Browsing by Subject "Biopsy"

Now showing 1 - 11 of 11
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    50 years of Emmonsia disease in humans: the dramatic emergence of a cluster of novel fungal pathogens
    (Public Library of Science, 2015) Schwartz, Ilan S; Kenyon, Chris; Feng, Peiying; Govender, Nelesh P; Dukik, Karolina; Sigler, Lynne; Jiang, Yanping; Stielow, J Benjamin; Muñoz, José F; Cuomo, Christina A; Botha, Alfred; Stchigel, Alberto M; De Hoog, G Sybren
    New species of Emmonsia-like fungi, with phylogenetic and clinical similarities to Blastomyces and Histoplasma, have emerged as causes of systemic human mycoses worldwide. They differ from classical Emmonsia species by producing a thermally-dependent, yeast-like phase rather than adiaspores, and by causing disseminated infections, predominantly in immunocompromised patients and often with high case-fatality rates. Such differences will be important for clinicians to consider in diagnosis and patient management, and for microbiologists who may encounter these fungi with increasing frequency.
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    Applications of aspiration lung biopsy with special reference to the pathogenesis of the resolution of acute and chronic lobar pneumonia
    (1951) Woolf, Colin Rael; Forman, F; Landau, A
    Lung biopsy is neither widely known nor practiced and it was only in 1949 that i first came across a paper on this subject. The title was: "Cellular analysis of the aspiration lung biopsy from normal and some pathological conditions by Z. Godlowski" (1949). The very term "lung biopsy" conjures up the picture of a needle being introduced into an air filled, very vascular structure where the bleeding of an injured vessel cannot readily be stopped, where the stage is set for air embolisms and where tension pneumothorax may occur. it was with great surprise but also an apparently innocuous procedure. Unfortunately, at that time, there was no opportunity to use the method. In 1950 I became the University Assistant at the New Somerset Hospital in Cape Town. Many of the cases admitted to the wards presented with chest pathology. Patients with pneumococcal lobar pneumonia were not infrequent and occasional cases did not resolve as expected but went on to become so-called chronic pneumonia. What happened when an acute lobar pneumonia went on to the chronic stage and why did this occur? it was suggested that investigae this problem.
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    Biopsying Southern right whales: their reactions and effects on reproduction
    (Wiley, 2005) Best, Peter B; Reeb, Desray; Rew, Mary Beth; Palsbøll, Per J; Schaeff, Cathy; Brandão, Anabela
    Collecting skin biopsies from large whales for genetic analysis is often subject to national permit, and in the case of cow-calf pairs, it may be prohibited. We present results of 906 biopsy attempts on southern right whales (Eubalaenaustralis) in South African waters between 1995 and 1997, including 147 cow-calf pairs. Our sampling success was higher for biopsy darts with a bore of 4 mm compared to 4.6 mm. Contact periods averaged 17.7 min for cow-calf pairs and 25.4 min for whales unaccompanied by calves. There were no significant differences in the short-term reactions of males and females to biopsying, but the reaction of single animals of either sex was greater than for larger groups. Cows accompanied by calves had the strongest reactions, which were significantly greater than even single females. We found evidence of sensitization to repeat biopsying (over periods of hours to 65 days) for cows but not calves (n = 20). We compared the subsequent reproductive history of 117 biopsied cows with that of 163 unbiopsied cows from the same years, and we compared the distribution of calving intervals for biopsied animals with 829 intervals recorded from 1985 to 1995. We did not detect any adverse effects on the proportion of successful reproductive cycles, and hence calf survival, or the proportion of longer-than-normal cycles, although the power of all the statistical tests was low. We concluded that any prohibition on the biopsy sampling of cow-calf pairs should be carefully reconsidered in the light of the valuable genetic insights such sampling could achieve.
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    Clinical diagnostic utility of IP-10 and LAM antigen levels for the diagnosis of tuberculous pleural effusions in a high burden setting
    (Public Library of Science, 2009) Dheda, Keertan; Van-Zyl Smit, Richard N; Sechi, Leonardo A; Badri, Motasim; Meldau, Richard; Symons, Gregory; Khalfey, Hoosein; Carr, Igshaan; Maredza, Alice; Dawson, Rodney
    BACKGROUND: Current tools for the diagnosis of tuberculosis pleural effusions are sub-optimal. Data about the value of new diagnostic technologies are limited, particularly, in high burden settings. Preliminary case control studies have identified IFN-γ-inducible-10kDa protein (IP-10) as a promising diagnostic marker; however, its diagnostic utility in a day-to-day clinical setting is unclear. Detection of LAM antigen has not previously been evaluated in pleural fluid. METHODS: We investigated the comparative diagnostic utility of established (adenosine deaminase [ADA]), more recent (standardized nucleic-acid-amplification-test [NAAT]) and newer technologies (a standardized LAM mycobacterial antigen-detection assay and IP-10 levels) for the evaluation of pleural effusions in 78 consecutively recruited South African tuberculosis suspects. All consenting participants underwent pleural biopsy unless contra-indicated or refused. The reference standard comprised culture positivity for M. tuberculosis or histology suggestive of tuberculosis. Principal FINDINGS: Of 74 evaluable subjects 48, 7 and 19 had definite, probable and non-TB, respectively. IP-10 levels were significantly higher in TB vs non-TB participants (p<0.0001). The respective outcomes [sensitivity, specificity, PPV, NPV %] for the different diagnostic modalities were: ADA at the 30 IU/L cut-point [96; 69; 90; 85], NAAT [6; 93; 67; 28], IP-10 at the 28,170 pg/ml ROC-derived cut-point [80; 82; 91; 64], and IP-10 at the 4035 pg/ml cut-point [100; 53; 83; 100]. Thus IP-10, using the ROC-derived cut-point, missed ∼20% of TB cases and mis-diagnosed ∼20% of non-TB cases. By contrast, when a lower cut-point was used a negative test excluded TB. The NAAT had a poor sensitivity but high specificity. LAM antigen-detection was not diagnostically useful. CONCLUSION: Although IP-10, like ADA, has sub-optimal specificity, it may be a clinically useful rule-out test for tuberculous pleural effusions. Larger multi-centric studies are now required to confirm our findings.
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    Epidemiology of histologically proven Glomerulonephritis in Africa: A systematic review and meta-analysis
    (Public Library of Science, 2016) Okpechi, Ikechi G; Ameh, Oluwatoyin I; Bello, Aminu K; Ronco, Pierre; Swanepoel, Charles R; Kengne, Andre P
    Background and aim: Glomerulonephritis (GN) is a leading cause of end-stage renal disease (ESRD) in Africa. Data on epidemiology and outcomes of glomerular diseases from Africa is still limited. We conducted a systematic review on the epidemiology of histologically proven glomerular diseases in Africa between 1980 and 2014. Materials and methods We searched literature using PubMed, AfricaWide, the Cumulative Index to Nursing and Allied Health Literature on EBSCO Host, Scopus, African Journals online databases, and the African Index Medicus, for relevant studies. The review was conducted using standard methods and frameworks using only biopsy-confirmed data. RESULTS: Twenty four (24) studies comprising 12,093 reported biopsies from 13 countries were included in this analysis. The median number of biopsies per study was 127.0 (50-4436), most of the studies (70.0%) originated from North Africa and the number of performed kidney biopsies varied from 5.2 to 617 biopsies/year. Nephrotic syndrome was the commonest indication of renal biopsy. The frequency of reported primary pathologic patterns included, minimal change disease (MCD); 16.5% (95%CI: 11.2-22.6), focal segmental glomerulosclerosis (FSGS); 15.9% (11.3-21.1), mesangiocapillary GN (MCGN); 11.8% (9.2-14.6), crescentic GN; 2.0% (0.9-3.5) and IgA nephropathy 2.8% (1.3-4.9). Glomerular diseases related to hepatitis B and systemic lupus erythematosus had the highest prevalence among assessed secondary diseases: 8.4% (2.0-18.4) and 7.7% (4.5-11.7) respectively. There was no evidence of publication bias and regional differences were seen mostly for secondary GNs. CONCLUSIONS: Glomerular diseases remain poorly characterized in sub-Saharan Africa due to declining renal biopsy rates and consequent paucity of data on pathologic patterns of key renal diseases. Development of renal biopsy registries in Africa is likely to enable adequate characterization of the prevalence and patterns of glomerular diseases; this could have a positive impact on chronic kidney disease evaluation and treatment in the African continent since most glomerulopathies are amenable to treatment.
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    Failure to eradicate Isospora belli diarrhoea despite immune reconstitution in adults with HIV--a case series
    (Public Library of Science, 2012) Boyles, Tom H; Black, John; Meintjes, Graeme; Mendelson, Marc
    Isospora belli causes diarrhoea in patients with AIDS. Most respond to targeted therapy and recommendations are that secondary prophylaxis can be stopped following immune reconstitution with ART. We report eight cases of chronic isosporiasis that persisted despite standard antimicrobial therapy, secondary prophylaxis, and good immunological and virological response to ART. Median CD4 nadir was 175.5 cells/mm 3 and median highest CD4 while symptomatic was 373 cells/mm 3 . Overall 34% of stool samples and 63% of duodenal biopsy specimens were positive for oocytes. Four patients died, two remain symptomatic and two recovered. Possible explanations for persistence of symptoms include host factors such as antigen specific immune deficiency or generalised reduction in gut immunity. Parasite factors may include accumulating resistance to co-trimoxazole. Research is required to determine the optimum dose and duration of co-trimoxazole therapy and whether dual therapy may be necessary. Mortality was high and pending more data we recommend extended treatment with high-dose co-trimoxazole in similar cases.
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    Optimizing viable leukocyte sampling from the female genital tract for clinical trials: an international multi-site study
    (Public Library of Science, 2014) McKinnon, Lyle R; Hughes, Sean M; De Rosa, Stephen C; Martinson, Jeffrey A; Plants, Jill; Brady, Kirsten E; Gumbi, Pamela P; Adams, Devin J; Vojtech, Lucia; Galloway, Christine G
    BACKGROUND: Functional analysis of mononuclear leukocytes in the female genital mucosa is essential for understanding the immunologic effects of HIV vaccines and microbicides at the site of HIV exposure. However, the best female genital tract sampling technique is unclear. Methods and FINDINGS: We enrolled women from four sites in Africa and the US to compare three genital leukocyte sampling methods: cervicovaginal lavages (CVL), endocervical cytobrushes, and ectocervical biopsies. Absolute yields of mononuclear leukocyte subpopulations were determined by flow cytometric bead-based cell counting. Of the non-invasive sampling types, two combined sequential cytobrushes yielded significantly more viable mononuclear leukocytes than a CVL (p<0.0001). In a subsequent comparison, two cytobrushes yielded as many leukocytes (∼10,000) as one biopsy, with macrophages/monocytes being more prominent in cytobrushes and T lymphocytes in biopsies. Sample yields were consistent between sites. In a subgroup analysis, we observed significant reproducibility between replicate same-day biopsies (r = 0.89, p = 0.0123). Visible red blood cells in cytobrushes increased leukocyte yields more than three-fold (p = 0.0078), but did not change their subpopulation profile, indicating that these leukocytes were still largely derived from the mucosa and not peripheral blood. We also confirmed that many CD4 + T cells in the female genital tract express the α4β7 integrin, an HIV envelope-binding mucosal homing receptor. CONCLUSIONS: CVL sampling recovered the lowest number of viable mononuclear leukocytes. Two cervical cytobrushes yielded comparable total numbers of viable leukocytes to one biopsy, but cytobrushes and biopsies were biased toward macrophages and T lymphocytes, respectively. Our study also established the feasibility of obtaining consistent flow cytometric analyses of isolated genital cells from four study sites in the US and Africa. These data represent an important step towards implementing mucosal cell sampling in international clinical trials of HIV prevention.
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    Outcome of patients with primary immune-complex type Mesangiocapillary Glomerulonephritis (MCGN) in Cape Town South Africa
    (Public Library of Science, 2014) Okpechi, Ikechi G; Dlamini, Thandiwe A L; Duffield, Maureen; Rayner, Brian L; Moturi, George; Swanepoel, Charles R
    Background and Aim Mesangiocapillary glomerulonephritis (MCGN) is a common cause of chronic kidney disease in developing countries. Data on the renal outcome of patients with idiopathic MCGN is limited. The aim of this study is to investigate the outcome of patients with idiopathic MCGN presenting to the Groote Schuur Hospital (GSH) Renal Unit in Cape Town. Materials and METHODS: A retrospective study of patients with idiopathic MCGN followed up at our clinic. Seventy-nine patients with no identifiable cause of MCGN were included for analysis. A composite renal outcome of persistent doubling of serum creatinine or end stage renal disease (ESRD) was used. Kaplan Meier survival and Cox regression analysis were used to assess survival and identify factors predicting the outcome. RESULTS: The mean age at biopsy was 33.9±13.6 years and 41.8% were black. Mean duration of follow up was 13.5±18.8 months. Twenty-three patients (34.2%) reached the composite endpoint. Overall, median renal survival was 38.7±11.7 months (95% CI 15.7-61.8) with 2-year and 5-year renal survival of 61% and 40.3% respectively. No significant difference was found for renal survival between males and females, treatment or non-treatment with immunosuppression, presence or absence of crescents or histological type of MCGN (p>0.05). On univariate Cox-regression analysis, factors found to be associated with the outcome were the estimated glomerular filtration rate at biopsy (OR 0.97 [95%CI: 0.95-0.99], p<0.0001), black race (OR 3.03 [95%CI: 1.27-7.21], p = 0.012) and presence of interstitial fibrosis in the biopsy (OR 2.64 [95%CI: 1.07-6.48], p = 0.034). Age, systolic blood pressure and attaining complete or partial remission approached significant values with the endpoint. CONCLUSIONS: The outcome of idiopathic MCGN in Cape Town is poor and requires further prospective studies to improve our understanding of this common disease.
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    Pre-operative diagnosis of thyroid cancer: Clinical, radiological and pathological correlation
    (2013) Cairncross, Lydia; Panieri, Eugenio
    AIM: Ultrasonography and fine-needle aspiration biopsy (FNAB) are the mainstays of diagnosing thyroid cancer accurately and reducing the number of diagnostic lobectomies. No benchmark for diagnostic accuracy has been published in the South African context. This single-institution study addresses this deficit. METHODS: The oncology, pathology and surgical records of all patients diagnosed with thyroid carcinoma from 2004 to 2010 at Groote Schuur Hospital, Cape Town, South Africa, were reviewed and data were recorded on a standardised confidential proforma. The findings on pre-operative clinical assessment, ultrasound and FNAB were correlated with the histopathology results. Diagnostic accuracy for thyroid cancer was determined by correlating pre-operative investigations with the final diagnosis. Sensitivity of ultrasound and FNAB were calculated. RESULTS: A total of 109 patients, 79 female and 30 male, were identified. The majority (99, 90.8%) had well-differentiated thyroid cancers (56 papillary, 30 follicular, 10 mixed and 3 Hurtle cell carcinomas). There were 6 anaplastic and 4 medullary carcinomas. Of the 109 patients 38 had a definite pre-operative diagnosis, in 61 a malignant tumour was suspected, and 10 had surgery for benign disease. FNAB was inadequate in 11 cases and the findings indicated a benign lesion in 47, a suspicious lesion in 13 and a malignant lesion in 38 patients diagnosed with thyroid carcinoma. FNAB diagnosed all patients with medullary and anaplastic carcinoma but less than half of those with well-differentiated thyroid carcinoma. Ultrasound scans detected at least one suspicious feature in 44 patients. Microcalcification was the most common sign. CONCLUSION: The rate of pre-operative diagnosis of well-differentiated thyroid carcinomas in this unit is under 50%, well below international norms. Our standard practice needs to change to include ultrasound-guided FNAB and standardised reporting of high-resolution ultrasound and cytology, before reassessment of our diagnostic accuracy.
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    Prospective One Year follow up of HIV infected women screened for cervical cancer using visual inspection with acetic acid, cytology and human papillomavirus testing in Johannesburg, South Africa
    (Public Library of Science, 2016) Firnhaber, Cynthia; Goeieman, Bridgette; Faesen, Mark; Levin, Simon; Williams, Sophie; Rameotshela, Sibongile; Swarts, Avril; Michelow, Pam; Omar, Tanvier; Williamson, Anna-Lise; Allan, Bruce; Schnippel, Kate; Smith, Jennifer S
    BACKGROUND: Cervical cancer is the most common cancer in Sub-Saharan Africa. There are little of HIV-infected women one-year after screening using visual inspection with acetic acid (VIA), HPV or cytology in sub-Saharan Africa. METHODS: HIV-infected women in Johannesburg South Africa were screened one year later by Pap smear, VIA and human papillomavirus (HPV) testing. Women qualified for the 12 month follow-up visit if they had a negative or cervical intra-epithelial neoplasia (CIN) 1 results at the baseline visit. Modified Poisson regression was used to analyse associations between patient baseline characteristics and progression. RESULTS: A total of 688 of 1,202 enrolled at baseline study who were CIN-2+ negative and qualified for a 12 month follow-up visit. Progression to CIN-2+ was higher in women with positive VIA results (12.6%; 24/191) than those VIA-negative (4.4%; 19/432). HPV-positive women at baseline were more likely to progress to CIN-2+ (12.3%; 36/293) than those HPV-negative (2.1%; 7/329). Cytology-positive women at baseline were more likely to progress to CIN-2+ (9.6%; 37/384) than cytology-negative women (2.5%; 6/237). Approximately 10% (10.4%; 39/376) of women with CIN 1 at baseline progressed to CIN 2+. Women who were VIA or HPV positive at baseline were more likely to progress aIRR 1.85, CI 95% (1.46 to 2.36), aIRR 1.41 CI 95% (1.14 to 1.75) respectively. CONCLUSION: Progression to CIN-2+ in HIV-infected women is significant when measured by baseline positive VIA, HPV or Pap and yearly screening by any method should be considered in this population if possible.
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    Satellite Tagging and Biopsy Sampling of Killer Whales at Subantarctic Marion Island: Effectiveness, Immediate Reactions and Long-Term Responses
    (Public Library of Science, 2014) Reisinger, Ryan R; Oosthuizen, W Chris; Péron, Guillaume; Toussaint, Dawn Cory; Andrews, Russel D; de Bruyn, P J Nico
    Remote tissue biopsy sampling and satellite tagging are becoming widely used in large marine vertebrate studies because they allow the collection of a diverse suite of otherwise difficult-to-obtain data which are critical in understanding the ecology of these species and to their conservation and management. Researchers must carefully consider their methods not only from an animal welfare perspective, but also to ensure the scientific rigour and validity of their results. We report methods for shore-based, remote biopsy sampling and satellite tagging of killer whales Orcinus orca at Subantarctic Marion Island. The performance of these methods is critically assessed using 1) the attachment duration of low-impact minimally percutaneous satellite tags; 2) the immediate behavioural reactions of animals to biopsy sampling and satellite tagging; 3) the effect of researcher experience on biopsy sampling and satellite tagging; and 4) the mid- (1 month) and long- (24 month) term behavioural consequences. To study mid- and long-term behavioural changes we used multievent capture-recapture models that accommodate imperfect detection and individual heterogeneity. We made 72 biopsy sampling attempts (resulting in 32 tissue samples) and 37 satellite tagging attempts (deploying 19 tags). Biopsy sampling success rates were low (43%), but tagging rates were high with improved tag designs (86%). The improved tags remained attached for 26±14 days (mean ± SD). Individuals most often showed no reaction when attempts missed (66%) and a slight reaction-defined as a slight flinch, slight shake, short acceleration, or immediate dive-when hit (54%). Severe immediate reactions were never observed. Hit or miss and age-sex class were important predictors of the reaction, but the method (tag or biopsy) was unimportant. Multievent trap-dependence modelling revealed considerable variation in individual sighting patterns; however, there were no significant mid- or long-term changes following biopsy sampling or tagging.