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PubMed1992

Segmentation, modelling and reconstruction of arterial bifurcations in digital angiography.

The paper presents a method to model an arterial bifurcation from a pair of X-ray angiographic images. It is the initial step of a reconstruction process aiming at detecting and quantifying abnormal sites located on bifurcations. The method proposed consists of two steps. First, each image is independently segmented to extract the vessels in the images. The algorithm uses dynamic programming first to find the bifurcation centrelines from the original images, and secondly to extract vessel edges from the morphological gradient images, under a constraint of parallelism with the previously detected centrelines. Then, a three-dimensional bifurcation model is built by adapting cylinders around the three-dimensional bifurcation centrelines. These cylinders are obtained as a stack of binary orientable ellipses fitted to the projection densities in the corresponding cross-sections. Results obtained on simulated data, phantom and femoral bifurcations are displayed.

Angiography, Digital Subtraction↗
PubMed2002

[Indicators of structural quality in palliative care for cancer pain patients in Lower-Saxony].

INTRODUCTION: Palliative care in Germany fails to reach established standards. To improve this situation the Chamber of Physicians of Lower-Saxony initiated SUPPORT in 1995. Prior to interventions structural quality of care was evaluated, specifically the rate of availability of opioid-prescription-forms and the ability to treat chronic pain (defined as a construct of knowledge, attitudes and skills) were examined. METHODS: The survey was carried out using a standardized questionnaire mailed to a representative stratified sample of 1200 physicians. RESULTS: Out of 865 answering physicians (response rate 72.1%) only 36.9% had their own opioid-prescription-forms. Differentiations regarding to specialty, working place (clinic vs. private practice) and treatment of cancer pain patients during the last three months shows a better result for GPs (84.6%), internists (48.6%), gynecologists (51%) and pain specialists (66.7%). Only 33.1% of respondents claimed knowledge of the WHO-3-step-analgesic-ladder. Again the aforementioned differentiations yield somewhat better results for GPs (49.2%), internists (51.5%), gynecologists (34.7%) and pain specialists (55.6%), however only two thirds of these physicians were able to identify the correct number of steps of the WHO-algorithm. CONCLUSIONS: These results verify an insufficient structural quality in palliative care in Lower-Saxony. In the authors' opinion effective improvements can only be achieved by implementing a parallel strategy:improvement of basic knowledge in pain management with sufficient transfer of this knowledge into practice as well as raising the rate of availability of opioid-prescription-forms,and, on the other hand, establishing local palliative-care-teams with nursing and medical expertise with 24/7 on-demand availability to optimize palliative care.

Adult↗
PubMed2004

[The quality-of-life questionnaire QLS-H: validation of the French language version of the questionnaire in patients with growth hormone deficiency and collection of reference data in the general population].

The QLS-H(c) (Questions on Life Satisfaction- Hypopituitarism) is new a quality of life (QoL) self-administered questionnaire addressing the complaints of adult patients with growth hormone deficiency. The French version of the QLS-H(c) (16 items) has been psychometrically evaluated during a randomized, open label study comparing two strategies of growth hormone (GH) replacement therapy. Seventy-three patients were included and received an 8-month GH replacement therapy. QoL was explored at baseline, 4 and 8 months using the QLS-H(c) questionnaire and the Nottingham Health Profile (NHP) reference scale. Acceptance of the QLS-H(c) was excellent as 92% of the questionnaires were suitable for analysis. All the items demonstrated good selectivity. The homogeneity of the questionnaire was confirmed (Cronbach's alpha, 0.87). The external validity construct was assessed and confirmed using the NHP scores. Sensitivity to change was confirmed. Following an 8-month replacement therapy, the perception of the QoL assessed with the QLS-H(c) questionnaire was significantly improved, irrespective to the treatment strategy. Finally, redundant items of the questionnaire were removed. As a result, the final version of the QLS-H(c) contained 9 items. In a parallel study, reference data of the QLS-H(c) (9 items) were collected from a representative sample of 989 subjects from the French population. With these reference ranges, algorithms to calculate Z scores adjusted for age and gender were developed as a measure for the deviation of patients' scores from those of the general population, and also to evaluate changes along time. In summary, the French version of the quality of life QLS-H(c) questionnaire is a relevant, validated investigational tool for the evaluation and follow-up of an adult patient with growth hormone deficiency.

Adult↗
PubMed2001

Similarity between condensed phase and gas phase chemistry: fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics.

Amino acid residues containing thioethers are easily oxidized during protein purification, derivatization, and/or digestion. For instance, oxidation of methionine residues in proteins during SDS-PAGE is commonly observed. Under low energy collision induced dissociation this gives rise to a second series of fragment ion of lower abundance that are shifted by -64 Da when compared to the oxidized methionine-containing fragments. We report here that alkylated cysteine residues can be found in their oxidized form too, indicating that the oxidation of thioethers can occur during and following protein digestion and not only during SDS-PAGE or reduction and alkylation. Collision induced dissociation experiments on the singly- and multiply-charged species reveals that these peptides preferentially undergo elimination reactions that forms a dehydroalanine from the oxidized, alkylated cysteine residue. This contrasts to the less abundant elimination reaction of peptides containing oxidized methionines which cannot form an alpha,beta-unsaturated compound, but parallels the condensed phased chemistry of sulfoxides. The masses of both precursor and product ions are shifted such that these peptides cannot be identified in database searches with current algorithms. Incorporation of this fragmentation pattern is important for the isotope-coded affinity tag approach since this method is based on peptides containing cysteine residues.

Cysteine↗
PubMed2002

From genomes to vaccines: Leishmania as a model.

The 35 Mb genome of Leishmania should be sequenced by late 2002. It contains approximately 8500 genes that will probably translate into more than 10 000 proteins. In the laboratory we have been piloting strategies to try to harness the power of the genome-proteome for rapid screening of new vaccine candidate. To this end, microarray analysis of 1094 unique genes identified using an EST analysis of 2091 cDNA clones from spliced leader libraries prepared from different developmental stages of Leishmania has been employed. The plan was to identify amastigote-expressed genes that could be used in high-throughput DNA-vaccine screens to identify potential new vaccine candidates. Despite the lack of transcriptional regulation that polycistronic transcription in Leishmania dictates, the data provide evidence for a high level of post-transcriptional regulation of RNA abundance during the developmental cycle of promastigotes in culture and in lesion-derived amastigotes of Leishmania major. This has provided 147 candidates from the 1094 unique genes that are specifically upregulated in amastigotes and are being used in vaccine studies. Using DNA vaccination, it was demonstrated that pooling strategies can work to identify protective vaccines, but it was found that some potentially protective antigens are masked by other disease-exacerbatory antigens in the pool. A total of 100 new vaccine candidates are currently being tested separately and in pools to extend this analysis, and to facilitate retrospective bioinformatic analysis to develop predictive algorithms for sequences that constitute potentially protective antigens. We are also working with other members of the Leishmania Genome Network to determine whether RNA expression determined by microarray analyses parallels expression at the protein level. We believe we are making good progress in developing strategies that will allow rapid translation of the sequence of Leishmania into potential interventions for disease control in humans.

Animals↗
PubMed2000

Maximum-likelihood transmission image reconstruction for overlapping transmission beams.

In many transmission imaging geometries, the transmitted "beams" of photons overlap on the detector, such that a detector element may record photons that originated in different sources or source locations and thus traversed different paths through the object. Examples include systems based on scanning line sources or on multiple parallel rod sources. The overlap of these beams has been disregarded by both conventional analytical reconstruction methods as well as by previous statistical reconstruction methods. We propose a new algorithm for statistical image reconstruction of attenuation maps that explicitly accounts for overlapping beams in transmission scans. The algorithm is guaranteed to monotonically increase the objective function at each iteration. The availability of this algorithm enables the possibility of deliberately increasing the beam overlap so as to increase count rates. Simulated single photon emission tomography transmission scans based on a multiple line source array demonstrate that the proposed method yields improved resolution/noise tradeoffs relative to "conventional" reconstruction algorithms, both statistical and nonstatistical.

Algorithms↗
PubMed2004

Review of STI and HIV epidemiological data from 1990 to 2001 in urban Burkina Faso: implications for STI and HIV control.

OBJECTIVES: To better understand the sexually transmitted infection (STI)/HIV dynamics in an urban west African setting in order to adapt STI/HIV control efforts accordingly. METHODS: Review of STI and HIV epidemiological studies performed over the past decade in Bobo-Dioulasso, the second city of Burkina Faso. Trends in STI prevalence among commercial sex workers and the general population were assessed over time through studies that used the same recruitment and laboratory diagnostic procedures. Variations in aetiologies of vaginal discharge, urethral discharge, and genital ulcers were also evaluated among patients consulting for genital infection complaints. Antenatal clinic based surveys provided data to assess HIV trend among the general population. RESULTS: We observed an important decline of classic bacterial STI such as syphilis, Neisseria gonorrhoea, Chlamydia trachomatis, and Haemophilus ducrey infections in all study groups. Trichomoniasis also declined but to a lesser extent. HIV infection followed the same trend at the same time, with a significant decline in the 15-19 year age group of pregnant women, suggesting a possible decrease of HIV incidence. Although no evidence of a causal relation can be drawn from this review, adoption of safer sex behaviour, introduction of the syndromic management (SM) approach, or higher antibiotic use may have contributed to these changes. CONCLUSIONS: Classic bacterial STI declined over the past decade in parallel with a stabilisation of HIV infection. Variations in syndromes aetiology and sexual behaviours should be monitored as part of STI surveillance in order to improve STI syndromic management algorithms and to adapt HIV/STI prevention efforts.

Burkina Faso↗
PubMed2004

Modeling of the signals of an optical particle counter for real nonspherical particles.

An optical particle counter (OPC) was exposed to atmospheric particles of diameters of 200, 300, and 400 nm. The OPC data were combined with the results of single-particle analysis with a transmission electron microscope (TEM) on samples taken in parallel with the OPC measurements. With a T-matrix-based optical model the measured OPC spectra of scattered light pulses could be approximated with good precision. With an algorithm that simulated the response of the OPC to a given population of model particles derived from the TEM results, average absorption properties of different particle types were retrieved. For mobility sizes of 400 nm, higher light absorption was retrieved with the optical model for soot aggregates than for the rest of the morphological particle types. At smaller mobility sizes no compositional information could be derived from the model particles derived from the TEM data. Despite the limited success of the new methodology applied to the present experiment the results encourage the use of OPCs in combination with electrical mobility analyzers to derive more than aerosol-size distributions. With state-of-the-art pulse-height analysis the light-scattering pulses could be resolved with much finer resolution than in the instrument used.

Aerosols↗
PubMedDate not supplied

Review of MR image segmentation techniques using pattern recognition.

This paper has reviewed, with somewhat variable coverage, the nine MR image segmentation techniques itemized in Table II. A wide array of approaches have been discussed; each has its merits and drawbacks. We have also given pointers to other approaches not discussed in depth in this review. The methods reviewed fall roughly into four model groups: c-means, maximum likelihood, neural networks, and k-nearest neighbor rules. Both supervised and unsupervised schemes require human intervention to obtain clinically useful results in MR segmentation. Unsupervised techniques require somewhat less interaction on a per patient/image basis. Maximum likelihood techniques have had some success, but are very susceptible to the choice of training region, which may need to be chosen slice by slice for even one patient. Generally, techniques that must assume an underlying statistical distribution of the data (such as LML and UML) do not appear promising, since tissue regions of interest do not usually obey the distributional tendencies of probability density functions. The most promising supervised techniques reviewed seem to be FF/NN methods that allow hidden layers to be configured as examples are presented to the system. An example of a self-configuring network, FF/CC, was also discussed. The relatively simple k-nearest neighbor rule algorithms (hard and fuzzy) have also shown promise in the supervised category. Unsupervised techniques based upon fuzzy c-means clustering algorithms have also shown great promise in MR image segmentation. Several unsupervised connectionist techniques have recently been experimented with on MR images of the brain and have provided promising initial results. A pixel-intensity-based edge detection algorithm has recently been used to provide promising segmentations of the brain. This is also an unsupervised technique, older versions of which have been susceptible to oversegmenting the image because of the lack of clear boundaries between tissue types or finding uninteresting boundaries between slightly different types of the same tissue. To conclude, we offer some remarks about improving MR segmentation techniques. The better unsupervised techniques are too slow. Improving speed via parallelization and optimization will improve their competitiveness with, e.g., the k-nn rule, which is the fastest technique covered in this review. Another area for development is dynamic cluster validity. Unsupervised methods need better ways to specify and adjust c, the number of tissue classes found by the algorithm. Initialization is a third important area of research. Many of the schemes listed in Table II are sensitive to good initialization, both in terms of the parameters of the design, as well as operator selection of training data.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗
PubMed1996

LIA: a location-independent transformation for ASOCS adaptive algorithm 2.

Most Artificial Neural Networks (ANNs) have a fixed topology during learning, and often suffer from a number of short-comings as a result. ANNs that use dynamic topologies have shown the ability to overcome many of these problems. Adaptive Self-Organizing Concurrent Systems (ASOCS) are a class of learning models with inherently dynamic topologies. This paper introduces Location-Independent Transformations (LITs) as a general strategy for implementing learning models that use dynamic topologies efficiently in parallel hardware. An LIT creates a set of location-independent nodes, where each node computes its part of the network output independent of other nodes, using local information. This type of transformation allows efficient support for adding and deleting nodes dynamically during learning. In particular, this paper presents the Location-Independent ASOCS (LIA) model as an LIT for ASOCS Adaptive Algorithm 2. The description of LIA gives formal definitions for LIA algorithms. Because LIA implements basic ASOCS mechanisms, these definitions provide a formal description of basic ASOCS mechanisms in general, in addition to LIA.

Algorithms↗
PubMed2006

Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins.

The ability to predict structure from sequence is particularly important for toxins, virulence factors, allergens, cytokines, and other proteins of public health importance. Many such functions are represented in the parallel beta-helix and beta-trefoil families. A method using pairwise beta-strand interaction probabilities coupled with evolutionary information represented by sequence profiles is developed to tackle these problems for the beta-helix and beta-trefoil folds. The algorithm BetaWrapPro employs a "wrapping" component that may capture folding processes with an initiation stage followed by processive interaction of the sequence with the already-formed motifs. BetaWrapPro outperforms all previous motif recognition programs for these folds, recognizing the beta-helix with 100% sensitivity and 99.7% specificity and the beta-trefoil with 100% sensitivity and 92.5% specificity, in crossvalidation on a database of all nonredundant known positive and negative examples of these fold classes in the PDB. It additionally aligns 88% of residues for the beta-helices and 86% for the beta-trefoils accurately (within four residues of the exact position) to the structural template, which is then used with the side-chain packing program SCWRL to produce 3D structure predictions. One striking result has been the prediction of an unexpected parallel beta-helix structure for a pollen allergen, and its recent confirmation through solution of its structure. A Web server running BetaWrapPro is available and outputs putative PDB-style coordinates for sequences predicted to form the target folds.

Algorithms↗
PubMed1994

Spiral CT of the lungs: optimal technique and resolution compared with conventional CT.

OBJECTIVE: The purpose of this study was to compare the resolution of spiral and conventional CT for imaging the lungs and to optimize spiral CT techniques for imaging lung parenchyma. MATERIALS AND METHODS: A line-pair phantom, a dried lung specimen, and three human subjects were scanned. Spiral CT scans obtained on a Somatom PLUS-S CT scanner were compared with conventional CT scans. In addition, the influence of different collimation (1,3, 5, and 8 mm), pitch (1 and 2), display kernel (UltraHi, Hi, Standard, and Soft), and interpolation algorithms (360 degrees and 180 degrees linear interpolation) on spiral CT scans was evaluated. Scans obtained by using different techniques were compared for edge sharpness, contrast resolution, overall visibility of vessels, and noise. RESULTS: With the line bars parallel to the z-axis, a spatial resolution of 7.7 Ip/cm was obtained at all four levels of collimation used for both spiral and conventional CT scanning. Resolution in the z-axis (i.e., direction of table movement) on spiral CT scans decreased markedly when alignment of the line-pair phantom bars was changed to 45 degrees. Resolution along the z-axis decreased with increasing collimation, and this effect was more marked on spiral CT scans than on conventional CT scans. The relative decrease in resolution on spiral CT scans was visible on scans of human subjects only at narrow collimation (1 and 3 mm). Optimal visualization of structures in the lung parenchyma was obtained by using 3-mm collimation and the UltraHi display kernel. The choice of table speed (pitch 1 vs 2) and interpolation algorithm (360 degrees vs 180 degrees linear interpolation) did not significantly affect the image quality of scans of human subjects. CONCLUSION: CT scans of the lung obtained by using spiral and conventional modes at wide collimation (5 and 8 mm) show no differences in resolution, although, at narrow collimation (1 and 3 mm), curved structures such as walls of bullae and fissures are somewhat indistinct. On spiral CT scans of the lungs, narrow collimation and the UltraHi display kernel provide the best image resolution and have more effect on image quality than does choice of table speed or linear interpolation algorithm.

Humans↗
PubMed1995

A distributed, scalable, community care network architecture for wide-area electronic patient records: modeling and simulation.

Principal systems issues relative to computerizing patient medical records that are yet to be addressed in the scientific literature include (1) the characteristics of networks, i.e. bandwidth and capacity, and their impact on the performance of the system, (2) the architecture and the underlying algorithm of the system, (3) the location and migration of medical records, (4) scalability of the system, and (5) the nature of the performance variation under heavy and light use of the network. Key parameters that affect performance include the number of patients, doctors, frequency of patient visits, and the number of electronic queries and record entries initiated during a patient-doctor interaction episode. This paper presents AMPReD, a Distributed, Scalable, Community Care Network Architecture that aims to provide Real-Time Access to Geographically-Dispersed Patient Medical Records. The AMPReD model includes stationary hospitals and medical clinics, mobile clinics, migrating doctors as well as patients, the communications network, and the patient medical record database. AMPReD's goals include (1) the accurate modeling of the propagation of medical records and (2) providing real-time access to patient medical records from anywhere in the system. To achieve these goals, an asynchronous, distributed algorithm must be developed that achieves concurrent access of multiple, autonomous databases. AMPReD is modeled and simulated for a representative community care network on a network of workstations configured as a loosely-coupled parallel processor, for different parametric combinations of number of doctors, patients, and number of queries or record entries generated corresponding to every patient-doctor interaction episode. AMPReD defines and obtains key performance measures including the idle times of the doctors, patient waiting times, the access times of queries as functions of their sizes, and the growth of the databases. In addition, AMPReD also measures the deviation of the actual time required for a patient-doctor interaction episode from the scheduled interaction interval, as a function of the network load. For the representative system selected, performance measures indicate that the network, utilizing 1/2T1 links, and the database system poses no bottleneck to the system even where the number of doctors and patients within a 30 minute interval are chosen at 192 and 200 respectively. A T1 is a standard, digital, transmission link that is rated at 1.44Mbits/sec.

Algorithms↗
PubMed2025

PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption.

MOTIVATION: Rare diseases affect millions of people worldwide, yet their genomic foundations remain poorly understood due to limited patient data and strict privacy regulations, such as the General Data Protection Regulation (GDPR) (https://gdpr.eu/tag/gdpr/) in March 2025. These restrictions can hinder the collaborative analysis of genomic data necessary for uncovering disease-causing variants. RESULTS: We present PRISM, a novel privacy-preserving framework based on fully homomorphic encryption (FHE) that facilitates rare disease variant analysis across multiple institutions without exposing sensitive genomic information. To address the challenges of centralized trust, PRISM is built upon a Threshold FHE scheme. This approach decentralizes key management across participating institutions and ensures no single entity can unilaterally decrypt sensitive data. Our method filters disease-causing variants under recessive, dominant, and de novo inheritance models entirely on encrypted data. We propose two algorithmic variants: a multiplication-intensive (MUL-IN) approach and an addition-intensive (ADD-IN) approach. The ADD-IN algorithms minimize the number of costly multiplication operations, enabling up to a 17× improvement in runtime for recessive/dominant filtering and 22× for de novo filtering, compared to MUL-IN methods. While ADD-IN produces larger ciphertexts, efficient parallelization via SIMD and multithreading allows it to handle millions of variants in reasonable time. To the best of our knowledge, this is the first study that utilizes FHE for privacy-preserving rare disease analysis across multiple inheritance models, demonstrating its practicality and scalability in a single-cloud setting. AVAILABILITY AND IMPLEMENTATION: The source code and the data used in this work can be found in https://github.com/mdppml/PRISM.git.

Computer Security↗
PubMed2000

Spiral interpolation algorithm for multislice spiral CT--part I: theory.

This paper presents the adaptive axial interpolator (AAI), a novel spiral interpolation approach for multislice spiral computed tomography (CT) implemented in a clinical multislice CT scanner, the SOMATOM Volume Zoom (Siemens Medical Systems, Forchheim, Germany). The method works on parallel-beam data generated from the acquired fan-beam data by azimuthal rebinning. Spiral interpolation is performed by distance-dependent weighting; i.e., for each ray, its distance to the image plane is evaluated and serves as an argument to a freely selectable weighting function, resulting in a weight factor. A normalization step is applied to the weight factors to ensure that the sum of all corresponding weights (i.e., the weights applied to rays that contribute to the same ray in the interpolated sinogram) is 1. By selection of appropriate weighting functions and suitable adjustment of the tube current, it is possible to keep the slice sensitivity profiles (SSP) as well as the pixel noise constant for all pitch values in the relevant range. Also, a large range of slice-thickness can be reconstructed from a given collimation. The method is, thus, very versatile. Further advantages are that it uses the entire applied dose for imaging and allows for efficient implementation using a table lookup approach.

Algorithms↗
PubMed2005

Uniaxial drawing of poly[(R)-3-hydroxybutyrate]/cellulose acetate butyrate blends and their orientation behavior.

Miscible blends of PHB and CAB were prepared by the solvent-casting method with various blend compositions, and their orientation behavior was investigated during uniaxial drawing. X-ray analysis revealed that the orientation of the crystallizable PHB component in the drawn PHB/CAB blends was changed from c-axis-orientation to a-axis-orientation with increasing CAB content. The a-axis-orientation was a result from the a-axis-oriented crystal growth caused by the intramolecular nucleation and the confined crystal growth. For quantitative assessment of the chain orientation, the Hermans orientation functions of the two respective components were obtained from the polarized FT-IR measurements. The orientation function of pure PHB stretched to 5 times of its initial length was approximately 0.8. However the value decreased rapidly with increasing CAB content, and it turned to a negative value from 30 wt.-% CAB content. This indicates that the PHB chains were aligned perpendicular to the drawing direction. On the contrary, the value of the CAB component remained almost unchanged at about 0.1 regardless of the blend composition and the annealing time, indicating that the CAB chains were constantly oriented parallel to the drawing direction without any chain relaxation. In addition, SAXS analysis suggested that the lamellar stacking direction also changed from parallel to perpendicular in the stretching direction with increasing CAB content.

Algorithms↗
PubMed2006

An introduction to coil array design for parallel MRI.

The basic principles of radiofrequency coil array design for parallel MRI are described from both theoretical and practical perspectives. Because parallel MRI techniques rely on coil array sensitivities to provide spatial information about the sample, a careful choice of array design is essential. The concepts of coil array spatial encoding are first discussed from four qualitative perspectives. These qualitative descriptions include using coil arrays to emulate spatial harmonics, choosing coils with selective sensitivities to aliased pixels, using coil sensitivities with broad k-space reception profiles, and relying on detector coils to provide a set of generalized projections of the sample. This qualitative discussion is followed by a quantitative analysis of coil arrays, which is discussed in terms of the baseline SNR of the received images as well as the noise amplifications (g-factor) in the reconstructed data. The complications encountered during the experimental evaluation of coil array SNR are discussed, and solutions are proposed. A series of specific array designs are reviewed, with an emphasis on the general design considerations that motivate each approach. Finally, a set of special topics is discussed, which reflect issues that have become important, especially as arrays are being designed for more high-performance applications of parallel MRI. These topics include concerns about the depth penetration of arrays composed of small elements, the use of adaptive arrays for systems with limited receiver channels, the management of inductive coupling between array elements, and special considerations required at high field strengths. The fundamental limits of spatial encoding using coil arrays are discussed, with a primary emphasis on how the determination of these limits impacts the design of optimized arrays. This review is intended to provide insight into how arrays are currently used for parallel MRI and to place into context the new innovations that are to come.

Algorithms↗
PubMed2003

Multiple parallel-pathway folding of proline-free Staphylococcal nuclease.

When a protein exhibits complex kinetics of refolding, we often ascribe the complexity to slow isomerization events in the denatured protein, such as cis/trans isomerization of peptidyl prolyl bonds. Does the complex folding kinetics arise only from this well-known reason? Here, we have investigated the refolding of a proline-free variant of staphylococcal nuclease by stopped-flow, double-jump techniques, to examine the folding reactions without the slow prolyl isomerizations. As a result, the protein folds into the native state along at least two accessible parallel pathways, starting from a macroscopically single denatured-state ensemble. The presence of intermediates on the individual folding pathways has revealed the existence of multiple parallel pathways, and is characterized by multi-exponential folding kinetics with a lag phase. Therefore, a "single" amino acid sequence can fold along the multiple parallel pathways. This observation in staphylococcal nuclease suggests that the multiple folding may be more general than we have expected, because the multiple parallel-pathway folding cannot be excluded from proteins that show simpler kinetics.

Algorithms↗