Novel citation-based search method for scientific literature: application to meta-analyses

Background

Finding eligible studies for meta-analysis and systematic reviews relies on keyword-based searching as the gold standard, despite its inefficiency. Searching based on direct citations is not sufficiently comprehensive. We propose a novel strategy that ranks articles on their degree of co-citation with one or more “known” articles before reviewing their eligibility.

Method

In two independent studies, we aimed to reproduce the results of literature searches for sets of published meta-analyses (n = 10 and n = 42). For each meta-analysis, we extracted co-citations for the randomly selected ‘known’ articles from the Web of Science database, counted their frequencies and screened all articles with a score above a selection threshold. In the second study, we extended the method by retrieving direct citations for all selected articles.

Results

In the first study, we retrieved 82 % of the studies included in the meta-analyses while screening only 11 % as many articles as were screened for the original publications. Articles that we missed were published in non-English languages, published before 1975, published very recently, or available only as conference abstracts. In the second study, we retrieved 79 % of included studies while screening half the original number of articles.

Conclusions

Citation searching appears to be an efficient and reasonably accurate method for finding articles similar to one or more articles of interest for meta-analysis and reviews.

Electronic supplementary material

The online version of this article (doi:10.1186/s12874-015-0077-z) contains supplementary material, which is available to authorized users.

Prioritizing genomic applications for action by level of evidence: a horizon-scanning method

As evidence accumulates on the use of genomic tests and other health-related applications of genomic technologies, decision makers may increasingly seek support in identifying which applications have sufficiently robust evidence to suggest they might be considered for action. As an interim working process to provide such support, we developed a horizon-scanning method that assigns genomic applications to tiers defined by availability of synthesized evidence. We illustrate an application of the method to pharmacogenomics tests.

Viral hepatitis C gets personal--the value of human genomics to public health

About 180 million people worldwide are chronically infected with hepatitis C virus (HCV), with 3-4 million newly infected each year. Only 15-25% of acute HCV infections clear spontaneously, and the remainder persists as chronic HCV infection. More than 350,000 people die every year from hepatitis C-related liver failure and cancer. There is currently no vaccine and the standard-of-care therapies--peg-interferon alpha (pegIFN) plus ribavirin (RBV)--are expensive and have serious side effects. Also, they may be effective in only 40-50% of patients infected with HCV genotype 1, the most common HCV genotype in the US. Interleukin 28B (IL28B) genotype was recently and convincingly associated with response to pegIFN and RBV therapy. It has emerged as a robust pretreatment predictor of sustained virological response (SVR, i.e. virologic clearance) to pegIFN and RBV as well as to new triple therapy regimens that include a direct-acting antiviral agent with pegIFN and RBV and increase SVR rates as much as 75% in patients infected with HCV genotype 1. Testing for IL28B genotype may contribute to clinical decision-making and could inform clinical guidelines and public health policies.

Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations

Summary: We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continuously updated from PubMed. These applications provide user-friendly interfaces for searching summarized information on human genetic associations, using either genes or diseases as the starting point.

Availability: Phenopedia and Genopedia can be freely accessed at http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do and http://www.hugenavigator.net/HuGENavigator/startPagePedia.do, respectively.

Contact:wby0@cdc.gov

Supplementary information:Supplementary data are available at Bioinformatics online.

The Gene Ontology (GO) database and informatics resource

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

Informed consent for population-based research involving genetics

Bridging the gap between gene discovery and our ability to use genetic information to benefit health requires population-based knowledge about the contribution of common gene variants and gene-environment interactions to the risk of disease. The risks and benefits associated with population-based research involving genetics, especially lower-penetrance gene variants, can differ in nature from those associated with family-based research. In response to the urgent need for appropriate guidelines, the Centers for Disease Control and Prevention formed a multidisciplinary group to develop an informed consent approach for integrating genetic variation into population-based research. The group used expert opinion and federal regulations, the National Bioethics Advisory Commission's report on research involving human biological materials, existing consent forms, and literature on informed consent to create suggested language for informed consent documents and a supplemental brochure. This language reflects the premise that the probability and magnitude of harm, as well as possible personal benefits, are directly related to the meaning of the results for the health of the participant and that appropriate disclosures and processes for obtaining consent should be based on an assessment at the outset of the likelihood that the results will generate information that could lead directly to an evidence-based intervention. This informed consent approach is proposed to promote discussion about how best to enable potential participants to make informed decisions about population-based research involving genetics and to suggest issues for consideration by research sponsors, institutional review boards, and investigators.

Public health impact of genetic tests at the end of the 20th century

PURPOSE

To evaluate genetics tests available for clinical, research, and public health purposes in terms of their public health impact as measured by the number of people who could potentially be tested.

METHODS

Genetic tests for the 751 inherited diseases or conditions listed in the GeneTests database as of November 2000, were classified on the basis of their use for population-based testing and the prevalence of the disease or condition being tested. The GeneTests database divides the tests into two groups: those offered for clinical use and those available for research only.

RESULTS

Of the 423 clinical tests, 51 had potentially greater impact on public health because of their use in statewide newborn screening programs, other population screening programs, or testing for common diseases with a prevalence over 1 in 2,000 people. Among the 328 tests performed for research purposes only, 18 met the criteria for potentially greater public health impact.

CONCLUSIONS

Our classification scheme indicated that fewer than 10% of the genetic tests listed in the GeneTests database at the end of 2000 are highly relevant to public health. The majority of genetic tests are used in diagnosis and/or genetic counseling for rare, single-gene disorders in a limited number of people. However, as more tests are being considered for newborn screening, and associations between genes and common diseases are being discovered, the impact of genetic testing on public health is likely to increase.

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae

The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.

Hemochromatosis-associated morbidity in the United States: an analysis of the National Hospital Discharge Survey, 1979-1997

PURPOSE

The recent discovery of the HFE gene and its association with hereditary hemochromatosis has renewed the attention directed to iron-overload diseases. Population screening for hereditary hemochromatosis is under debate, and population-based estimates of morbidity associated with hereditary hemochromatosis are needed. The purpose of this study is to estimate the number of hemochromatosis-associated hospitalizations in the United States using a population-based dataset.

METHODS

National Hospital Discharge Survey and census data were used to estimate hemochromatosis-associated hospitalization rates for persons 18 years of age and over.

RESULTS

From 1979 through 1997, the rate of hemochromatosis-associated hospitalizations was 2.3 per 100,000 persons in the United States. The rate among persons 60 years of age and over increased more than 60% during this time period.

CONCLUSION

The increase in the rate of hereditary hemochromatosis-associated hospitalizations among older persons is consistent with recent trends in mortality data and may reflect the rising awareness of iron-overload disorders in the United States.

Incidence of HIV among injection drug users entering drug treatment programs in four US cities

We estimated seroincidence of human immunodeficiency virus (HIV) and prevalence of risk behaviors among injection drug users (IDUs) who accepted voluntary HIV testing on entry to drug treatment. Record-based incidence studies were conducted in 12 drug treatment programs in New York City (n = 890); Newark, New Jersey (n = 521); Seattle, Washington (n = 1,256); and Los Angeles, California (n = 733). Records of confidential HIV tests were abstracted for information on demographics, drug use, and HIV test results. More detailed data on risk behaviors were obtained by a standardized questionnaire. Although overall incidence rates were relatively low in this population (<1/100 person-years), there was a high prevalence of risk behaviors. Needle sharing was reported by more than one-third of the participants in each of the cities. HIV seroincidence rates were up to three-fold higher among younger ID Us. We found that HIV continued to be transmitted among ID Us who had received both drug treatment and HIV counseling and testing. HIV/AIDS (acquired immunodeficiency syndrome) prevention education should continue to be an important component of drug treatment.

Surveillance of HIV-1 genetic subtypesand diversity in the US blood supply

BACKGROUND

Recent reports of variant (non-subtype B) HIV infections in US populations have raised concerns about the sensitivity of subtype B virus-based donor screening and diagnostic assays. This study was designed to determine the prevalence and genetic diversity of HIV subtypes in US blood donors over the last two decades.

STUDY DESIGN AND METHODS

Three groups were studied: hemophiliacs infected by clotting factor concentrates in the early 1980s (n = 49), blood donors retrospectively identified as being seropositive in 1985 (n = 97), and blood donors identified as seropositive between 1993 and 1996 (n = 405). Subtype assignment was based primarily on heteroduplex mobility analysis (HMA) of HIV-1 env, with DNA sequence confirmation of selected specimens. HIV peptide-based EIA serotyping was used to rule out HIV-2 and group O infections and to serotype HMA-refractory specimens.

RESULTS

Of 551 specimens, 535 (97%) were assigned subtypes; 532 (99%) of these were subtype B. Three postscreening donations (1%) were assigned non-B subtypes (2 A, 1 C). Two of these three donors were born in Africa; the third was born in the United States and reported no risk factors other than heterosexual activity. HMA distribution plots showed an increase in env diversity among HIV-1 group B strains over time.

CONCLUSION

The results support the need for continued surveillance of HIV subtype diversity and ongoing validation of the sensitivity of HIV diagnostic assays to non-B subtype infections.

Prevalence of mutations associated with reduced antiretroviral drug susceptibility among human immunodeficiency virus type 1 seroconverters in the United States, 1993-1998

To assess the prevalence of mutations associated with decreased antiretroviral drug susceptibility, specimens were tested from persons infected with human immunodeficiency virus (HIV) during 1993-1998. Subjects were drug naive and were attending sexually transmitted disease clinics in 6 US cities. All were enrolled consecutively and had tested negative for HIV during the 2 years before enrollment. Plasma specimens from patients having >/=1 reverse transcriptase (RT) or primary protease mutation were tested phenotypically with a recombinant virus assay. Of 99 patients, 6 (6%) had mutations associated with zidovudine resistance, 2 (2%) had mutations associated with nonnucleoside RT inhibitor resistance, and 1 (1%) had a primary protease mutation. Overall, the prevalence of resistance-associated primary mutations was 5%, although high levels of decreased drug susceptibility (IC(50)s >/=10 times that of a reference virus) were observed in just 1%. These findings confirm the transmission of these mutations to drug-naive persons.

HIV/AIDS among African Americans: progress or progression?

OBJECTIVES

To review data on the extent of HIV infection and associated risk behaviors, the occurrence of AIDS, and HIV-related mortality in African Americans and to suggest what can be done to reduce HIV exposure and infection in this population.

DESIGN/METHODS

Review of epidemiologic, published, multisite data on HIV infection in, and related behaviors of, African Americans.

RESULTS

On every epidemiologic measure in common use, African Americans, compared with the four other federally recognized racial/ethnic groups, have the most severe epidemic. The trend data show continuing growth in the African American epidemic despite the availability of effective behavioral interventions and biomedical treatments. Few published intervention studies with African American populations have been adequately evaluated; nor have they focused proportionately on men who have sex with men, a group in the African American community with continuing high rates of infection.

CONCLUSIONS

Rates of HIV transmission and disease among African Americans are high, disproportionate, and are not declining as significantly in response to effective interventions as they are among whites. Attention is urgently needed to increase our understanding of risk behaviors, social networks, and specific factors in the African American community that can be altered to reduce HIV infection. Macroenvironmental factors--poverty, social class, racism--need to be studied to suggest possible intervention components to reduce rates of HIV transmission and to increase the use of therapies that are more effectively slowing disease progression and lowering death rates among whites.

Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39

The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.

Geographic variation of HIV infection in childbearing women with syphilis in the United States

OBJECTIVES

Substantial biologic and epidemiologic data indicate the importance of syphilis as a potential cofactor for sexual transmission of HIV infection, but few detailed data exist on the geographic covariation of these two important sexually transmitted infections.

DESIGN

HIV prevalence in childbearing women and primary and secondary (P&S) syphilis data from 29 states were examined to explore the importance of the epidemiology of syphilis as a factor in facilitating HIV transmission.

METHOD

The spatial relationship between P&S syphilis and HIV infection in the health districts of 29 states was analyzed and adjusted for demographic and socioeconomic factors such as racial composition, income, housing, education levels, and access to medical services using the 1990 US census, and geographic location.

RESULTS

In 29 states and the District of Colombia, 448 health districts, representing more than 75% of the US population, reported HIV prevalence rates for mothers' district of residence. The HIV seroprevalence ranged from 0 to 1258/10 000 in these health districts. The incidence of P&S syphilis from 1984-1994 in these districts ranged from 0 to 87/100 000. The P&S syphilis incidence was positively associated with the prevalence of HIV infection among childbearing women (P < 0.0001).

CONCLUSIONS

Syphilis that persists in communities in the United States appears to represent a 'sentinel public health event' reflecting risk for sexual HIV transmission. These findings, along with other biologic and epidemiologic information, reinforce the importance of syphilis as an indicator for targeting HIV prevention efforts generally, as well as syphilis control as a specific HIV-prevention strategy.

A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi

We have determined that Borrelia burgdorferi strain B31 MI carries 21 extrachromosomal DNA elements, the largest number known for any bacterium. Among these are 12 linear and nine circular plasmids, whose sequences total 610 694 bp. We report here the nucleotide sequence of three linear and seven circular plasmids (comprising 290 546 bp) in this infectious isolate. This completes the genome sequencing project for this organism; its genome size is 1 521 419 bp (plus about 2000 bp of undetermined telomeric sequences). Analysis of the sequence implies that there has been extensive and sometimes rather recent DNA rearrangement among a number of the linear plasmids. Many of these events appear to have been mediated by recombinational processes that formed duplications. These many regions of similarity are reflected in the fact that most plasmid genes are members of one of the genome's 161 paralogous gene families; 107 of these gene families, which vary in size from two to 41 members, contain at least one plasmid gene. These rearrangements appear to have contributed to a surprisingly large number of apparently non-functional pseudogenes, a very unusual feature for a prokaryotic genome. The presence of these damaged genes suggests that some of the plasmids may be in a period of rapid evolution. The sequence predicts 535 plasmid genes >/=300 bp in length that may be intact and 167 apparently mutationally damaged and/or unexpressed genes (pseudogenes). The large majority, over 90%, of genes on these plasmids have no convincing similarity to genes outside Borrelia, suggesting that they perform specialized functions.

Human formyl peptide receptor function role of conserved and nonconserved charged residues

In this study, we investigated the role of charged residues in ligand binding interactions of f-Met-Leu-Phe receptors (FPR). Charged residues of FPR, both conserved and nonconserved, which are located close to the membrane interface were mutated to alanine to determine their role in ligand binding. The mutated residues belonged to specific domains of FPR which have previously been implicated in FPR ligand binding interactions. We demonstrate that nonconserved charged residues such as Arg84, Lys85, Arg205 and Asp284 and conserved charge residue Arg163 seem to play a role in ligand binding. However, alteration of nonconserved charged residue Asp106 did not have any effect. In conclusion, specific charged residues of FPR, both conserved nonconserved, may contribute to FPR function either directly or indirectly.

Trends in perinatal transmission of HIV/AIDS in the United States

CONTEXT

Since 1994, the US Public Health Service (PHS) has recommended routine, voluntary prenatal human immunodeficiency virus (HIV) testing and zidovudine therapy to reduce perinatal HIV transmission.

OBJECTIVE

To describe trends in incidence of perinatal AIDS and factors contributing to these trends, particularly the effect of PHS perinatal HIV recommendations.

DESIGN, SETTING, AND PARTICIPANTS

Analysis of nationwide AIDS surveillance data and data from HIV-reporting states through June 1998.

MAIN OUTCOME MEASURES

Trends in AIDS by year of diagnosis, incidence rates of AIDS and Pneumocystis carinii pneumonia (PCP) among infants younger than 1 year from US natality data for birth cohorts 1988 to 1996; expected number of infants with AIDS from national serosurvey data; and zidovudine use data from selected HIV-reporting states.

RESULTS

Perinatal AIDS cases peaked in 1992 and then declined 67% from 1992 through 1997, including an 80% decline in infants and a 66% decline in children aged 1 to 5 years. Rates of AIDS among infants (per 100000 births) declined 69%, from 8.9 in 1992 to 2.8 in 1996 compared with a 17% decline in births to HIV-infected women from 1992 (n = 6990) to 1995 (n = 5797). Among infants, PCP rates per 100000 declined 67% (from 4.5 in 1992 to 1.5 in 1996), similar to the decline in other AIDS conditions. The percentage of perinatally exposed children born from 1993 through 1997 whose mothers were tested for HIV before giving birth increased from 70% to 94%; the percentage who received zidovudine increased from 7% to 91%.

CONCLUSIONS

According to these data, substantial declines in AIDS incidence were temporally associated with an increase in zidovudine use to reduce perinatal HIV transmission, demonstrating substantial success in implementing PHS guidelines. Reductions in the numbers of births and effects of therapy in delaying AIDS do not explain the decline.

HIV seroincidence and risk factors among patients repeatedly tested for HIV attending sexually transmitted disease clinics in the United States, 1991 to 1996. STD Clinic HIV Seroincidence Study Group

To assess the incidence of HIV infection and risk factors associated with HIV seroconversion among patients attending clinics for sexually transmitted diseases (STD), medical record reviews were conducted in 12 clinics in 7 U.S. cities. The records of all patients who initially tested negative for HIV from 1991 through 1996 and who received at least one additional HIV test during the study period were reviewed. In each of 7 cities, 5 to 112 patients seroconverted. Of the 286 seroconverters identified in total, 53% (152 of 286) were heterosexual men and 28% (81 of 286) were women. HIV incidence rates among men who have sex with men (MSM) ranged by city from 0.81 to 7.0 new infections/100 person-years. Rates among heterosexual men and women ranged from 0.018 to 1.2 infections/100 person-years. Multivariate analyses showed that drug use was associated with HIV seroconversion only among heterosexuals. Most new HIV infections in these clinics are being transmitted heterosexually and are associated with drug use. Nevertheless, MSM, particularly young MSM, are at greatest risk for HIV in this population: 1 of 47 seroconvert/year. The effective use of targeted prevention efforts depends upon the continued ability to monitor the incidence of HIV infection.

Trends in HIV prevalence among childbearing women in the United States, 1989-1994

We used data from a national serosurvey to describe national and regional trends in the prevalence of HIV among women giving birth in the United States from 1989 through 1994, and to estimate the number of women between 15 and 44 years old with HIV infection who had not yet developed opportunistic infections defining AIDS. We compared these estimates with AIDS prevalence and mortality estimates from the national AIDS case surveillance system. HIV seroprevalence among childbearing women remained stable nationwide from 1989 through 1994, ranging from 1.5 to 1.7/1000 women. In the Northeast, seroprevalence declined significantly after 1989. Seroprevalence increased significantly in the South through 1991 and then stabilized, although seroprevalence among black women continued to increase through 1994 in some southern states. Although AIDS prevalence and mortality increased nationwide each year from 1989 through 1994, the number of women infected with HIV who had not yet developed AIDS changed little and was approximately 86,000 in 1994. Our data suggest that new HIV infections among women of reproductive age are occurring at a rate that offsets losses from this population due to aging, disease progression, and death.

Complete genome sequence of Treponema pallidum, the syphilis spirochete

The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.

Radioimmunoassay for monitoring zidovudine in dried blood spot specimens

We modified and evaluated a RIA for serum and used the modified RIA to measure zidovudine in dried blood spot specimens (DBSs) routinely collected for newborn screening and tested anonymously for maternally acquired HIV antibodies in the national HIV Seroprevalence Survey Among Childbearing Women. DBS calibration and quality-control materials were used to adapt the serum assay to the DBS matrix. The assay had a limit of detection of 24 micrograms/L serum and was used to measure zidovudine from both whole DBSs and the eluate remaining after HIV antibody screening. We initiated a pilot study to investigate the assay's performance and assess its potential to determine the implementation of the US Public Health Service recommendations that HIV-infected pregnant women and newborns receive zidovudine treatment to reduce the risk of perinatal HIV transmission.

Projection of AIDS and HIV incidence among children born infected with HIV

By 31 December 1995, 6285 children with perinatally acquired immunodeficiency syndrome (AIDS) had been reported to the Centers for Disease Control and Prevention (CDC) by the state and local health departments of all 50 states, the District of Columbia, Puerto Rico, and the U.S. territories. We present here the statistical methods used to estimate the number of infants born with HIV and to predict the number of diagnoses of perinatally acquired AIDS among children to 1997. We estimate that there were 13,900 children who had perinatally acquired HIV infection by the end of 1995 and who will eventually be reported with AIDS. If 85 per cent of all diagnoses are reported, this represents a total of more than 16,300 diagnoses. Of these, 6600 had developed AIDS by the end of 1995 and will eventually be reported to CDC. We project that, during 1996 and 1997, another 1500 HIV-infected children will be born.

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.

Prevalence of HIV infection in the United States, 1984 to 1992

OBJECTIVE

To estimate the number of persons infected with the human immunodeficiency virus (HIV) living in the United States and the change in HIV infection prevalence since 1984.

DESIGN

We estimated HIV prevalence from 3 data sources. We estimated past HIV infection rates from a statistical procedure based on national acquired immunodeficiency syndrome (AIDS) case surveillance data and estimates of the time from HIV infection to AIDS diagnosis. We also analyzed HIV prevalence data from 2 national surveys, a survey of childbearing woman and a household survey of current health status. We used other data sources to adjust these survey estimates to include groups not covered in the surveys.

RESULTS

Approximately 0.3% of US residents (650,000-900,000 persons) were infected with HIV in 1992. Approximately 0.6% of men (including adolescent boys > or = 13 years of age) were infected, including approximately 2% of non-Hispanic black men and 1% of Hispanic men. Approximately 0.1% of women (including adolescent girls > or = 13 years of age) were infected, including approximately 0.6% of non-Hispanic black women. Approximately half of all infected persons were men who had sex with men, and one fourth were injecting drug users. The prevalence of HIV infection increased from 1984 to 1992, with a greater relative increase among women than men.

CONCLUSIONS

The 3 different data sources and methods are consistent in estimating that 650,000 to 900,000 persons were infected with HIV in the United States in 1992. Among adolescents and adults of both sexes, the proportion infected was substantially higher among non-Hispanic blacks and Hispanics than among non-Hispanic whites. HIV-related illness will be a major clinical and public health problem in the United States for years to come.

Trends in human immunodeficiency virus seroprevalence among injection drug users entering drug treatment centers, United States, 1988-1993

National unlinked sentinel surveillance data were used to describe trends in prevalent human immunodeficiency virus infection among injection drug users entering drug treatment programs in the United States from 1988 through 1993. During this 6-year period, unlinked testing was performed on 70,882 specimens from injection drug users at 60 sentinel sites. The annual change in seroprevalence was estimated for each site by odds ratios obtained from logistic regression models fit within site-specific age and race/ethnicity subgroups. Overall trends for age and race/ethnicity subgroups across sites were described by summary odds ratios calculated using the inverse variance method. A decrease was observed among younger (age less than 30 years) whites both in areas with high (10% or higher) and low (less than 10%) prevalence, although this decrease was significant only in high-prevalence areas (odds ratio = 0.90, 95% confidence interval 0.81-0.99). Seroprevalence also decreased among older whites in high-prevalence areas, although this decrease was not significant (odds ratio = 0.95, 95% confidence interval 0.89-1.00). Seroprevalence remained stable among all other age and race/ethnicity subgroups. Stable seroprevalence among the dynamic population of injection drug users entering treatment suggests continued transmission among these individuals in both high- and low-prevalence areas of the United States.

Prevalence and incidence of vertically acquired HIV infection in the United States

OBJECTIVE

To estimate human immunodeficiency virus (HIV) type I prevalence among childbearing women, HIV incidence in infants, and the number of children living with HIV infection and acquired immunodeficiency syndrome as a result of transmission from mother to infant (vertical transmission).

DESIGN

The national HIV serosurvey of childbearing women was used to estimate the incidence of vertically acquired HIV infection in children born between 1988 and 1993. Data from the national acquired immunodeficiency syndrome case surveillance system and a multicenter pediatric HIV surveillance project were modeled to estimate incidence in children born between 1978 and 1987.

SETTING

Surveillance conducted by the Centers for Disease Control and Prevention, Atlanta, Ga, in collaboration with state and local health departments.

RESULTS

Approximately 14,920 HIV-infected infants were born in the United States between 1978 and 1993. Of these, an estimated 12,240 children were living at the beginning of 1994; 26% were younger than 2 years, 35% were aged 2 to 4 years, and 39% were aged 5 years or older. Approximately 6530 HIV-infected women gave birth in the United States in 1993, and, based on a 25% vertical transmission rate, an estimated 1630 of their infants were HIV infected.

CONCLUSIONS

These results provide a basis for estimating medical and other resource needs for HIV-infected women and their children and for measuring the impact of interventions to reduce vertical transmission of HIV.

Trends in HIV seroprevalence among persons attending sexually transmitted disease clinics in the United States, 1988-1992

Trends in seroprevalence of the human immunodeficiency virus (HIV) were examined among patients attending sentinel clinics for sexually transmitted diseases (STDs) throughout the United States. Cross-sectional, unlinked (blinded) surveys of HIV seroprevalence were conducted annually within clinics in 40 metropolitan areas. From 1988 to 1992, 552,665 specimens were tested in 80 STD clinics. The overall HIV seroprevalence was 33% (range among metropolitan areas: 5-52%) among gay and bisexual men, 3% (range: 0.3-11%) among heterosexual men, 2% (range: 0.1-11%) among women, and 10% (range: 0.5-45%) among heterosexual injecting drug users (IDUs). Controlling for clinic, age, and race/ethnicity, HIV seroprevalence decreased among all gay and bisexual men, but especially among white gay and bisexual men from 32% in 1989 to 22% in 1992. Among heterosexual men and women, HIV seroprevalence decreased among whites and, to a lesser degree, Hispanics, but remained essentially stable among African-Americans over time. Among heterosexual IDUs, seroprevalence was also unchanged. These results reflect changes in the HIV epidemic, which is becoming increasingly characterized by infected heterosexuals and IDUs, especially within minority populations.

Applications of data from the CDC Family of Surveys

The CDC Family of Surveys is a national serologic surveillance system set up to characterize the extent of human immunodeficiency virus (HIV) infection in the United States. The now Centers for Disease Control and Prevention (CDC) and participating State and local health departments began the system in 1987. HIV seroprevalence data are collected by unlinked (anonymous) surveys of particular components of the population that include childbearing women; clients of sexually transmitted disease clinics; injecting drug users; tuberculosis patients; and several special populations, such as adolescents, prisoners, and homeless persons. The data obtained have been used extensively on both national and local levels to assist HIV-prevention programs. Data from the surveys have been used to identify specific demographic groups at risk for HIV infection so that health education programs may be planned and made available to them in clinical settings. Local serosurvey results have been used in planning and implementing prevention programs and in planning health services for HIV-positive persons. The completeness, or coverage, of HIV counseling and testing programs has been evaluated by comparing seroprevalences among clients tested voluntarily with those tested in the unlinked survey. Survey data are used in formulating recommendations and standards of care for health practitioners, in allocating resources, and in carrying out long-range planning for HIV prevention and treatment services for at-risk groups. Such data are essential to the decision-making process in forming public health policy and recommending practices involving the HIV epidemic.

Urban-nonurban distribution of HIV infection in childbearing women in the United States

Women account for an increasing proportion of AIDS cases in the United States, and the number reported from small cities and rural areas is growing. To better describe the geographic characteristics of the human immunodeficiency virus (HIV) epidemic in women, we analyzed data for more than 1.6 million newborn specimens tested for maternal antibody to HIV-1 in 35 states in 1989. To provide comparable geographic units for analysis, seroprevalence rates were calculated for state-designated health districts, which are groups of counties defined for the planning and delivery of health services. Health districts with > or = 75% of the population residing in urban areas as defined by the 1990 census were considered urban. Prevalence of HIV infection ranged from 0 to 12.2 per 1,000, with the highest rates found in urban health districts, primarily those on the East coast; however, high rates were also found in some nonurban districts, particularly in the South. Rates among black women were three to 35 times higher than in white women in nine states, regardless of urbanicity. These findings should be used to focus prevention activities and direct health care planners to urban and rural areas in need of HIV-related services for women.

Trends in HIV prevalence among disadvantaged youth. Survey results from a national job training program, 1988 through 1992

OBJECTIVE

To describe trends in the prevalence of human immunodeficiency virus (HIV) among socially and educationally disadvantaged US youth.

DESIGN

Analysis of demographic and geographic trends of HIV infection among Job Corps students from January 1988 through December 1992.

SETTING

The Job Corps is a national training program for disadvantaged and out-of-school youth. POPULATION SCREENED: Youths aged 16 to 21 years who entered the Job Corps residential training centers during the survey period.

MAIN OUTCOME MEASURE

Trends in prevalence of HIV infection among Job Corps students stratified by sex, age, race, and region of the country.

RESULTS

Of the 269,956 Job Corps students screened, 812 (0.3%) tested positive for the antibody to HIV type 1. Seroprevalence of HIV for young men decreased from 3.6 per 1000 in 1988 to 2.2 per 1000 in 1992 (chi 2 test for trend, P < .001). Seroprevalence for young women increased from 2.1 per 1000 in 1988 to 4.2 per 1000 in 1990 (P = .001), with seroprevalence remaining stable from 1990 through 1992. The decreasing trends in HIV prevalence among men and increasing trends among women were primarily due to changes in seroprevalence in African-American students.

CONCLUSIONS

The overall prevalence of HIV infection of three per 1000 is high, given the youth of Job Corps students. The significant rise in HIV rates among female Job Corps students provides evidence of the increasing risk of infection for socioeconomically disadvantaged young women. Reasons for the declining trend in HIV prevalence among male Job Corps students are not clear. Efforts to prevent the spread of HIV infection among adolescents must focus on the group that is hardest to reach--out-of-school and impoverished youth.

Factors influencing HIV-1 banding patterns in miniaturized western blot testing of dried blood spot specimens

In the HIV Seroprevalence Survey among Childbearing Women (SCBW), antibodies to human immunodeficiency virus type 1 are detected using enzyme immunoassays (EIA) and Western blot (WB) methods modified to accommodate samples of blood dried on special collection paper. Dried blood spot (DBS) eluates positive by EIA are tested by one of two WB methods, the miniblot technique using equipment from Immunetics Corporation and the PBS Integra assay (pageblot) from Genetic Systems. In this report we compared the performance of the two WB methods. The identity and position of the viral proteins on the WB were identified using monoclonal antibodies and monospecific antisera. The blots differed substantially in their composition and concentration of viral glycoproteins. Performance of the WB assays with DBS elution buffers from different EIA kits was equivalent except for samples eluted in the Abbott buffer, which reduced detection of antibodies to the p31, p51, p55, and p66 viral proteins. Case classification of DBS, positive sera, dilution curve samples, and seroconversion panels was equivalent by both tests in the presence of all elution buffers. Proficiency evaluation panels sent to SCBW participating laboratories over a 3-year period were used to note the differences between the two WB methods in detection of antibodies to the viral glycoproteins.

Prevalence of HIV infection in childbearing women in the United States. Surveillance using newborn blood samples

A national, population-based survey was initiated in 1988 to measure the prevalence of human immunodeficiency virus (HIV) infection in women giving birth to infants in the United States. Following standardized procedures, residual dried-blood specimens collected on filter paper for newborn metabolic screening were tested anonymously in state public health laboratories for maternal antibody to HIV. As of September 1990, annual survey data were available from 38 states and the District of Columbia. The highest HIV seroprevalence rates were observed in New York (5.8 per 1000), the District of Columbia (5.5 per 1000), New Jersey (4.9 per 1000), and Florida (4.5 per 1000). Nationwide, an estimated 1.5 per 1000 women giving birth to infants in 1989 were infected with HIV. Assuming a perinatal transmission rate of 30%, we estimate that approximately 1800 newborns acquired HIV infection during one 12-month period. Preventing transmission of HIV infection to women and infants is an urgent public health priority.

Magnitude and time course of extracellular potassium inhomogeneities during acute ischemia in pigs. Effect of verapamil

Prior studies have demonstrated the presence of inhomogeneities in myocardial [K+]e after serial 10-minute occlusions of the left anterior descending coronary artery in the pig, even within restricted locations of an ischemic zone. These inhomogeneities are thought to underlie the electrophysiological abnormalities responsible for lethal ventricular arrhythmias through reentrant and nonreentrant pathways, but a clear association has not been demonstrated. As a prerequisite to establishing this association, these studies were performed to establish measurement standards for [K+]e inhomogeneity, to quantify the magnitude and time course of these inhomogeneities, to determine whether the inhomogeneities are greater in the ischemic border where lethal ventricular arrhythmias are known to originate, and to assess the effect of a known antifibrillatory drug on [K+]e inhomogeneities. [K+]e (expressed as the change in potassium equilibrium potential, dEK [mV]) was measured in 15 preparations using an average of 17 closely spaced, critically calibrated K(+)-sensitive electrodes having stable response characteristics. A series of four 10-minute occlusions each separated by a 50-minute reperfusion period were performed in each study. In half of the studies, intravenous verapamil (0.2 mg/kg bolus followed by 0.0065 mg/kg/hr) was administered before the fourth occlusion. In nine studies (five control and four verapamil), electrodes were placed in the marginal ischemic zone (from 2 mm outside to 5 mm inside the visible cyanotic border). In six other studies (three control and three verapamil), electrodes were placed in the central ischemic zone (10-20 mm within the ischemic region). We determined that the standard deviation is the best measure of inhomogeneity and that 12 equivalent measurement sites are required to estimate it with a satisfactory degree of statistical confidence. We found that after 10 minutes of ischemia, mean dEK was 1.6 times greater in the central than in the marginal ischemic zone, whereas mean standard deviation at the same time was 1.5 times greater in the marginal than in the central ischemic zone. Verapamil reduced mean dEK and mean standard deviation in both ischemic zones for most of the occlusion by delaying the rise in [K+]e and the inhomogeneity of that rise by 3-5 minutes. Comparisons of mean dEK with mean standard deviation revealed a steep linear relation in the marginal zone and a curvilinear relation in the central zone where higher mean dEK values were not accompanied by higher values for mean standard deviation. Furthermore, we determined that these relations were not altered by verapamil.(ABSTRACT TRUNCATED AT 400 WORDS)

HIV seroprevalence surveys of childbearing women--objectives, methods, and uses of the data

A seroprevalence survey of human immunodeficiency virus (HIV) among childbearing women is being conducted in 43 States and Territories as one of the family of HIV seroprevalence surveys. This blinded survey, in which serologic test results are not linked to identifiable persons, uses neonatal dried blood specimens on filter paper to test for maternal antibodies to HIV. This survey provides relatively unbiased estimates of prevalence of HIV infection in the population of women delivering live children during given survey periods, by month or quarter of delivery, geographic area, and demographic subgroup. This objective will be met while protecting the integrity and efficient conduct of neonatal screening programs and ensuring patient anonymity. Information from this survey will be used to (a) assess the levels and trends of HIV infection in women and infants, (b) help develop and evaluate prevention programs, and (c) project the number of women and children who will develop HIV infection and the acquired immunodeficiency syndrome (AIDS) and will require health care and social services in the future.