GeneLynx: a gene-centric portal to the human genome.

GeneLynx is a meta-database providing an extensive collection of hyperlinks to human gene-specific information in diverse databases available on the Internet. The GeneLynx project is based on the simple notion that given any gene-specific identifier (accession number, gene name, text, or sequence), scientists should be able to access a single location that provides a set of links to all the publicly available information pertinent to the specified human gene. GeneLynx was implemented as an extensible relational database with an intuitive and user-friendly Web interface. The data are automatically extracted from more than 40 external resources, using appropriate approaches to maximize coverage of the available data. Construction and curation of the system is mediated by a custom set of software tools. An indexing utility is provided to facilitate the establishment of hyperlinks in external databases. A unique feature of the GeneLynx system is a communal curation system for user-aided annotation. GeneLynx can be accessed freely at http://www.genelynx.org.

Pneumococcal conjugate vaccine for young children.

UNLABELLED: Pneumococcal disease is a common cause of morbidity and mortality in the pediatric population. Pneumococcal infections, which account for most serious bacterial disease in infancy and early childhood, are a major cause of acute otitis media, sinusitis, pneumonia, bacterial meningitis, and bacteremia. Streptococcus pneumoniae is the causative agent in a large percentage of these infections, although other microorganisms also play a role. The recent emergence of drug-resistant strains has provided a strong incentive for preventing pneumococcal infections by vaccination. However, the capsular polysaccharide pneumococcal vaccines used to immunize adults are neither immunogenic nor protective in young children due to poor antibody responses. Therefore, research has focused on development of additional immunogenic pneumococcal vaccines to provide long-term immunity in children < 2 years of age. The most promising approach has been the development of a protein-polysaccharide conjugate vaccine for the seven serotypes (4, 6B, 9V, 14, 18C, 19F, and 23F) that most commonly cause infections in childhood. An effective conjugate vaccine that protects against these serotypes has the potential to prevent 85 percent of bacteremia episodes, 83 percent of meningitis episodes, and 65 percent of otitis media cases in the U.S. among children younger than 6 years. The Food and Drug Administration (FDA) recently approved the first protein-polysaccharide conjugate vaccine to prevent invasive pneumococcal diseases in infants and toddlers < 2 years of age. This conjugated vaccine against pneumococcus uses the same technology as the successful vaccine against Haemophilus influenzae type b. It consists of an immunogenic but inert protein coupled covalently to the polysaccharide coat of the selected strains of pneumococci. The conjugated antigen induces a more powerful, T-cell-based immune response in infants, which is developed by the time they are 2 months of age. Some important questions regarding this vaccine for children < 2 years of age: Is the vaccine safe? Is it immunogenic? Is it efficacious in preventing invasive pneumococcal disease and controlling otitis media? FINDINGS: Results of three randomized double-blind trials designed to evaluate the safety and immunogenicity of this vaccine in healthy children < 2 years of age were reported within the last three years. The studies found that the vaccine is safe and highly immunogenic for all seven serotypes. The most recent study, involving over 37,000 young children, also evaluated the vaccine's efficacy, and reported that the vaccine is highly effective in preventing invasive disease and has had an impact on otitis media. CONCLUSIONS: The heptavalent pneumococcal conjugate vaccine is safe and highly effective in preventing pneumococcal meningitis and bacteremic pneumonia in young children < 2 years of age; it is less effective in preventing otitis media. Based on the results of three well-designed studies demonstrating the vaccine's safety, immunogenicity, and efficacy, the vaccine is safe and effective for active immunization of children < 2 years of age against invasive disease caused by seven Streptococcus pneumoniae serotypes included in the vaccine. At this time, there is no clear medical consensus regarding its safety and efficacy for control of otitis media in children < 2 years of age. This application has not been evaluated by the FDA. The pneumococcal conjugate vaccine should be considered experimental, and has not been shown to be safe or efficacious for Streptococcus pneumoniae disease other than that caused by the serotypes included in the vaccine and for invasive infection, such as bacteremia or meningitis, caused by other microorganisms.

An evidence-based evaluation of percutaneous vertebroplasty.

BACKGROUND INFORMATION: Percutaneous vertebroplasty is a therapeutic, interventional radiologic procedure that involves injection of bone cement into a cervical, thoracic, or lumbar vertebral body lesion for the relief of pain and the strengthening of bone. This procedure only recently has been introduced, and is being used for patients with lytic lesions due to bone metastases, aggressive hemangiomas, or multiple myeloma, and for patients who have medically intractable debilitating pain resulting from osteoporotic vertebral collapse. FINDINGS: Results from two uncontrolled prospective studies and several case series reports, including one with 187 patients, indicate that percutaneous vertebroplasty can produce significant pain relief and increase mobility in 70 percent to 80 percent of patients with osteolytic lesions in the vertebrae from hemangiomas, metastases, or myeloma, or with osteoporotic compression fractures. In these reports, pain relief was apparent within one to two days after injection, and persisted for at least several months up to several years. While experimental studies and preliminary clinical results suggest that percutaneous vertebroplasty can also strengthen the vertebral bodies and increase mobility, it remains to be proven whether this procedure can prevent additional fractures in the injected vertebrae. In addition, the duration of effect is not known; there were no long-term follow-up data on most of these patients, and these data may be difficult to obtain and interpret in patients with an underlying malignant process, because disease progression may confound evaluation of the treatment effect. Complications were relatively rare, although some studies reported a high incidence of clinically insignificant leakage of bone cement into the paravertebral tissues. In a few cases, the leakage of polymer caused compression of spinal nerve roots or neuralgia. Several instances of pulmonary embolism were also reported. Although patient selection criteria have not been definitely established, percutaneous vertebroplasty is considered appropriate treatment for patients with vertebral lesions resulting from osteolytic metastasis and myeloma, hemangioma, and painful osteoporotic compression fractures if the following criteria have been met: o Severe debilitating pain or loss of mobility that cannot be relieved by correct medical therapy. o Other causes of pain, such as herniated intervertebral disk have been ruled out by computed tomography or magnetic resonance imaging. o The affected vertebra has not been extensively destroyed and is at least one third of its original height. o Radiation therapy or concurrent surgical interventions, such as laminectomy, may also be required in patients with compression of the spinal cord due to ingrowth of a tumor. CONCLUSIONS: Percutaneous vertebroplasty has only recently been introduced as a treatment for osteolytic lesions and osteoporotic compression fractures of the vertebrae, but early results are promising. Up to 80 percent of patients with pain unresponsive to correct medical treatment experience a significant degree of pain relief, and few serious complications have been reported. However, relatively few patients have undergone this procedure, and there are no data from controlled clinical trials or from studies with long-term follow-up. At the present time this procedure is still in the investigational stages, but may be appropriate for patients with no other reasonable options for medical treatment.

Bacterial start site prediction.

With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. Although the existing tools predict genes in bacterial genomes with high overall accuracy, their ability to pinpoint the translation start site remains unsatisfactory. In this paper, we present a novel approach to bacterial start site prediction that takes into account multiple features of a potential start site, viz., ribosome binding site (RBS) binding energy, distance of the RBS from the start codon, distance from the beginning of the maximal ORF to the start codon, the start codon itself and the coding/non-coding potential around the start site. Mixed integer programing was used to optimize the discriminatory system. The accuracy of this approach is up to 90%, compared to 70%, using the most common tools in fully automated mode (that is, without expert human post-processing of results). The approach is evaluated using Bacillus subtilis, Escherichia coli and Pyrococcus furiosus. These three genomes cover a broad spectrum of bacterial genomes, since B.subtilis is a Gram-positive bacterium, E.coli is a Gram-negative bacterium and P. furiosus is an archaebacterium. A significant problem is generating a set of 'true' start sites for algorithm training, in the absence of experimental work. We found that sequence conservation between P. furiosus and the related Pyrococcus horikoshii clearly delimited the gene start in many cases, providing a sufficient training set.

How to interpret an anonymous bacterial genome: machine learning approach to gene identification.

In this report we address the problem of accurate statistical modeling of DNA sequences, either coding or noncoding, for a bacterial species whose genome (or a large portion) was sequenced but not yet characterized experimentally. Availability of these models is critical for successful solution of the genome annotation task by statistical methods of gene finding. We present the method, GeneMark-Genesis, which learns the parameters of Markov models of protein-coding and noncoding regions from anonymous bacterial genomic sequence. These models are subsequently used in the GeneMark and GeneMark.hmm gene-finding programs. Although there is basically one model of a noncoding region for a given genome, several models of protein-coding region are automatically obtained by GeneMark-Genesis. The diversity of protein-coding models reflects the diversity of oligonucleotide compositions, particularly the diversity of codon usage strategies observed in genes from one and the same genome. In the simplest and the most important case, there are just two gene models-typical and atypical ones. We show that the atypical model allows one to predict genes that escape identification by the typical model. Many genes predicted by the atypical model appear to be horizontally transferred genes. The early versions of GeneMark-Genesis were used for annotating the genomes of Methanoccocus jannaschii and Helicobacter pylori. We report the results of accuracy testing of the full-scale version of GeneMark-Genesis on 10 completely sequenced bacterial genomes. Interestingly, the GeneMark.hmm program that employed the typical and atypical models defined by GeneMark-Genesis was able to predict 683 new atypical genes with 176 of them confirmed by similarity search.

Deriving ribosomal binding site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction.

Accurate prediction of the position of translation initiation (N-terminal prediction) is a difficult problem. N-terminal prediction from DNA sequence alone is ambiguous is several candidate start sites are close to each other. Protein similarity search is usually unable to indicate the true start of a gene as it would require a strong protein sequence similarity at the N-terminal portion of a protein where conservative regions are rarely situated. With the aid of the GeneMark program for gene identification, we extract DNA sequence fragments presumably containing ribosome binding sites (RBS) from unannotated complete genomic sequences. These DNA segments are aligned to generate the RBS model using the Gibbs' sampling method. N-terminal prediction is then performed by using the RBS model in conjunction with the GeneMark start codon prediction to aid in determining the true N-terminal site.

A telemedicine consultative service for the evaluation of patients with urolithiasis.

OBJECTIVES: A 6-month pilot teleconsultative project linking Georgetown University Medical Center (GUMC) in Washington, DC, and City Hospital in Martinsburg, West Virginia, 90 miles away, was designed to assess the effectiveness of telemedicine on the clinical decision-making process for patients with urolithiasis. METHODS: The telemedicine system designed and tested for this project was based on a PC-based platform. Videoconferencing and review of the patient's imaging studies were performed over an Integrated Service Digital Network (ISDN) with 3 Basic Rate (BRI) ISDN lines providing a 336-kilobytes/s bandwidth through an Inverse Multiplexor (IMUX). Treatment options were recorded for the clinical trial group and a simulated study group by the consulting urologist after the initial telephone consultation, after the telemedicine consultation, and after examination of those patients transferred to GUMC. RESULTS: A total of 32 telemedicine consultations were performed: 14 in the clinical trial group and 18 in the simulated study group. The recommendation of the consulting urologist at the tertiary center was altered in 12 patients (37.5%) after the telemedicine consultation compared with the recommended treatment after the initial telephone consultation. CONCLUSIONS: In the evaluation of patients with urolithiasis, this telemedicine application enhanced the clinical decision-making process by allowing for improved quality of care through immediate access and effective transfer of information between the referring urologist, the patient, and the stone center specialist.

The complete genome sequence of the gastric pathogen Helicobacter pylori.

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

Requirements for urology and renal dialysis PC-based telemedicine applications: comparative analysis.

The Imaging Science and Information Systems (ISIS) Center of the Department of Radiology at Georgetown University Medical Center (GUMC) has been developing technical requirements for different telemedicine applications. This paper details the process through which those technical requirements are determined and shows how they may differ substantially, depending on the clinical need. This information is presented in light of two telemedicine applications being undertaken at GUMC: a urology application for the management of patients with surgical stone disease and a nephrology application for monitoring of renal dialysis patients.

Helical CT of renal masses: the value of delayed scans.

OBJECTIVE: Routine scanning techniques used for helical CT of the abdomen result in dense cortical opacification of the kidney, whereas the medulla and collecting system are not well opacified, which potentially compromises detection of renal masses. The purpose of this retrospective study was to determine if additional delayed views (taken approximately 2-4 min after the start of injection of contrast material) are necessary for the detection and characterization of renal masses. MATERIALS AND METHODS: Early (60-70 sec after the start of the injection of contrast material) and delayed scans of 40 patients with suspected renal masses were blindly evaluated by two observers. The patients harbored a total of 187 renal masses (including 62 solid masses). Each region of the kidney (upper, middle, and lower pole) was scored for the presence of a mass. Scoring was done as a binary decision and also as a five-point confidence score for receiver operating characteristic analysis. RESULTS: We found 97 regions that contained renal masses and 114 regions that did not. Receiver operating characteristic analysis revealed the observers to have significantly greater confidence in detection of renal masses on the delayed scans. The binary data showed the two observers to have a sensitivity of 97% for delayed scans versus 77% (p = .0002) and 89% (p = .027), respectively, for the early scans. For the first observer, early and delayed scans were of equal specificity, but for the second observer, the delayed scans yielded greater specificity (94% versus 85%, p = .024). On the early scans, both observers were significantly more likely to miss a neoplastic lesion than a nonneoplastic lesion. The less experienced of the two observers also tended to have greater difficulty in characterizing the lesions on the early scans. CONCLUSION: Because of the significant risk of missing a renal mass, especially a neoplasm, on early cortical-phase scans, additional delayed scans appear justified when a renal mass is suspected on the basis of other imaging tests or clinical history.

Management of locally advanced prostate cancer.

The staging and treatment of prostate cancer are complex, particularly in patients with clinical disease that has advanced locally beyond the confines of the gland. Management choices are made more difficult by a paucity of quality randomized and controlled studies. Staging has traditionally relied on digital rectal examination, which is now being augmented by improved noninvasive radiologic studies. Radiation is the most common form of treatment today, and newer techniques are being examined and compared to external-beam therapy. Surgical intervention as monotherapy has failed to show a survival advantage. Current approaches treatment appear to be evolving toward combination therapies, potentially incorporating hormonal manipulation. Patients with locally advanced disease should be encouraged to enter prospective clinical trials.

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.

BACKGROUND: The 1.83 Megabase (Mb) sequence of the Haemophilus influenzae chromosome, the first completed genome sequence of a cellular life form, has been recently reported. Approximately 75 % of the 4.7 Mb genome sequence of Escherichia coli is also available. The life styles of the two bacteria are very different - H. influenzae is an obligate parasite that lives in human upper respiratory mucosa and can be cultivated only on rich media, whereas E. coli is a saprophyte that can grow on minimal media. A detailed comparison of the protein products encoded by these two genomes is expected to provide valuable insights into bacterial cell physiology and genome evolution. RESULTS: We describe the results of computer analysis of the amino-acid sequences of 1703 putative proteins encoded by the complete genome of H. influenzae. We detected sequence similarity to proteins in current databases for 92 % of the H. influenzae protein sequences, and at least a general functional prediction was possible for 83 %. A comparison of the H. influenzae protein sequences with those of 3010 proteins encoded by the sequenced 75 % of the E. coli genome revealed 1128 pairs of apparent orthologs, with an average of 59 % identity. In contrast to the high similarity between orthologs, the genome organization and the functional repertoire of genes in the two bacteria were remarkably different. The smaller genome size of H. influenzae is explained, to a large extent, by a reduction in the number of paralogous genes. There was no long range colinearity between the E. coli and H. influenzae gene orders, but over 70 % of the orthologous genes were found in short conserved strings, only about half of which were operons in E. coli. Superposition of the H. influenzae enzyme repertoire upon the known E. coli metabolic pathways allowed us to reconstruct similar and alternative pathways in H. influenzae and provides an explanation for the known nutritional requirements. CONCLUSIONS: By comparing proteins encoded by the two bacterial genomes, we have shown that extensive gene shuffling and variation in the extent of gene paralogy are major trends in bacterial evolution; this comparison has also allowed us to deduce crucial aspects of the largely uncharacterized metabolism of H. influenzae.

Health systems evaluation of telemedicine: a staged approach.

Telemedicine promises greater access to health care of higher quality, potentially at lower cost. The diverse applications of telemedicine technology developed to date have not been evaluated systematically in terms of their ability to achieve these goals. Furthermore, the great variety in telemedicine applications and the far-reaching consequences of new information systems for health care delivery pose challenges to traditional methods of technology assessment. Methods appropriate for mature technologies may not be suitable for emerging ones and, indeed, may risk stifling their development with premature negative conclusions. The staged approach to technology assessment proposed here matches the analysis to the technology's stage of development. It focuses on access, quality, and cost and considers the communication pathway employed in the telemedicine application. A staged approach to technology assessment can inform and foster the development of new telemedicine technology while allowing health care delivery systems to make rational decisions about adopting telemedicine.

Applications of GeneMark in multispecies environments.

This paper is supposed to bridge the gap between practical experience in using GeneMark for a rapidly widening repertoire of genomes, and the available publications that determine and compare the gene prediction accuracy of the GeneMark method for different genomes. Here we focus on the genome-specific variability of prediction error rates and their sources. DNA sequence inhomogeneity is present both in training and control sets of coding and non-coding regions. Coding region inhomogeneity, caused by differences in sequence composition between "native" and horizontally transferred genes or between genes expressed at different levels, contributes to the false negative error rate. Inhomogeneity of non-coding region may frequently be caused by the presence of unnoticed genes and contributes to the false positive error rate. We have documented such unnoticed genes in GenBank sequences for several species Some of protein products of these genes have been characterized by similarity search methods. For others, which we call "pioneer genes", no significant similarity has been found at a protein sequence level although the confidence of GeneMark prediction is high. For instance, to date a majority of those pioneer gene predictions made for E. coli now show strong similarity to more recently characterized proteins that have been added to protein sequence database. Another practical question is related to genomic sequence inhomogeneity at interspecies level: if GeneMark has not been trained for a particular species, is it possible to apply models derived for phylogenetically close genomes? The answer is, yes. The results of cross-species gene prediction experiments show that cross-species prediction can often be reasonably accurate.

Computer survey for likely genes in the one megabase contiguous genomic sequence data of Synechocystis sp. strain PCC6803.

Using the computer program GeneMark, the open reading frames (ORFs) previously assigned within the one megabase sequence data of the genome of the cyanobacterium, Synechocystis sp. strain PCC6803 (Kaneko et al., DNA Res. 2: 153-166, 1995), were re-examined. Matrices required by GeneMark for its statistical calculation were generated and modified by running a script termed GeneMark-Genesis that performed recursive application of GeneMark against the Synechocystis data and evaluated the probability scores for optimization. Based on the matrices thus generated, 752 of the 818 previously assigned ORFs (92%) were supported by GeneMark as likely coding sequences, of which 26 were predicted to start at more internal positions than previously assigned. In addition, 50 ORFs were newly identified as likely coding sequences, most of them being shorter than 300 bp. Thus, the procedure was proven to be very powerful to locate likely coding regions within the genomic sequence data of Synechocystis without having prior information concerning their similarity to the genes of other organisms. However, GeneMark did not predict 66 previously assigned ORFs as likely genes: 14 of them showed significant degrees of similarity to known genes and 10 others were found within IS-like elements. It seems that these genes, many of which appear to be exogenous origin, escaped detection by GeneMark as in the case of "class 3 (horizontally transferred) genes" of E. coli, which in turn suggests that genes of different phylogenetic origins might also be detected as such by modifying the matrices.

Primary extragonadal germ cell tumors of the retroperitoneum: differentiation of primary and secondary tumors.

Primary extragonadal germ cell tumors (EGCTs) of the retroperitoneum are rarely encountered. In most cases, they arise from remnants of the genital ridge, whereas the majority of retroperitoneal germ cell tumors are metastases from primary testicular tumors. Differentiating between these primary and secondary tumors can be difficult because gonadal germ cell tumors can regress or develop slowly. Careful examination of the testes with ultrasound (US) is crucial for this determination, but asynchronous or metachronous lesions in both the testes and retroperitoneum can occur. Symptoms are often nonspecific, and diagnosis is frequently delayed. Serum markers such as beta-human chorionic gonadotropin and alpha-fetoprotein are often helpful in the diagnosis and follow-up of these tumors. Imaging techniques such as US and computed tomography play a major role in the localization and differentiation of primary and secondary retroperitoneal EGCTs. Treatment of EGCTs usually requires a combination of surgery, irradiation, and chemotherapy.

Renal oncocytoma and carcinoma: failure of differentiation with CT.

The authors studied the hypothesis that oncocytoma and adenocarcinoma of the kidney can be differentiated with computed tomographic (CT) criteria and that differences would become more apparent as tumors enlarged. On contrast material-enhanced scans, homogeneous attenuation throughout the tumor and a central, sharply marginated, stellate area of low attenuation were considered predictors of oncocytoma. Any area of decreased attenuation in the tumor except for a stellate, central area was used as a predictor of adenocarcinoma. Among oncocytomas larger than 3 cm in diameter, 67% exhibited the criteria for oncocytoma and 33% met the criterion for adenocarcinoma; among smaller oncocytomas, the respective results were 82% and 18%. Among adenocarcinomas larger than 3 cm in diameter, 84% fulfilled the criterion for malignancy and 16% were incorrectly predicted to be oncocytomas; among smaller adenocarcinomas, the respective results were 58% and 42%. The authors conclude that the CT criteria used are poor predictors of the diagnosis of oncocytoma or adenocarcinoma regardless of tumor size.

The natural history of renal lesions in von Hippel-Lindau disease: a serial CT study in 28 patients.

OBJECTIVE: Von Hippel-Lindau disease is a multisystem disorder predisposing to renal cysts and cancer. The growth and development of these renal lesions have not been documented previously. We reviewed serial CT scans to determine the rates and patterns of growth of renal lesions associated with von Hippel-Lindau disease. SUBJECTS AND METHODS: Twenty-eight patients with von Hippel-Lindau disease and renal involvement, including the spectrum from simple cysts to solid masses, had follow-up examinations for at least 1 year (mean, 2.4 years; range, 1-12 years) with serial contrast-enhanced abdominal CT. Renal lesions were measured and characterized. Surgical correlation was available in 12 patients. RESULTS: Two hundred twenty-eight lesions (eight lesions per patient) were detected. On the basis of their CT appearance, 168 lesions (74%) were classified as cysts, 18 (8%) as cysts with solid components, and 42 (18%) as solid masses. Among 12 patients with pathologic confirmation, the solid components of cystic lesions and solid lesions almost always contained renal carcinoma. The majority of cysts remained the same size (71%) or enlarged (20%); 9% became smaller or entirely involuted during the follow-up period. Although it is generally presumed that renal cysts are precursors to cancers, the transformation of a simple cyst to a solid lesion was observed in only two patients. Among the 42 solid lesions, all but two enlarged with time, with a mean doubling time of 10 months. CONCLUSION: The renal lesions associated with von Hippel-Lindau disease exhibited wide differences in growth. The majority of renal cysts grew slowly but some involuted. Transition to solid renal cancer was rare among cysts. Complex cystic and solid lesions contained neoplastic tissue that uniformly enlarged. These data may be used to help predict the progression of renal lesions in von Hippel-Lindau disease.