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At least 1,135 records · Page 63Linked to original sources
PubMed2006

SVRMHC prediction server for MHC-binding peptides.

BACKGROUND: The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. RESULTS: Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. CONCLUSION: SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.

Amino Acid Sequence↗
PubMedDate not supplied

Measuring community benefits provided by for-profit and nonprofit hospitals.

Nonprofit hospitals are expected to provide benefits to their community in return for being exempt from most taxes. In this paper we develop a new method of identifying activities that should qualify as community benefits and of determining a benchmark for the amount of community benefits a nonprofit hospital should be expected to provide. We then compare estimates of nonprofits' current level of community benefits with our benchmark and show that actual provision appears to fall short. Either nonprofit hospitals as a group ought to provide more community benefits, or they are performing activities that cannot be measured. In either case, better measurement and accounting of community benefits would improve public policy.

Benchmarking↗
PubMed2000

Quality improvement in a managed care organization from a medical director's perspective: an interview with Bruce Perry. Interview by Douglas Roblin.

BACKGROUND: In late 1994 the Quality Forum commissioned the Interdisciplinary Prevention Committee [IPC]. One of the IPC's charges was to identify priorities for QI in preventive health services. The IPC established priorities through a review of scientific literature, identification of national and state health initiative priorities, and consideration of what services to establish as priorities and of the practicality of implementing low-cost interventions to achieve specific QI goals. Breast cancer screening was selected as a top-ten priority for guideline development and for focused intervention because of the disease's prevalence, morbidity, and mortality and because of the fact that it is most treatable and curable when it is found early through routine screening. The national HEDIS (Health Plan Employer Data and Information Set; National Committee on Quality Assurance (NCQA), Washington, DC] result of 71%, reported in May 1995, provided our baseline performance measurement. This result fell short of our goal of being in the 90th percentile of performance on each HEDIS effectiveness of care measure. In August 1995 the Quality Forum accepted the IPC's recommendations, which had been endorsed by the department of medicine. These recommendations emphasized the importance of annual clinical breast exam and mammography for women of targeted age groups. In November 1997, a new "Excellence in Quality: HEDIS Improvement Team" began work. Its charge was to undertake analyses of underlying causes of reduced performance and to develop additional steps to improve performance by changes in care delivery processes in 1998. In March 1998 the Quality Forum's executive committee designated breast cancer screening one of the six organizationwide quality priorities for 1998 and designated two "owners" who would be accountable for this performance--the chief and director of radiology. RESULTS: The screening rate increased from 73.8% in 1996 to 84.0% in 1999. National benchmarks [90th percentile] in 1998 were 81% for commercially insured members and 84% for Medicare members. The 84% screening rate made the Georgia region the Kaiser Permanente national leader and put the region in the top 10% of all health plans in the United States. CONCLUSIONS: The program has achieved these results with a broad array of activities: Saturday hours, mobile mammography, medical record reminders (fuschia-colored inserts), patient and physician reminders, call-center outreach, provider feedback on performance, and provider financial incentives. Several of these innovations demonstrate the ability to integrate improved care management into evolving service delivery in Kaiser Permanente--such as use of call-center technologies and redesign of primary care delivery. While we cannot point to any one of these innovations as a key driver of improvement, it is clear that substantial improvements in care delivery can be achieved. All these activities are relatively low cost and easily implemented in other managed care organizations and in other areas of medical care.

Child↗
PubMed2004

Comparative performance data for critical access hospitals.

CONTEXT: Among small rural hospitals, there is a growing recognition of the need to measure and report on the use of resources and the safety and quality of the services provided. Dashboards, clinical value compasses, and balanced scorecards are approaches to performance measurement that have been adopted by many health care organizations. However, there exists very little comparative performance data specific for critical access hospitals. PURPOSE: To identify how comparative performance data for critical access hospitals (CPD-CAH) might facilitate performance and quality improvement, to assess the potential benefits and drawbacks of such data, and to identify some of the critical issues in the development and implementation of CPD-CAH. METHODS: Assessment of discussions by participants at a rural hospital performance improvement summit and authors' analyses. FINDINGS: CPD-CAH potentially could improve quality of care and patient outcomes, provide comparative data and benchmarks, inform policy development, facilitate collaboration, and enhance community relations. However, CPD-CAH could also impose an unaffordable cost, produce poor information, require complex coordination, induce a negative public reaction, and result in perverse hospital behavior. Development and implementation of CPD-CAH would require including stakeholders' assessment of its desirability and feasibility, setting objectives, establishing guiding principles, developing a method, collecting and analyzing data, and disseminating results. CONCLUSIONS: CPD-CAH could significantly advance CAH performance and quality improvement. However, development and implementation would be a complicated exercise requiring academic expertise and practitioner consultation. The potential value of CPD-CAH should be carefully weighed against its potential cost.

Benchmarking↗
PubMed2005

Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si).

To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S(N)2@C) and at silicon in chlorosilane (S(N)2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl(-), CH(3)Cl] reactant complex, the [Cl-CH(3)-Cl](-) transition state and the stable [Cl-SiH(3)-Cl](-) transition complex is -10.42, +2.52, and -27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triple-zeta quality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S(N)2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP).

Journal Article↗
PubMed2026

PepGen: conditional generation of peptides for MHC binding.

MOTIVATION: Peptide-MHC II binding drives adaptive immunity, yet discovery of novel binder peptides remains challenging due to open binding grooves of MHC-II that accommodate variable-length peptides. While discriminative models perform well, they are unfeasible for generation via enumeration due to vast peptide space (2013≈8×1016 for peptides of length 13 amino acids). Generative AI approaches could accelerate binder design to enable vaccines targeted to particular MHC-II alleles or optimize other peptide chemical properties. RESULTS: We introduce PepGen, the first protein language model for MHC II peptide generation building on Generalized Language Modeling. PepGen conditions on alleles, arbitrary partial peptides including putative TCR-interacting motifs, and continuous binding affinity. Across multiple benchmarks including infilling and de novo generation, PepGen outperformed frequency sampling, Gibbs clustering, and autoregressive baselines. Adjusted log-probabilities enable good classification performance. Experimental validation confirmed that the SARS-CoV-2 peptide TEGALNTPKDHIGTR binding the HLA-DQA101:03-DQB106:03 allele can be redesigned to bind the HLA-DQA101:02-DQB105:02 allele. PepGen generated three putative TCR-motif-preserving binders gaining up to 70% of original MFI. Overall, PepGen provides scalable, motif-constrained MHC II peptide redesign and de novo generation, validated through thorough benchmarks and functional assays. AVAILABILITY AND IMPLEMENTATION: Code and Data are available at https://github.com/DaniTheOrange/PepGen.

Peptides↗
PubMed1997

Biomechanical analysis of four-strand extensor tendon repair techniques.

Experience with flexor tendon repairs has suggested the superiority of the augmented Becker (MGH) technique for strength, toughness, and gap resistance. In an effort to apply these findings to the extensor tendons, 3 four-strand extensor tendon repair techniques were biomechanically tested in fresh human cadaver limbs: modified Bunnell, modified Krackow-Thomas, and MGH. Repairs were performed in Verdan's zone VI. Repaired tendons were distracted at constant speed until rupture. Tendon load and tendon distraction were continuously monitored. Benchmark values for load were measured as fingers were pulled from full metacarpophalangeal (MP) joint flexion to full extension, to 1-mm gap formation at the tenorrhaphy, and to complete rupture of the repair. The MGH repair proved significantly more resistant to gap formation (stronger and tougher) than the Bunnell and Krackow-Thomas repairs (p < .02). No differences were seen between groups in repair performance at MP joint extension and at complete rupture. This study suggests that the MGH technique has superior gap resistance to the other four-strand methods tested for extensor tendon repair in Verdan's zone VI. The MGH repair is recommended for extensor tendon repairs in zone VI when early postoperative motion regimens are considered.

Biomechanical Phenomena↗
PubMed1997

Protein secondary structure prediction using local alignments.

The accuracy of secondary structure prediction methods has been improved significantly by the use of aligned protein sequences. The PHD method and the NNSSP method reach 71 to 72% of sustained overall three-state accuracy when multiple sequence alignments are with neural networks and nearest-neighbor algorithms, respectively. We introduce a variant of the nearest-neighbor approach that can achieve similar accuracy using a single sequence as the query input. We compute the 50 best non-intersecting local alignments of the query sequence with each sequence from a set of proteins with known 3D structures. Each position of the query sequence is aligned with the database amino acids in alpha-helical, beta-strand or coil states. The prediction type of secondary structure is selected as the type of aligned position with the maximal total score. On the dataset of 124 non-membrane non-homologous proteins, used earlier as a benchmark for secondary structure predictions, our method reaches an overall three-state accuracy of 71.2%. The performance accuracy is verified by an additional test on 461 non-homologous proteins giving an accuracy of 71.0%. The main strength of the method is the high level of prediction accuracy for proteins without any known homolog. Using multiple sequence alignments as input the method has a prediction accuracy of 73.5%. Prediction of secondary structure by the SSPAL method is available via Baylor College of Medicine World Wide Web server.

Algorithms↗
PubMed2002

Performance characteristics of the Pantak Therapax-150 superficial X-ray treatment machine: measurements and calculations.

The beam and operating performance characteristics of a superficial X-ray unit, the Pantak Therapax-150 have been evaluated and benchmarked against the Monte Carlo code-MCNP. Parameters which were studied included beam quality, central axis depth dose and field uniformity for several applicator sizes and focal skin distances (FSDs) with the tube operating between 50 and 150 kVp accelerating potential. MCNP calculations were compared with five published qualities: 3.75 mm Al, 3.27 mm Al, 2.43 mm Al, 7.15 mm Al and 1.65 mm Cu half value layer (HVL). The unit has been found to provide beam characteristics similar to those reported for other superficial therapy machines. For most of the combinations of radiation qualities and applicators, good agreement between experiments an dcalculations was obtained. Calculated data when compared with other workers was not worse than 8.8%.

Equipment Failure Analysis↗
PubMed2006

Is there an indication for ETV in young infants in aetiologies other than isolated aqueduct stenosis?

OBJECTIVES: The objective was to determine whether endoscopic third ventriculostomy (ETV) has a role in the management of obstructive hydrocephalus in aetiologies other than idiopathic aqueduct stenosis (AS) in infants. MATERIALS AND METHODS: In addition to reviewing the literature, we performed a retrospective analysis of our endoscopy database, which was established in 1998, and analysed the outcome results of all cases of ETV in those under 1 year of age which were performed between 1998 and 2003. We included cases of idiopathic AS in the outcome analysis as a benchmark of successful outcome. Successful outcome was assessed by resolution of the presenting clinical features and shunt freedom. RESULTS: Aetiologies that were identified included, in addition to idiopathic AS, suprasellar arachnoid cysts, AS in association with post-haemorrhagic hydrocephalus (PHH), post-infectious hydrocephalus (PIH), tumour-related hydrocephalus and a heterogenous group including Dandy-Walker malformation and other developmental anomalies. Suprasellar arachnoid cysts had a 100% outcome success. Idiopathic AS had a 50% outcome success and the successful outcome of PHH cases was poor at 18%. A statistical analysis revealed no effect of age at the time of ETV on the outcome in the aetiological groups. CONCLUSIONS: The definitive initial neurosurgical management of suprasellar arachnoid cysts causing significant hydrocephalus is ETV, whereas that for PHH and PIH is probably that of a ventriculo-peritoneal shunt placement. We speculate that there may be a sub-group of AS cases, termed pure or idiopathic AS, which have a higher rate of successful outcome that may be durable from a younger age. The role of repeat ETV is controversial.

Age Factors↗
PubMed1999

Faithful representations with topographic maps.

Topographic map algorithms that are aimed at building "faithful representations" also yield maps that transfer the maximum amount of information available about the distribution from which they receive input. The weight density (magnification factor) of these maps is proportional to the input density, or the neurons of these maps have an equal probability to be active (equiprobabilistic map). As MSE minimization is not compatible with equiprobabilistic map formation in general, a number of heuristics have been devised in order to compensate for this discrepancy in competitive learning schemes, e.g. by adding a "conscience" to the neurons' firing behavior. However, rather than minimizing a modified MSE criterion, we introduce a new unsupervised competitive learning rule, called the kernel-based Maximum Entropy learning Rule (kMER), for topographic map formation, that optimizes an information-theoretic criterion directly. To each neuron a radially symmetric kernel is associated, with a given center and radius, and the two are updated in such a way that the (unconditional) information-theoretic entropy of the neurons' outputs is maximized. We review a number of competitive learning rules for building equiprobabilistic maps. As benchmark tests for the faithfulness of the representations, we consider two types of distributions and compare the performances of these rules and kMER, for batch and incremental learning. As a first example application, we consider non-parametric density estimation where the maps are used for generating "pilot" estimates in kernel-based density estimation. The second application we envisage for kMER is "on-line" adaptive filtering of speech signals, using Gabor functions as wavelet filters. The topographic feature maps that are developed in this way differ in several respects from those obtained with Kohonen's Adaptive-Subspace SOM algorithm.

Journal Article↗
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

Determination of drug glucuronidation and UDP-glucuronosyltransferase selectivity using a 96-well radiometric assay.

A rapid and sensitive radiometric assay for UDP-glucuronosyltransferase (UGT) is described. UGT substrates are incubated in 96-well plates with microsomes in the presence of [14C]UDP-glucuronic acid, and 14C-labeled glucuronidation products are separated from the unreacted nucleotide sugar by solid-phase extraction using 96-well extraction plates. The assay was validated with 15 structurally diverse UGT substrates containing acidic, phenolic, and hydroxyl reacting groups. Glucuronidation velocities for these compounds were determined using human, rat, and dog liver microsomes, and reaction kinetics were studied with 1-naphthol and 4-methylumbelliferone. Results obtained with the new assay confirmed the previously reported rank order of glucuronidation velocity of several typical UGT substrates and the finding that the glucuronidation of most of these compounds is significantly faster in dog than in human liver microsomes. UGT specificity of five compounds was determined using recombinant human UGTs. The major UGT isoforms identified were UGT1A6, UGT1A7, and UGT1A9 for 4-methylumbelliferone; UGT1A6 and UGT1A8 for 1-naphthol; UGT2B7 for naloxone; UGT1A3 and UGT2B7 for ketoprofen; and UGT1A4 for trifluoperazine. Identical results were obtained with a conventional high-performance liquid chromatography method coupled to mass spectrometric detection. The new assay should prove valuable for rapidly benchmarking recombinant UGTs and microsomal preparations from different species and tissues, identifying high-turnover compounds during drug discovery, and reaction phenotyping studies.

Animals↗
PubMed1997

Factors affecting the valuation of physician practices.

Valuation of physician practices provides physicians with a benchmark of their business success and helps purchasers negotiate a purchase price. The Center for Healthcare Industry Performance Studies (CHIPS) recently conducted a survey of physician practice acquisitions. The survey collected data on salaries and benefits paid to physicians after practice acquisition, historical profitability of the acquired practice, and specific values assigned to both tangible and intangible assets in the practice. Some of the survey's critical conclusions include: hospitals tend to acquire unprofitable practices, value is based on historical revenues rather than historical profits, the importance of valuation methodology and payer mix is underestimated, tangible assets represent a large part of the purchase price, and hospitals tend to pay higher physician compensation than do other purchasers.

Data Collection↗
PubMed2003

[A novel approach for peptide identification by tandem mass spectrometry].

High throughput scoring algorithms that are used to find the match of a tandem mass spectrum to a predicted mass spectrum of a peptide within a database have been applied in shotgun proteomics. However, these algorithms could produce a significant number of incorrect peptide identifications. Here a novel approach was developed to scoring tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental and theoretical spectrum were considered. Benchmarking the novel scorer on a large set of experimental MS/MS spectra, it is demonstrated that PepSearch performs significantly better than the widely used software SEQUEST. The PepSearch software is available at http://compbio.sibsnet.org/projects/pepsearch.

Databases, Protein↗