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PubMed2002

PGAAS: a prokaryotic genome assembly assistant system.

MOTIVATION: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. RESULTS: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. AVAILABILITY: We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.

Algorithms↗
PubMed1995

Surgical indications in low lumbar burst fractures: experiences with Anterior Locking Plate System and the reduction-fixation system.

A study of 14 surgically treated patients with low lumbar burst fractures (L3 to L5) is reported. Initially, 13 patients presented with incomplete neurologic deficits below the level of injury. The follow-up period ranged from 24 to 40 months, with an average of 30 months. In group 1, seven patients underwent one-stage anterior decompression, fusion, and Anterior Locking Plate System (ALPS) fixation. In Group 2, seven patients had posterior surgery with decompression, portero-lateral fusion, and a short segment fixation, one above and one below the injuried level, with the reduction-fixation transpediculate system. Indications for one-stage anterior surgery consisted of patients with incomplete neurologic deficits, segmental kyphotic deformity caused by loss of anterior vertebral height (< 50%), or canal encroachment < 50%. When there is significant radiologic evidence of lamina fractures, displaced or greenstick type, or injuries that occurred at the L5 level, the posterior approach was undertaken initially. This may be followed by anterior surgery if satisfactory vertebral height restoration or canal clearance was not achieved. Five dura tears (36%) were noted during surgery: two tears in group 1 and three tears in group 2. There were two patients in group 2 (29%) who had screws broken; however, none in group 1 demonstrated implant failure. In the low lumbar region, the step-off ALPS plate is preferable to the straight plate because of the increasing size of the vertebral body toward the caudal area. A low profile and easy application were its advantages. However, the ALPS could not be distracted or compressed anteriorly.

Adolescent↗
PubMedDate not supplied

Clinical trial of time-resolved scanning optical mammography at 4 wavelengths between 683 and 975 nm.

The first time-resolved optical mammograph operating beyond 900 nm (683, 785, 913, and 975 nm) is presently being used in a clinical trial to test the diagnostic potential of the technique in detecting and characterizing breast lesions. Between November 2001 and October 2002, 101 patients with malignant and benign lesions were analyzed retrospectively. Scattering plots, as derived from a homogeneous model, and late gated intensity images, to monitor spatial changes in the absorption properties, are routinely used. The intensity images available at four wavelengths provide sensitivity to the main tissue constituents (oxy- and deoxyhemoglobin, water, and lipids), in agreement with expected tissue composition and physiology, while the scattering plots mirror structural changes. Briefly, tumors are usually identified due to the strong blood absorption at short wavelengths, cysts to the low scattering, and fibroadenomas to low absorption at 913 nm and high at 975 nm, even though the optical features of fibroadenomas seem not to be uniquely defined. The effectiveness of the technique in localizing and discriminating different lesion types is analyzed as a function of various parameters (lesion size, compressed breast thickness, and breast parenchymal pattern). .

Algorithms↗
PubMed2003

Post-beamforming second-order Volterra filter for pulse-echo ultrasonic imaging.

We present a new algorithm for deriving a second-order Volterra filter (SVF) capable of separating linear and quadratic components from echo signals. Images based on the quadratic components are shown to provide contrast enhancement between tissue and ultrasound contrast agents (UCAs) without loss in spatial resolution. It is also shown that the quadratic images preserve the low scattering regions due to their high dynamic range when compared with standard B-mode or harmonic images. A robust algorithm for deriving the filter has been developed and tested on real-time imaging data from contrast and tissue-mimicking media. Illustrative examples from image targets containing contrast agent and tissue-mimicking media are presented and discussed. Quantitative assessment of the contrast enhancement is performed on both the RF data and the envelope-detected log-compressed image data. It is shown that the quadratic images offer levels of enhancement comparable or exceeding those from harmonic filters while maintaining the visibility of low scattering regions of the image.

Algorithms↗
PubMed1985

Real-time analysis of sperm motion using automatic video image digitization.

A methodology is described for automatic, real-time analysis of sperm movement characteristics. Video micrographic images of spermatozoa are digitized, compressed, and then analyzed using a Motion Analysis Corporation Expert Vision system. The system includes a VP-100 video processor, a video camera, and a Sun-2/120 minicomputer. Algorithms for detection of and discrimination among sperm are described, and desirable operating characteristics of the system are considered. Salient parameters which characterize the kinematics of sperm swimming trajectories are discussed.

Analog-Digital Conversion↗
PubMed1996

A comparison of prolonged manual and mechanical external chest compression after cardiac arrest in dogs.

The effects of manual and a new mechanical chest compression device (Heartsaver 2000) during prolonged CPR with respect to haemodynamics and outcome were tested in a prospective, randomized, controlled experimental trial during ventricular fibrillation in 12 dogs of 9-13 kg body weight after 1 min of cardiac arrest. During the first 10 min of CPR the dogs were resuscitated according to the Basic Life Support (BLS) algorithm, followed by 20 min of Advanced Life Support (ALS) algorithm. After 30 min of CPR both manual and mechanical CPR groups were resuscitated following a standardized ALS protocol. During CPR, coronary perfusion pressure and end tidal CO2 were greater with mechanical CPR. All animals were successfully resuscitated and neurological deficit scores were not different. The CPR trauma score was less in the mechanical group. Mechanical external chest compression provided better haemodynamics than the manual technique, though outcome did not differ. Both optimally performed manual and mechanical techniques produce flow sufficient to maintain organ viability for 30 min of CPR after a 1 min arrest interval.

Animals↗
PubMed1998

Virtual endoscopy (VE) of the basal cisterns: its value in planning the neurosurgical approach.

Virtual endoscopy (VE) is a postprocessing technique based on a diverging ray casting algorithm to create perspective 3 D-images from computed tomographic angiography (CTA) and high resolution magnetic resonance imaging (MR) data. By applying VE to aneurysms, tumors, and vascular compression syndromes within the basal cisterns, endoscopic-like views of these structures are achieved from an intracisternal point above the cranial base. These views closely simulate the surgeon's impression during intraoperative endoscopy or microscopy and facilitate preoperative planning of different approaches.

Adult↗
PubMed1985

The frozen shoulder.

The clinical entity of frozen shoulder has been the subject of considerable controversy concerning pathogenesis and treatment. This is a review and interpretation of the literature against the background of my personal experience and a formulation of a treatment algorithm based on a practical synthesis of these sources. The separate stages of the disease are clearly definable and must be considered in prescribing treatment for the purpose of compressing the natural history and morbidity of this self-limited though disabling condition.

Diagnosis, Differential↗
PubMedDate not supplied

A cryptologic based trust center for medical images.

OBJECTIVE: To investigate practical solutions that can integrate cryptographic techniques and picture archiving and communication systems (PACS) to improve the security of medical images. DESIGN: The PACS at the University of California San Francisco Medical Center consolidate images and associated data from various scanners into a centralized data archive and transmit them to remote display stations for review and consultation purposes. The purpose of this study is to investigate the model of a digital trust center that integrates cryptographic algorithms and protocols seamlessly into such a digital radiology environment to improve the security of medical images. MEASUREMENTS: The timing performance of encryption, decryption, and transmission of the cryptographic protocols over 81 volumetric PACS datasets has been measured. Lossless data compression is also applied before the encryption. The transmission performance is measured against three types of networks of different bandwidths: narrow-band Integrated Services Digital Network, Ethernet, and OC-3c Asynchronous Transfer Mode. RESULTS: The proposed digital trust center provides a cryptosystem solution to protect the confidentiality and to determine the authenticity of digital images in hospitals. The results of this study indicate that diagnostic images such as x-rays and magnetic resonance images could be routinely encrypted in PACS. However, applying encryption in teleradiology and PACS is a tradeoff between communications performance and security measures. CONCLUSION: Many people are uncertain about how to integrate cryptographic algorithms coherently into existing operations of the clinical enterprise. This paper describes a centralized cryptosystem architecture to ensure image data authenticity in a digital radiology department. The system performance has been evaluated in a hospital-integrated PACS environment.

Algorithms↗
PubMed2005

Algorithmic approaches for computing elementary modes in large biochemical reaction networks.

The concept of elementary (flux) modes provides a rigorous description of pathways in metabolic networks and proved to be valuable in a number of applications. However, the computation of elementary modes is a hard computational task that gave rise to several variants of algorithms during the last years. This work brings substantial progresses to this issue. The authors start with a brief review of results obtained from previous work regarding (a) a unified framework for elementary-mode computation, (b) network compression and redundancy removal and (c) the binary approach by which elementary modes are determined as binary patterns reducing the memory demand drastically without loss of speed. Then the authors will address herein further issues. First, a new way to perform the elementarity tests required during the computation of elementary modes which empirically improves significantly the computation time in large networks is proposed. Second, a method to compute only those elementary modes where certain reactions are involved is derived. Relying on this method, a promising approach for computing EMs in a completely distributed manner by decomposing the full problem in arbitrarity many sub-tasks is presented. The new methods have been implemented in the freely available software tools FluxAnalyzer and Metatool and benchmark tests in realistic networks emphasise the potential of our proposed algorithms.

Algorithms↗
PubMed1987

Differentiation of vascular and neurogenic claudication.

Lower extremity pain caused by exercise but relieved by rest is usually a reliable symptom of chronic arterial insufficiency. However, similar discomfort often occurs in patients who have neurospinal compression. Furthermore, both arterial occlusive disease and neurogenic causes of lower extremity discomfort may present simultaneously. Forty patients with symptoms that suggested intermittent claudication comprised our study group. All had non-arterial cause of their complaint. The nonvascular origin of the symptoms was suggested initially by clinical evaluation in 30 patients and by noninvasive evaluation in 25 patients. The neurospinal origin of symptoms was obscured in 15 patients because of the concomitant presence of significant arterial occlusive disease as demonstrated by noninvasive arterial testing. Twelve of these 15 patients underwent arterial reconstruction, which did not relieve their symptoms. Subsequently, the neurospinal origin of their symptoms was proven by appropriate evaluation and therapy. Forms of evaluation that proved helpful in the differential diagnosis were lumbosacral spine x-rays, electromyography, nerve conduction velocity studies, computerized tomography, Doppler noninvasive assessment and, at times arteriography and contrast myelography.

Adult↗
PubMed2003

Spinal cord compression: a review of 70 pediatric patients.

The authors report their experience with 70 pediatric patients with spinal cord compression (SCC) due to malignancies identified among 898 patients with solid tumors. An extradural tumor was the most frequent cause of SCC (71%); 54% of these were soft tissue sarcomas and neuroblastoma. Most intradural tumors (70%) were outside the spinal cord, 9/12 being metastatic medulloblastomas. The SCC localized mainly to the dorsal and lumbosacral regions (42% each). Pain was the most common symptom (94%). MRI proved diagnostic in all cases in which it was used, while myelography was diagnostic in 85% of 26 patients. CT scan demonstrated the lesion in 83% of the patients. Laminectomy was provided for patients with paraplegia of less than 96 h evolution; isolated recurrence of the main tumor; a primary spinal cord tumor; progression of neurologic symptoms after chemotherapy/radiotherapy; chemotherapy and radiotherapy-resistant tumor (when known); resection of a paraspinal tumor. Surgery was avoided when prognosis of primary disease was poor or risks exceeded possible benefits. Twelve/twenty-one (57%) patients with paraplegia were able to walk after laminectomy only, while 14% (2/14) improved after chemotherapy and radiotherapy. Survival rates were 38% for the former and 36% for the latter. Overall survival was related to the original malignancy. All patients (12) admitted without paraplegia and submitted to laminectomy were able to walk, and of these, 6 presented a primary spinal cord tumor. The remaining had paraspinal tumors that extended to the spinal canal. Almost 87% (20/23) of the patients without paraplegia who submitted to medical treatment were able to walk, while only one progressed to paraplegia. Patients with SCC may entertain radio- and chemotherapy when harboring tumors responding to such therapies and present no evidence of neurologic damage progression. The latter manifestation is a strong indication for laminectomy without delay.

Adolescent↗
PubMed2000

Imaging of tinnitus: a review.

Tinnitus, a buzzing or ringing in the ear, may be pulsatile or continuous (nonpulsatile). The distinction, with a detailed clinical evaluation, determines the most appropriate imaging study. Pulsatile tinnitus suggests a vascular neoplasm, vascular anomaly, or vascular malformation. Most of the neoplasms are glomus tympanicum and glomus jugulare tumors. Vascular anomalies may cause pulsatile tinnitus, but the mechanism is unknown, and another (treatable) cause should be sought. Most neoplasms and anomalies are best seen on bone algorithm computed tomographic (CT) studies. Dural vascular malformations are often elusive on all cross-sectional imaging studies; conventional angiography may be necessary to make this diagnosis. Flow-sensitive magnetic resonance (MR) images show vascular loops compressing the eighth cranial nerve. Carotid dissections, aneurysms, atherosclerosis, and fibromuscular dysplasia can be identified on both MR imaging or MR angiographic studies and CT or CT angiographic studies. Otosclerosis and Paget disease are CT diagnoses. Benign intracranial hypertension often has no abnormal imaging findings. For patients with nonpulsatile tinnitus, MR imaging is the study of choice to exclude a vestibular schwannoma or other neoplasm of the cerebellopontine angle cistern. Multiple sclerosis and a Chiari I malformation are rare causes of pulsatile tinnitus, also best seen on MR studies. Many patients with tinnitus have no abnormal imaging findings.

Algorithms↗
PubMed2004

The study of diagnostic accuracy of chest nodules by using different compression methods.

BACKGROUND: The purpose of this study was to compare the diagnostic accuracy of small nodules in the chest by using different compression methods. METHOD: Two radiologists with 5 years experience twice interpreted 39 chest images by using lossless and lossy compression methods. The time interval was 3 weeks. Each time the radiologists interpreted one kind of compressed images. The image browser used the Unisight software provided by Atlastiger Company in Shanghai. The interpreting results were analyzed by the ROCKIT software and the ROC curves were painted by Excel 2002. RESULTS: In studies of receiver operating characteristics for scoring the presence or absence of nodules, the images with lossy compression method showed no statistical difference as compared with the images with lossless compression method. CONCLUSION: The diagnostic accuracy of chest nodules by using the lossless and lossy compression methods had no significant difference, we could use the lossy compression method to transmit and archive the chest images with nodules.

Algorithms↗
PubMed2000

New real-time strain imaging concepts using diagnostic ultrasound.

Two real-time strain imaging concepts and systems are presented. Both systems are based on a conventional ultrasound scanner that is connected to a PC with an A/D converter card for real-time data acquisition of rf data. Differential strain between successively acquired rf frames are estimated using phase root seeking. The first concept uses a special real-time implementation of manual elastography. In the second concept, denoted 'vibrography', the static compression is replaced by low-frequency axial vibration of the probe, still operating in quasistatic acquisition mode. The properties of both concepts are discussed with regard to noise and motion artefacts, and it is shown, using simulations and phantom experiments, that both imaging concepts yield the same kind of strain images. Vibrography has the advantage that no manual compression has to be applied, total compression can be very low and some motion artefacts are better suppressed.

Algorithms↗
PubMed2005

A space-efficient construction of the Burrows-Wheeler transform for genomic data.

Algorithms for exact string matching have substantial application in computational biology. Time-efficient data structures which support a variety of exact string matching queries, such as the suffix tree and the suffix array, have been applied to such problems. As sequence databases grow, more space-efficient approaches to exact matching are becoming more important. One such data structure, the compressed suffix array (CSA), based on the Burrows-Wheeler transform, has been shown to require memory which is nearly equal to the memory requirements of the original database, while supporting common sorts of query problems time efficiently. However, building a CSA from a sequence in efficient space and time is challenging. In 2002, the first space-efficient CSA construction algorithm was presented. That implementation used (1+2 log2 |summation|)(1+epsilon) bits per character (where epsilon is a small fraction). The construction algorithm ran in as much as twice that space, in O(| summation|n log(n)) time. We have created an implementation which can also achieve these asymptotic bounds, but for small alphabets, and only uses 1/2 (1+|summation|)(1+epsilon) bits per character, a factor of 2 less space for nucleotide alphabets. We present time and space results for the CSA construction and querying of our implementation on publicly available genome data which demonstrate the practicality of this approach.

Animals↗
PubMed2001

Prostate cancer and spinal cord compression.

Prostate cancer metastasis to the spine is an extremely difficult clinical problem to treat. However, it occurs commonly, and all clinicians--not only oncologists--should undertake to understand its pathogenesis, diagnosis, clinical presentation, and current treatment options. This review emphasizes the surgical treatment of prostate cancer metastasis to the spine. The goals of this article are to (1) present an overview of the pathophysiology of this disease, with an emphasis on the mechanisms of metastasis and invasion, (2) provide a general overview of the clinical presentation and diagnosis of metastatic prostate carcinoma, and (3) discuss currently available treatment options. Such options include best medical management, nonsurgical treatments (radiation, chemotherapy), and surgical treatment of newly diagnosed and previously irradiated metastatic prostate carcinoma to the spine. Algorithms for the treatment of this disease are presented.

Algorithms↗
PubMed2005

Geometric diffusions for the analysis of data from sensor networks.

Harmonic analysis on manifolds and graphs has recently led to mathematical developments in the field of data analysis. The resulting new tools can be used to compress and analyze large and complex data sets, such as those derived from sensor networks or neuronal activity datasets, obtained in the laboratory or through computer modeling. The nature of the algorithms (based on diffusion maps and connectivity strengths on graphs) possesses a certain analogy with neural information processing, and has the potential to provide inspiration for modeling and understanding biological organization in perception and memory formation.

Algorithms↗