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Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Res 2003; 31:51-4. [PMID: 12519945 PMCID: PMC165576 DOI: 10.1093/nar/gkg129] [Citation(s) in RCA: 1179] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.
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Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006; 34:D590-8. [PMID: 16381938 PMCID: PMC1347506 DOI: 10.1093/nar/gkj144] [Citation(s) in RCA: 1030] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .
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Research Support, Non-U.S. Gov't |
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1030 |
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Ledergerber B, Egger M, Opravil M, Telenti A, Hirschel B, Battegay M, Vernazza P, Sudre P, Flepp M, Furrer H, Francioli P, Weber R. Clinical progression and virological failure on highly active antiretroviral therapy in HIV-1 patients: a prospective cohort study. Swiss HIV Cohort Study. Lancet 1999; 353:863-8. [PMID: 10093977 DOI: 10.1016/s0140-6736(99)01122-8] [Citation(s) in RCA: 698] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND The efficacy of highly active antiretroviral therapy (HAART) in suppression of HIV-1 is well documented. We investigated virological and clinical outcomes of HAART in routine practice. METHODS We analysed prospective data from the Swiss HIV Cohort Study on suppression of viral load and progression to AIDS or death in 2674 outpatients (median age 36 years, 27.3% women) who started HAART in 1995-98. Viral rebound was defined as two consecutive HIV-1-RNA measurements of more than 400 copies/mL. We analysed separately outcomes in patients with a history of antiretroviral treatment and in treatment-naïve patients. FINDINGS An estimated 90.7% of treatment-naïve patients reached undetectable viral load (<400 copies/mL) by 12 months. Among pretreated patients, estimates ranged from 70.3% treated with one new drug to 78.7% on three new drugs. 2 years after reaching undetectable concentrations, an estimated 20.1% of treatment-naïve patients and 35.7-40.1% of pretreated patients had viral rebound. At 30 months, an estimated 6.6% (95% CI 4.6-8.6) of patients who had maintained undetectable concentrations, 9.0% (5.5-12.5) who had viral rebound, and 20.1% (15.3-24.9) who had never reached undetectable concentrations developed AIDS or died. Compared with patients who maintained undetectable viral load, the adjusted relative hazard of AIDS or death was 1.00 (0.66-1.55) for patients with viral rebound, and 2.40 (1.72-3.33) for patients who failed to reach undetectable concentrations. INTERPRETATION The rate of virological failure of HAART was high among these patients, but the probability of clinical progression was low even in patients with viral rebound.
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Matricardi PM, Kleine-Tebbe J, Hoffmann HJ, Valenta R, Hilger C, Hofmaier S, Aalberse RC, Agache I, Asero R, Ballmer-Weber B, Barber D, Beyer K, Biedermann T, Bilò MB, Blank S, Bohle B, Bosshard PP, Breiteneder H, Brough HA, Caraballo L, Caubet JC, Crameri R, Davies JM, Douladiris N, Ebisawa M, EIgenmann PA, Fernandez-Rivas M, Ferreira F, Gadermaier G, Glatz M, Hamilton RG, Hawranek T, Hellings P, Hoffmann-Sommergruber K, Jakob T, Jappe U, Jutel M, Kamath SD, Knol EF, Korosec P, Kuehn A, Lack G, Lopata AL, Mäkelä M, Morisset M, Niederberger V, Nowak-Węgrzyn AH, Papadopoulos NG, Pastorello EA, Pauli G, Platts-Mills T, Posa D, Poulsen LK, Raulf M, Sastre J, Scala E, Schmid JM, Schmid-Grendelmeier P, van Hage M, van Ree R, Vieths S, Weber R, Wickman M, Muraro A, Ollert M. EAACI Molecular Allergology User's Guide. Pediatr Allergy Immunol 2016; 27 Suppl 23:1-250. [PMID: 27288833 DOI: 10.1111/pai.12563] [Citation(s) in RCA: 535] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology User's Guide (MAUG) provides comprehensive information on important allergens and describes the diagnostic options using CRD. Part A of the EAACI MAUG introduces allergen molecules, families, composition of extracts, databases, and diagnostic IgE, skin, and basophil tests. Singleplex and multiplex IgE assays with components improve both sensitivity for low-abundance allergens and analytical specificity; IgE to individual allergens can yield information on clinical risks and distinguish cross-reactivity from true primary sensitization. Part B discusses the clinical and molecular aspects of IgE-mediated allergies to foods (including nuts, seeds, legumes, fruits, vegetables, cereal grains, milk, egg, meat, fish, and shellfish), inhalants (pollen, mold spores, mites, and animal dander), and Hymenoptera venom. Diagnostic algorithms and short case histories provide useful information for the clinical workup of allergic individuals targeted for CRD. Part C covers protein families containing ubiquitous, highly cross-reactive panallergens from plant (lipid transfer proteins, polcalcins, PR-10, profilins) and animal sources (lipocalins, parvalbumins, serum albumins, tropomyosins) and explains their diagnostic and clinical utility. Part D lists 100 important allergen molecules. In conclusion, IgE-mediated reactions and allergic diseases, including allergic rhinoconjunctivitis, asthma, food reactions, and insect sting reactions, are discussed from a novel molecular perspective. The EAACI MAUG documents the rapid progression of molecular allergology from basic research to its integration into clinical practice, a quantum leap in the management of allergic patients.
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Practice Guideline |
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535 |
5
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Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VVB, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003; 424:788-93. [PMID: 12917688 DOI: 10.1038/nature01858] [Citation(s) in RCA: 421] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2003] [Accepted: 06/16/2003] [Indexed: 11/08/2022]
Abstract
The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.
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Comparative Study |
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Abstract
Microsporidia are obligate intracellular spore-forming protozoal parasites belonging to the phylum Microspora. Their host range is extensive, including most invertebrates and all classes of vertebrates. More than 100 microsporidial genera and almost 1,000 species have now been identified. Five genera (Enterocytozoon spp., Encephalitozoon spp., Septata spp., Pleistophora sp., and Nosema spp.) and unclassified microsporidia (referred to by the collective term Microsporidium) have been associated with human disease, which appears to manifest primarily in immunocompromised persons. The clinical manifestations of microsporidiosis are diverse and include intestinal, pulmonary, ocular, muscular, and renal disease. Among persons not infected with human immunodeficiency virus, ten cases of microsporidiosis have been documented. In human immunodeficiency virus-infected patients, on the other hand, over 400 cases of microsporidiosis have been identified, the majority attributed to Enterocytozoon bieneusi, an important cause of chronic diarrhea and wasting. Diagnosis of microsporidiosis currently depends on morphological demonstration of the organisms themselves. Initial detection of microsporidia by light microscopic examination of tissue sections and of more readily obtainable specimens such as stool, duodenal aspirates, urine, sputum, nasal discharge, bronchoalveolar lavage fluid, and conjunctival smears is now becoming routine practice. Definitive species identification is made by using the specific fluorescein-tagged antibody (immunofluorescence) technique or electron microscopy. Treatment options are limited, but symptomatic improvement of Enterocytozoon bieneusi infection may be achieved with the anthelmintic-antiprotozoal drug albendazole. Preliminary observations suggest that Septata intestinalis and Encephalitozoon infections may be cured with albendazole. Progress is being made with respect to in vitro propagation of microsporidia, which is crucial for developing antimicrosporidial drugs. Furthermore, molecular techniques are being developed for diagnostic purposes, taxonomic classification, and analysis of phylogenetic relationships of microsporidia.
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392 |
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Weber R, Bryan RT, Owen RL, Wilcox CM, Gorelkin L, Visvesvara GS. Improved light-microscopical detection of microsporidia spores in stool and duodenal aspirates. The Enteric Opportunistic Infections Working Group. N Engl J Med 1992; 326:161-166. [PMID: 1370122 DOI: 10.1056/nejm199201163260304] [Citation(s) in RCA: 356] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The diagnosis of infection with Enterocytozoon bieneusi, a microsporidian organism that causes chronic diarrhea in patients infected with the human immunodeficiency virus (HIV), has depended on invasive procedures. We have developed a new method to detect microsporidia spores in feces and duodenal aspirates. METHODS Stool was obtained from four HIV-infected patients with biopsy-confirmed intestinal microsporidiosis. Slides prepared from unconcentrated, formalin-fixed stool specimens were stained with a new chromotrope-based technique and examined by light microscopy. Methods of stool concentration were also compared. The technique was then evaluated by examining 215 specimens from 134 HIV-infected persons with or without diarrhea. In addition, duodenal aspirates from 10 patients with unexplained chronic diarrhea were examined by light microscopy after staining according to the new and the traditional techniques. RESULTS E. bieneusi spores were found in all unconcentrated stool specimens from the four patients with microsporidiosis. The use of various methods of stool concentration did not improve the detection of microsporidia spores. In the prospective study, microsporidiosis was detected in samples from 6 of 27 patients with chronic diarrhea, but in none of those from 42 patients with acute diarrhea or 65 patients without diarrhea. The presence of microsporidia spores in stool specimens and duodenal aspirates allowed the successful prediction of the presence of microsporidia in small-bowel biopsy specimens from all four patients who subsequently underwent endoscopy. CONCLUSIONS E. bieneusi is an important cause of chronic diarrhea in HIV-infected persons. This new diagnostic technique serves as a practical, noninvasive means to detect microsporidia spores in stool specimens and is also applicable to the examination of duodenal aspirates.
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Ledergerber B, Egger M, Erard V, Weber R, Hirschel B, Furrer H, Battegay M, Vernazza P, Bernasconi E, Opravil M, Kaufmann D, Sudre P, Francioli P, Telenti A. AIDS-related opportunistic illnesses occurring after initiation of potent antiretroviral therapy: the Swiss HIV Cohort Study. JAMA 1999; 282:2220-6. [PMID: 10605973 DOI: 10.1001/jama.282.23.2220] [Citation(s) in RCA: 331] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Acquired immunodeficiency syndrome-related opportunistic illnesses (Ols) continue to occur after initiation of potent antiretroviral therapy in patients with human immunodeficiency virus (HIV) infection. Risk factors for clinical progression to Ols during potent therapy are not well defined. OBJECTIVE To examine the incidence of and risk factors for Ols among patients treated with potent antiretroviral therapy in a population-based study. DESIGN The Swiss HIV Cohort Study, a prospective cohort study of adult HIV-infected persons. SETTING Seven study centers throughout Switzerland. PATIENTS A total of 2410 cohort study participants with a potential follow-up of at least 15 months after starting potent therapy between September 1995 and December 1997. MAIN OUTCOME MEASURES Disease-specific incidence of Ols during the 6 months preceding potent antiretroviral therapy and at 3 intervals after initiating therapy; risk factors for development of Ols during therapy. RESULTS Of the 2410 participants, 143 developed 186 Ols after initiation of potent antiretroviral therapy. Incidence of any OI decreased from 15.1 per 100 person-years in the 6 months before therapy to 7.7 in the first 3 months after starting treatment, 2.6 in the following 6 months, and 2.2 per 100 person-years between 9 and 15 months. Reductions in incidence ranged from 38% per month for Kaposi sarcoma (P<.001) to 5% per month for non-Hodgkin lymphoma (P = .31). Baseline CD4 cell count continued to predict the risk of disease progression after initiating potent therapy. Compared with CD4 cell counts above 200 x 10(6)/L, the hazard ratio for developing Ols was 2.5 (95% confidence interval [CI], 1.4-4.5) for counts between 51 and 200 x 10(6)/L and 5.8 (95% CI, 3.2-10.5) for counts below 51 x 10(6)/L at baseline. Independent of baseline CD4 cell count, a rise in CD4 cell count by 50 x 10(6)/L or more and undetectable HIV-1 RNA in plasma (<400 copies/mL) by 6 months reduced risk of subsequent events, with hazard ratios of 0.32 (95% CI, 0.20-0.52) and 0.39 (0.24-0.65), respectively. CONCLUSIONS Our data indicate that the risk of developing an OI for a person receiving potent antiretroviral therapy is highest during the initial months of therapy. Baseline CD4 cell count and immunologic and virologic response to treatment were strong predictors of disease progression in patients receiving potent therapy. Individuals with CD4 cell counts of 50 x 10(6)/L or below may need close clinical surveillance after initiation of potent therapy.
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Weber R, Ruppik M, Rickenbach M, Spoerri A, Furrer H, Battegay M, Cavassini M, Calmy A, Bernasconi E, Schmid P, Flepp M, Kowalska J, Ledergerber B. Decreasing mortality and changing patterns of causes of death in the Swiss HIV Cohort Study. HIV Med 2012; 14:195-207. [PMID: 22998068 DOI: 10.1111/j.1468-1293.2012.01051.x] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2012] [Indexed: 01/29/2023]
Abstract
BACKGROUND Mortality among HIV-infected persons is decreasing, and causes of death are changing. Classification of deaths is hampered because of low autopsy rates, frequent deaths outside of hospitals, and shortcomings of International Statistical Classification of Diseases and Related Health Problems (ICD-10) coding. METHODS We studied mortality among Swiss HIV Cohort Study (SHCS) participants (1988-2010) and causes of death using the Coding Causes of Death in HIV (CoDe) protocol (2005-2009). Furthermore, we linked the SHCS data to the Swiss National Cohort (SNC) cause of death registry. RESULTS AIDS-related mortality peaked in 1992 [11.0/100 person-years (PY)] and decreased to 0.144/100 PY (2006); non-AIDS-related mortality ranged between 1.74 (1993) and 0.776/100 PY (2006); mortality of unknown cause ranged between 2.33 and 0.206/100 PY. From 2005 to 2009, 459 of 9053 participants (5.1%) died. Underlying causes of deaths were: non-AIDS malignancies [total, 85 (19%) of 446 deceased persons with known hepatitis C virus (HCV) status; HCV-negative persons, 59 (24%); HCV-coinfected persons, 26 (13%)]; AIDS [73 (16%); 50 (21%); 23 (11%)]; liver failure [67 (15%); 12 (5%); 55 (27%)]; non-AIDS infections [42 (9%); 13 (5%); 29 (14%)]; substance use [31 (7%); 9 (4%); 22 (11%)]; suicide [28 (6%); 17 (7%), 11 (6%)]; myocardial infarction [28 (6%); 24 (10%), 4 (2%)]. Characteristics of deceased persons differed in 2005 vs. 2009: median age (45 vs. 49 years, respectively); median CD4 count (257 vs. 321 cells/μL, respectively); the percentage of individuals who were antiretroviral therapy-naïve (13 vs. 5%, respectively); the percentage of deaths that were AIDS-related (23 vs. 9%, respectively); and the percentage of deaths from non-AIDS-related malignancies (13 vs. 24%, respectively). Concordance in the classification of deaths was 72% between CoDe and ICD-10 coding in the SHCS; and 60% between the SHCS and the SNC registry. CONCLUSIONS Mortality in HIV-positive persons decreased to 1.33/100 PY in 2010. Hepatitis B or C virus coinfections increased the risk of death. Between 2005 and 2009, 84% of deaths were non-AIDS-related. Causes of deaths varied according to data source and coding system.
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Research Support, Non-U.S. Gov't |
13 |
299 |
10
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Brown SS, Ryerson TB, Wollny AG, Brock CA, Peltier R, Sullivan AP, Weber RJ, Dubé WP, Trainer M, Meagher JF, Fehsenfeld FC, Ravishankara AR. Variability in Nocturnal Nitrogen Oxide Processing and Its Role in Regional Air Quality. Science 2006; 311:67-70. [PMID: 16400145 DOI: 10.1126/science.1120120] [Citation(s) in RCA: 298] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nitrogen oxides in the lower troposphere catalyze the photochemical production of ozone (O3) pollution during the day but react to form nitric acid, oxidize hydrocarbons, and remove O3 at night. A key nocturnal reaction is the heterogeneous hydrolysis of dinitrogen pentoxide, N2O5. We report aircraft measurements of NO3 and N2O5, which show that the N2O5 uptake coefficient, g(N2O5), on aerosol particles is highly variable and depends strongly on aerosol composition, particularly sulfate content. The results have implications for the quantification of regional-scale O3 production and suggest a stronger interaction between anthropogenic sulfur and nitrogen oxide emissions than previously recognized.
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11
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Ratner LE, Kavoussi LR, Sroka M, Hiller J, Weber R, Schulam PG, Montgomery R. Laparoscopic assisted live donor nephrectomy--a comparison with the open approach. Transplantation 1997; 63:229-33. [PMID: 9020322 DOI: 10.1097/00007890-199701270-00009] [Citation(s) in RCA: 282] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Live donor renal transplantation provides significant advantages when compared with cadaveric donor renal transplantation in terms of improved patient and graft survival, a lower incidence of delayed function, and a shorter waiting time. Yet despite these advantages, live donors continue to be an under utilized source of kidneys for transplantation. Disincentives to live donation include the length of hospitalization, postoperative pain, cosmetic concerns, and the prolonged convalescence associated with the donor operation. In many instances minimally invasive video-assisted techniques have proven more efficacious than standard open procedures in terms of patient discomfort, length of hospital stay, cost, and length of time until the patient can return to full activity. Laparoscopic live donor nephrectomies are being performed at our institution in an attempt to make live donation more attractive to the potential donor. The purpose of this study was to retrospectively review the results of laparoscopic live donor nephrectomy (LapNx) and to compare them with those obtained using the standard open approach (OpenNx). Ten consecutive LapNx were performed from February 1995 through April 1996. The control group consisted of the 20 consecutive OpenNx performed at the same institution from January 1991 through January 1995 immediately before the initiation of the LapNx program. Live donors were considered candidates for LapNx if they possessed at least one kidney with normal renal anatomy with single renal vessels and a single ureter. LapNx was safely performed in all cases. No patients required open conversion or blood transfusions. The allograft warm ischemic time for the laparoscopic cases was 4.2+/-1.3 min. All kidneys harvested laparoscopically produced urine on the table immediately upon revascularization. Presently nine of the ten recipients have functioning allografts. At three months posttransplant the calculated recipient creatinine clearances were 67.0+/-11.5 ml/min and 64.8+/-21.4 ml/min for the LapNx and OpenNx groups, respectively (P=NS). The LapNx donors had a significantly decreased estimated blood loss, shorter time until resumption of oral intake, decreased postoperative pain (in terms of decreased analgesic requirements), shorter hospitalization, and a shorter interval until the resumption of full activities (P<0.05 for all). In addition, the LapNx group donors returned to work sooner than the OpenNx group (3.9+/-1.6 wk vs. 6.4+/-3.1 wk, respectively) (P=0.024). Four individuals agreed to donate a kidney only after learning of the availability of the laparoscopic approach. We conclude that laparoscopic live donor nephrectomy is technically feasible. In addition, it may offer significant advantages over the standard open approach in terms of patient comfort and convenience. These advantages may make live donor renal transplantation more attractive to prospective donors. The potential decrease in hospitalization and convalescence may also prove to be financially advantageous. We believe that further careful study of this procedure is warranted.
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Clinical Trial |
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282 |
12
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Abstract
Vitellogenin is synthesized under estrogen control in the liver, extensively modified, transported to the ovary, and there processed to the yolk proteins lipovitellin and phosvitin. In the frog Xenopus laevis there are at least four distinct but related vitellogenin genes. The two genes A1 and A2 have a 95 percent sequence homology in their messenger RNA coding regions, and contain 33 introns that interrupt the coding region (exons) at homologous positions. Sequences and lengths of analogous introns differ, and many introns contain repetitive DNA elements. The introns in these two genes that have apparently arisen by duplication have diverged extensively by events that include deletions, insertions, and probably duplications. Rapid evolutionary change involving rearrangements and the presence of repeated DNA suggests that the bulk of the sequences within introns may not have any specific function.
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256 |
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Biben C, Weber R, Kesteven S, Stanley E, McDonald L, Elliott DA, Barnett L, Köentgen F, Robb L, Feneley M, Harvey RP. Cardiac septal and valvular dysmorphogenesis in mice heterozygous for mutations in the homeobox gene Nkx2-5. Circ Res 2000; 87:888-95. [PMID: 11073884 DOI: 10.1161/01.res.87.10.888] [Citation(s) in RCA: 246] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heterozygous mutations in the cardiac homeobox gene, NKX2-5, underlie familial cases of atrial septal defect (ASD) with severe atrioventricular conduction block. In this study, mice heterozygous for Nkx2-5-null alleles were assessed for analogous defects. Although ASD occurred only rarely, atrial septal dysmorphogenesis was evident as increased frequencies of patent foramen ovale and septal aneurysm, and decreased length of the septum primum flap valve. These parameters were compounded by genetic background effects, and in the 129/Sv strain, septal dysmorphogenesis bordered on ASD in 17% of Nkx2-5 heterozygotes. In a proportion of neonatal heterozygotes, as well as in adults with ASD, we found that the size of the foramen ovale was significantly enlarged and altered in shape, potentially exposing the normally thin septum primum to excessive hemodynamic forces. Therefore, defective morphogenesis of the septum secundum may be one contributing factor in the generation of patent foramen ovale, septal aneurysm, and certain ASDs. Mild prolongation of P-R interval in females and an increased frequency of stenotic bicuspid aortic valves were also features of the Nkx2-5 heterozygous phenotype. Our data demonstrate that the complex effects of Nkx2-5 haploinsufficiency in mice are weaker but convergent with those in humans. As in the mouse, the phenotype of human NKX2-5 mutations may be modulated by interacting alleles.
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246 |
14
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Law MG, Friis-Møller N, El-Sadr WM, Weber R, Reiss P, D'Arminio Monforte A, Thiébaut R, Morfeldt L, De Wit S, Pradier C, Calvo G, Kirk O, Sabin CA, Phillips AN, Lundgren JD. The use of the Framingham equation to predict myocardial infarctions in HIV-infected patients: comparison with observed events in the D:A:D Study. HIV Med 2006; 7:218-30. [PMID: 16630034 DOI: 10.1111/j.1468-1293.2006.00362.x] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The D:A:D (Data Collection on Adverse Events of Anti-HIV Drugs) Study, a prospective observational study on a cohort of 23 468 patients with HIV infection, indicated that the incidence of myocardial infarction (MI) increased by 26% per year of exposure to combination antiretroviral treatment (CART). However, it remains unclear whether the observed increase in the rate of MI in this population can be attributed to changes in conventional cardiovascular risk factors. OBJECTIVE To compare the number of MIs observed among participants in the D:A:D Study with the number predicted by assuming that conventional cardiovascular risk equations apply to patients with HIV infection. METHODS The Framingham equation, a conventional cardiovascular risk algorithm, was applied to individual patient data in the D:A:D Study to predict rates of MI by duration of CART. A series of sensitivity analyses were performed to assess the effect of model and data assumptions. Predictions were extrapolated to provide 10-year risk estimates, and various scenarios were modelled to assess the expected effect of different interventions. RESULTS In patients receiving CART, the observed numbers of MIs during D:A:D follow up were similar to or somewhat higher than predicted numbers: 9 observed vs 5.5 events predicted, 14 vs 9.8, 22 vs 14.9, 31 vs 23.2 and 47 vs 37.0 for<1 year, 1-2 years, 2-3 years, 3-4 years and >4 years CART exposure, respectively. In patients who had not received CART, the observed number of MIs was fewer than predicted (3 observed vs 7.6 predicted). Nine per cent of the study population have a predicted 10-year risk of MI above 10%, a level usually associated with initiation of intervention on risk factors. CONCLUSIONS A consistent feature of all analyses was that observed and predicted rates of MI increased in a parallel fashion with increased CART duration, suggesting that the observed increase in risk of MI may at least in part be explained by CART-induced changes in conventional risk factors. These findings provide guidance in terms of choosing lifestyle or therapeutic interventions to decrease those risk factors in much the same way as in persons without HIV infection.
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Abstract
The periaqueductal gray matter of the mesencephalon (PAG) subserves a variety of diverse autonomic functions and also appears to be a site for opiate action in the induction of immunosuppression. Microinjections of morphine into the PAG, but not into other opiate receptor-containing neuroanatomical sites, result in a rapid suppression of natural killer (NK) cell activity. The NK cell suppression can be blocked by prior peripheral administration of the opiate antagonist naltrexone. These findings demonstrate that certain central actions of opiates that produce changes in NK cell function are mediated through opiate receptors in the PAG and identify a brain region involved in opiate regulation of immune function.
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Brandt T, Orberk E, Weber R, Werner I, Busse O, Müller BT, Wigger F, Grau A, Grond-Ginsbach C, Hausser I. Pathogenesis of cervical artery dissections: association with connective tissue abnormalities. Neurology 2001; 57:24-30. [PMID: 11445623 DOI: 10.1212/wnl.57.1.24] [Citation(s) in RCA: 216] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The etiology of spontaneous cervical artery dissection (CAD) is largely unknown. An underlying connective tissue disorder has often been postulated. OBJECTIVE To further assess the association of CAD with ultrastructural abnormalities of the dermal connective tissue. METHODS In a multicenter study, skin biopsies of 65 patients with proven nontraumatic CAD and 10 control subjects were evaluated. The ultrastructural morphology of the dermal connective tissue components was assessed by transmission electron microscopy. RESULTS Only three patients (5%) had clinical manifestations of skin, joint, or skeletal abnormalities. Ultrastructural aberrations were seen in 36 of 65 patients (55%), consisting of the regular occurrence of composite fibrils within collagen bundles that in some cases resembled the aberrations found in Ehlers-Danlos syndrome type II or III and elastic fiber abnormalities with minicalcifications and fragmentation. A grading scale according to the severity of the findings is introduced. Intraindividual variability over time was excluded by a second biopsy of the skin in eight patients with pronounced aberrations. Recurrent CAD correlated with connective tissue aberrations. In addition, similar connective tissue abnormalities were detected in four first-degree relatives with familial CAD. CONCLUSION CAD is associated with ultrastructural connective tissue abnormalities, mostly without other clinical manifestations of a connective tissue disease. A structural defect in the extracellular matrix of the arterial wall leading to a genetic predisposition is suggested. The dermal connective tissue abnormalities detected can serve as a phenotypic marker for further genetic studies in patients with CAD and large families to possibly identify the underlying basic molecular defect(s).
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Multicenter Study |
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Weber R, Bryan RT, Bishop HS, Wahlquist SP, Sullivan JJ, Juranek DD. Threshold of detection of Cryptosporidium oocysts in human stool specimens: evidence for low sensitivity of current diagnostic methods. J Clin Microbiol 1991; 29:1323-7. [PMID: 1715881 PMCID: PMC270109 DOI: 10.1128/jcm.29.7.1323-1327.1991] [Citation(s) in RCA: 205] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To determine the minimum number of Cryptosporidium oocysts that can be detected in stool specimens by diagnostic procedures, stool samples seeded with known numbers of Cryptosporidium parvum oocysts were processed by the modified Formalin-ethyl acetate (FEA) stool concentration method. FEA concentrates were subsequently examined by both the modified cold Kinyoun acid-fast (AF) staining and fluorescein-tagged monoclonal antibody (immunofluorescence [IF]) techniques. Oocysts were more easily detected in watery diarrheal stool specimens than they were in formed stool specimens. For watery stool specimens, a 100% detection rate was accomplished at a concentration of 10,000 oocysts per g of stool by both the AF staining and IF techniques. In formed stool specimens, 100% of specimens seeded with 50,000 oocysts per gram of stool were detected by the IF technique, whereas 500,000 oocysts per g of stool were needed for a 100% detection rate by AF staining. Counting of all oocysts on IF slides indicated a mean oocyst loss ranging from 51.2 to 99.6%, depending on the stool consistency as determined by the FEA concentration procedure. Our findings suggest that the most commonly used coprodiagnostic techniques may fail to detect cryptosporidiosis in many immunocompromised and immunocompetent individuals.
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research-article |
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Wahli W, Dawid IB, Wyler T, Jaggi RB, Weber R, Ryffel GU. Vitellogenin in Xenopus laevis is encoded in a small family of genes. Cell 1979; 16:535-49. [PMID: 455441 DOI: 10.1016/0092-8674(79)90028-x] [Citation(s) in RCA: 198] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Vitellogenin, the yolk protein precursor, is produced in X. laevis liver from a 6.3 kilobase (kb) mRNA. Sequences of this mRNA have been transcribed into cDNA and cloned in E. coli. Some properties of 21 of these cloned DNAs, ranging in size from 1 to 3.7 kb, have been reported by Wahli et al. (1978b). This paper reports restriction endonuclease mapping, cross hybridization, heteroduplex mapping in the electron microscope and heteroduplex melting experiments with these DNAs. We conclude that the cloned DNAs fall into two main groups of sequences which differ from each other in approximately 20% of their nucleotides. Each main group contains two subgroups which differ from each other by about 5% sequence divergence. By hybridizing cloned DNAs with restricted genomic DNA, we showed that sequences corresponding to all four sequence groups are present in a single animal. Furthermore, we have obtained tentative evidence for the presence of large intervening sequences in genomic vitellogenin DNA. Analysis of R loop molecules demonstrated that all four sequences are present in the vitellogenin mRNA population purified from individual animals. While some alternate explanations are not entirely excluded, we suggest that vitellogenin is encoded by a small family of related genes in Xenopus.
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Ruff MR, Pert CB, Weber RJ, Wahl LM, Wahl SM, Paul SM. Benzodiazepine receptor-mediated chemotaxis of human monocytes. Science 1985; 229:1281-3. [PMID: 2994216 DOI: 10.1126/science.2994216] [Citation(s) in RCA: 196] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Benzodiazepines, which are widely prescribed for their antianxiety effects, are shown to be potent stimulators of human monocyte chemotaxis. The chemotactic effects of benzodiazepine receptor agonists were blocked by the peripheral benzodiazepine receptor antagonist PK-11195, suggesting that these effects are mediated by the peripheral-type benzodiazepine receptor. Diazepam was also active in inducing chemotaxis. Binding studies on purified monocytes revealed high-affinity peripheral benzodiazepine receptors, and the displacement potencies of various benzodiazepines correlated with their relative potencies in mediating chemotaxis. The demonstration of functional benzodiazepine receptors on human monocytes, together with recent evidence of receptor-mediated monocyte chemotaxis by other psychoactive peptides (such as opiate peptides), suggests a biochemical substrate for psychosomatic communication.
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Phillips AN, Staszewski S, Weber R, Kirk O, Francioli P, Miller V, Vernazza P, Lundgren JD, Ledergerber B. HIV viral load response to antiretroviral therapy according to the baseline CD4 cell count and viral load. JAMA 2001; 286:2560-7. [PMID: 11722270 DOI: 10.1001/jama.286.20.2560] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT It is unclear whether delay in initiation of antiretroviral therapy (ART) may lead to a poorer viral load response for patients with human immunodeficiency virus (HIV). OBJECTIVE To characterize the relationship of viral load response to ART with baseline CD4 cell count and baseline viral load. DESIGN Inception cohort of 3430 therapy-naive patients with HIV, of whom 3226 patients had at least 1 viral load count after the start of ART. SETTING Three cohort studies of patients cared for in HIV clinics in Europe between 1996 and 2000. PATIENTS All patients initiating ART consisting of at least 3 drugs initiated in or after 1996 and for whom CD4 cell count and viral load were available in the prior 6 months (at most). MAIN OUTCOME MEASURES Viral load decrease to below 500 copies/mL; viral load rebound to above 500 copies/mL (2 consecutive values). RESULTS Of 3226 patients during the median follow-up of 119 weeks, 2741 (85%) experienced viral suppression to less than 500 copies/mL by 32 weeks. Relative hazards (RHs) of achieving this were 1.08 (95% confidence interval [CI], 0.98-1.21) and 0.94 (95% CI, 0.84-1.04) for baseline CD4 cell counts between 200 and 349 x 10(6)/L and baseline CD4 cell counts lower than 200 x 10(6)/L, respectively, compared with baseline CD4 cell counts of 350 x 10(6)/L or higher, after adjustment for several factors including baseline viral load. For baseline viral load, the RHs were 0.95 (95% CI, 0.84-1.07) and 0.65 (95% CI, 0.58-0.74), for 10 000 to 99 999 and 100 000 copies/mL or greater, respectively, compared with less than 10 000 copies/mL, but the probability of viral load lower than 500 copies/mL at week 32 was similar in all 3 groups. Subsequent rebound above 500 copies/mL was no more likely with a lower baseline CD4 cell count or higher viral load. CONCLUSION In this study, lower CD4 cell counts and higher viral loads at baseline were not associated with poorer virological outcome of ART. Those with baseline viral loads of greater than 100 000 copies/mL had a slower rate of achieving viral suppression.
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Multicenter Study |
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d'Arminio A, Sabin CA, Phillips AN, Reiss P, Weber R, Kirk O, El-Sadr W, De Wit S, Mateu S, Petoumenos K, Dabis F, Pradier C, Morfeldt L, Lundgren JD, Friis-Møller N. Cardio- and cerebrovascular events in HIV-infected persons. AIDS 2004; 18:1811-7. [PMID: 15316342 DOI: 10.1097/00002030-200409030-00010] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Recent results from the D:A:D Study indicated that the incidence of myocardial infarction (MI) increased by 26% per year of exposure to combination antiretroviral treatment (CART). The present study was performed to investigate whether this risk was similar when including other cardio- and cerebro-vascular disease events (CCVE). DESIGN D:A:D is an international collaboration of 11 cohorts, following 23 468 HIV-infected patients prospectively at 188 clinics in 21 countries situated in Europe, USA and Australia. METHODS The end-point was the occurrence of a first CCVE during prospective follow-up, defined as the first of: acute MI, invasive cardiovascular procedures, stroke, or death from other cardiovascular disease. Relative rates (RR) for CCVE from Poisson regression models and 95% confidence intervals (CI) are reported. All models are adjusted for other risk factors for CCVE, including age, gender, ethnicity, family history, body mass index, and smoking status as well as cohort and HIV transmission group. RESULTS Over 36 145 person-years of follow-up, 207 patients experienced at least one CCVE (23.7% fatal). The first event was MI in 126 patients, invasive cardiovascular procedure in 39 patients, stroke in 38 patients, and death from other cardiovascular disease in four patients. The incidence of first CCVE was 5.7 per 1000 person-years [95% confidence interval (CI) 5.0-6.5] and increased with longer exposure to CART (RR per year of exposure, 1.26; 95% CI, 1.14-1.38; P < 0.0001). CONCLUSION CART increases the risk of CCVD, and this increase is comparable with how CART affects the risk of MI. This finding is consistent with the hypothesis that atherosclerosis is a side-effect of CART.
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Research Support, U.S. Gov't, P.H.S. |
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Grohmann GS, Glass RI, Pereira HG, Monroe SS, Hightower AW, Weber R, Bryan RT. Enteric viruses and diarrhea in HIV-infected patients. Enteric Opportunistic Infections Working Group. N Engl J Med 1993; 329:14-20. [PMID: 8099429 DOI: 10.1056/nejm199307013290103] [Citation(s) in RCA: 186] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Diarrhea occurs frequently among persons with the acquired immunodeficiency syndrome, but the cause often remains unknown. We used a group of diagnostic assays to determine which viruses were etiologic agents of diarrhea in a group of persons infected with the human immunodeficiency virus (HIV). METHODS Stool and serum specimens were obtained from HIV-infected patients enrolled in a longitudinal study in Atlanta. Fecal specimens from patients with diarrhea and from control patients without diarrhea were screened by electron microscopy, polyacrylamide-gel electrophoresis, and enzyme immunoassays for rotaviruses, enteric adenoviruses, caliciviruses, picobirnaviruses, and astroviruses. Paired serum samples were tested for antibody responses to Norwalk virus and picobirnavirus. RESULTS Viruses were detected in 35 percent of 109 fecal specimens from patients with diarrhea but in only 12 percent of 113 specimens from those without diarrhea (P < 0.001). Specimens from patients with diarrhea were more likely than those from patients without diarrhea to have astrovirus (12 percent vs. 2 percent, P = 0.003); picobirnavirus (9 percent vs. 2 percent, P = 0.017); caliciviruses, including small round structured viruses (6 percent vs. 1 percent, P = 0.062); and adenoviruses (9 percent vs. 3 percent, P = 0.047). They were also more likely to have a mixed viral infection (6 percent vs. 0 percent, P = 0.006). With the use of polyacrylamide-gel electrophoresis to analyze concentrated RNA extracts from stool, picobirnavirus was detected in fecal specimens from 6 of the 65 patients with diarrhea and was associated with prolonged viral shedding and chronic diarrhea. No rotaviruses, enteric adenoviruses, or instances of seroconversion to positivity for Norwalk virus were observed. CONCLUSIONS Novel enteric viruses such as astrovirus and picobirnavirus may be more important etiologic agents of diarrhea in HIV-infected patients than previously recognized and may be more common than either bacterial or parasitic enteropathogens.
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Review |
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Morgan U, Weber R, Xiao L, Sulaiman I, Thompson RC, Ndiritu W, Lal A, Moore A, Deplazes P. Molecular characterization of Cryptosporidium isolates obtained from human immunodeficiency virus-infected individuals living in Switzerland, Kenya, and the United States. J Clin Microbiol 2000; 38:1180-3. [PMID: 10699017 PMCID: PMC86369 DOI: 10.1128/jcm.38.3.1180-1183.2000] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 22 Cryptosporidium isolates from human immunodeficiency virus-infected patients from Kenya, Switzerland, and the United States were examined at three genetic loci: the 18S ribosomal DNA, HSP-70, and acetyl coenzyme A synthetase genes. Four distinct Cryptosporidium genotypes were identified: (i) the Cryptosporidium parvum "human" genotype, (ii) the C. parvum "cattle" genotype, (iii) Cryptosporidium felis, and (iv) Cryptosporidium meleagridis. This is the first report of C. meleagridis in a human host. These results and those of others indicate that immunocompromised individuals are susceptible to a wide range of Cryptosporidium species and genotypes. Future studies are required to understand the full public health significance of Cryptosporidium genotypes and species in immunocompromised hosts.
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Abstract
OBJECTIVES/HYPOTHESIS To validate the endonasal surgical approach to frontal sinus in inflammatory sinus disease, trauma, and selective tumor surgery, and to define the role of external approaches to the frontal sinus. Endonasal frontal sinusotomy can range from endoscopic removal of obstructing frontal recess cells or uncinate process to the more complex unilateral or bilateral removal of the frontal sinus floor as described in the Draf II-III drainage procedures. In contrast, the osteoplastic frontal sinusotomy remains the "gold standard" for external approaches to frontal sinus disease. METHODS A retrospective review of 1286 patients undergoing either endonasal or external frontal sinusotomy by the authors at four university teaching programs from 1977. Prior author reports were updated and previously unreported patient series were combined. RESULTS Six hundred thirty-five patients underwent type I frontal sinusotomy, 312 type II sinusotomy, and 156 type III sinusotomy. A successful result was seen in these groups, 85.2% to 99.3%, 79% to 93.3%, and 91.5% to 95%, respectively. External frontal sinusotomy or osteoplastic frontal sinusotomy was successfully performed in 187 of 194 patients. Clinical symptoms, endoscopic findings, computed tomography, and magnetic resonance image scanning, and reoperation rate measured postoperative success. CONCLUSIONS A stepwise approach to the surgical treatment of frontal sinusitis, trauma, and selective benign tumors yields successful results as defined by specific criteria which vary from 79% to 97.8%. The details of specific techniques are discussed, essential points emphasized, and author variations noted.
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Multicenter Study |
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Ratner LE, Hiller J, Sroka M, Weber R, Sikorsky I, Montgomery RA, Kavoussi LR. Laparoscopic live donor nephrectomy removes disincentives to live donation. Transplant Proc 1997; 29:3402-3. [PMID: 9414765 DOI: 10.1016/s0041-1345(97)00955-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Comparative Study |
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163 |