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PubMed2005

A simple method for faster nonbonded force evaluations.

Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent "dielectric constant" in implicit solvent models. Benchmarks are provided for the all-atom, implicit solvent dynamics of Met-enkephalin, the villin headpiece, the B1 domain of protein-G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look-up tables for other implicit solvent models such as the generalized Born models.

Algorithms↗
PubMed2026

DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.

Determining the structures of unknown metabolites remains a fundamental bottleneck in plant metabolomics, as the vast chemical diversity of plant secondary metabolites far exceeds the coverage of existing spectral libraries. Here, we present DeepMASS v.2, a substantially enhanced platform for annotating unknown metabolites from liquid chromatography-tandem mass spectrometry data, designed to address this challenge at scale. DeepMASS v.2 leverages a semantic spectral representation model trained on millions of spectra from GNPS, NIST, and in-house resources. By integrating Spec2Vec-based embeddings with HNSW (hierarchical navigable small world) graph retrieval and a unified chemical space defined by molecular fingerprints, DeepMASS v.2 identifies structurally related neighbors of unknown spectra and ranks candidate structures according to their proximity to the predicted structural neighborhoods within chemical space. Benchmarking against Critical Assessment of Small Molecule Identification datasets and a curated natural product collection demonstrated that DeepMASS v.2 outperforms state-of-the-art in silico annotation tools, including SIRIUS, CFM-ID, MetFrag, and MS-Finder. Importantly, DeepMASS v.2 maintains strong performance for metabolites absent from spectral libraries, highlighting its capacity to annotate genuinely unknown compounds. Application of DeepMASS v.2 to large-scale plant metabolomics datasets demonstrated its ability to expand accessible metabolome coverage. Implemented as an intuitive web platform, DeepMASS v.2 provides the community with a scalable, interpretable, and high-throughput solution for structural annotation, enabling more comprehensive characterization of plant chemical diversity and accelerating natural product discovery in molecular plant science. The DeepMASS v.2 web server is publicly available at http://deepmass.cn.

Metabolomics↗
PubMed2002

Confidence measures for protein fold recognition.

MOTIVATION: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one. For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures. RESULTS: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures. For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods. In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores. The methods for assessing the statistical significance of predictions are compared using specificity--sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best. By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable. AVAILABILITY: The benchmark set is available upon request.

Amino Acid Sequence↗
PubMed2026

CircExor enables interpretable prediction of circRNA localization into extracellular vesicles.

Certain circular RNAs (circRNAs) are selectively enriched in extracellular vesicles (EVs), in which they contribute to intercellular communication and represent promising biomarkers, yet the sequence determinants of their sorting remain unclear. Existing computational predictors are optimized mainly for linear RNAs and rarely address circRNA localization into EVs. Here we introduce circExor, the first framework specifically designed for circRNA EV localization. We curate a dedicated benchmark data set of 2102 circRNAs and implement a variable-length end-to-end concatenation strategy together with k-mer frequency encoding to accommodate circular topology, long sequence length, and length heterogeneity. Using a tree-based classifier, circExor achieves superior performance compared with RNAlocate-v3 and ExoGRU, reaching an AUROC of 0.743 on the internal test set and an average AUROC of 0.680 on the held-out test set. SHAP-based analysis, sequence perturbation analysis, motif mapping, and cell-based experimental validation support the predicted EV tendency and identify YBX1, HNRNPK, HNRNPL, and NOVA2 as candidate RBPs potentially associated with circRNA sorting. CircExor therefore provides a predictive and interpretable framework that links in silico modeling to mechanistic hypotheses, and supports biomarker discovery and candidate prioritization for downstream studies of EV-associated circRNAs.

Journal Article↗
PubMed1999

Performance of an algorithm to detect Pneumocystis carinii pneumonia in symptomatic HIV-infected persons. Pulmonary Complications of HIV Infection Study Group.

STUDY OBJECTIVES: To determine whether an algorithm consisting of a chest radiograph and the diffusing capacity of the lung for carbon monoxide (D(LCO)) is effective in detecting Pneumocystis carinii pneumonia (PCP) in symptomatic HIV-infected persons; and to establish a benchmark for future comparisons of alternative algorithms. DESIGN: Prospective, 64-month study. SETTING: Multicenter, ambulatory care. PATIENTS: 306 HIV-infected subjects enrolled in the Pulmonary Complications of HIV Infection Study who developed 467 episodes of new or worsening respiratory symptoms. MEASUREMENTS: Chest radiography followed by D(LCO) measurement, if the radiograph was normal or unchanged. RESULTS: An algorithm combining a chest radiograph followed by a D(LCO) measurement, if the radiograph was normal or unchanged, was effective and detected abnormalities that led to a diagnosis of PCP in 78 of 80 evaluable episodes (97.5%). The radiograph (specific parenchymal abnormality, number of lung zones involved) and the D(LCO) (degree of decrease, degree of decrease from baseline) also provided additional information on the probability of PCP. CONCLUSIONS: In symptomatic HIV-infected patients suspected of having PCP, the diagnostic evaluation should begin with a chest radiograph, followed by a D(LCO) measurement, if the radiograph is normal or unchanged. If both of these tests are normal, it may be reasonable to conclude the evaluation rather than to proceed on to additional testing. This algorithm can serve as a benchmark for future comparisons.

AIDS-Related Opportunistic Infections↗
PubMed2005

Developing first-level leaders.

Oil and energy corporation BP was well aware of the importance of its work group managers on the front lines. Their decisions, in aggregate, make an enormous difference in BP's turnover, costs, quality control, safety, innovation, and environmental performance. There were about 10,000 such supervisors, working in every part of the company-from solar plants in Spain, to drilling platforms in the North Sea, to marketing teams in Chicago. Some 70% to 80% of BP employees reported directly to these lower-level managers. Yet, until recently, the corporation didn't have a comprehensive training program--let alone an official name--for them. For their part, the frontline managers felt disconnected; it was often hard for them to understand how their individual decisions contributed to the growth and reputation of BP as a whole. In this article, BP executive Andreas Priestland and Dialogos VP Robert Hanig describe how BP in the past five years has learned to connect with this population of managers. After one and a half years of design and development, there is now a companywide name--"first-level leaders"--and a comprehensive training program for this cohort. The authors describe the collaborative effort they led to create the program's four components: Supervisory Essentials, Context and Connections, the Leadership Event, and Peer Partnerships. The design team surveyed those it had deemed first-level leaders and others throughout BP; extensively benchmarked other companies' training efforts for lower-level managers; and conducted a series of pilot programs that involved dozens of advisers. The training sessions were first offered early in 2002, and since then, more than 8000 of BP's first-level leaders have attended. The managers who've been through training are consistently ranked higher in performance than those who haven't, both by their bosses and by the employees who report to them, the authors say.

Commerce↗
PubMed1998

The Quality of Surgical Care Project: benchmark standards of open resection for abdominal aortic aneurysm in Western Australia.

BACKGROUND: The Quality of Surgical Care Project (QSCP) was established in May 1996, to evaluate surgical outcomes and where indicated, recommend changes to improve the quality of surgical care in Western Australia (WA). The purpose of this study is to establish benchmark standards in WA for operative mortality, 5-year survival and length of stay in all patients who were surgically treated for aneurysm of the abdominal aorta (AAA) in WA. METHODS: The WA Linked Database was used to link the morbidity and mortality records of all patients admitted and surgically treated for AAA in WA from 1985 to 1994. The linked chains of de-identified hospital morbidity and death records were selected using diagnostic and procedure codes pertaining to AAA. Three groups were separated for analysis: those admitted for rupture, those admitted for elective repair, and those who were admitted to hospital as an emergency without mention of rupture but who underwent repair for AAA. Independent analysis for gender and patients 80 years or more were included in the study. Patients were excluded from the study if they were less than 55 years of age. RESULTS: A total of 1475 cases (1257 males, 218 females) were identified. The mean age in elective cases was 70.4 years in males and 72.4 years in females, and for rupture the mean ages were 71.9 and 74.8 years, respectively. Median length of stay for males was 12 days for elective cases. Admission type or age did not significantly influence length of stay. Thirty-day mortality in males was 4.4% for elective repair and 36.7% for ruptured AAA and 5-year survival was 71.7 and 47.7%, respectively. The overall case fatality rate for ruptured AAA was 79.3% which included those cases who died from rupture without being admitted to hospital. CONCLUSIONS: These community-wide data provide a realistic measure of surgical performance for open repair of AAA. The outcomes for elective and rupture repair for AAA compare favourably with standards reported by international centres of excellence. They also support the use of this procedure in patients over 80 years of age with rupture. This information can be used for ongoing audit purposes and as a benchmark for the introduction of new treatment modalities.

Aged↗
PubMed1999

Experience measuring performance improvement in multiphase picture archiving and communications systems implementations.

When planning a picture archiving and communications system (PACS) implementation and determining which equipment will be implemented in earlier and later phases, collection and analysis of selected data will aid in setting implementation priorities. If baseline data are acquired relative to performance objectives, the same information used for implementation planning can be used to measure performance improvement and outcomes. The main categories of data to choose from are: (1) financial data; (2) productivity data; (3) operational parameters; (4) clinical data; and (5) information about customer satisfaction. In the authors' experience, detailed workflow data have not proved valuable in measuring PACS performance and outcomes. Reviewing only one category of data in planning will not provide adequate basis for targeting operational improvements that will lead to the most significant gains. Quality improvement takes into account all factors in production: human capacity, materials, operating capital and assets. Once we have identified key areas of focus for quality improvement in each phase, we can translate objectives into implementation requirements and finally into detailed functional and performance requirements. Here, Integration Resources reports its experience measuring PACS performance relative to phased implementation strategies for three large medical centers. Each medical center had its own objectives for overcoming image management, physical/geographical, and functional/technical barriers. The report outlines (1) principal financial and nonfinancial measures used as performance indicators; (2) implementation strategies chosen by each of the three medical centers; and (3) the results of those strategies as compared with baseline data.

Benchmarking↗
PubMed2005

Mimicking cellular sorting improves prediction of subcellular localization.

Predicting the native subcellular compartment of a protein is an important step toward elucidating its function. Here we introduce LOCtree, a hierarchical system combining support vector machines (SVMs) and other prediction methods. LOCtree predicts the subcellular compartment of a protein by mimicking the mechanism of cellular sorting and exploiting a variety of sequence and predicted structural features in its input. Currently LOCtree does not predict localization for membrane proteins, since the compositional properties of membrane proteins significantly differ from those of non-membrane proteins. While any information about function can be used by the system, we present estimates of performance that are valid when only the amino acid sequence of a protein is known. When evaluated on a non-redundant test set, LOCtree achieved sustained levels of 74% accuracy for non-plant eukaryotes, 70% for plants, and 84% for prokaryotes. We rigorously benchmarked LOCtree in comparison to the best alternative methods for localization prediction. LOCtree outperformed all other methods in nearly all benchmarks. Localization assignments using LOCtree agreed quite well with data from recent large-scale experiments. Our preliminary analysis of a few entirely sequenced organisms, namely human (Homo sapiens), yeast (Saccharomyces cerevisiae), and weed (Arabidopsis thaliana) suggested that over 35% of all non-membrane proteins are nuclear, about 20% are retained in the cytosol, and that every fifth protein in the weed resides in the chloroplast.

Animals↗
PubMed2004

[Zoom on the excellence of biomedical research in France].

Among the key benchmarks in assessing research excellence is the production and recognition of scientific discoveries for innovation. Despite the growing use of bibliometric indicators for policy-making purposes, there is still no consensus concerning the appropriate measures of research excellence. In this study, we examine the performance of France in biomedical sciences using several ISI-based indicators. We focus on the results provided by these two selective indicators: the absolute numbers and proportion of papers published in the very high-impact journals (above 20) and in the 1 % of the most highly cited papers. Furthermore, we present the detailed analysis of the Top 1 % French biomedical articles. On this basis we identify the crucial fields, the most active centres per speciality and the networks and the degree of international collaboration resulting from different types of research. These results provide an objective demonstration that the French biomedical research meets with high international standards and contributes to the world core research.

Biomedical Research↗
PubMed2003

Use of audit tools to evaluate the efficacy of cleaning systems in hospitals.

BACKGROUND: Recent publicity has highlighted both the inadequacies of hospital cleaning and high levels of methicillin-resistant Staphylococcus aureus infections in UK hospitals. "Standards for Environmental Cleanliness" (SEC) was a checklist developed in April 1999 by the Infection Control Nurses Association and the Association of Domestic Managers to evaluate cleaning services regardless of who is the provider. More recently, the National Health Service plan (July 2000) was an attempt to generate a rapid improvement in the cleanliness and tidiness of hospitals via a National Health Service patient environment audit (PEA). On the basis of models used in the food industry to manage cleaning practices cost-effectively, a risk-based audit checklist incorporating rapid hygiene monitoring was developed to assess the adequacy of cleaning programs and standards in hospitals. This checklist (Audit for Cleaning Efficacy, or ACE) as well as the SEC and PEA approaches were applied at 4 hospitals, and environmental microbial surface counts were compared. SEC and PEA rely on visual assessment, whereas the ACE approach is more comprehensive and included more specific questions relating to the management and monitoring of cleaning as well as standards on the basis of rapid hygiene monitoring. METHODS: Two wards in each of the 4 hospitals were visited on 3 separate occasions immediately after cleaning was completed. Visual assessment, adenosine triphosphate bioluminescence, and microbiologic sampling of selected environmental sites were performed to evaluate the effectiveness of cleaning. The 3 audits were completed during the final hospital visit. RESULTS: Visual assessment indicated that 90% of sites were satisfactory, whereas adenosine triphosphate bioluminescence showed that 100% and microbiologic sampling showed that 90% of sites did not meet benchmark values. There was no significant difference between the SEC and PEA audits (P =.311), which used visual assessment, and the results suggest that they both are similar in passing surfaces that have microbiologic benchmark values that are too high. However, the ACE audit showed a significant difference (P = <.001) in results compared with the SEC and the PEA audits and did not pass surfaces with microbiologic benchmark values that were too high. The ACE audit, which incorporates rapid hygiene testing, showed a much stronger association with the microbial counts; this was not apparent with the SEC and the PEA audits. CONCLUSION: The data suggest that visual assessment is a poor indicator of cleaning efficacy and that the ACE audit gives a better assessment of cleaning programs compared with the other 2 audit methods in relation to microbial surface counts. It is recommended that hospital cleaning regimes be designed to ensure that surfaces are cleaned adequately and that efficacy is assessed with use of internal auditing and rapid hygiene testing.

Adenosine Triphosphate↗
PubMed2003

Shear-slip Mesh Update Method: implementation and applications.

The Shear-slip Mesh Update Method (SSMUM) is being used in flow simulations involving large but regular displacements of one or more boundaries of the computational domain. We follow up the earlier discussion of the method with notes on practical implementation aspects. In order to establish a benchmark problem for this class of flow problems, we define and report results from a two-dimensional viscous flow around a rotating stirrer in a square chamber. The application potential of the method is demonstrated in the context of biomedical design problem, as we perform an analysis of blood flow in a centrifugal left ventricular assist device, or blood pump, which involves a rotating impeller in a non-axisymmetric housing.

Blood Flow Velocity↗
PubMed2000

DPM, a fast, accurate Monte Carlo code optimized for photon and electron radiotherapy treatment planning dose calculations.

A new Monte Carlo (MC) algorithm, the 'dose planning method' (DPM), and its associated computer program for simulating the transport of electrons and photons in radiotherapy class problems employing primary electron beams, is presented. DPM is intended to be a high accuracy MC alternative to the current generation of treatment planning codes which rely on analytical algorithms based on an approximate solution of the photon/electron Boltzmann transport equation. For primary electron beams, DPM is capable of computing 3D dose distributions (in 1 mm3 voxels) which agree to within 1% in dose maximum with widely used and exhaustively benchmarked general-purpose public-domain MC codes in only a fraction of the CPU time. A representative problem, the simulation of 1 million 10 MeV electrons impinging upon a water phantom of 128(3) voxels of 1 mm on a side, can be performed by DPM in roughly 3 min on a modern desktop workstation. DPM achieves this performance by employing transport mechanics and electron multiple scattering distribution functions which have been derived to permit long transport steps (of the order of 5 mm) which can cross heterogeneity boundaries. The underlying algorithm is a 'mixed' class simulation scheme, with differential cross sections for hard inelastic collisions and bremsstrahlung events described in an approximate manner to simplify their sampling. The continuous energy loss approximation is employed for energy losses below some predefined thresholds, and photon transport (including Compton, photoelectric absorption and pair production) is simulated in an analogue manner. The delta-scattering method (Woodcock tracking) is adopted to minimize the computational costs of transporting photons across voxels.

Algorithms↗
PubMed2004

Is cross-validation valid for small-sample microarray classification?

MOTIVATION: Microarray classification typically possesses two striking attributes: (1) classifier design and error estimation are based on remarkably small samples and (2) cross-validation error estimation is employed in the majority of the papers. Thus, it is necessary to have a quantifiable understanding of the behavior of cross-validation in the context of very small samples. RESULTS: An extensive simulation study has been performed comparing cross-validation, resubstitution and bootstrap estimation for three popular classification rules-linear discriminant analysis, 3-nearest-neighbor and decision trees (CART)-using both synthetic and real breast-cancer patient data. Comparison is via the distribution of differences between the estimated and true errors. Various statistics for the deviation distribution have been computed: mean (for estimator bias), variance (for estimator precision), root-mean square error (for composition of bias and variance) and quartile ranges, including outlier behavior. In general, while cross-validation error estimation is much less biased than resubstitution, it displays excessive variance, which makes individual estimates unreliable for small samples. Bootstrap methods provide improved performance relative to variance, but at a high computational cost and often with increased bias (albeit, much less than with resubstitution).

Algorithms↗
PubMed2003

Is there a difference in hip joint position sense between young and older groups?

BACKGROUND: Joint position sense (JPS) in the knee has been shown by many authors to decline with age. It has been speculated that this decrease contributes to abnormal joint mechanics during load-bearing activities and putatively results in joint degeneration. Surprisingly little research has been conducted on the human hip to determine benchmarks for normal JPS. METHOD: Fifty-nine community dwelling subjects, 30 young (mean age 21.7 years) and 29 older (mean age 75 years), were recruited to determine normal reference ranges for the effect of age on hip JPS. Active and passive repositioning tasks were performed in inner and outer ranges of the hip abduction plane of movement. An electromagnetic tracking system was used to obtain accurate error measurements of the angular displacement. RESULTS: Results indicated no difference in hip JPS between the young and older subjects (F(1,57) = 0.011, p = .917). However, it was found that for both age groups, accurate reproduction of position at the hip joint occurred in the inner range (F(1,57) = 13.760, p < .001). For both groups, active repositioning was more accurate than passive (F(1,57) = 9.265, p = .004). CONCLUSIONS: In this study, no difference in hip JPS was found between young and older subjects. Accuracy was greater in the inner range, with active repositioning demonstrating higher precision compared to passive repositioning of the limb.

Adult↗
PubMed1995

Physicians' response to length-of-stay profiling.

One of the techniques adopted recently by certain hospitals to meet the competitive pressure for reducing costs is physician profiling. Profiling produces periodic reports that compare a physician's resource consumption to a benchmark figure. This study analyzes the effectiveness and implications of one hospital's introduction of physician patient length-of-stay profiling. Data for 24,000 patients treated by 400 physicians in 450 diagnosis-related groups over 42 months were analyzed, including both preprofiling and postprofiling periods. Statistical tests examined whether more physicians achieved the length-of-stay benchmark after profiling was introduced, controlling for physician, disease category (diagnosis-related group), and patient severity level. First, the results establish a significant increase in the percentage of physicians who achieve the length-of-stay benchmark after the introduction of profiling. Second, it was found that physicians who had initially failed to meet the benchmark reduced their patients' average length of stay much more than those physicians who initially achieved the benchmark. Further, reductions occurred primarily at intermediate severity levels, and in diagnosis-related groups with a large economic impact for the hospital. Although the profiling program did achieve the objective of reducing patient length of stay, further improvement may be possible. First, providing different benchmarks or targets for different physicians may extend the improvement to a greater percentage of all physicians involved. Second, an analysis of monthly data on total weighted procedures reveals that the reduction in length of stay resulted in an increase in the number of procedures performed per patient day. This finding suggests that to achieve a reduction in hospital costs and charges, profiling programs should be combined with process improvement initiatives.

Diagnosis-Related Groups↗