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PubMedDate not supplied

Finding anchors for genomic sequence comparison.

Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole genomes generally use a seed-and-extend technique, starting from exact or near-exact matches and selecting a reliable subset of these, called anchors, and then filling in the remaining portions between the anchors using a combination of local and global alignment algorithms, but their choices for the parameters so far have been primarily heuristic. We present a statistical framework and practical methods for selecting a set of matches that is both sensitive and specific and can constitute a reliable set of anchors for a one-to-one mapping of two genomes from which a whole-genome alignment can be built. Starting from exact matches, we introduce a novel per-base repeat annotation, the Z-score, from which noise and repeat filtering conditions are explored. Dynamic programming-based chaining algorithms are also evaluated as context-based filters. We apply the methods described here to the comparison of two progressive assemblies of the human genome, NCBI build 28 and build 34 (www.genome.ucsc.edu), and show that a significant portion of the two genomes can be found in selected exact matches, with very limited amount of sequence duplication.

Algorithms↗
PubMed2026

Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.

MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty. RESULTS: We present Perseus, a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches. AVAILABILITY AND IMPLEMENTATION: Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus.

Journal Article↗
PubMed1999

Health-related quality of life in dialysis patients. A report from an Italian study using the SF-36 Health Survey. DIA-QOL Group.

BACKGROUND: Interest in measuring health-related quality of life (HRQoL) has increased together with an awareness that such humanistic outcomes require valid and reliable measures. In the last decade short, simple and multidimensional generic and disease-specific questionnaires have been developed. Among the several generic questionnaires available, the Short Form 36 Items Health Survey (SF-36) was translated and validated in several languages, and applied to different settings and diseases. METHODS: Within the framework of a larger, prospective, multicentre study (DIA-QOL project) the SF-36 was administered to 304 patients to test its characteristics in terms of patient acceptability, and psychometric and clinical validity. Standard psychometric techniques were used to evaluate its validity in terms of convergence, divergence and internal consistency reliability (Cronbach's alpha). Correlations between clinical variables and HRQoL scores were performed to test the questionnaire's capability to capture differences across patients groups. RESULTS: Overall, the findings show that, in this sample, the SF-36's performance was very good. Acceptability was satisfactory, with a response rate higher than 80%. All the questionnaire scales met the psychometric standards suggested in terms of grouping and scaling assumptions. The internal reliability coefficients actually replicate the satisfactory findings reported previously for the original SF-36. In terms of the ability of the questionnaire scales to discriminate between groups expected to differ in a given health concept in relation to clinical variables, the results were also good. On average, females reported lower scores, the impact of ageing was more evident for physical scales. Diabetic patients score significantly worse on the physical function scale and patients with mental health problems score significantly lower on the mental health scale. No significant association was found with the index KtV, haemoglobin levels, body mass index, parathyroid hormone and type of dialysis. A strong association was indeed found between SF-36 scales measuring physical health concepts and the serum albumin level. This association held after adjusting for the confounding effect of age. Comparison of the health profile of the present sample with others from the US and UK and from a representative sample of the Italian general population highlights the potential of such questionnaire in dialysis setting. CONCLUSIONS: The SF-36 questionnaire is easy to use in Italian dialysis patients and SF-36 scores are related to important clinical aspects. This approach can help in caring for dialysis patients and can be useful in outcome assessment programmes.

Adult↗
PubMed2006

Development of the combined assessment of residential environments (CARE) profiles.

AIM: This paper reports the development and initial testing of the combined assessment of residential environments (CARE) profiles, which identify the frequency of positive events over a specified time based on the perceptions of residents, relatives and staff in care home settings. BACKGROUND: Despite the well-known benefits of positive events for subjective well-being, little is known about the nature of positive events experienced by residents, relatives and staff in care homes. There is also a dearth of tools capable of systematically evaluating how frequently these events occur in this context. METHODS: The CARE profiles were developed and tested between February 2004 and June 2005 with a combined sample of 372 residents, relatives and staff drawn from 11 care homes. An Event Frequency Approach was adopted to create three questionnaires (residents, relatives and staff), each containing 30 consensually valid positive events. The thematic content of these events was balanced for each questionnaire using the Senses Framework as a theoretical model. Once completed, the CARE profiles were tested in four care homes. RESULTS: Test data from the CARE profiles were used to produce a bar chart showing median frequencies of positive events experienced by residents, relatives and staff during the timeframe in question (e.g. 1 month). These profiles were shown to be internally consistent, with alpha scores ranging from 0.70 to 0.89 for residents, 0.91 to 0.94 for relatives and 0.78 to 0.92 for staff. CONCLUSION: We envisage that feedback from the CARE profiles will both reinforce good care home practice and identify areas for change based on the experiences of all major stakeholders. However, further development of the profiles is needed if the experiences of cognitively impaired residents are to be included in the assessment process.

Adaptation, Psychological↗
PubMed1998

Relationship between interpersonal psychotherapy problem areas with temperament and character: a pilot study.

OBJECTIVE: To examine the relationships between dimensions of personality assessed by using the Temperament and Character Inventory and presenting problem areas in Interpersonal Psychotherapy. METHOD: One hundred two depressed patients completed the Temperament and Character Inventory (TCI), and Interpersonal Psychotherapy (IPT) problem areas were assessed using a clinician-rated questionnaire. RESULTS: Following multiple regression analysis, patients rated as having problems with grief scored low on self transcendence, those with disputes had low cooperativeness, those with role transitions had low novelty seeking, and those with deficits had low reward dependence. CONCLUSIONS: Both temperament and character may be relevant to the nature of presenting problems related to Interpersonal Psychotherapy. An understanding of how personality is relevant to presenting interpersonal problems may provide both a framework and a focus with which to work in this form of psychotherapy.

Adult↗
PubMed2000

Linkage of mood disorders with D2, D3 and TH genes: a multicenter study.

BACKGROUND: It has been suggested that the dopaminergic system is involved in the pathophysiology of mood disorders. We conducted a multicenter study of families with mood disorders, to investigate a possible linkage with genes coding for dopamine receptor D2, dopamine receptor D3 and tyrosine hydroxylase (TH). METHODS: Twenty three mood disorder pedigrees collected within the framework of the European Collaborative Project on Affective Disorders were analyzed with parametric and non-parametric linkage methods. Various potential phenotypes were considered, from a narrow (only bipolar as affected) to a broad (bipolar+major depressive+schizoaffective disorders) definition of affection status. RESULTS: Parametric analyses excluded linkage for all the candidate genes, even though small positive LOD (Limit of Detection) scores were observed for TH in three families. Non-parametric analyses yielded negative results for all markers. CONCLUSION: The D2 and D3 dopamine receptors were, therefore, not a major liability factor for mood disorders in our sample, whereas TH may play a role in a subgroup of patients.

Bipolar Disorder↗
PubMed2001

Development and evaluation of a moral distress scale.

AIM OF THE STUDY: This methodological research developed and evaluated the moral distress scale from 1994 to 1997. BACKGROUND/RATIONALE: Although nurses confront moral questions in their practice daily, few instruments are available to measure moral concepts. The methodological design used a convenience sample consisted of 214 nurses from several Unites States hospitals. The framework guiding the development of the moral distress scale (MDS) included Jameton's conceptualization of moral distress, House and Rizzo's role conflict theory, and Rokeach's value theory. Items for the MDS were developed from research on the moral problems that nurses confront in hospital practice. The MDS consists of 32 items in a 7-point Likert format; a higher score reflects a higher level of normal distress. RESULTS: Mean scores on each item ranged from 3.9 to 5.5, indicating moderately high levels of moral distress. The item with the highest mean score (M=5.47) was working where the number of staff is so low that care is inadequate. Factor analysis yielded three factors: individual responsibility, not in the patient's best interest, and deception. No demographic or professional variables were related to moral distress. Fifteen percent of the nurses had resigned a position in the past because of moral distress. CONCLUSION: The results support the reliability and validity of the MDS.

Adult↗
PubMed1999

Quality of life of cardiac arrhythmia patients after radiofrequency catheter ablation.

UNLABELLED: Radiofrequency catheter ablation (RFCA) has been used to treat cardiac arrhythmias in Thailand since 1992. The effect of this procedure on quality of life has not been systematically studied. The purpose of this study was to assess the impact of RFCA on quality of life in patients with cardiac arrhythmias. Data were collected by interviewing 30 patients from February 1998 to August 1998, before and two months after RFCA. The questionnaire used for this study was created by researchers using Zhan's conceptual framework and SF36 in 4 dimensions--life satisfaction, self-concept and psycho-social well being, health functioning and physical well being, socio-economic and social well being. The questionnaire was validated by experts. Its reliability was tested by using Cronbach's test that gave an alpha coefficient of 0.81. Our study showed that the overall quality of life scores 2 months after RFCA (mean = 179.467, SD = 17.005) were higher than before RFCA (mean = 131.567, SD = 18.680). The results also showed a statistically significant difference (p = 0.000). CONCLUSION: It was found that RFCA significantly improved the quality of life of patients with various cardiac arrhythmias. However, this study consisted of a small sample size. Further work in this area with a large sample size is needed to confirm this finding.

Adolescent↗
PubMed2003

Women's decision-making needs regarding place of care at end of life.

Little is known about the decision-making needs of terminally ill women who are considering options for place of care at the end of life. A pilot study was conducted with a sample of 20 terminally ill women with advanced cancer to identify factors taken into consideration in making this decision. Participants were interviewed using a semistructured questionnaire incorporating the domains of quality of end-of-life care and based on the Ottawa Decision Support Framework. Results suggested a gap between the preferred (home, n = 13) and the actual (palliative care unit, n = 16) place of care. Discrepancies about place of care may be related to conflicting subjective factors such as being a burden to family versus having the opportunity to strengthen relationships with family and friends. Participants who were actively engaged in making the decision scored the highest levels of decisional conflict. Previous studies have shown an association between high decisional conflict scores and decision delay. Although findings from this small study are preliminary, they suggest that the decision regarding place of terminal care is complex with multiple competing factors being considered.

Adult↗
PubMed1993

[Sleep apnea screening in a pulmonary-internal medicine rural practice in Mecklenburg-Vorpommern].

In a screening study of a total of 230 patients covered on the occasion of an x-ray mass screening (Group A: 157 patients) or within the framework of a pulmonology-cardiology-orientated medical consulting-room practice (Group B: 73 patients), 178 patients said "snoring" was their major symptom, whereas 35 patients considered "apnoea" to be the main complaint. Looking at both groups more closely and with greater differentiation we find in Group B a high incidence of the characteristic symptoms "snoring" and "apnoea" and a score of more than +2, compared with Group A, concomitant with a high coincidence of a positive finding in the MESAM study (Group A: ration 55.5:1, Group B: ratio 4.3:1). 18 patients were found to be suffering from sleep apnoea syndrome. Due to limited facilities we have so far been able to adjust only two of these patients to CPAP/BiPAP in the sleep laboratory of the Hospital for Pulmonological Diseases in Schwerin. We conclude that it seems problematic to conduct mass screening on a broad basis of the population (another argument being the cost/benefit ratio), whereas it appears to be more effective to conduct an on-target search for sleep apnoea syndrome (SAS) in high-risk groups. A prerequisite for appropriate coverage and treatment of sleep apnoea patients is to provide patients with on-target and wide-scope information on the disease pattern; furthermore, both doctors and the population must be provided with examination facilities also on an outpatient basis.

Adult↗
PubMed2025

Sparse polygenic risk score inference with the spike-and-slab LASSO.

MOTIVATION: Large-scale biobanks, with rich phenotypic and genomic data across hundreds of thousands of samples, provide ample opportunities to elucidate the genetics of complex traits and diseases. Consequently, there is growing demand for robust and scalable methods for disease risk prediction from genotype data. Inference in this setting is challenging due to the high-dimensionality of genomic data, especially when coupled with smaller sample sizes. Popular Polygenic Risk Score (PRS) inference methods address this challenge by adopting sparse Bayesian priors or penalized regression techniques, such as the Least Absolute Shrinkage and Selection Operator (LASSO). However, the former class of methods are not as scalable and do not produce exact sparsity, while the latter tends to over-shrink large coefficients. RESULTS: In this study, we present SSLPRS, a novel PRS method based on the Spike-and-Slab LASSO (SSL) prior, which offers a theoretical bridge between the two frameworks. We extend previous work to derive a coordinate-ascent inference algorithm that operates on GWAS summary statistics, which is orders-of-magnitude more efficient than corresponding individual-level-based implementations. To illustrate the statistical properties of the proposed model, we conducted experiments involving nine simulation configurations and nine quantitative phenotypes from the UK Biobank. Our results demonstrate that SSLPRS is competitive with state-of-the-art methods in terms of prediction accuracy and exhibits superior variable selection performance, especially in sparse genetic architectures. In simulations, this translates to upwards of 50% improvement in positive predictive value. In analysis of real phenotypes, we show that selected variants are highly enriched for meaningful genomic annotations and have better replication rates in larger meta-analyses. AVAILABILITY AND IMPLEMENTATION: SSLPRS is available in the open-source package https://github.com/li-lab-mcgill/penprs.

Multifactorial Inheritance↗
PubMedDate not supplied

The role of religious and spiritual beliefs in coping with malignant melanoma.

This study investigated the role of spiritual and religious beliefs in ambulatory patients coping with malignant melanoma. One-hundred and seventeen patients with melanoma being seen in an outpatient clinic completed a battery of measurements including the newly validated Systems of Belief Inventory (SBI-54). No correlation was found between SBI-54 scores and levels of distress. However, there was a correlation between greater reliance on spiritual and religious beliefs and use of an active-cognitive coping style (r = 0.46, p < 0.0001). Data suggest that use of religious and spiritual beliefs is associated with an active rather than passive form of coping. We suggest that such beliefs provide a helpful active-cognitive framework for many individuals from which to face the existential crises of life-threatening illness.

Adaptation, Psychological↗
PubMed2003

Priority setting in surgery: improve the process and share the learning.

Surgeons and surgical programs encounter priority-setting challenges every day, such as in regard to purchasing new technologies or managing waiting lists for elective surgery. The purpose of this paper was to explore priority setting in surgery. Traditionally in surgery, priority-setting decisions for new technologies have been based on evidence of effectiveness and cost-effectiveness; and decisions about managing waiting lists for elective surgery have been based on urgency rating scores. The fairness of priority-setting processes in surgical programs should be enhanced to permit all relevant information and values to be considered. The quality of these decisions can be improved by using an approach that captures and shares lessons from each priority-setting experience. The approach we propose in this paper- describe, evaluate, and improve using a leading conceptual framework for priority setting, called "accountability for reasonableness"-can be used by any surgical program to improve its priority setting, share lessons with others, and develop an evidence base for how these important health policy decisions should be made.

Biomedical Technology↗
PubMed1999

The Conners-28 teacher questionnaire in clinical and nonclinical samples of Greek children 6-12 years old.

It is accepted practice in child psychiatry to use more than one source of information in assessing behavioural problems in children and adolescents. Employing standardized tools for these assessments allows cross-cultural comparisons and better interchange of the findings. Achenbach's Child Behavior Checklist (CBCL) and Teacher's Report Form (TRF) are two widely accepted instruments that were standardized in Greece within the framework of the European Network for the Study of Hyperkinetic Disorder. We studied the Conners-28 teacher questionnaire in a Greek community sample of primary schoolchildren aged 6-12 years. The factor structure showed to be similar to that originally reported from the USA. Discrimination between the referred and nonreferred sample was high, especially for the Inattentive-passive scale. Conners-28 scores were highly correlated with the TRF (scored by the same informant), much less so with the CBCL (scored by a different informant). Our study demonstrates the usefulness and applicability of the Conners-28 item questionnaire.

Adolescent↗
PubMedDate not supplied

Coping with the stress of premature labor.

UNLABELLED: Premature birth, the leading cause of perinatal morbidity and mortality in the United States affects between 8% and 12% of all live births. Approximately 80% of premature births are proceeded by premature labor. Significant progress has been made in the physical treatment of premature labor; however, the psychological cost to women being treated needs further study. My purpose in conducting this study was to assess the stress experienced by women treated at home for premature labor and to examine methods used by the women to cope. The theoretical framework was provided by Lazarus's model of Stress, Coping, and Emotion. A total of 50 women participated. Twenty responded to a questionnaire that included the Perceived Stress Scale (PSS) and the Ways of Coping Questionnaire only, 10 were interviewed only, and 20 completed the questionnaire and the interview. RESULTS: The women reported experiencing a moderate amount of stress. Their mean stress score was 26.75, just below the mean for the instrument (M = 28) and slightly less than the stress score of 27.52 reported by women experiencing a "normal" pregnancy. Appraisal was assessed by analyzing the data from the interviews. The women appraised their situation as both threatening and challenging. They described their emotional response most frequently as frustration because of fear concerning the pregnancy outcome, loss of control over their life, and inability to perform their usual roles of mother, wife, and worker. The women reported on the Ways of Coping Questionnaire that they used strategies from three subscales to cope with the premature labor. Those subscales were Seeking Social Support, Planful Problem-Solving, and Positive Reappraisal.

Adaptation, Psychological↗
PubMed1991

Origin of aneuploidy in relation to disturbances of cell-cycle progression. II: Cytogenetic analysis of various parameters in mouse bone marrow cells after colchicine or hydroquinone treatment.

The relationship between in vivo aneuploidy and cell-cycle perturbation induced by potential aneugens was investigated in mouse bone marrow cells. This work was performed within the framework of a research programme coordinated by the European Community to study the ability of 10 selected chemicals to induce aneuploidy in different systems. In this context, the effects of colchicine (COL) and hydroquinone (HQ) on cell-cycle progression, aneuploidy, polyploidy, micronucleus and sister chromatid exchange induction in mouse bone marrow cells after bromodeoxyuridine incorporation are reported. Hyperploidy and polyploidy were scored in metaphases of cells that had undergone only one division after treatment. Both chemicals induced cell-cycle lengthening, hyperploidy and micronuclei. The kinetics of hyperploidy induction by the two compounds differed in that COL was positive at 24 h, whereas HQ was positive 18 h after treatment. Only colchicine was positive for polyploidy induction and neither chemical induced sister chromatid exchange. These results are compared with similar data obtained after vinblastine (VBL) treatment. The results suggest that VBL and COL induce chromosome malsegregation via a mechanism associated with perturbations in the cell-cycle, whereas HQ induces aneuploidy independently of cell-cycle lengthening, possibly altering a chromosomal component of chromosome segregation rather than a spindle component.

Aneuploidy↗
PubMed2003

A non-parametric model for transcription factor binding sites.

We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly interpolates between the empirical distribution of binding sites and the standard position-specific scoring matrix (PSSM). In a test of generalization to unseen binding sites using 10-fold cross-validation on known binding sites for 95 TRANSFAC transcription factors, this representation outperforms PSSMs on between 65 and 89 of the 95 transcription factors, depending on the choice of the two adjustable parameters. We also discuss how the non- parametric representation may be incorporated into frameworks for finding binding sites given only a collection of unaligned promoter regions.

Base Sequence↗
PubMed2002

Health-promoting self-care in family caregivers.

Caregiving for family members with cognitive impairment is stressful and time consuming. Because of the attention needed to manage the memory and behavior problems of the care receiver, family caregivers have little time to attend to their own health needs. Most research related to the health of family caregivers has been conducted within a stress-illness framework. Fewer researchers have studied caregiver health from a health-promotion paradigm. The purpose of this study was to compare health-promoting self-care behavior infamily caregivers with demographically matched noncaregivers and to investigate the mediational effect of health-promoting self-care behavior on the relationship between stress and well-being. Findings revealed that family caregivers scored significantly lower on all measures of health promotion, with the exception of Nutrition and Number of Medications, and significantly higher on Barriers to Health-Promoting Actions. Health-promoting self-care behavior acted as a mediator to reduce the effect of caregiver stress on general well-being.

Caregivers↗