1) among these participants suggest that Hong Kong Chinese men experience uncertainty and psychological distress when undergoing cardiac catheterization. Strong relationships between uncertainty and mood disturbance (r=0.57, P=0.01), trait-anxiety and mood disturbance (r=0.65, P=0.01) and state-anxiety and external coping strategies (r=0.50, P=0.05) were found. These findings suggest that relationships between uncertainty, psychological distress and external coping strategies exist in Chinese men hospitalized for cardiac catheterization. Moreover, these findings may help nurses' design culturally specific interventions for their patients.

Adaptation, Psychological↗

PubMed1986

The Thompson-Patterson Scale of Psychosocial Development: I. Theoretical basis.

This paper presents a theoretical framework for describing childhood psychopathology in terms of coping styles and introduces a scale to measure psychosocial development in young children. It is hypothesized that coping styles characteristic of specific stages of development evolve in a predictable sequence with treatment. The term coping style rather than disorder is used to reflect the opinion that the child's behaviour constitutes an attempt to find a solution to difficulties encountered during the normal course of psychosocial development. These styles of relating are not static. The coping styles are presumed to arise from partial blocks to normal development during the period of early attachment and separation and individuation. A computer scored behaviour rating instrument, the Thompson-Patterson Scale, allows for the determination of the child's predominant coping style at a particular point in time. Clinical work and research has shown the utility of this paradigm and supports the hypothesis that changes in pathological behaviour patterns which emerge during treatment are predictable.

Adaptation, Psychological↗

PubMedDate not supplied

Nursing care delivery in Japanese psychiatric units.

Japan has the largest number of psychiatric beds per population in the world. At the same time, little research had been done to describe nursing care delivered in psychiatric units. To describe contents of nursing care, the framework for care classification and measuring methods must be examined. The purpose of this study was to develop a nursing intervention classification and examine the correlation between amount of care and patients' mental states. Data were collected from 39 patient care records from 4 randomly selected psychiatric hospitals. Patients' function and condition were evaluated by their doctors using the Global Assessment of Functioning (GAF) and the Brief Psychiatric Rating Scale (BPRS). Six care categories were extracted: basic activities of daily living, psychological support/interpersonal skills, medical support, monitoring, family support and miscellaneous. By examining three cases with this classification, there were significant correlations between the GAF and BPRS scores and amount of care for two acutely ill psychotic patients.

Activities of Daily Living↗

PubMed2007

Per-sextant localization and staging of prostate cancer: correlation of imaging findings with whole-mount step section histopathology.

OBJECTIVE: The objective of our study was to determine the diagnostic accuracy and interobserver agreement of 1.5-T prostatic MRI for per-sextant tumor localization and staging of prostate cancer as compared with whole-mount step section histopathology. MATERIALS AND METHODS: Combined endorectal-pelvic phased-array prostatic MRI scans obtained at 1.5 T of 106 patients with biopsy-proven prostate cancer who had undergone radical prostatectomy with whole-mount step section histopathology within 28 days of MRI were retrospectively analyzed by three independent abdominal radiologists (reviewers 1, 2, and 3). Sextants of the prostate (right and left base, middle, and apex) were evaluated for the presence of prostate cancer and extracapsular extension (ECE) using a 5-point confidence scale. Data were statistically analyzed using receiver operating characteristic (ROC) analysis. Interobserver variability was assessed by kappa statistics. For calculation of sensitivity and specificity, data from the 5-point confidence scale were dichotomized into negative (score of 1-3) or positive (score of 4 or 5) findings. RESULTS: Forty-one patients had ECE (tumor stage T3), and 65 patients had organ-confined disease (stage T2). Of 636 prostatic sextants, 417 were positive for prostate cancer and 135 were positive for ECE at histopathology. For prostate cancer localization, ROC analysis yielded area under the ROC curve (AUC) values ranging from 0.776 +/- 0.023 (SD) to 0.832 +/- 0.027. For the detection of ECE, the AUC values ranged from 0.740 +/- 0.054 to 0.812 +/- 0.045. Interobserver agreement (kappa) ranged from 0.49 to 0.60 for prostate cancer localization and from 0.59 to 0.67 for the detection of ECE. CONCLUSION: Using the sextant framework, independent observers reach similar accuracy with moderate to substantial agreement for the localization of prostate cancer and ECE by means of MRI of the prostate.

Anatomy, Cross-Sectional↗

PubMed1991

Copying strategies and memory on the Complex Figure Test in psychiatric patients.

We assessed three copying strategies on the Rey-Osterrieth Complex Figure Test among 50 psychiatric patients. The strategies were featural (detail-focused), contextual (framework-focused), and mixed. Reliable classification of each patient's copying strategy showed 7 patients used a featural and 7 patients used a contextual strategy. The remaining 36 used a mixed strategy involving both elements. Analysis indicated that patients who met DSM-III-R criteria for schizophrenia tended to use a mixed strategy. Nonschizophrenic patients also favoured the mixed approach. Moreover, when subjects were divided into groups based on their strategies, there were no differences in copying accuracy. However, the groups differed on immediate and delayed recall of the Complex Figure Test. Patients who adopted a featural strategy on the copy trial had the lowest recall scores. "Process" variables may be important in understanding neurocognitive functioning in schizophrenia; however, there is little evidence that schizophrenic patients use copying strategies consistent with lateralized impairment of brain function.

Adult↗

PubMed2026

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7.

UNLABELLED: The outermost surface layers of Gram-negative bacteria determine phage access to terminal receptors, yet their genetic basis has been mapped almost exclusively in laboratory strains that lack them. Here we apply genome-wide RB-TnSeq fitness profiling to four Escherichia coli O157:H7 strains from distinct phylogenetic clades sharing the O157 O-antigen, using 38 phages with terminal receptors previously mapped in E. coli K-12 strain. RB-TnSeq fitness landscapes across all four pathogenic backgrounds were mostly similar, and dominated by surface-associated loci, including the gfc-etk group 4 capsule operon, O-antigen biosynthesis genes, LPS core assembly genes and outer membrane proteins. Disruption of gfc-etk abolished infection in 11 genetically diverse myoviruses, establishing the O-antigen capsule as a widespread required primary recognition substrate. O-antigen loci generated two classes of fitness score patterns. For 10 phages, disruption increased infectivity, indicating it is a barrier to receptor access; for 3 others, disruption abolished infectivity, demonstrating it can also be a primary recognition substrate. Outer membrane protein receptor identity was conserved across laboratory and pathogenic backgrounds, with the same proteins recognized in both K-12 and O157:H7, while glycan layer state determines whether these receptors are reached. These results demonstrate that outer surface glycan layers can act as primary and optional recognition substrates for phage infection, or as physical barriers preventing terminal receptor access. Extending the ability to probe phage-targeted receptors beyond outer membrane proteins provides a framework for incorporating glycan layer state into predictive models of phage-host interactions. IMPORTANCE: Bacteriophage-based interventions for controlling Escherichia coli O157:H7, a major foodborne pathogen responsible for tens of thousands of illnesses annually in the United States, require a mechanistic understanding of the factors governing strain-level susceptibility. Predictive frameworks developed in laboratory model strains lacking O-antigen and capsular polysaccharides can map the terminal protein receptors that phages bind, but are currently limited in their ability to determine whether those receptors are accessible in pathogenic isolates carrying full outer surface complexity. This study provides the first genome-scale, functional genetic map of phage susceptibility determinants in O157:H7 and demonstrates that the state of the outer surface layers, specifically the O-antigen and the gfc-etk capsule, determines whether phages can reach conserved terminal receptors. This finding explains differences in phage susceptibility between strains sharing nearly identical gene content, and identifies the molecular layers that must be characterized to predict phage host interaction in pathogenic E. coli backgrounds.

Journal Article↗

PubMed1992

[Study on the relationship between toddler temperament and development (second report)--the relationship between toddler temperament and developmental delay].

The purpose of this study is to clarify the relationship between toddler temperament and developmental delay, and to examine whether the result could be adapted to the health practice of mother and child. As the conceptual framework, we used A. J. Sameroff's transactional model. Questionnaires concerning toddler temperament, rearing environment and toddler development were sent to mothers whose children were scheduled to receive 1 year and 6 months child health examinations, and collected 306 responses. We assessed the developmental status of 41 children among the 306 by means of the Japanese edition of the Denver Developmental Screening Test. All 306 children were classified into either the developmental delayed group (30) or the normal group (275). The data analyses were conducted both quantitatively and qualitatively with the following results. Compared with normal children, developmentally delayed children showed these characteristics: (1) The temperamental category scores of adaptability and persistence were higher, indicating low adaptability and persistence. The prevalence of difficult child, slow to warm up (STWU) child and intermediate high child was relatively higher, with STWU child the highest. (2) The score for the rearing environment was lower. (3) There were cases where disagreement between a child's temperament and the mother's rearing behavior had an influence on the child's development. As a conclusion, these results indicate that a child's temperament must be considered developmental and child-rearing counseling in child health examinations.

Child, Preschool↗

PubMed2005

Dyslexia in English as a second language.

This study focused on English as L2 in a group of Norwegian dyslexic 12 year olds, compared to an age and gender matched control group. Norwegian school children learn English from the first grades on. The subjects were assessed with a test battery of verbal and written tasks. First, they were given a comprehension task; second, a model sentence task; third, two pragmatic tasks, and fourth, three tasks of literacy. The verbal tasks were scored according to comprehension, morphology, syntax and semantics, while the literacy tasks were scored by spelling, translation and reading skills. It was hypothesized that the results of the control group and the dyslexia group would differ on all tasks, but that subgrouping the dyslexia group by comprehension skills would show heterogeneity within the dyslexia group. The data analyses confirmed these hypotheses. Significant differences were seen between the dyslexia group and the control group. However, the subgrouping revealed minor differences between the control group and the subgroup with good comprehension skills, and major differences between the control group and the subgroup with poor comprehension skills. Especially morphology and spelling were difficult for the dyslexia group. The results were tentatively discussed within the framework of biological and cognitive models of how to interpret L2 performance in dyslexia, underlining the importance of further research in L2 acquisition in dyslexia.

Child↗