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PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗
PubMed1992

'References'.

Explore the source record for details and available documents.

Databases, Bibliographic↗
PubMed1994

Dose-response assessment for developmental toxicity. I. Characterization of database and determination of no observed adverse effect levels.

Developmental toxicity risk assessment currently relies on the estimation of reference doses (RfDDTs) or reference concentrations (RfCDTS) based on the use of no observed adverse effect levels (NOAELs) and uncertainty factors. The benchmark dose (BMD) has been proposed as an alternative basis for reference value calculations. A large database of 246 developmental toxicity experiments (Segment II-type studies) representing 1825 data subsets for various endpoints was compiled for use in comparing NOAEL and BMD approaches to developmental toxicity risk assessment. This paper describes the characteristics of the database used and the estimation of NOAELs using several approaches. For each endpoint evaluated, two NOAELs were calculated using the NOSTASOT procedure (Tukey et al., 1985). The first NOAEL calculation, the QNOAEL, was based on a quantal response where a litter was defined as "affected" if one or more fetuses or implants in the litter had the endpoint of interest. The second NOAEL calculation, the CNOAEL, was based on the proportion of fetuses or implants affected within each litter and was treated as a continuous response variable. Fifty-seven percent of the 246 experiments had at least one endpoint that showed a significant trend with dose. A total of 386 data sets were significant with respect to both the quantal and continuous test of trend. An additional 44 data sets were identified with significant trend only by the quantal approach whereas 177 additional data sets were identified with significant trend tests only by the continuous approach. Thus, the continuous approach appeared to be more powerful in detecting dose-related toxicity, but the patterns detected by the two approaches differed.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMedDate not supplied

The frequency of chromosomal abnormalities in patients referred for fragile X analysis.

The present paper summarizes our existing database on chromosomal abnormalities found in patients referred because of a question of the Fragile X Syndrome during the period from January 1, 1990 to June 30, 1995. Cytogenetic results were derived from testing performed at the cytogenetics laboratory at Rhode Island Hospital. All positive fragile X individuals detected among our sample population represent index patients from separate kindreds. Of a total of 327 cases referred for fragile X testing, 10 (3.06 percent) were found to be positive for fragile X by either cytogenetics alone or by both cytogenetics and DNA testing, 12 (3.60 percent) were found to be positive for either a numerical or structural chromosomal abnormality, while 10 (3.06 percent) were found to exhibit a heteromorphism. Positive chromosomal findings included numerical chromosomal abnormalities of the sex chromosomes and autosomes, deletions, and translocations. Heteromorphism mostly involved an increase in the length of heterochromatic regions of certain chromosomes as well as a pericentric inversion of a chromosome 9, usually considered normal variants. It is concluded that chromosomal abnormalities other than fragile X are found with equal and, in some cases, higher frequency than the frequency of fragile X positivity in patients referred for a question of the Fragile X Syndrome. Our figures, consistent with those reported in the literature, underscore the value of routine karyotyping in this population of patients. Except under special circumstances, it is important that GTG-banding analysis be performed so that the entire human genome be examined in addition to scoring for the fragile X mutation on Xq27.3. Especially in view of the recent finding of the relative rarity of this condition, the exclusive use of DNA analysis is not advised.

Chromosome Aberrations↗
PubMed1996

Cytomegalovirus prophylaxis and treatment following bone marrow transplantation.

OBJECTIVE: To provide an overview of the role of cytomegalovirus (CMV) in the bone marrow transplant (BMT) population and update the current methods of prevention and treatment of CMV infection and disease, with emphasis on CMV interstitial pneumonia (CMV-IP). DATA SOURCES: The current medical literature, including abstracts presented at recent national and international meetings, is reviewed. References were identified by searching the MEDLINE database from January 1988 through June 1994. The reference lists of the published studies and reviews obtained from the initial literature search were reviewed as well. STUDY SELECTION: Data regarding the epidemiology of CMV, the risk factor associated with CMV infection and disease, as well as data on the prevention and the treatment of CMV infection and disease in the BMT population are cited. Specific attention was focused on randomized, placebo-controlled studies pertaining to the prevention of CMV infection and disease in CMV-immunoglobulin G positive recipients undergoing allogeneic BMT. Information from nonrandomized, placebo-controlled studies was included in the absence of stronger data. DATA EXTRACTION: Information contributing to CMV in the BMT population was reviewed. Data supporting and disputing specific preventive and treatment modalities are presented. DATA SYNTHESIS: The incidence of CMV seropositivity in the general population is high and while BMT becomes a widely accepted treatment modality, CMV reactivation and subsequent disease, especially CMV-IP, becomes a significant prognostic factor of morbidity and mortality. Even though antiviral agents such as ganciclovir and foscarnet can inhibit the viral replication in vivo, they have not been able to treat CMV-IP effectively. It has been suggested that CMV-IP is an immunopathologic process that can cause irreversible damage, hence, the low efficacy of antiviral therapy and the associated high mortality. Immunomodulating agents such as intravenous immune globulin and cytomegalovirus hyperimmune globulin can increase the efficacy of antivirals in the treatment of CMV-IP. This further supports the postulated immunopathologic process of this disease. The lack of understanding of the pathophysiology of the disease compromised the efforts of treatment and led to the development of preventive interventions with antiviral and immunomodulatory regimens that resulted in a significantly lower incidence of infection and disease. As a result of current data, the Eastern Cooperative Oncology Group has published guidelines for the prevention and treatment of CMV infection and disease. CONCLUSIONS: The prognosis of CMV disease in the BMT recipients has improved as a result of a wide variety of modifications in the management of BMT recipients. These include an increased understanding of the risk factors associated with CMV infection, routine screening for CMV replication and excretion, and more effective prophylactic regimens. Still, more than half of the patients who develop pneumonia will die, indicating that more studies are needed to increase the understanding of the pathophysiology and refine the preventive and therapeutic regimens against CMV.

Antiviral Agents↗
PubMedDate not supplied

Computerized Dysmorphology Database Mackay (CDDM): preliminary report.

A computerized dysmorphology database is useful for the pediatrician and geneticist in the task of diagnosing multiple malformation syndromes in children. We set up a new dysmorphology database "Computerized Dysmorphology Database Mackay (CDDM)" managed by the Clipper program. At present 278 disease entities with their clinical features and references are stored in the database. In this article, we report a practice analysis of ten dysmorphic patients by CDDM. A specific syndrome was accurately and rapidly diagnosed with the aid of CDDM in all ten cases. They serve as examples on how CDDM can be efficiently applied to obtain a short list of syndromes for differential diagnosis.

Abnormalities, Multiple↗
PubMed1995

A study of intracranial volume in Apert syndrome.

The present study was undertaken to characterize the intracranial volume in patients with Apert syndrome. Radiographic and CT-based techniques for measuring intracranial volume were found to show close correlation when validated in dry normal adult skulls. A standard-deviation score of intracranial volume, determined from CT scans in 20 patients with Apert syndrome from birth to 30 years of age, was calculated with reference to a normative database of age- and sex-matched controls. Analysis of the data showed no significant difference in standard-deviation score between Apert patients with or without ventriculomegaly, before or after cranial vault surgery, or between male and female patients. The mean standard-deviation score among all Apert CT scans compared with normative data was 3.1, which was highly significant (p < 0.001). However, the growth curves showed no significant difference in intracranial volume between Apert and normal patients below 3.5 months of age. In summary, intracranial volume in Apert syndrome is within normal range at birth but increases to greater than 3 standard deviations above normal after 3.5 months of age, a finding independent of cranial vault surgery.

Acrocephalosyndactylia↗
PubMed1998

Proteins of rat serum: I. Establishing a reference two-dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography-electrospray mass spectrometry.

In the present investigation, we have identified 56 major spots, or spot rows, corresponding to 22 proteins, in the 2-DE pattern of adult male rats. This was done mainly by applying two complementary techniques, namely immunoblotting and high performance liquid chromatography-mass spectrometry (HPLC-MS) peptide mapping. Glycoproteins were characterized by affinity blotting with six lectins. We have also detailed how rat serum differs from human serum in two main respects: (i) relative abundance of individual proteins, which amounts in some cases to a complete absence in either sample, and (ii) varying molecular parameters for homologous proteins. It was thus possible to establish a first-generation reference map of rat serum proteins, which can be accessed through http://weber.u.washington.edu/ruedilab/aebersold++ +.html. We hope the present database will be a useful reference for the evaluation of changes in serum protein distribution in the course of pharmacological and toxicological studies. The recognition of species-specific proteins appears of special relevance in this respect.

Animals↗
PubMed1995

Review of dental materials citations: Part A, January to June 1995.

OBJECTIVE: Electronic databases are an excellent resource for identifying relevant references for research and education projects. However, these databases are not yet a substitute for direct inspection of the literature because: (a) there still is a lag of many months between journal issue publication and updates of the database, and (b) most databases selectively report a portion of the entire literature. The objective was to identify and categorize all the dental materials citations in biomedical journals that were published from January 1995 through June 1995. METHODS: Seventeen primary and 56 secondary dental journals were manually searched via their tables of contents to detect dental materials publications from January to June of 1995. Dental materials citations were categorized into 17 major sections and further divided into several subsections. The review excluded case reports and literature primarily related to dental implants or biomedical materials outside of dentistry. RESULTS: Three hundred-sixty-nine citations were identified. The greatest number of citations were associated with dentin bonding, composites, and glass ionomers. There was no significant increase in dental materials publications vs. the number reported for 1994. SIGNIFICANCE: This list provides a comprehensive source for review by academicians and researchers to bridge the gap between initial publication and electronic citation.

Dental Materials↗
PubMed1996

Acephalgic migraines of childhood.

Migraine aura without headache (acephalgic migraines) is a recognized subset of migrainous phenomena in the adult population. No reports of its prevalence or characteristics in a series of children exists. Using diagnostic criteria for migraine aura without headache established by the International Headache Society, a retrospective review of a computerized database of all patients referred over a 4-year period (July 1991 to June 1995 inclusive) to a single university-based pediatric neurologist was performed. Fourteen patients were identified, representing 2% of all patients with a primary diagnosis of migraine. Nine were females and 13 had a strong family history of migraines. Age of onset of symptoms ranged from 5 to 12 years with a mean of 8 years. Symptoms were episodic in all, varying in frequency from weekly to more typically monthly, lasting generally less than 10 min. In 9 patients the aura described was that of often colorful photopsias or scintillating scotomas. Two had micropsia, one had temporal distortion (time "speeded up"), one had hyperacusis, and the final patient had a vague sense of disconnection from her surroundings. Only 2 patients had a headache occasionally associated with the described aura. In addition to the acephalgic migraines, 9 patients had either common or classical migraines, the latter typically featuring aura distinct from those observed in these patients' acephalgic episodes. Neurologic examination, electrophysiologic investigation (EEG/evoked potentials), and neuroimaging were noncontributory in all instances. Migraine aura without headache is a recognizable benign migraine syndrome of late childhood.

Child↗
PubMed1997

An epidemiologic review of dietary intake studies among American Indians and Alaska Natives: implications for heart disease and cancer risk.

PURPOSE: Dietary factors play an important role in the occurrence of heart disease and cancer. While American Indians and Alaska Natives (AIANs) have unique heart disease and cancer mortality profiles, little is known about the effect of diet on heart disease and cancer risk in these populations. This paper reviews existing nutritional intake data from adult AIANs, and considers the potential impact of diet on heart disease and cancer in these communities. METHODS: A review of the literature was conducted using the Medline database system and other reference materials. Studies documenting nutrient intakes only were included in this review. Studies were limited to those among healthy, non-pregnant adults. RESULTS: A total of twelve reports from 1959 to 1996 were found. Sample sizes for the studies ranged from 20 to 575 subjects. Most studies were done among women, and a variety of nutritional assessment techniques (24 hour recall, food frequency questionnaire, multiple-day food record) were used. Most studies also had limited nutrient intake data, especially for dietary fiber and vitamin E. The majority of studies reported moderately high intakes of fat and saturated fat, and low intakes of polyunsaturated fat and fiber. CONCLUSIONS: Based on the limited data, diet may play an important role in the heterogeneity of heart disease and cancer mortality in AIAN communities. More research is needed to assess the impact of diet on heart disease and cancer risk, including more longitudinal data, and data to assess the validity and reliability of traditional methods of dietary assessment.

Adult↗
PubMed1993

Free radicals and antioxidants in sepsis.

OBJECTIVES: The clinical condition of sepsis is caused by the release of numerous mediators from many cells. The purpose of this review is to describe the results of studies in which the role of free radicals and/or the potential therapeutic value of antioxidants are assessed. DATA SOURCES: The studies described in this review come from a variety of sources, including Med-Line CD-ROM computerized database, Index Medicus, and references identified from the bibliographies of pertinent articles and books. Reports were confined to English language articles from 1966 to 1992. STUDY SELECTION: All retrieved references in which free-radical activity was assessed or antioxidants were measured or administered in sepsis or endotoxemia were included. This selection process encompassed clinical, animal and in vitro cell culture work. DATA EXTRACTION: Cited literature was found in reputable peer-reviewed clinical or basic science journals. DATA SYNTHESIS: Any contradictions in the results of studies are discussed. CONCLUSIONS: There is evidence that free radicals play an important role in the pathogenesis of sepsis. Antioxidant therapy has the potential to protect against such injury. It is suggested that combination therapy, which augments the endogenous antioxidant defenses, is likely to be the best approach.

Animals↗
PubMed1991

Classification and identification of bacteria by Fourier-transform infrared spectroscopy.

This study describes a computer-based technique for classifying and identifying bacterial samples using Fourier-transform infrared spectroscopy (FT-IR) patterns. Classification schemes were tested for selected series of bacterial strains and species from a variety of different genera. Dissimilarities between bacterial IR spectra were calculated using modified correlation coefficients. Dissimilarity matrices were used for cluster analysis, which yielded dendrograms broadly equated with conventional taxonomic classification schemes. Analyses were performed with selected strains of the taxa Staphylococcus, Streptococcus, Clostridium, Legionella and Escherichia coli in particular, and with a database containing 139 bacterial reference spectra. The latter covered a wide range of Gram-negative and Gram-positive bacteria. Unknown specimens could be identified when included in an established cluster analysis. Thirty-six clinical isolates of Staphylococcus aureus and 24 of Streptococcus faecalis were tested and all were assigned to the correct species cluster. It is concluded that: (1) FT-IR patterns can be used to type bacteria; (2) FT-IR provides data which can be treated such that classifications are similar and/or complementary to conventional classification schemes; and (3) FT-IR can be used as an easy and safe method for the rapid identification of clinical isolates.

Antigens, Bacterial↗
PubMed1994

Blinking and the release reflexes: are they clinically useful?

OBJECTIVE: To review the clinical utility of blinking and the release reflexes, palmomental, glabellar, grasp, and snout, as an important part of the bedside neurological examination. DESIGN: Articles published from 1966 to 1993 that addressed blinking or the release reflexes were identified by searching the MEDLINE database. Thirty-seven references provided clinically useful and applicable information. RESULTS: There is controversy regarding the optimal method of clinical elicitation of these reflexes. The release reflexes are frequently seen as an incidental abnormality in the elderly. A positive grasp reflex, especially if asymmetrical, is sensitive but not specific for abnormal brain function. Lack of habituation is more important than the mere presence or absence of a reflex. The brainstem circuits involved in the regulation of blinking and the release reflexes are discussed, as are their abnormalities in a variety of clinical settings. CONCLUSION: Blinking and the release reflexes have clinical utility in the diagnosis and bedside clinical assessment of diseases as diverse as frontal lobe lesions, hydrocephalus, multiple sclerosis, Parkinson's disease, Alzheimer's disease and other dementias, falls in the elderly, ageing, HIV-encephalopathy, schizophrenia, tumors in the region of the sylvian aqueduct and recovery from head trauma.

Blinking↗
PubMed1999

Homogeneity of 16S-23S ribosomal intergenic spacer regions of Tropheryma whippelii in Swiss patients with Whipple's disease.

The current genetic strategies used to identify Tropheryma whippelii, the putative agent of Whipple's disease, are based on PCR-mediated amplification of a part of its 16S rRNA gene (16S rDNA). Because there is very little intraspecies variation in these molecules, they are not suitable as targets for epidemiologic investigations. However, the intergenic spacer region between the 16S and 23S rDNAs is usually much more variable and has repeatedly been used for epidemiologic purposes. We have therefore amplified the spacer region of T. whippelii directly from clinical specimens from nine independent Swiss patients with Whipple's disease by PCR with primers complementary to the 3' and 5' ends of the 16S and 23S rDNAs, respectively. The amplicons were directly sequenced and the sequences were compared to the T. whippelii reference sequence in GenBank/EMBL (accession no. X99636). Complete sequence homogeneity was found between the samples from our nine patients; the spacer sequence was also identical to the reference sequence. However, the sequences corresponding to the 3' and 5' ends of the 16S and the 23S rDNAs of T. whippelii, respectively, differed from the respective sequences in GenBank/EMBL. The same sequence found in our patients was then found in a sample from the German patient from which the published sequence had been derived. We conclude that the 16S-23S rDNA spacer region seems to be very conserved in T. whippelii and that the respective reference entry in public databases should be revised.

Actinobacteria↗
PubMed1996

Palliative Mustard operation for transposition of the great arteries: late results after 15-20 years.

OBJECTIVE: To assess the clinical, functional state, and complications late (15-20 years) after palliative Mustard operation. DESIGN: Examination and evaluation of all patients presenting in adolescence and adult life after palliative Mustard operation for transposition of the great arteries and pulmonary vascular disease. SETTING: Grown-up Congenital Heart Unit specialised in the care of adolescents and adults with congenital heart disease, designated as having "quaternary" status within a tertiary referral centre for cardiac diseases. PATIENTS AND METHODS: Database searched for patients referred after palliative Mustard for classic transposition of the great arteries. Ten patients aged 18-31 (mean (SD) 25.9 (5.2)) years with a palliative Mustard operation performed at age 1.7-15 (mean (SD) 9 (4.6)) years were fully evaluated by echocardiography, exercise testing, Holter monitoring, and magnetic resonance imaging or radionuclide ventriculography, or both 15-20 years later. RESULTS: One patient died aged 25 years with biventricular failure (ability index 3/4), haemoptysis, and atrial flutter, eight were well (ability index 2), and one disabled (ability index 3). Arterial oxygen saturation at rest was 85-98% (mean (SD) 93.8 (4)%) decreasing to 59-87% (mean 77 (9.5)%) after limited exercise. Symptomatic arrhythmias occurred in four patients, atrial flutter being the most common, and two had sinus node dysfunction. Significant tricuspid regurgitation occurred in four patients. CONCLUSION: Patients with palliative Mustard operation have a low incidence of symptomatic ventricular dysfunction and despite exercise limitation by hypoxia, continue to live active, near normal lives until their thirties.

Adolescent↗
PubMed1998

Assessment of bibliographic databases performance in information retrieval for occupational and environmental toxicology.

OBJECTIVE: To determine the efficiency of the major bibliographic databases by assessing the percentage of references among the total literature available that can be retrieved from each database. We also evaluated the best database combinations to carry out an exhaustive search. METHODS: BIOSIS, EMBASE, MEDLINE, NIOSH-TIC, and TOXLINE were searched on two topics: allergy to latex and asbestos and mesothelioma, in the title, abstract, or keywords (textwords). This search was performed for the years 1994 and 1995. All the records were classified by journal and author's name and were verified for each record whether or not it was indexed in each database. Statistical analysis was performed with chi 2 test. RESULTS: 777 articles in 510 issues were found. The efficiency of each database (percentage of articles recovered) and of combinations varied between 11% and 63% for one database and between 42% and 86% for a combination of two databases. The reasons why these differences exist between databases, and within a database, between two different subjects or two different years are reported. CONCLUSION: Firstly, it is not advisable to assert that a bibliography is complete when only one database is searched. Secondly, the efficiency of the databases may be quite different. Finally, it is suggested that the best way to be as exhaustive as possible is to search two or more databases-for example, in EMBASE and TOXLINE, or to a lesser extent EMBASE and MEDLINE. This seems to be the best compromise solution between time consumed for searching and efficiency.

Asbestos↗