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Towards benchmark second-order correlation energies for large atoms: Zn2+ revisited.

To provide very accurate reference results for the second-order Møller-Plesset (MP2) energy and its various components for Zn(2+), which plays for 3d-electron systems a similar role as Ne for smaller atoms and molecules, we have performed extensive calculation by two completely different implementations of the MP2 method: the finite element method (FEM) and the variation-perturbation (VP) method. The FEM and VP calculations yield partial wave contributions up to l(max)=45 and 12, respectively. Detailed comparison of all FEM and VP energy components for l(max)=12 has disclosed an extraordinary similarity, which justifies using the present results as benchmarks. The present correlation energies are compared with other works. The dependability of an earlier version of FEM, already applied to very large closed-shell atoms, is confirmed. It has been found that for larger atoms the accuracy of the analytical Hartree-Fock results has an impact on the accuracy of the MP2 energies greater than for smaller atoms. Fields of applications of the present results in studies of various electron correlation effects in 3d-electron atoms and molecules are indicated.

Journal Article↗

Business Ethics 101 for the biotech industry.

Biotechnology companies face ethical challenges of two distinct types: bioethical challenges faced on account of the nature of work in the life sciences, and corporate ethical challenges on account of their nature as commercial entities. The latter set of challenges has received almost no attention at all in the academic literature or media. This paper begins to remedy that lacuna, examining ethical issues that arise specifically on account of the status of biotech companies as commercial entities. The focus here is on three representative issues: product safety, corporate social responsibility, and corporate governance. It is argued that each of these issues poses particular ethical challenges for companies in the biotech sector. In the area of product safety, it is noted that biotech companies face particular challenges in determining what counts as a "safe" product, given the contentious nature of what might count as a "harm" in the biotech field. In the area of corporate social responsibility, the adoption of a "stakeholder approach" and an attempt to manage the social consequences of products pose special challenges for biotech companies. This is due to the enormous range of groups and individuals claiming to have a stake in the doings of such companies, and the trenchant controversies over just what the social consequences of various biotechnologies might be. In the area of corporate governance, biotech companies need to seek out and follow best practices regarding the ways in which information, authority, and influence flow between a company's shareholders, managers, and Board of Directors, if they are to avoid duplicating the ethical and financial scandal that brought down ImClone. An important meta-issue, here--one that renders each of these corporate ethical challenges more vexing--is the difficulty of finding the appropriate benchmarks for ethical corporate behavior in a field as controversial, and as rapidly evolving, as biotechnology. Three programmatic suggestions can be made: Firstly, scholars and others interested in the ethical performance of the biotech sector must seek out and build opportunities for richer interdisciplinary collaboration. Secondly, companies within the biotech sector must seek out expertise and build capacity and competency in dealing with the corporate ethical issues that arise in their sector. Finally, companies in the biotech sector should explore the opportunities for collective problem solving afforded by the existence of local, national, and international industry associations such as the Biotechnology Industry Organization, BIOTECanada, and EuropaBio.

Benchmarking↗

Despite cost and risk, ORYX PLUS offers benchmarking bonanza.

The Joint Commission's ORYX-PLUS option offers standardized measurement, risk adjustment, and reporting of outcomes not available in the less comprehensive ORYX program. This should create a wealth of truly comparable data against which to benchmark. There are additional costs: $2,500 to the Joint Commission, plus more expensive software and maintenance. This means the program is probably best suited for those systems that already have significant investments in information systems. As ORYX-PLUS eventually will issue performance report cards to the public on participants, there are the risks associated with disclosure. On the other hand, participating hospitals will be able to boast participation in a voluntary disclosure program aimed at excellence.

Accreditation↗

Lesion segmentation and manual warping to a reference brain: intra- and interobserver reliability.

The study of subjects with acquired brain damage has been an invaluable tool for exploring human brain function, and the description of lesion locations within and across subjects is an important component of this method. Such descriptions usually involve the separation of lesioned from nonlesioned tissue (lesion segmentation) and the description of the lesion location in terms of a standard anatomical reference space (lesion warping). The objectives of this study were to determine the sources and magnitude of variability involved in lesion segmentation and warping using the MAP-3 approach. Each of two observers segmented the lesion volume in ten brain-damaged subjects twice, so as to permit pairwise comparisons of both intra- and interobserver agreement. The segmented volumes were then warped to a reference brain using both a manual (MAP-3) and an automated (AIR-3) technique. Observer agreement between segmented and warped volumes was analyzed using four measures: volume size, distance between the volume surfaces, percentage of nonoverlapping voxels, and percentage of highly discrepant voxels. The techniques for segmentation and warping produced high agreement within and between observers. For example, in most instances, the warped volume surfaces created by different observers were separated by less than 3 mm. The performance of the automated warping technique compared favorably to the manual technique in most subjects, although important exceptions were found. Overall, these results establish benchmark parameters for expert and automated lesion transfer, and indicate that a high degree of confidence can be placed in the detailed anatomical interpretation of focal brain damage based upon the MAP-3 technique.

Brain Damage, Chronic↗

Lower limb amputations during 3 years in Hungary.

We reviewed nationwide hospital data of amputations during 3 years to provide a comparison with similar data gathered about 20 years ago. Data were provided by the National Medical Records Centre and processed by our personally developed programmes. The cause of amputation was most often vascular disease, amputees were usually elderly, and the large majority of amputation surgery was carried out on the lower limb. The rate of transtibial amputation has increased favourably in the last 2 decades, but there are large regional differences within the country. Mortality parameters remarkably exceed those of foreign countries. Although the data accuracy is compromised, there are still ways of exploiting the data in favour of quality improvement of care, e.g. improve transtibial amputation rate, reduce mortality. The publication of data can be of benchmarking importance for hospitals by enabling them to compare their own results with those of other hospitals, as well as to develop and improve performance.

Adult↗

Synthetic sling options for stress urinary incontinence.

In the past decade, sling surgery has become the preferred technique for the management of female stress urinary incontinence. A greater understanding of the pathogenesis of stress urinary incontinence and a greater durability and effectiveness for sling surgery has allowed this technique to become the benchmark for treatment of female stress urinary incontinence. As a consequence, a multitude of products have been developed using various techniques and materials to perform sling surgery. This article reviews the materials and techniques available and the complications associated with each. Most importantly, the outcomes are discussed so that the readers can best understand the impact of these surgeries on our patients.

Biocompatible Materials↗

Evaluating outcomes of hospital care following coronary artery bypass surgery in Rome, Italy.

OBJECTIVE: Monitoring health outcomes across hospitals has become a growing interest as a potential means to promote quality of care, but in Italy it is at the beginning stage. We aimed at comparing the performance of different cardiac surgery units and testing the utility of routinely collected data in this respect. METHODS: From the Lazio region hospital information system (HIS), we selected a cohort of 1603 individuals (84% males; mean age 63 years, SD 8) residing in Rome (2,685,890 inhabitants), who underwent isolated coronary artery bypass surgery (CABG, ICD-9-CM code: 36.1) in the period 1996-97 in seven major cardiac surgery units in the city. They were identified as A, B, C (teaching), D and E (non-teaching) units. Information on vital status at 30 days after the CABG surgery was obtained through an automatic record linkage with the Municipal Registry of Rome. The association between cardiac surgery units and outcome was evaluated through logistic regression taking into account the following a priori risk factors in different models: gender, age, socio-economic status, type of ischaemic heart disease and comorbidities. RESULTS: The overall mortality was 5.4% (range 2.1-11.4%). Statistically significant predictors of outcome included: age (OR=7.5 for age> or =70 vs. 35-49 years), acute myocardial infarction (OR=32.7 vs. acute-subacute forms/angina), chronic myocardial ischaemia (OR=4.2 vs. acute-subacute forms/angina), other heart diseases (OR=4.8), chronic renal disease (OR=16.0) and peripheral arterial disease (OR=2.9). Statistically significant variability in mortality was observed across hospitals; taking hospital A as reference, hospital D showed the highest risk (OR=5.7, 95% CI=1.9-17.3, in the fully adjusted model). CONCLUSIONS: We suggest that a true variation in quality of care play a role in the observed differences across hospitals, although chance and inaccurately measured risk factors cannot be excluded. Despite some limitations, the HIS is a valid tool for screening cardiac surgery units with poor performance.

Adult↗

Pd-mBDPP-catalyzed regioselective internal arylation of electron-rich olefins by aryl halides.

meso-2,4-Bis(diphenylphosphino)pentane (mBDPP) has proved to be an effective regiocontrolling ligand for palladium-catalyzed internal arylation by aryl bromides of electron-rich olefins in a common solvent DMSO with no need for any halide scavengers. The arylation of the benchmark electron-rich olefin butyl vinyl ether took place smoothly to afford exclusively alpha-arylated product with high isolated yields. The better performance of mBDPP, compared with that of the commonly used DPPP [1,3-bis(diphenylphosphino)propane], highlights the important but subtle effect of ligand on the regioselectivity of the Heck arylation reactions.

Alkenes↗

De novo assembly of transcriptomes of six Hua species (Semisulcospiridae, Cerithioidea, Gastropoda).

Species in Semisulcospiridae are important in freshwater ecology and have great research value, yet their genomic resources remain very limited. Here, we present de novo assembled transcriptomes from six species of Hua in Semisulcospiridae, including Hua textrix (Heude, 1888), H. yangi L.-N. Du, J.-X. Yang & Chen, 2023, H. wujiangensis L.-N. Du, J.-X. Yang & Chen, 2023, and three undescribed species. Assembly was performed using Trinity, resulting in average contig lengths ranging from 716.6 to 883.3 bp and transcript numbers ranging from 147,147 to 268,741. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis was used to assess the transcriptome completeness. The functional annotation of transcripts for each species had over 18,000 BLAST hits, 17,000 GO terms, 15,000 KEGG pathways, 8,000 Pfam accessions, and 140 COG functional categories. This study provides valuable transcriptomic resources for the six Hua species, which can be used for various research of Semisulcospiridae, including biodiversity, phylogeny, and comparative genomics.

Transcriptome↗

High-order correlation effects on dynamic hyperpolarizabilities and their geometric derivatives: a comparison with density functional results.

Second harmonic generation hyperpolarizabilities and their geometric derivatives have been calculated for HF, HCl, CO, and LiF, using the coupled cluster hierarchies, CCS, CC2, CCSD, CC3, and large correlation-consistent basis sets. The full configuration interaction results have been used to test the accuracy of the coupled cluster results. The CCS and CC2 methods do not improve on the Hartree-Fock results while CCSD is robust and gives significant improvements compared to CCS and CC2. The effects of triples in CC3 are in some cases substantial. Higher order correlation effects are significant for LiF. Including core-valence correlation effects is required only if high accuracy is desired. The coupled cluster results have been used as benchmarks for the results obtained by means of density functional theory using various exchange-correlation functionals. For the hyperpolarizability B3LYP was found to perform best, i.e., to give the results closest to the CC3 ones, while for the geometric derivatives none of the considered functionals was able to give a consistent description for all the considered molecules.

Journal Article↗

PROSPECT II: protein structure prediction program for genome-scale applications.

A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key features. (i) We have developed an efficient way to utilize the evolutionary information for evaluating the threading potentials including singleton and pairwise energies. (ii) We have developed a two-stage threading strategy: (a) threading using dynamic programming without considering the pairwise energy and (b) fold recognition considering all the energy terms, including the pairwise energy calculated from the dynamic programming threading alignments. (iii) We have developed a combined z-score scheme for fold recognition, which takes into consideration the z-scores of each energy term. (iv) Based on the z-scores, we have developed a confidence index, which measures the reliability of a prediction and a possible structure-function relationship based on a statistical analysis of a large data set consisting of threadings of 600 query proteins against the entire FSSP templates. Tests on several benchmark sets indicate that the evolutionary information and other new features of PROSPECT II greatly improve the alignment accuracy. We also demonstrate that the performance of PROSPECT II on fold recognition is significantly better than any other method available at all levels of similarity. Improvement in the sensitivity of the fold recognition, especially at the superfamily and fold levels, makes PROSPECT II a reliable and fully automated protein structure and function prediction program for genome-scale applications.

Algorithms↗

National Committee on Quality Assurance health-plan accreditation: predictors, correlates of performance, and market impact.

CONTEXT: Accreditation of health care organizations has traditionally been considered a building block of quality assurance. However, the differences between accredited and nonaccredited health plans and the impact of accreditation on plan enrollment are not well understood. OBJECTIVES: To determine the characteristics of plans that have submitted to accreditation review, the performance of accredited plans on quality indicators and the impact of accreditation on enrollment. DESIGN: The databases containing 1996 data on health plans' National Committee on Quality Assurance (NCQA) accreditation status, organizational characteristics, Health Plan Employer Data and Information Set (HEDIS) scores, and patient-reported quality and satisfaction scores were linked to compare accredited health plans to nonaccredited plans. We also combined longitudinal data sets (1993-1998) on accreditation and health plan enrollment. MAIN OUTCOME MEASURES: Mean performance of accredited and nonaccredited plans on HEDIS measures and patient-reported measures of quality; health plan enrollment changes. RESULTS: Accredited plans have higher HEDIS scores but similar or lower performance on patient-reported measures of health plan quality and satisfaction. Furthermore, a substantial number of the plans in the bottom decile of quality performance were accredited suggesting that accreditation does not ensure high quality care. Receipt of accreditation has been associated with increased enrollment in the early years of the accreditation program; however, plans denied NCQA accreditation do not appear to suffer enrollment losses. CONCLUSION: NCQA accreditation is positively associated with some measures of quality but does not assure a minimal level of performance. Efforts now underway to incorporate plan performance on HEDIS into criteria for accreditation seem warranted.

Accreditation↗

How robust are hospital ranks based on composite performance measures?

BACKGROUND: Composite indices of healthcare performance are an aggregation of underlying individual performance measures. They are increasingly being used to rank healthcare organizations. Although composite indicators present the "big picture" in a way that is easy to interpret, misleading conclusions may be drawn if attention is not paid to key methodological issues in their construction. OBJECTIVES: We examine variability in performance measures in the context of the construction and use of composite measures. We illustrate how variability in the underlying data and the resulting composite may undermine the robustness of performance measures in health care. We also illustrate how variation in the methodological rules applied to aggregate the individual indicators can have an important impact on composite scores. METHODS: We use data for 117 English acute hospitals to illustrate the generic methodological issues. The variance in performance measures is partitioned into "controllable" and "uncontrollable" elements. We create a composite index from the underlying performance indicators and use Monte Carlo simulations to examine the robustness of the composite. RESULTS: Random variation beyond the control of organizations gives rise to considerable uncertainty in hospital scores. Composites are also sensitive to changes made to the weighting system and to the aggregation rules. Some hospitals can jump almost half of the league table as a result of subtle changes. CONCLUSIONS: Great care is warranted in interpreting the results of composite performance measures. Suggestions for their future development are made.

Benchmarking↗

A new X-ray spectrometer with large focusing crystal analyzer.

A new focusing spectrometer employing Johann geometry has been built and permanently installed at the wiggler beamline W1 at the Hamburger Synchrotron Strahlungslabor (HASYLAB) am Deutschen Elektronen Synchrotron (DESY). It is now available for user operation. The design of the spectrometer is optimized for the use of a large source spot size at the DORIS storage ring as well as for simple operation and robustness under user-mode conditions. Nevertheless, the ideal source for enlarging the number of possible applications in the future would be an undulator at one of the PETRA III beamlines. In the following the spectrometer design is described and boundary conditions such as the available energy range for future experiments are discussed. Two benchmark experiments, resonant inelastic X-ray scattering (RIXS) and X-ray absorption fluorescence spectroscopy (XAFS), on samples with complicated matrices demonstrate the performance of the new instrument.

Calibration↗

Improved gait recognition by gait dynamics normalization.

Potential sources for gait biometrics can be seen to derive from two aspects: gait shape and gait dynamics. We show that improved gait recognition can be achieved after normalization of dynamics and focusing on the shape information. We normalize for gait dynamics using a generic walking model, as captured by a population Hidden Markov Model (pHMM) defined for a set of individuals. The states of this pHMM represent gait stances over one gait cycle and the observations are the silhouettes of the corresponding gait stances. For each sequence, we first use Viterbi decoding of the gait dynamics to arrive at one dynamics-normalized, averaged, gait cycle of fixed length. The distance between two sequences is the distance between the two corresponding dynamics-normalized gait cycles, which we quantify by the sum of the distances between the corresponding gait stances. Distances between two silhouettes from the same generic gait stance are computed in the linear discriminant analysis space so as to maximize the discrimination between persons, while minimizing the variations of the same subject under different conditions. The distance computation is constructed so that it is invariant to dilations and erosions of the silhouettes. This helps us handle variations in silhouette shape that can occur with changing imaging conditions. We present results on three different, publicly available, data sets. First, we consider the HumanlD Gait Challenge data set, which is the largest gait benchmarking data set that is available (122 subjects), exercising five different factors, i.e., viewpoint, shoe, surface, carrying condition, and time. We significantly improve the performance across the hard experiments involving surface change and briefcase carrying conditions. Second, we also show improved performance on the UMD gait data set that exercises time variations for 55 subjects. Third, on the CMU Mobo data set, we show results for matching across different walking speeds. It is worth noting that there was no separate training for the UMD and CMU data sets.

Algorithms↗

Developing an assessment tool for evaluating community involvement.

BACKGROUND: Current UK policy has resulted in greater requirements for public and patient participation in health service planning and decision making. Organizations and services need to be able to monitor and evaluate the effectiveness and quality of their community involvement processes, but there are few appropriate evaluation tools or sets of indicators available. This paper reports on work within Bradford Health Action Zone to develop a self-assessment tool for organizations on community involvement. METHODS: A multi-agency working group developed the tool. A literature search was undertaken and evaluation resources were reviewed. A set of benchmarks for community involvement in regeneration was utilized in developing the assessment areas. A range of individuals with expertise on community involvement practice and performance management was consulted. The tool was then piloted in two primary care trusts prior to final modifications. RESULTS: The process resulted in the production of Well Connected--a self-assessment tool on community involvement designed for organizations to assess their progress and identify areas for improvement. A scoring system assesses evidence of a strategic approach to community involvement, good practice throughout the organization, and a range of opportunities and support. Feedback from the pilots revealed that the tool had facilitated assessment of the strengths and weaknesses of organizational practices. CONCLUSION: The paper discusses some of the methodological challenges pertaining to the measurement of community involvement. Notwithstanding those challenges, it is argued that Well Connected provides a robust and practical framework that health organizations and their partners can use to assess practice.

Community Participation↗

Homology induction: the use of machine learning to improve sequence similarity searches.

BACKGROUND: The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS: We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to bootstrap from standard sequence similarity search methods. First a standard method is run, then HI learns rules which are true for sequences of high similarity to the target (assumed homologues) and not true for general sequences, these rules are then used to discriminate sequences in the twilight zone. To learn the rules HI describes the sequences in a novel way based on a bioinformatic knowledge base, and the machine learning method of inductive logic programming. To evaluate HI we used the PDB40D benchmark which lists sequences of known homology but low sequence similarity. We compared the HI methodology with PSI-BLAST alone and found HI performed significantly better. In addition, Receiver Operating Characteristic (ROC) curve analysis showed that these improvements were robust for all reasonable error costs. The predictive homology rules learnt by HI by can be interpreted biologically to provide insight into conserved features of homologous protein families. CONCLUSIONS: HI is a new technique for the detection of remote protein homology--a central bioinformatic problem. HI with PSI-BLAST is shown to outperform PSI-BLAST for all error costs. It is expect that similar improvements would be obtained using HI with any sequence similarity method.

Algorithms↗