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Stephen J O'Brien

Publications and source records attributed to Stephen J O'Brien.

At least 55 records · Page 3Linked to original sources
PubMed2005

Arthroscopic release of the long head of the biceps tendon: functional outcome and clinical results.

BACKGROUND: Treatment of chronic, refractory biceps tendinitis remains controversial. The authors sought to evaluate clinical and functional outcomes of arthroscopic release of the long head of the biceps tendon. HYPOTHESIS: In specific cases of refractory biceps tendinitis, site-specific release of the long head of the biceps tendon may yield relief of pain and symptoms. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: Fifty-four patients diagnosed with biceps tendinitis underwent arthroscopic release of the long head of the biceps tendon as an isolated procedure or as part of a concomitant shoulder procedure over a 2-year period. Patients were not excluded for concomitant shoulder abnormality, including degenerative joint disease, rotator cuff tears, Bankart lesions, or instability. Nine of 40 patients had an isolated arthroscopic release of the biceps tendon. At a minimum of 2 years, the American Shoulder and Elbow Surgeons; the University of California, Los Angeles; and the L'Insalata shoulder questionnaires as well as ipsilateral and contralateral metrics were used for evaluation. RESULTS: The L'Insalata; University of California, Los Angeles; and American Shoulder and Elbow Surgeons scores were 77.6, 27.6, and 75.6, respectively. Seventy percent had a Popeye sign at rest or during active elbow flexion; 82.7% of men and 36.5% of women had a positive Popeye sign (P < .05); 68% were rated as good, very good, or excellent. No patient reported arm pain at rest distally or proximally; 38% of patients complained of fatigue discomfort (soreness) isolated to the biceps muscle after resisted elbow flexion. CONCLUSION: Arthroscopic release of the long head of the biceps tendon is an appropriate and reliable intervention for patients with chronic, refractory biceps tendinitis. Cosmetic deformity presenting as a positive Popeye sign and fatigue discomfort were the primary complaints. CLINICAL RELEVANCE: Although tenotomy is not the ideal intervention for patients of all ages with various shoulder abnormalities, data suggest that it may be an acceptable surgical intervention for a specifically selected cohort of individuals.

Adolescent↗
PubMed2005

An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples.

A forensic genotyping panel of 11 tetranucleotide STR loci from the domestic cat was characterized and evaluated for genetic individualization of cat tissues. We first examined 49 candidate STR loci and their frequency assessment in domestic cat populations. The STR loci (3-4 base pair repeat motifs), mapped in the cat genome relative to 579 coding loci and 255 STR loci, are well distributed across the 18 feline autosomes. All loci exhibit Mendelian inheritance in a multi-generation pedigree. Eleven loci that were unlinked and were highly heterozygous in cat breeds were selected for a forensic panel. Heterozygosity values obtained for the independent loci, ranged from 0.60-0.82, while the average cat breed heterozygosity obtained for the 11 locus panel was 0.71 (range of 0.57-0.83). A small sample set of outbred domestic cats displayed a heterozygosity of 0.86 for the 11 locus panel. The power of discrimination of the panel is moderate to high in the cat breeds examined, with an average P(m) of 3.7E-06. The panel shows good potential for genetic individualization within outbred domestic cats with a P(m) of 5.31E-08. A multiplex protocol, designed for the co-amplification of the 11 loci and a gender-identifying locus, is species specific and robust, generating a product profile with as little as 0.125 nanograms of genomic DNA.

Animals↗
PubMed2004

Cats.

Explore the source record for details and available documents.

Animals↗
PubMed2004

Cytonuclear genomic dissociation in African elephant species.

African forest and savanna elephants are distinct species separated by a hybrid zone. Because hybridization can affect the systematic and conservation status of populations, we examined gene flow between forest and savanna elephants at 21 African locations. We detected cytonuclear dissociation, indicative of different evolutionary histories for nuclear and mitochondrial genomes. Both paternally (n = 205 males) and biparentally (n = 2,123 X-chromosome segments) inherited gene sequences indicated that there was deep genetic separation between forest and savanna elephants. Yet in some savanna locales distant from present-day forest habitats, many individuals with savanna-specific nuclear genotypes carried maternally transmitted forest elephant mitochondrial DNA. This extreme cytonuclear dissociation implies that there were ancient episodes of hybridization between forest females and savanna males, which are larger and reproductively dominant to forest or hybrid males. Recurrent backcrossing of female hybrids to savanna bulls replaced the forest nuclear genome. The persistence of residual forest elephant mitochondria in savanna elephant herds renders evolutionary interpretations based on mitochondrial DNA alone misleading and preserves a genomic record of ancient habitat changes.

Africa South of the Sahara↗
PubMed2004

Phylogeography and genetic ancestry of tigers (Panthera tigris).

Eight traditional subspecies of tiger (Panthera tigris),of which three recently became extinct, are commonly recognized on the basis of geographic isolation and morphological characteristics. To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for three molecular markers: (1) 4.0 kb of mitochondrial DNA (mtDNA) sequence; (2) allele variation in the nuclear major histocompatibility complex class II DRB gene; and (3) composite nuclear microsatellite genotypes based on 30 loci. Relatively low genetic variation with mtDNA,DRB,and microsatellite loci was found, but significant population subdivision was nonetheless apparent among five living subspecies. In addition, a distinct partition of the Indochinese subspecies P. t. corbetti in to northern Indochinese and Malayan Peninsula populations was discovered. Population genetic structure would suggest recognition of six taxonomic units or subspecies: (1) Amur tiger P. t. altaica; (2) northern Indochinese tiger P. t. corbetti; (3) South China tiger P. t. amoyensis; (4) Malayan tiger P. t. jacksoni, named for the tiger conservationist Peter Jackson; (5) Sumatran tiger P. t. sumatrae; and (6) Bengal tiger P. t. tigris. The proposed South China tiger lineage is tentative due to limited sampling. The age of the most recent common ancestor for tiger mtDNA was estimated to be 72,000-108,000 y, relatively younger than some other Panthera species. A combination of population expansions, reduced gene flow, and genetic drift following the last genetic diminution, and the recent anthropogenic range contraction, have led to the distinct genetic partitions. These results provide an explicit basis for subspecies recognition and will lead to the improved management and conservation of these recently isolated but distinct geographic populations of tigers.

Alleles↗
PubMed2004

Lack of associations between HLA class II alleles and resistance to HIV-1 infection among white, non-Hispanic homosexual men.

HLA class II alleles were molecularly typed for 100 high-risk seronegative men and 184 low-risk seroconverters from the Multicenter AIDS Cohort Study (MACS). Seven resistant individuals homozygous for CCR5 Delta32 deletions were excluded from analysis. In the univariate analysis, no significant HLA class II associations with resistance/susceptibility to HIV type 1 infection were identified. However, the transporter associated with antigen presentation 2 (TAP2) Ala 665 variant associated with resistance in earlier analyses in the MACS was in linkage disequilibrium with some HLA class II alleles. After adjusting for the established associations with HLA-A*0205 subgroup and TAP2 Ala 665 variant, no HLA class II alleles were independently associated with resistance/susceptibility to HIV-1 infection. Other genetic factors in the HLA class II-TAP region of the major histocompatibility complex might be involved.

Alleles↗
PubMed2004

HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection.

Natural killer (NK) cells provide a central defense against viral infection by using inhibitory and activation receptors for major histocompatibility complex class I molecules as a means of controlling their activity. We show that genes encoding the inhibitory NK cell receptor KIR2DL3 and its human leukocyte antigen C group 1 (HLA-C1) ligand directly influence resolution of hepatitis C virus (HCV) infection. This effect was observed in Caucasians and African Americans with expected low infectious doses of HCV but not in those with high-dose exposure, in whom the innate immune response is likely overwhelmed. The data strongly suggest that inhibitory NK cell interactions are important in determining antiviral immunity and that diminished inhibitory responses confer protection against HCV.

Adolescent↗
PubMed2004

Mesozoic origin for West Indian insectivores.

The highly endangered solenodons, endemic to Cuba (Solenodon cubanus) and Hispaniola (S. paradoxus), comprise the only two surviving species of West Indian insectivores. Combined gene sequences (13.9 kilobases) from S. paradoxus established that solenodons diverged from other eulipotyphlan insectivores 76 million years ago in the Cretaceous period, which is consistent with vicariance, though also compatible with dispersal. A sequence of 1.6 kilobases of mitochondrial DNA from S. cubanus indicated a deep divergence of 25 million years versus the congeneric S. paradoxus, which is consistent with vicariant origins as tectonic forces separated Cuba and Hispaniola. Efforts to prevent extinction of the two surviving solenodon species would conserve an entire lineage as old or older than many mammalian orders.

Animals↗
PubMed2004

A high-density admixture map for disease gene discovery in african americans.

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with approximately 100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing approximately 450000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3011 as a MALD map (1.2 cM average spacing). We estimate that this map is approximately 70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations.

Black or African American↗
PubMed2004

Methods for high-density admixture mapping of disease genes.

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) has been proposed as an efficient approach to localizing disease-causing variants that differ in frequency (because of either drift or selection) between two historically separated populations. Near a disease gene, patient populations descended from the recent mixing of two or more ethnic groups should have an increased probability of inheriting the alleles derived from the ethnic group that carries more disease-susceptibility alleles. The central attraction of admixture mapping is that, since gene flow has occurred recently in modern populations (e.g., in African and Hispanic Americans in the past 20 generations), it is expected that admixture-generated linkage disequilibrium should extend for many centimorgans. High-resolution marker sets are now becoming available to test this approach, but progress will require (a). computational methods to infer ancestral origin at each point in the genome and (b). empirical characterization of the general properties of linkage disequilibrium due to admixture. Here we describe statistical methods to estimate the ancestral origin of a locus on the basis of the composite genotypes of linked markers, and we show that this approach accurately estimates states of ancestral origin along the genome. We apply this approach to show that strong admixture linkage disequilibrium extends, on average, for 17 cM in African Americans. Finally, we present power calculations under varying models of disease risk, sample size, and proportions of ancestry. Studying approximately 2500 markers in approximately 2500 patients should provide power to detect many regions contributing to common disease. A particularly important result is that the power of an admixture mapping study to detect a locus will be nearly the same for a wide range of mixture scenarios: the mixture proportion should be 10%-90% from both ancestral populations.

Alleles↗
PubMed2004

Seroprevalence of Toxoplasma gondii in American free-ranging or captive pumas (Felis concolor) and bobcats (Lynx rufus).

Toxoplasma gondii is a major zoonotic agent infecting a wide range of mammals, including wild felids. Like domestic cats, wild felids are involved in the complete infective cycle of T. gondii, as they can host in their gastrointestinal tract sexually mature parasites and shed infective oocysts in their feces. In order to evaluate the importance of this wildlife reservoir, 438 serum samples collected between 1984 and 1999 from 438 pumas (Felis concolor) and from 58 bobcats (Lynx rufus) from North America, Central America and South America were screened for antibodies to T. gondii. The overall prevalence of T. gondii antibodies was 22.4% in pumas and 51.7% in bobcats, with regional variations. Adults were more likely to be seropositive than juveniles and kittens (prevalence ratio (PR) = 2.61; confidence interval (CI) = 1.15, 4.04). In the US, pumas from the southwestern states (Arizona, California and New Mexico) were more likely to be seropositive for T. gondii ( PR = 2.61; 95% CI = 1.32-5.18 ) than pumas from the northwestern and mountain states (Colorado, Idaho, Oregon, Utah and Wyoming). Male pumas from the US were more likely to be seropositive than females (PR = 2.08; 95% CI = 1.11-3.92), whereas female pumas from Mexico, Central America and South America were more likely to be seropositive than female pumas from Canada and the US (PR = 2.49; 95% CI = 1.09-5.69). Captive pumas were also more likely to be seropositive (21.7%, 29/92) for T. gondii than free-ranging animals (19.9%, 69/346) (PR = 1.85; 95% CI = 1.06, 3.17).

Animals↗
PubMed2004

Patterns of ethnic diversity among the genes that influence AIDS.

Although HIV-1/AIDS emerged late in the last century, more than 42 million individuals have been infected and 25 million have died worldwide, making AIDS, like malaria, a strong selective force for disease-associated genetic factors. Many of the genes that mediate immune response or that are co-opted by HIV-1 for completion of its lifecycle show differences in allele frequencies, as a result of drift, migration or selection. Here we show that the majority of AIDS candidate genes and AIDS restriction genes show significant differences in allele frequencies, possibly the result of historic selective pressures. These genes are undergoing present day natural selection in populations with high AIDS prevalence.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Mammalian phylogenomics comes of age.

The relatively new field of phylogenomics is beginning to reveal the potential of genomic data for evolutionary studies. As the cost of whole genome sequencing falls, anticipation of complete genome sequences from divergent species, reflecting the major lineages of modern mammals, is no longer a distant dream. In this article, we describe how comparative genomic data from mammals is progressing to resolve long-standing phylogenetic controversies, to refine dogma on how chromosomes evolve and to guide annotation of human and other vertebrate genomes.

Animals↗
PubMed2004

Human genes that limit AIDS.

Discernable genetic variation among people and populations has an important role in infectious disease epidemics, including that of acquired immune deficiency syndrome (AIDS). Genetic association analysis of several large AIDS cohorts implicate 14 AIDS restriction genes, polymorphic variants in loci that regulate HIV-1 cell entry, acquired and innate immunity, and cytokine defenses to HIV-1. The influence and translational impact of these genes on individual and population sensitivity to AIDS is considerable.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Revision anterior cruciate ligament reconstruction: etiology of failures and clinical results.

A retrospective study was performed to determine the etiology of failed primary anterior cruciate ligament (ACL) reconstruction and evaluate the clinical results of revision ACL surgery. From January 1989 to January 1996, 90 patients with failed ACL reconstructions underwent revision ACL surgery. The etiology of failed ACL reconstruction included 47 surgical technical errors, 22 traumatic reinjuries, 7 lack of graft incorporation, 3 loss of motion, 3 related to synthetic grafts, and 8 alignment or combined ligamentous instability patterns not addressed. Of 52 revision ACL patients with minimum 2-year follow-up, 43 responded to a questionnaire and underwent a comprehensive physical examination. The Hospital for Special Surgery knee ligament evaluation revealed 63% good/excellent results. Objective laxity test revealed 77% of all patients had 0/+1 grade on Lachman and a mean 2.86-mm KT 1000. The overall results of revision ACL surgery are encouraging in providing symptomatic relief and restoring stability; however, they are significantly lower than primary ACL surgery.

Adolescent↗
PubMed2004

APOBEC3G genetic variants and their influence on the progression to AIDS.

The cytosine deaminase APOBEC3G, in the absence of the human immunodeficiency virus type 1 (HIV-1) accessory gene HIV-1 viral infectivity factor (vif), inhibits viral replication by introducing G-->A hypermutation in the newly synthesized HIV-1 DNA negative strand. We tested the hypothesis that genetic variants of APOBEC3G may modify HIV-1 transmission and disease progression. Single nucleotide polymorphisms were identified in the promoter region (three), introns (two), and exons (two). Genotypes were determined for 3,073 study participants enrolled in six HIV-AIDS prospective cohorts. One codon-changing variant, H186R in exon 4, was polymorphic in African Americans (AA) (f = 37%) and rare in European Americans (f < 3%) or Europeans (f = 5%). For AA, the variant allele 186R was strongly associated with decline in CD4 T cells (CD4 slope on square root scale: -1.86, P = 0.009), The 186R allele was also associated with accelerated progression to AIDS-defining conditions in AA. The in vitro antiviral activity of the 186R enzyme was not inferior to that of the common H186 variant. These studies suggest that there may be a modifying role of variants of APOBEC3G on HIV-1 disease progression that warrants further investigation.

APOBEC-3G Deaminase↗
PubMed2004

Cytotoxic T-lymphocyte antigen 4 gene and recovery from hepatitis B virus infection.

Cytotoxic T-lymphocyte antigen 4 (CTLA-4) is an inhibitory T-cell receptor expressed by activated and regulatory T cells. We hypothesized that single-nucleotide polymorphisms (SNPs) in the gene encoding CTLA-4 may affect the vigor of the T-cell response to hepatitis B virus (HBV) infection, thus influencing viral persistence. To test this hypothesis, we genotyped six CTLA4 SNPs, from which all frequent haplotypes can be determined, using a large, matched panel of subjects with known HBV outcomes. Haplotypes with these SNPs were constructed for each subject using PHASE software. The haplotype distribution differed between those with viral persistence and those with clearance. Two haplotypes were associated with clearance of HBV infection, which was most likely due to associations with the SNPs -1722C (odds ratio [OR] = 0.60, P = 0.06) and +49G (OR = 0.73, P = 0.02). The wild-type haplotype, which contains an SNP leading to a decreased T-cell response (+6230A), was associated with viral persistence (OR = 1.32, P = 0.04). These data suggest that CTLA4 influences recovery from HBV infection, which is consistent with the emerging role of T regulatory cells in the pathogenesis of disease.

Adult↗