Endobronchial ultrasound-guided transbronchial needle aspiration in the diagnosis of lymphoma.

BACKGROUND: The diagnostic accuracy of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) for the diagnosis of lymphoma in patients with mediastinal lymphadenopathy is not well defined. METHODS: A retrospective review was performed of all patients with mediastinal lymphadenopathy referred for EBUS-TBNA between August 2005 and December 2006 in whom lymphoma was suspected based on prior history or clinical presentation. Mediastinal biopsy specimens were taken using a linear array ultrasonic bronchoscope (Olympus XBF-UC 160F) and a 22-gauge cytology needle (NA-202C Olympus) with on-site cytopathological support. The EBUS-TBNA result was compared with a reference standard of pathological tissue diagnosis or a composite of > or =6 months of clinical follow-up with radiographic imaging. RESULTS: Of 236 patients who underwent EBUS-TBNA, 25 were eligible for inclusion. Indications for EBUS-TBNA were suspected mediastinal recurrence of lymphoma (n = 13) and mediastinal lymphadenopathy of unknown cause (n = 12). Adequate lymph node sampling was accomplished in 24/25 patients (96%); there were no complications. EBUS-TBNA identified lymphoma in 10 patients and benign disease in 14 patients. There was one false negative EBUS-TBNA for lymphoma (lymphoma prevalence 11/25 (44%)). Follow-up over a median of 10.5 months (range 1-19) confirmed stable or regressive lymphadenopathy in all 14 patients without a lymphoma diagnosis, consistent with a benign diagnosis. Overall, EBUS-TBNA had a sensitivity of 90.9%, specificity of 100%, positive predictive value of 100% and negative predictive value of 92.9% for the diagnosis of lymphoma. CONCLUSIONS: EBUS-TBNA is an accurate, safe and useful tool in the investigation of suspected lymphoma with isolated mediastinal adenopathy, and may diminish the need for more invasive procedures such as mediastinoscopy.

Proventricular dilatation disease: an emerging exotic disease of parrots in Australia.

Proventricular dilatation disease is a viral disease seen as a segmental neuropathy in parrots. It has always been believed to be a disease exotic to Australia, with the only reported case being a legally imported Green Wing Macaw (Ara chloroptera) in 1993. This paper reports a cluster of cases seen in south-east Queensland in 2005 to 2006. Clinical signs, autopsy findings and histopathological findings are described. No pattern or common source for these cases could be identified. The implications for Australian aviculture and avifauna are discussed.

Relationship of pre-1918 avian influenza HA and NP sequences to subsequent avian influenza strains.

Wild waterfowl that were captured between 1915 and 1919 and preserved in 70% ethyl alcohol were tested for influenza A virus RNA. Most of the HA1 domain of the hemagglutinin (HA) gene segment was sequenced from one bird, captured in 1917, that was infected with a virus of the same HA subtype as the 1918 human pandemic virus. The 1917 HA sequence is closely related to modern avian HA sequences, suggesting little drift in avian sequences in 80 years and that the 1918 pandemic virus probably did not acquire its hemagglutinin directly from a bird. A 151-bp fragment of the nucleoprotein gene segment was sequenced from two pre-1918 birds and compared to avian and mammalian influenza strains. The 1917 avian NP sequences are also closely related to modern avian sequences and distinct from the mammalian clade in which the 1918 NP sequence is found.

Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes.

The influenza A virus pandemic of 1918-1919 resulted in an estimated 20-40 million deaths worldwide. The hemagglutinin and neuraminidase sequences of the 1918 virus were previously determined. We here report the sequence of the A/Brevig Mission/1/18 (H1N1) virus nonstructural (NS) segment encoding two proteins, NS1 and nuclear export protein. Phylogenetically, these genes appear to be close to the common ancestor of subsequent human and classical swine strain NS genes. Recently, the influenza A virus NS1 protein was shown to be a type I IFN antagonist that plays an important role in viral pathogenesis. By using the recently developed technique of generating influenza A viruses entirely from cloned cDNAs, the hypothesis that the 1918 virus NS1 gene played a role in virulence was tested in a mouse model. In a BSL3+ laboratory, viruses were generated that possessed either the 1918 NS1 gene alone or the entire 1918 NS segment in a background of influenza A/WSN/33 (H1N1), a mouse-adapted virus derived from a human influenza strain first isolated in 1933. These 1918 NS viruses replicated well in tissue culture but were attenuated in mice as compared with the isogenic control viruses. This attenuation in mice may be related to the human origin of the 1918 NS1 gene. These results suggest that interaction of the NS1 protein with host-cell factors plays a significant role in viral pathogenesis.

The 1918 Spanish influenza: integrating history and biology.

In 1918 an influenza pandemic killed 40 million people. It is now possible to study the genetic features of the 1918 virus. Such analyses will try to answer questions about the origin and the unusual virulence of this pandemic virus.

Integrating historical, clinical and molecular genetic data in order to explain the origin and virulence of the 1918 Spanish influenza virus.

The Spanish influenza pandemic of 1918-1919 caused acute illness in 25-30% of the world's population and resulted in the death of 40 million people. The complete genomic sequence of the 1918 influenza virus will be deduced using fixed and frozen tissues of 1918 influenza victims. Sequence and phylogenetic analyses of the complete 1918 haemagglutinin (HA) and neuraminidase (NA) genes show them to be the most avian-like of mammalian sequences and support the hypothesis that the pandemic virus contained surface protein-encoding genes derived from an avian influenza strain and that the 1918 virus is very similar to the common ancestor of human and classical swine H1N1 influenza strains. Neither the 1918 HA genes nor the NA genes possessed mutations that are known to increase tissue tropicity, which accounts for the virulence of other influenza strains such as A/WSN/33 or fowl plague viruses. The complete sequence of the nonstructural (NS) gene segment of the 1918 virus was deduced and tested for the hypothesis that the enhanced virulence in 1918 could have been due to type I interferon inhibition by the NS1 protein. The results from these experiments were inconclusive. Sequence analysis of the 1918 pandemic influenza virus is allowing us to test hypotheses as to the origin and virulence of this strain. This information should help to elucidate how pandemic influenza strains emerge and what genetic features contribute to their virulence.

Influenza A virus neuraminidase: regions of the protein potentially involved in virus-host interactions.

Phylogenetically informative amino acid positions (PIPs) were identified in influenza A neuraminidases of subtypes N1 and N2. Neuraminidase evolves in a lineage-specific way as the virus adapts to a new host or changes to evade the host's immune system. Thus, many PIPs undoubtedly identify positions involved in virus-host interactions. Phylogenetically important regions (PIRs) are defined as several PIPs near one another. There are 15 PIRs on N1 and 12 on N2, seven of which are shared between the two subtypes. Many PIRs are coincident with antigenic or glycosylation sites. Other PIRs may represent additional antigenic sites or may be involved in other aspects of virus-host biology.

Characterization of the 1918 "Spanish" influenza virus neuraminidase gene.

The "Spanish" influenza pandemic of 1918 was characterized by exceptionally high mortality, especially among young adults. The surface proteins of influenza viruses, hemagglutinin and neuraminidase, play important roles in virulence, host specificity, and the human immune response. The complete coding sequence of hemagglutinin was reported last year. This laboratory has now determined the complete coding sequence of the neuraminidase gene of the 1918 virus. Influenza RNA fragments were isolated from lung tissue of three victims of the 1918 flu; complete sequence was generated from A/Brevig Mission/1/18, with confirmatory sequencing carried out on A/South Carolina/1/18 and A/New York/1/18. The 1918 neuraminidase gene sequence was compared with other N1 subtype neuraminidase genes, including 9 N1 strains newly sequenced for this study. The 1918 neuraminidase shares many sequence and structural characteristics with avian strains, including the conserved active site, wild-type stalk length, glycosylation sites, and antigenic sites. Phylogenetically, the 1918 neuraminidase gene appears to be intermediate between mammals and birds, suggesting that it was introduced into mammals just before the 1918 pandemic.

Molecular genetic evidence of a novel morbillivirus in a long-finned pilot whale (Globicephalus melas).

A long-finned pilot whale with morbilliviral disease was stranded in New Jersey. An immunohistochemical stain demonstrated morbilliviral antigen. Reverse transcriptase-polymerase chain reaction for morbillivirus P and N genes was positive. Novel sequences most closely related to, but distinct from, those of dolphin and porpoise morbilliviruses suggest that this virus may represent a third member of the cetacean morbillivirus group.

Improved birth outcomes among HIV-infected women with enhanced Medicaid prenatal care.

OBJECTIVES: This study evaluated the impact of enhanced prenatal care on the birth outcomes of HIV-infected women. METHODS: Medicaid claims files linked to vital statistics were analyzed for 1723 HIV-infected women delivering a live-born singleton from January 1993 to October 1995. Prenatal care program visits were indicated by rate codes. Logistic models controlling for demographic, substance use, and health care variables were used to assess the program's effect on preterm birth (less than 37 weeks) and low birthweight (less than 2500 g). RESULTS: Of the women included in the study, 75.3% participated in the prenatal care program. Adjusted program care odds were 0.58 (95% confidence interval [CI] = 0.42, 0.81) for preterm birth and 0.37 (95% CI = 0.24, 0.58) for low-birthweight deliveries in women without a usual source of prenatal care. Women with a usual source had lower odds of low-birthweight deliveries if they had more than 9 program visits. The effect of program participation persisted in sensitivity analyses that adjusted for an unmeasured confounder. CONCLUSIONS: A statewide prenatal care Medicaid program demonstrates significant reductions in the risk of adverse birth outcomes for HIV-infected women.

Sources of prenatal care data and their association with birth outcomes of HIV-infected women.

OBJECTIVES: Different sources of prenatal care data were used to examine the association between birth outcomes of HIV-infected women and the Adequacy of Prenatal Care Utilization (APNCU) index. METHODS: Adjusted odds ratios of birth outcomes for 1858 HIV-positive mothers were calculated for APNCU indexes on the basis of birth certificate data or 3 types of physician visits on Medicaid claims. RESULTS: Claims- and birth certificate-based APNCU indexes agreed poorly (kappa < 0.3). Only the broadest claims-based APNCU index had lower adjusted odds ratios for low birthweight (0.64; 95% confidence interval [CI] = 0.49, 0.84) and preterm birth (0.70; 95% CI = 0.54, 0.91). The birth certificate-based index had a reduced adjusted odds ratio (0.73; 95% CI = 0.56, 0.95) only for preterm birth. CONCLUSIONS: The association of birth outcomes and adequacy of prenatal care in this HIV-infected cohort differed significantly depending on the source of prenatal care data.

Effect of enhanced prenatal and HIV-focused services for pregnant women who are infected by human immunodeficiency virus on emergency department use.

OBJECTIVES: This study examines whether the receipt of enhanced prenatal or human immunodeficiency virus (HIV) medical services is associated with in-pregnancy emergency department (ED) utilization by HIV-infected women. METHODS: Medicaid and vital statistics records were linked for 1,826 women who are infected by HIV and who were delivered from 1993 to 1995 while receiving New York State Medicaid. The authors examined two types of ambulatory care--the Prenatal Care Assistance Program (PCAP) and enhanced care focused on HIV--that offer additional services in exchange for increased Medicaid reimbursement. From logistic regression models, the authors estimated adjusted associations of these types of care with ED use during pregnancy not leading directly to hospitalization. RESULTS: Fifty-three percent of pregnant women visited the ED. Women with ED use averaged 2.0 visits (SD = 1.1). After adjustment for demographic and substance use factors, enhanced care focused on HIV was not associated with any ED use (OR = 1.11, 95% CI 0.94, 1.30) or, among those using the ED at least once, with number of visits (P = 0.84). Interactions of receipt of PCAP care with the Adequacy of Prenatal Care Utilization Index (APNCU) and having a usual source of care in pregnancy improved model fit (P < 0.001 and P = 0.06, respectively). PCAP was associated with increased ED use only among women with inadequate APNCU or no usual source of prenatal care. CONCLUSION: Pregnant women infected with HIV receiving Medicaid relied heavily on ED care. Use of the ED was not associated with services focused on HIV but was positively associated with enhanced prenatal care. The association of enhanced prenatal care with greater ED use was curbed for women with more timely and adequate prenatal care visits or a usual source of prenatal care.

Characterization of Escherichia coli 50S ribosomal protein L31.

The published C-terminal sequence of Escherichia coli 50S ribosomal protein L31, ellipsisRFNK (Brosius, J. (1978) Biochemistry 17, 501-508), differs from that predicted by the gene sequence, ellipsisRFNKRFNIPGSK (GenBank accession no. X78541). This discrepancy might be due to post-translational processing of the protein. To examine this possibility, we have isolated L31 from E. coli strain MRE600 and sequenced the C-terminal tryptic peptide. We find the sequence to be FBIPGSK. Size comparisons of L31 from several E. coli strains demonstrate that all are identical in size to the protein isolated from MRE600 and larger than the previously described protein, indicating that ellipsisRFNKRFNIPGSK represents the true C-terminus of L31. In addition, we show that the failure to identify L31 in many ribosome preparations is probably due to the protein's loose association with the ribosome and its ability to form various intramolecular disulfide bonds, leading to L31 forms with distinct mobilities in gels.

Phylogenetically important regions of the influenza A H1 hemagglutinin protein.

A parsimony approach was used to construct phylogenetic trees of the H1, H2 and H3 influenza hemagglutinin subtypes. The parsimony trees were then compared with randomly generated trees to identify regions of the proteins containing the most phylogenetic information, i.e. those regions making the parsimony trees shorter. We reasoned that any areas of the hemagglutinin protein that were phylogenetically 'information-rich' would be good candidates for sites involved in virus-host interactions and their identification might lead to a better understanding of the protein. Molecular modelling, based upon the crystal structure of the H3 hemagglutinin, demonstrated that most phylogenetically important regions of the H1 subtype were on the surface of the hemagglutinin trimer, primarily in the globular region. Many corresponded to known antigenic or receptor binding sites, while others appear to be novel and specific for H1.

Relationship between ambulatory care accessibility and hospitalization for persons with advanced HIV disease.

Specific features of ambulatory care, such as accessibility, may influence hospital use for patients with HIV infection. To identify clinic features associated with a lower risk of hospitalization, 6,280 New York state Medicaid enrollees diagnosed with AIDS in 1987-1992 and managed by one of 157 surveyed clinics were studied. The odds of hospitalization in the year before AIDS diagnosis were associated with five clinic features that facilitate the accessibility of care: (1) evening/weekend hours, (2) case manager, (3) appointments within 48 hours, (4) telephone consultation, and (5) whether the clinic handled urgent care. Hospitalization in the year before AIDS diagnosis occurred for 49 percent of patients. Three of the five accessibility features had unadjusted associations with lower hospitalization rates. The adjusted odds of hospitalization were lower for patients in clinics with extended hours (OR = 0.77, 95% CI = 0.63, 0.93) and for patients in clinics with four or more accessibility features compared with those in clinics with less than two features (OR = 0.67; 95% CI = 0.50, 0.89).

Translating clinical trial results into practice: the effect of an AIDS clinical trial on prescribed antiretroviral therapy for HIV-infected pregnant women.

BACKGROUND: The success of Pediatric AIDS Clinical Trials Group (PACTG) Protocol 076 in preventing vertical HIV transmission prompted intensive efforts to inform lay-persons and professionals about the trial's results. OBJECTIVE: To explore community responsiveness to these efforts by assessing temporal, maternal, and health care factors associated with prescribed antiretroviral therapy before and after PACTG Protocol 076. DESIGN: Retrospective cohort study. SETTING: New York State Medicaid program. PATIENTS: 2607 HIV-infected women who delivered a living child between January 1993 and September 1996. MEASUREMENTS: Adjusted odds of being prescribed antiretroviral treatment in the second or third trimester for women who delivered in period 1 (during the trial [January 1993 to February 1994]), period 2 (after the trial's end and announcement of the results to publication of the results [March 1994 to November 1994]), and period 3 (after publication of the trial results [December 1994 to September 1996]). RESULTS: The adjusted odds of being prescribed antiretroviral therapy increased 21% per month in period 2 and decreased to 3% per month in period 3. In all time periods, the adjusted odds of being prescribed antiretroviral therapy were at least 60% greater (P < 0.05) for women who were treated at an institution that performed HIV clinical trials, received HIV-focused ambulatory care, or had adequate prenatal care visits. After the trial, women receiving methadone treatment had at least twofold (95% CI, 1.5- to 4.3-fold) greater adjusted odds of being prescribed antiretroviral therapy than women who did not take any illicit drugs. Latin-American women, older women, and women born in the United States had greater adjusted odds (P < 0.05) of being prescribed treatment in period 3. CONCLUSION: Community practice responded rapidly to efforts to disseminate the results of PACTG Protocol 076; however, the absolute increase in prescribed therapy was greatest for women who had adequate prenatal visits or were receiving HIV-focused care, care at a site that performed clinical trials, or methadone therapy.

Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene.

The "Spanish" influenza pandemic killed over 20 million people in 1918 and 1919, making it the worst infectious pandemic in history. Here, we report the complete sequence of the hemagglutinin (HA) gene of the 1918 virus. Influenza RNA for the analysis was isolated from a formalin-fixed, paraffin-embedded lung tissue sample prepared during the autopsy of a victim of the influenza pandemic in 1918. Influenza RNA was also isolated from lung tissue samples from two additional victims of the lethal 1918 influenza: one formalin-fixed, paraffin-embedded sample and one frozen sample obtained by in situ biopsy of the lung of a victim buried in permafrost since 1918. The complete coding sequence of the A/South Carolina/1/18 HA gene was obtained. The HA1 domain sequence was confirmed by using the two additional isolates (A/New York/1/18 and A/Brevig Mission/1/18). The sequences show little variation. Phylogenetic analyses suggest that the 1918 virus HA gene, although more closely related to avian strains than any other mammalian sequence, is mammalian and may have been adapting in humans before 1918.

Clinic characteristics associated with reduced hospitalization of drug users with AIDS.

OBJECTIVE: To identify features of ambulatory care associated with reduced hospitalization among drug users with acquired immunodeficiency syndrome (AIDS). METHODS: A nonconcurrent prospective study of hospital use by 1,369 drug users with AIDS was conducted using data from New York State Medicaid research data files linked to telephone interview data from directors of ambulatory care clinics serving this group. RESULTS: Follow-up averaged 29 months, during which 88% of subjects were hospitalized at least once. On average, those hospitalized spent 14% of follow-up time as inpatients. Hospitalization was less likely for patients in clinics with case managers (adjusted odds ratio = 0.42, 95% confidence interval 0.25, 0.69) or high director's rating of coordination of care (adjusted odds ratio = 0.50, 95% confidence interval 0.29, 0.89). Multivariate analysis showed significantly less time in hospital for patients in clinics with methadone maintenance, case managers, high continuity ratings, and clinic physicians attending for hospitalized clinic patients. CONCLUSIONS: Drug users with AIDS rely heavily on inpatient care, but those followed in clinics featuring greater coordination and offering special services, including methadone treatment and case management, appear to have significantly less hospital use.