Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Scoring framework”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed2025

acmgscaler: an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework.

MOTIVATION: A genome-wide variant effect calibration method was recently developed under the guidelines of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP), following ClinGen recommendations for variant classification. While genome-wide approaches offer clinical utility, emerging evidence highlights the need for gene- and context-specific calibration to improve accuracy. Building on previous work, we have developed an algorithm tailored to converting functional scores from both multiplexed assays of variant effects (MAVEs) and computational variant effect predictors (VEPs) into ACMG/AMP evidence strengths. RESULTS: Our method is designed to deliver consistent performance across different genes and score distributions, with all variables adaptively determined from the input data, preventing selective adjustments or overfitting that could inflate evidence strengths beyond empirical support. To facilitate adoption, we introduce acmgscaler, a lightweight R package and a plug-and-play Google Colab notebook for the calibration of custom datasets. This algorithmic framework bridges the gap between MAVEs/VEPs and clinically actionable variant classification. AVAILABILITY AND IMPLEMENTATION: The R package and Colab notebook are available at https://github.com/badonyi/acmgscaler.

Software↗
PubMedDate not supplied

OLAV-PMF: a novel scoring scheme for high-throughput peptide mass fingerprinting.

We propose a new type of probabilistic scoring scheme framework for protein identification from peptide masses. We first introduce the framework itself and explain its requirements. In a second part, we describe a particular implementation and test it on a data set of more than 8000 MALDI-TOF spectra with known contents. Doing so, we also compare its performance to two widely used scoring schemes, thereby demonstrating the potential of the proposed approach.

Algorithms↗
PubMed2005

QUASAR--scoring and ranking of sequence-structure alignments.

SUMMARY: Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Computational Biology↗
PubMed2005

Initial use of a novel instrument to measure professionalism in surgical residents.

BACKGROUND: No universally accepted method to measure professionalism exists. We developed an instrument to measure specific aspects of professionalism in surgical residents. METHODS: Professionalism was deconstructed into 15 domains. Behavioral descriptors were determined for extreme and selected intermediate anchors. It became evident that residents could "go too far" in some professional behaviors. Therefore, although a 7-point continuous ordinal scale forms the framework, a score of 7 does not necessarily indicate the ideal. This characteristic minimizes the problem of inflated ratings. RESULTS: The instrument was utilized by attending faculty to evaluate residents and also by residents as a self-evaluation. Calculated from ordinal values, mean (SD) of the ratings across domains for faculty evaluations of residents was 4.95 (0.38) while mean for self-evaluations was 4.95 (0.39). Reliability was high (coefficient alpha 0.85). CONCLUSIONS: This instrument provides a means to measure professional behaviors during surgical residency. Repeated use will be required to thoroughly establish validity and reliability.

Accreditation↗
PubMed1999

The item generation methodology of an empiric simulation project.

The American Board of Family Practice (ABFP) is developing a computer-based testing system that will create realistic clinical encounters using an adaptation of an item generation process. Simulated patients' entire lives will be stochastically produced from a knowledge base, with constraints applied to prevent implausible simulations. The constraint mechanisms include knowledge acquisition decisions about grouping closely related medical concepts and widespread use of Bayesian networks to manage dependencies between concepts. Bayesian networks and fuzzy definitions provide stochastic variability between simulations produced from the same data. Examinees will interact with these patients using a large and stable set of queries and interventions. Multiple management plans associated with patient simulations provide a framework for scoring performance. All major components, including Health States, history generating "Lead To" objects, and Plans are reusable and often substitutable. Although initial knowledge acquisition demands are enormous, the system has good potential for low cost maintenance of content areas, and economies of scale as simulations and components are reused.

Journal Article↗
PubMed2006

Framework for parsing, visualizing and scoring tissue microarray images.

Increasingly automated techniques for arraying, immunostaining, and imaging tissue sections led us to design software for convenient management, display, and scoring. Demand for molecular marker data derived in situ from tissue has driven histology informatics automation to the point where one can envision the computer, rather than the microscope, as the primary viewing platform for histopathological scoring and diagnoses. Tissue microarrays (TMAs), with hundreds or even thousands of patients' tissue sections on each slide, were the first step in this wave of automation. Via TMAs, increasingly rapid identification of the molecular patterns of cancer that define distinct clinical outcome groups among patients has become possible. TMAs have moved the bottleneck of acquiring molecular pattern information away from sampling and processing the tissues to the tasks of scoring and results analyses. The need to read large numbers of new slides, primarily for research purposes, is driving continuing advances in commercially available automated microscopy instruments that already do or soon will automatically image hundreds of slides per day. We reviewed strategies for acquiring, collating, and storing histological images with the goal of streamlining subsequent data analyses. As a result of this work, we report an implementation of software for automated preprocessing, organization, storage, and display of high resolution composite TMA images.

Cytodiagnosis↗
PubMed1995

A model for predicting HEAL repayment patterns and its implications for medical student financing.

BACKGROUND: The current level of Health Education Assistance Loan (HEAL) defaults has exceeded the original estimate, and as such is producing an unforeseen federal expenditure. Predicting repayment patterns of HEAL borrowers is an important step in assessing the impact that this unforeseen expenditure will have on HEAL and other financial aid programs. METHOD: Since prior research on educational lending has not identified a practical model for predicting repayment patterns, the authors turned in 1994 to an alternative discipline, research on consumer lending. Using the multivariate discriminant analysis credit scoring model framework, the authors incorporated operational definitions of the borrower's character, capacity, and capital. To identify factors that are significant in establishing repayment category membership, the framework was applied to a group of 233 HEAL borrowers who graduated from five medical schools in 1988. Because of the small numbers of delinquent borrowers and defaulters, the repayment categories were restricted to repayment, deferment, and forbearance. RESULTS: The level of unsubsidized debt, in conjunction with financial resources (including the potential resource of parental support), may be significant in identifying those HEAL borrowers who may confront repayment difficulty. CONCLUSION: While the results are not surprising, they do lend documented support for a review of financial aid policies at both institutional and governmental levels, and a framework within which this review may be conducted.

Education, Medical, Undergraduate↗
PubMedDate not supplied

[Assessing the accuracy of the practice of a method of scoring the body condition of ewes within a professional framework].

The accuracy of the body condition scoring for ewes using lumbar palpation was assessed by mean of an experiment conducted under conditions close to those occurring everyday on the farms. Thirteen operators evaluated the body condition score twice in a sample of 48 Lacaune breed dairy ewes, using a semi-quantitative grid (from 0 to 5 points, with a 0.25 point precision). Under the experimental conditions, the repeatability of the method, i.e. the comparison between the scores given by the same operator to the same animals for the two successive scoring notations, was good and even very good (Kappa test), if a 0.25 point precision is tolerated. On the other hand, the reproducibility, i.e. the comparison between the scores given to the same animals by differents operators was poor. Therefore, this method is easy to master for the management of a given flock by a single person. However in order to make comparisons between flocks, in reference to body condition standards set up for different farming systems, this method needs greater precision. Some of the application conditions required for this are discussed.

Animal Husbandry↗
PubMedDate not supplied

Genetic linkage studies.

Linkage analysis is used to map genetic loci by use of observations of related individuals. We provide an introduction to methods commonly used to map loci that predispose to disease. Linkage analysis methods can be applied to both major gene disorders (parametric linkage) and complex diseases (model-free or non-parametric linkage). Evidence for linkage is most commonly expressed as a logarithm of the odds score. We provide a framework for interpretation of these scores and discuss the role of simulation in assessment of statistical significance and estimation of power. Genetic and phenotypic heterogeneity can also affect the success of a study, and several methods exist to address such problems.

Chromosome Mapping↗
PubMed2026

Comparison of short-term clinical outcomes and patient satisfaction between intraoral scanning and conventional impressions for complete-arch implant prostheses: a pilot RCT.

OBJECTIVE: To compare framework passive fit, subjective evaluations, and short-term clinical outcomes between conventional impressions (CI) and intraoral scanning (IOS) for complete-arch implant-supported fixed dental prostheses (CIFDPs). METHODS: In this randomized controlled trial, 22 patients were allocated to the CI or IOS groups. All participants received a definitive one-piece CIFDP. The primary outcome was framework passive fit, assessed using the Vision and Tactile Score (V&T score), which included framework lift-off, the single-screw test, the full-screw test, smoothness of screw insertion, and radiographic gap assessment. Secondary outcomes included operator evaluation, patient satisfaction using a visual analog scale (VAS), early implant survival, marginal bone loss (MBL), modified Plaque Index (mPII), and complications at the 6-month follow-up. RESULTS: Twenty-two patients were enrolled (CI: n = 11; IOS: n = 11), and one patient in the CI group was lost to follow-up. No statistically significant difference in the V&T score was observed between the CI and IOS groups (4.66 &#xb1; 0.17 vs. 4.65 &#xb1; 0.28; P = 0.93). The operator reported greater nervousness during the CI procedure than during IOS (21.82 &#xb1; 15.69 vs. 8.64 &#xb1; 7.47; P < 0.05). Patients in the CI group reported significantly greater discomfort, including nausea and anxiety, than those in the IOS group (P < 0.05). At the 6-month follow-up, the early implant survival rate was 100% in both groups. No significant differences were found between the groups in MBL (0.09 &#xb1; 0.09 vs. 0.06 &#xb1; 0.10 mm; P = 0.43) or mPII (0.10 &#xb1; 0.12 vs. 0.10 &#xb1; 0.28; P = 0.99). CONCLUSION: IOS and CI achieved comparable short-term clinical outcomes in patients who met the predefined inclusion criteria, including controlled implant number, spacing, and angulation. IOS provided a more favorable experience for both operators and patients. CLINICAL SIGNIFICANCE: In complete-arch implant restorations, intraoral scanning may provide clinical outcomes comparable to those of conventional impressions while improving patient comfort.

Humans↗
PubMed2006

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MOTIVATION: Tandem mass spectrometry (MS/MS) identifies protein sequences using database search engines, at the core of which is a score that measures the similarity between peptide MS/MS spectra and a protein sequence database. The TANDEM application was developed as a freely available database search engine for the proteomics research community. To extend TANDEM as a platform for further research on developing improved database scoring methods, we modified the software to allow users to redefine the scoring function and replace the native TANDEM scoring function while leaving the remaining core application intact. Redefinition is performed at run time so multiple scoring functions are available to be selected and applied from a single search engine binary. We introduce the implementation of the pluggable scoring algorithm and also provide implementations of two TANDEM compatible scoring functions, one previously described scoring function compatible with PeptideProphet and one very simple scoring function that quantitative researchers may use to begin their development. This extension builds on the open-source TANDEM project and will facilitate research into and dissemination of novel algorithms for matching MS/MS spectra to peptide sequences. The pluggable scoring schema is also compatible with related search applications P3 and Hunter, which are part of the X! suite of database matching algorithms. The pluggable scores and the X! suite of applications are all written in C++. AVAILABILITY: Source code for the scoring functions is available from http://proteomics.fhcrc.org

Algorithms↗
PubMed2006

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

MOTIVATION AND RESULTS: The position weight matrix (PWM) is a popular method to model transcription factor binding sites. A fundamental problem in cis-regulatory analysis is to "count" the occurrences of a PWM in a DNA sequence. We propose a novel probabilistic score to solve this problem of counting PWM occurrences. The proposed score has two important properties: (1) It gives appropriate weights to both strong and weak occurrences of the PWM, without using thresholds. (2) For any given PWM, this score can be computed while allowing for occurrences of other, a priori known PWMs, in a statistically sound framework. Additionally, the score is efficiently differentiable with respect to the PWM parameters, which has important consequences for designing search algorithms. The second problem we address is to find, ab initio, PWMs that have high counts in one set of sequences, and low counts in another. We develop a novel algorithm to solve this "discriminative motif-finding problem", using the proposed score for counting a PWM in the sequences. The algorithm is a local search technique that exploits derivative information on an objective function to enhance speed and performance. It is extensively tested on synthetic data, and shown to perform better than other discriminative as well as non-discriminative PWM finding algorithms. It is then applied to cis-regulatory modules involved in development of the fruitfly embryo, to elicit known and novel motifs. We finally use the algorithm on genes predictive of social behavior in the honey bee, and find interesting motifs. AVAILABILITY: The program is available upon request from the author.

Algorithms↗
PubMed2005

A review of the Apgar score indicated that contextualization was required within the contemporary perinatal and neonatal care framework in different settings.

OBJECTIVE: To triangulate the Apgar score by using a crossdisciplinary approach and highlighting the differences that exist between actual everyday practice and accepted standards of scoring in contrasting populations of the world. STUDY DESIGN AND SETTING: Clinimetrics review of Apgar scoring. RESULTS: The Apgar scoring has weighting problems, rigid categorization, redundancy and subjectivity in its variables. Poor inter-rater reliability and equivocal validity mark its use in the present milieu. The ceiling and floor effects further hamper the evaluative responsiveness of scoring. Moreover, despite some recent evidence in its favor, the Apgar score has poor calibration when used as an isolated criterion to predict mortality and long-term morbidity, particularly in preterms. Also, the vigor of resuscitation (nature and duration), in essence, is beyond the realm of the Apgar score in contemporary resuscitation guidelines. In developed nations, with rapidly decreasing age of viability, and alternative modes of childbearing, threats to Apgar are more ominous today than before. On the other hand, in developing countries, feasibility problems due to unattended home deliveries and barriers to effective scoring in the overburdened and understaffed hospitals cast doubts about its accuracy as a measure of neonatal well-being. CONCLUSION: Use of the Apgar score definitely needs to be contextualized within the contemporary perinatal and neonatal care framework in different settings.

Apgar Score↗
PubMed2026

iMTSS: an integrated framework for biology- and patient-driven prognosis in myelofibrosis undergoing transplantation.

BACKGROUND: Allogeneic hematopoietic cell transplantation is the only curative treatment for myelofibrosis, but failure occurs by two mechanistically distinct routes: relapse of the neoplasm, which reflects its underlying genetics, and non-relapse mortality, which reflects whether the patient and graft tolerate the procedure. Established prognostic systems either lack molecular granularity or were derived in the non-transplant setting, and all collapse these two routes into a single survival estimate. None can indicate why an individual patient is at risk, or which class of intervention might reduce that risk. OBJECTIVE: To determine why an individual patient is at risk and to develop and validate an integrated framework that quantifies biology- and patient-driven prognosis. STUDY DESIGN: We analyzed 1,550 adults undergoing first allogeneic transplantation for primary or secondary myelofibrosis across international centers, the largest genomically annotated transplant cohort in this disease. The cohort was split into development (n=930) and validation (n=620) sets. Overall survival was modeled by Cox regression; relapse and non-relapse mortality were modeled as competing events by Fine-Gray subdistribution-hazard regression at 2 years. Discrimination was assessed by the concordance index with bootstrap confidence intervals. The molecular contribution was quantified by variance decomposition of, and robustness to the analytic choices was examined by resampling. RESULTS: A genetically defined disease-intrinsic axis, including TP53 allelic state, RAS pathway mutations, ASXL1 and driver genotype, blasts and blood counts, predicted 2 year relapse incidence (validation concordance 0.69, 95% CI 0.63 to 0.74), whereas a non-overlapping host and structural axis, including portal vein thrombosis, donor type, patients' performance status, and age predicted 2-year non-relapse mortality (0.63, 95% CI 0.59 to 0.68). The two scores shared only 3.4% of their variance, indicating that a patient's disease genetics carried almost no information about non-relapse mortality. Variance decomposition showed that TP53 allelic state alone accounted for 30% of the relapse score. Recombined, the framework discriminated overall survival (concordance 0.640, 95% CI 0.616 to 0.662) better than every established prognostic system. For proof of concept, 3 risk groups separated in the validation cohort, with 5 year survival of 72%, 58%, and 39% (P<0.001), and the models were well calibrated. CONCLUSIONS: Relapse and non-relapse mortality after transplantation for myelofibrosis are governed by distinct dimensions. Estimating both outcomes independently with genetic and clinical information, in addition to overall survival, establishes an individualized basis for transplant decision-making. The calculator is openly available (https://imtss-calculator.com).

mortality↗
PubMed2001

Epidermal growth factor receptor immunohistochemical reactivity in patients with American Joint Committee on Cancer Stage IV colon adenocarcinoma: implications for a standardized scoring system.

BACKGROUND: An epidermal growth factor receptor (EGFR) immunohistochemical detection system currently is being developed. The current study attempts to address background EGFR reactivity issues before determining the optimum EGFR scoring system. METHODS: Tissue sections from 102 patients with T3N1-2M1 colon adenocarcinoma were stained with a prototype EGFR detection system. The number of cases, location, percentage, and intensity of reactive cells (0+ [none] to 3+ [strong]) were scored and compared with the length of survival. RESULTS: Approximately 75.5% of the adenocarcinoma cases had EGFR reactivity; 31.4% of the tumors had 3+ reactivity in 10-50% of the neoplastic cells and 3.9% had 3+ reactivity in > 50% of cells. Increased numbers of reactive cells per case predominantly resulted from increased 3+ reactivity. The mean percentage of 2+ (moderate) and 3+ reactive cells per case increased in the regions of deepest invasion. The mean percentage of 3+ reactivity per case was significantly greater in the deepest tumor region compared with the superficial region (16.9% vs. 7.9%; P = 0.004). EGFR reactivity in metastases appeared to have the strongest correlation with reactivity in the deep regions of colon adenocarcinoma. An increasing percentage of 2+ and 3+ or 3+ only reactivity in the deep region was found to have the strongest correlation with decreased survival (P = 0.0252). CONCLUSIONS: EGFR reactivity of 2+ and 3+ may provide a framework for a scoring system. It may be important to evaluate EGFR reactivity in the deepest region of tumor invasion because this region appears to contain the largest percentage of 3+ reactive cells and appears to have the strongest correlation with survival length and EGFR reactivity in lymph node and liver metastases.

Adenocarcinoma↗
PubMed2006

Referral to cancer genetic counseling: are there stages of readiness?

As genetic awareness spreads among healthcare providers and the general public, and evidence mounts to show the efficacy of cancer control methods, referrals to cancer genetic counseling services for risk assessment are becoming more common. However, few studies have examined referral patterns to genetics and even less is known about referral uptake to clinical cancer genetic counseling. We investigated outcome of genetics referral in 43 affected women attending a breast cancer treatment program who were referred based on having BRCA mutation carrier risks > or =10%. Within 6 months, of the 36 women we were able to recontact, 13 (36%) came to an appointment at the cancer genetic counseling clinic (Acceptors), 10 (27%) said they intended to come in the future (Intenders), and 13 (36%) said they would not consider genetic counseling (Decliners). Referral uptake was framed by elements of the Transtheoretical model (TTM) to determine if decisional balance scores (DBSs), a summary of an individual's "Pro" and "Con" opinions related to genetic testing, correlated with their decision to follow through. Mean DBS's were strongly negative for the Decliner group (-7.4), weakly negative for the Intender group (-1.1), and positive for the Acceptor group (5.4). The difference in the DBS along the continuum was due more to the mean "Con" score decreasing, rather than the mean "Pro" score increasing. Theoretical frameworks are needed to study adherence to referral for cancer genetic counseling. Stage-based theories may have a role to play.

Adult↗
PubMed1996

Stress, coping, HIV status, psychosocial resources, and depressive mood in African American gay, bisexual, and heterosexual men.

The associations between stress, physical health, psychosocial resources, coping, and depressive mood were examined in a community sample of African American gay, bisexual, and heterosexual men (N = 139). Data were collected from physical exams and in-person interviews. In our theoretical framework, depressive mood scores were regressed first on stressors, next on psychosocial resources, and finally on coping strategy variables. Results revealed that psychosocial resources mediate the effects of stressors, including health symptoms, hassles, and life events, on depressive mood. There were no significant differences in depressive mood associated with HIV status or sexual orientation. Results are discussed in terms of community interventions needed to provide social support as a buffer between stress and psychological distress in African American men.

Adaptation, Psychological↗
PubMed2006

The relationship of perfectionism, depression, and therapeutic alliance during treatment for depression: latent difference score analysis.

The authors examined the longitudinal relationship of patient-rated perfectionism, clinician-rated depression, and observer-rated therapeutic alliance using the latent difference score (LDS) analytic framework. Outpatients involved in the Treatment for Depression Collaborative Research Program completed measures of perfectionism and depression at 5 occasions throughout treatment, with therapeutic alliance measured early in therapy. First, LDS analyses of perfectionism and depression established longitudinal change models. Further LDS analyses revealed significant longitudinal interrelationships, in which perfectionism predicted the subsequent rate of depression change, consistent with a personality vulnerability model of depression. In the final LDS model, the strength of the therapeutic alliance significantly predicted longitudinal perfectionism change, and perfectionism significantly predicted the rate of depression change throughout therapy. These results clarify the patterns of growth and change for these indicators throughout depression treatment, demonstrating an alternative method for evaluating longitudinal dynamics in therapy.

Adult↗