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The biotic ligand model: a historical overview.

During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. This is an important consideration because it is the bioavailability and bioreactivity of metals that control their potential to cause adverse effects. The BLM approach has gained widespread interest amongst the scientific, regulated and regulatory communities because of its potential for use in developing water quality criteria (WQC) and in performing aquatic risk assessments for metals. Specifically, the BLM does this in a way that considers the important influences of site-specific water quality. This journal issue includes papers that describe recent advances with regard to the development of the BLM approach. Here, the current status of the BLM development effort is described in the context of the longer-term history of advances in the understanding of metal interactions in the environment upon which the BLM is based. Early developments in the aquatic chemistry of metals, the physiology of aquatic organisms and aquatic toxicology are reviewed first, and the degree to which each of these disciplines influenced the development of water quality regulations is discussed. The early scientific advances that took place in each of these fields were not well coordinated, making it difficult for regulatory authorities to take full advantage of the potential utility of what had been learned. However, this has now changed, with the BLM serving as a useful interface amongst these scientific disciplines, and within the regulatory arena as well. The more recent events that have led to the present situation are reviewed, and consideration is given to some of the future needs and developments related to the BLM that are envisioned. The research results that are described in the papers found in this journal issue represent a distinct milestone in the ongoing evolution of the BLM approach and, more generally, of approaches to performing ecological assessments for metals in aquatic systems. These papers also establish a benchmark to which future scientific and regulatory developments can be compared. Finally, they demonstrate the importance and usefulness of the concept of bioavailability and of evaluative tools such as the BLM.

Animals↗

Validation of a Monte Carlo dose calculation tool for radiotherapy treatment planning.

A new EGS4/PRESTA Monte Carlo user code, MCDOSE, has been developed as a routine dose calculation tool for radiotherapy treatment planning. It is suitable for both conventional and intensity modulated radiation therapy. Two important features of MCDOSE are the inclusion of beam modifiers in the patient simulation and the implementation of several variance reduction techniques. Before this tool can be used reliably for clinical dose calculation, it must be properly validated. The validation for beam modifiers has been performed by comparing the dose distributions calculated by MCDOSE and the well-benchmarked EGS4 user codes BEAM and DOSXYZ. Various beam modifiers were simulated. Good agreement in the dose distributions was observed. The differences in electron cutout factors between the results of MCDOSE and measurements were within 2%. The accuracy of MCDOSE with various variance reduction techniques was tested by comparing the dose distributions in different inhomogeneous phantoms with those calculated by DOSXYZ without variance reduction. The agreement was within 1.0%. Our results demonstrate that MCDOSE is accurate and efficient for routine dose calculation in radiotherapy treatment planning, with or without beam modifiers.

Bone and Bones↗

KCFtools: rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

MOTIVATION: In the era of multiple genome references, researchers often align sequencing reads against distinct assemblies or even multiple references simultaneously. This enables applications such as the detection of introgressed segments or highly variable genomic regions, which are especially prevalent in large-genome crop species such as lettuce or wheat. However, these applications come at the cost of increased computational burden, inconsistencies in mapping methods, and reduced reproducibility across studies. To address these limitations, we developed KCFtools, a Java-based toolkit that identifies the presence and absence of k-mers in nonoverlapping genomic or transcriptomic windows by comparing query and reference genomes. This alignment-free approach enables the efficient computation of an identity score for each window, thereby facilitating robust detection of introgressed or variable regions across genomes. RESULTS: We systematically evaluated the performance and accuracy of the k-mer-based method implemented in KCFtools, benchmarking it against conventional single nucleotide variation-based introgression detection pipelines. Our results demonstrate that KCFtools effectively captures introgressed segments and structurally diverse regions, even in species with fragmented or highly divergent reference genomes. In addition, we extended KCFtools to generate genotype matrices from k-mer variation tables. These matrices are compatible with genome-wide association studies software and allow the identification of loci associated with phenotypic traits. We showcase the utility of this approach by detecting known and novel associations for downy mildew resistance in lettuce, underscoring the pipeline's potential for high-resolution, reference-agnostic population genetic analysis. AVAILABILITY AND IMPLEMENTATION: https://github.com/sivasubramanics/kcftools.

Software↗

Hospice quality improvement programs: an initial examination.

Recognizing that little is known about use of quality improvement (QI) processes to enhance care of the dying, 11 large hospices exchanged information about their QI programs. These hospices reported monitoring from 3 to 50 outcomes measured by various indicators and methods. Agencies that related QI to their organization's mission, goals, and strategic plan were more likely to have dedicated QI staff; a more intense, comprehensive, and participatory QI program; and more QI projects resulting in performance enhancement. Both accomplishments and difficulties were identified in several areas, including establishing benchmarks, involving staff, and using computer technology to manage and analyze QI data.

Attitude of Health Personnel↗

Characteristics of best gastroenterology practices.

OBJECTIVE: As health care costs continue to rise, competition among providers is increasing. Although this competition is currently based on price, quality of care will become an increasingly important issue. One popular method to assess quality is by comparing physicians' performance with that of a representative group of physicians, in a process called benchmarking. The purpose of this study was to survey private practice gastroenterologists to identify the practice characteristics, so-called "best practices," associated with high-quality health care delivery to provide data for use as benchmarks. METHODS: Three hundred randomly selected gastroenterology practices were surveyed regarding practice demographics, administration, financial management, and use of outcomes techniques by mail questionnaire. Analogous questionnaires were completed by representatives of the gastroenterology practices comprising the Gastroenterology Practice Management Group, LLC (GMPG). RESULTS: One hundred and eighty-two (61%) of the 300 eligible practices responded to the questionnaire. Increasing differences between survey and benchmark GPMG practices were observed as the complexity of quality measures increased. Among structure measures, the groups were similar. By contrast, significant differences were observed between survey and benchmark groups with regards to outcomes measures such as the use of practice guidelines, continuous quality improvement, and outcomes assessment. CONCLUSIONS: These results provide a snapshot of gastroenterology practices across the country and can be used as a benchmark for quality assessment purposes to compare with one's practice, suggesting areas for change or improvement. It seems clear that the defining characteristic of best gastroenterology practices is the demonstration of quality patient care. It also appears that many practices' efforts in this regard could be increased.

Gastroenterology↗

Establishment of paediatric biochemical reference intervals.

BACKGROUND: The standard method for the determination of reference values in a population by testing a number of healthy volunteers is difficult within the paediatric age group; this study explores an alternative approach. METHODS: Biochemical blood test results collected by the Woman's and Children's Hospital over a 1 year period were used and the data selected to ensure, as far as possible, that the results were from patients who were "healthy". This was achieved using various selection criteria, such as the exclusion of patients with more than one test episode. Some of the data were skewed, making standard statistical approaches difficult. In such cases, transformations were used to ensure that the resulting information had a distribution that was approximately Gaussian. RESULTS: Data from different biochemical tests covering both genders and ages in the range 0-18 years were collected; this included more than 250 000 laboratory test results. After elimination of non-representative data and tests with insufficient results, there were approximately 23 500 results covering almost 3000 individuals and 16 different biochemical tests. There were no results from very young children (< 1 year) after the data selection process; hence the derivation of reference values from that age group was not possible. CONCLUSIONS: This approach permitted better delineation of reference intervals for common biochemical tests performed on paediatric patients than is currently readily available. In addition, some important benchmarks for transformation of medical data have been found.

Adolescent↗

The Veterans Health Administration: quality, value, accountability, and information as transforming strategies for patient-centered care.

The Veterans Health Administration is the United States' largest integrated health system. Once disparaged as a bureaucracy providing mediocre care, the Department of Veterans Affairs (VA) reinvented itself during the past decade through a policy shift mandating structural and organizational change, rationalization of resource allocation, explicit measurement and accountability for quality and value, and development of an information infrastructure supporting the needs of patients, clinicians, and administrators. Today, the VA is recognized for leadership in clinical informatics and performance improvement, cares for more patients with proportionally fewer resources, and sets national benchmarks in patient satisfaction and for 18 indicators of quality in disease prevention and treatment.

Cooperative Behavior↗

Techniques for managing quality.

The science of quality management is an eclectic collection of concepts and methods primarily borrowed from other fields. Techniques roughly fall into three categories involving quality improvement, planning, and measurement. Improvement techniques include models to guide team-based efforts, tools for process description, and tools for data analysis. These methods are the most visible artifacts of CQI efforts in health care organizations today. Less widely known, but equally powerful, are the techniques of quality planning. There are models to guide both process design and strategic planning, methods for identifying customer needs, and tools to support these efforts. Finally, while measurement is a traditionally well-developed area in health care, industrial quality management science broadens our outlook about what is important to measure. It also provides the technique of benchmarking, which suggests that we look beyond our own organization when we measure performance.

Data Display↗

Hospice quality improvement programs: an initial examination.

Recognizing that little is known about use of quality improvement (QI) processes to enhance care of the dying, 11 large hospices exchanged information about their QI programs. These hospices reported monitoring from 3 to 50 outcomes measured by various indicators and methods. Agencies that related QI to their organization's mission, goals, and strategic plan were more likely to have dedicated QI staff; a more intense, comprehensive, and participatory QI program; and more QI projects resulting in performance enhancement. Both accomplishments and difficulties were identified in several areas, including establishing benchmarks, involving staff, and using computer technology to manage and analyze QI data.

Benchmarking↗

Financial modeling: Rx for financial success.

In an era of managed care, cost cutting and finding ways to increase revenue are key goals in the survival of group practices. Many practices find that they have to boost their revenue by a certain amount (for example, 20-30% within the next three years) to maintain viability in the health care marketplace. Understanding how to generate that revenue and influence short-term and long-term financial outcomes is a far trickier process. This article details how practice administrators can influence a practice's bottom line through a three-step process: (1) identify the components of the practice's financial performance and drivers of performance results, (2) diagnose the practice's current financial situation, and (3) pinpoint benchmarks and targets for success.

Economic Competition↗

The Veterans Health Administration: quality, value, accountability, and information as transforming strategies for patient-centered care.

The Veterans Health Administration is the United States' largest integrated health system. Once disparaged as a bureaucracy providing mediocre care, the Department of Veterans Affairs (VA) reinvented itself during the past decade through a policy shift mandating structural and organizational change, rationalization of resource allocation, explicit measurement and accountability for quality and value, and development of an information infrastructure supporting the needs of patients, clinicians, and administrators. Today, the VA is recognized for leadership in clinical informatics and performance improvement, cares for more patients with proportionally fewer resources, and sets national benchmarks in patient satisfaction and for 18 indicators of quality in disease prevention and treatment.

Delivery of Health Care, Integrated↗

[Quality assurance measures in surgical gynecology. Program development and routine introduction in Hessia].

Frequently, quality assurance measures fail during application in routine practice despite showing very promising results in the developmental stage. Using the project 'Quality assurance in gynecological surgery' as an example which has made the leap into routine practice, we describe the development of a successful quality assurance measure. We name some of the elements which have proved to be crucial for the assumption of a new quality assurance measure. First of all, decisive was the development of the measure by renowned experts of the scientific medical society together with methodologists. All current professional and legal demands on medical quality assurance were included as were methodological knowledge for the optimal formation of such a measure. The evaluation of the measure on approximately 50,000 gynecological surgical procedures showed that the new quality assurance measure is suitable in gynecological surgery as an instrument both for making transparent the quality of health care delivery as well as for supporting comprehensive internal and external assessments of performance, outcomes, and processes of care and comparisons with the "best" care provider ("benchmarking"). Secondly, a favorable point in time--here the introduction of a diagnosis related payment system--and the early and close cooperation on the part of the program developers with political decision-makers helped to ensure that the newly developed quality assurance measure in gynecological surgery was accepted for routine practice.

Benchmarking↗

The performance impact of context in TQM implementation: the nursing facility industry.

This study develops a model and empirically assesses how# organizational context mediates the impact of total quality management (TQM) implementation on perceived performance in the nursing facility industry. Outcomes are analysed for financial, human resources and resident-care performance. Contextual factors related to TQM implementation include managerial control, reward systems, organizational structure and the extent of implementation. Duration of TQM implementation is included as a control variable. Benchmarking has a positive impact on financial outcomes, and the extent of TQM implementation and required reporting of quality improvement activity results have a positive impact on both financial and human resources performance. The presence of a Quality Steering Council has a positive impact on financial performance, but only among larger facilities.

Benchmarking↗

Improving fold recognition of protein threading by experimental distance constraints.

We present a comprehensive analysis of methods for improving the fold recognition rate of the threading approach to protein structure prediction by the utilization of few additional distance constraints. The distance constraints between protein residues may be obtained by experiments such as mass spectrometry or NMR spectroscopy. We applied a post-filtering step with new scoring functions incorporating measures of constraint satisfaction to ranking lists of 123D threading alignments. The detailed analysis of the results on a small representative benchmark set show that the fold recognition rate can be improved significantly by up to 30% from about 54%-65% to 77%-84%, approaching the maximal attainable performance of 90% estimated by structural superposition alignments. This gain in performance adds about 10% to the recognition rate already achieved in our previous study with cross-link constraints only. Additional recent results on a larger benchmark set involving a confidence function for threading predictions also indicate notable improvements by our combined approach, which should be particularly valuable for rapid structure determination and validation of protein models.

Nuclear Magnetic Resonance, Biomolecular↗