Quantitative evaluation of recall and precision of CAT Crawler,a search engine specialized on retrieval of Critically Appraised Topics

Background

Critically Appraised Topics (CATs) are a useful tool that helps physicians to make clinical decisions as the healthcare moves towards the practice of Evidence-Based Medicine (EBM). The fast growing World Wide Web has provided a place for physicians to share their appraised topics online, but an increasing amount of time is needed to find a particular topic within such a rich repository.

Methods

A web-based application, namely the CAT Crawler, was developed by Singapore's Bioinformatics Institute to allow physicians to adequately access available appraised topics on the Internet. A meta-search engine, as the core component of the application, finds relevant topics following keyword input. The primary objective of the work presented here is to evaluate the quantity and quality of search results obtained from the meta-search engine of the CAT Crawler by comparing them with those obtained from two individual CAT search engines. From the CAT libraries at these two sites, all possible keywords were extracted using a keyword extractor. Of those common to both libraries, ten were randomly chosen for evaluation. All ten were submitted to the two search engines individually, and through the meta-search engine of the CAT Crawler. Search results were evaluated for relevance both by medical amateurs and professionals, and the respective recall and precision were calculated.

Results

While achieving an identical recall, the meta-search engine showed a precision of 77.26% (±14.45) compared to the individual search engines' 52.65% (±12.0) (p < 0.001).

Conclusion

The results demonstrate the validity of the CAT Crawler meta-search engine approach. The improved precision due to inherent filters underlines the practical usefulness of this tool for clinicians.

     

A screening assay for detecting CD8+ cell non-cytotoxic anti-HIV responses

The rate of HIV-1 disease progression is influenced by several factors that include pathogen and host genetic variations and the quality of antiviral immune responses. The CD8+ cell non-cytotoxic antiviral response (CNAR) substantially suppresses HIV replication in CD4+ cells and is positively associated with an asymptomatic clinical state. Traditionally, the measurement of CNAR has required several culture procedures and costly reagents. Here we report the development and validation of a screening assay for detection of CNAR that accurately identifies individuals benefiting from this response. Use of the CNAR screening assay should facilitate the evaluation of this important immune parameter in studies of HIV pathogenesis, resistance to infection, and vaccine development.     

Genetic imbalances in pleomorphic xanthoastrocytoma detected by comparative genomic hybridization and literature review.

Pleomorphic xanthoastrocytoma (PXA) is a rare, low-grade astrocytic tumor found in the central nervous system. Histologically, the tumor is characterized by markedly pleomorphic and lipidized cells. Although most of the patients have a favorable prognosis, a small number of cases undergoing recurrence or progression to anaplastic astrocytoma were reported. Very few genetic studies have been performed on PXA because of its rarity and the pathogenesis of this neoplasm is largely unknown. In order to provide an overview of genetic alterations in PXA, we performed comparative genomic hybridization to identify chromosomal imbalances (DNA gains and losses) in three cases of PXA. Genetic imbalance was detected on at least one chromosome for each case. One case, which revealed multiple genetic alterations, showed a poor prognosis. DNA gain on chromosome 7 and loss on 8p were demonstrated in two of three cases, suggesting that the candidate gene(s) located on these regions may play a role in the development of PXA. Further studies are needed to identify the residing candidate genes that are involved in the tumorigenesis of PXA. In addition, the histopathological features and previous genetic studies on PXA are reviewed.     

Tyrosine phosphatase-like protein (IA-2) and glutamic acid decarboxylase (GAD65) autoantibodies: a study of Chinese patients with diabetes mellitus

Type 1 diabetes in most Asian populations may not have a salient autoimmune basis when assessed with single determinations of the major markers, islet cell antibodies (ICAs) and glutamic acid decarboxylase antibodies (GAD65ab). With the inclusion of antibodies to tyrosine phosphatase-like protein IA-2 (IA-2ab) as an additional major marker, we re-examined autoimmune diabetes in a group of Chinese patients. We studied 272 subjects at various stages of disease with blood samples procured for biochemical analysis. ICAs were measured by immunofluorescence, GAD65ab and IA-2ab by radioimmunoassay. Sixty-seven patients fulfilled clinical diagnosis of type 1 diabetes and the remaining 205 patients were type 2. Prevalence of single autoantibody type in recent-onset type 1 diabetes ( < 1 year duration; n = 47) showed 10.6% with ICAs, 44.7% GAD65ab and 36.2% IA-2ab. GAD65ab account for more than two-thirds of the markers found in type 1 diabetes. Combined analysis further showed that 51.1% had at least one antibody type, 31.9% with two or more antibodies and 8.5% with all three antibodies. Islet autoimmunity presence in childhood-onset type 1 diabetes improved with the addition of IA-2ab, though less impact was seen in the adult-onset. Similarly, combined analysis for type 2 patients with recent diabetes showed a modest increase to 13% with islet autoimmunity compared to 8% when assessed by GAD65ab alone. Combining IA-2ab and GAD65ab assays results detected slightly more immune-mediated diabetes, compared to using a single GAD65ab determination. Non-autoimmune causes need to be considered in the pathogenesis of type 1 diabetes in Chinese, particularly in adults.     

Human micro-insemination by injection of single or multiple sperm: ultrastructure

The process of micro-insemination by single or muhiple spermtransfer into the perivitelline space (PVS) or by direct sperminjection into oocytes was examined by transmission electronmicroscopy. Spermatozoa from normal and oligozoospermic menwere injected into oocytes, obtained from consenting IVF patients,mostly by zona-puncture using micromanipulators. Spermatozoawere washed by the Percoll or Ficoll methods and capacitatedusing Whittingham's T₆ or modified Tyrode's medium or incubatedin strontium medium before injection. The women were stimulatedby three IVF methods and oocytes were recovered by laparoscopyor ultrasonography. Sixty-one oocytes were cultured in T₆ orHam's F-10 media (3–24 h) and were subjected to micromanipulation.Four oocytes were also studied after zona-drilling. Normal 2-pronuclearova were developed after single-sperm transfer satisfying allmorphological criteria of fertilization. Both monospermic andpolyspermic fertilization resulted after multiple sperm transfer,indicating that a vitelline block to polyspermy may exist inhumans. The majority of oocytes examined were unfertilized.Spermatozoa with intact or reacted acrosomes and those undergoingthe acrosome reaction were found in the PVS and in the ooplasm.Abnormal spermatozoa were also seen in these locations. Quantitatlonof acrosomal status in 16 oocytes after multiple-sperm transfer,revealed that 24% of spermatozoa were acrosome reacted or reactingin the PVS following Ficoll entrapment, while 76% of spermatozoawere intact (33% of these abnormal). Sperm transfer seemed tobe the least invasive, while direct sperm injection was comparativelydestructive to oocytes. Drilling with acid made larger breachesin the zona when compared with mechanical perforation and spermatozoaoccasionally escaped through breaches. Three 2-pronuclear ovaobtained after multiple sperm transfer have resulted in twopregnancies, in cases of severe oligozoo spermia, during thecourse of this study.     

What can natural infection of African monkeys with simian immunodeficiency virus tell us about the pathogenesis of AIDS?

The simian immunodeficiency viruses are a diverse group of viruses that naturally infect a wide range of African primates, including chimpanzees, African green monkeys (AGM) and sooty mangabey monkeys (SM). Although natural infection is widespread in feral populations of AGMs and SMs, this infection does not result in immunodeficiency. However, experimental inoculation of Asian macaque species results in an immunodeficiency syndrome that is remarkably similar in pathogenesis to human AIDS. Thus, SIVsm infection of macaques results in AIDS, and similarly experimental inoculation of pigtailed macaques with at least one SIVagm isolate, SIVIhoest or SIVsun, results in AIDS. The extent of plasma viremia in pathogenic infection is an excellent prognostic indicator of clinical course, with higher viral load being predictive of shorter survival and low viremia being predictive of long-term non-progression. Based upon this paradigm, one would have expected naturally infected animals to exhibit low levels of viremia. In reality, AGMs, SMs, mandrills and chimpanzees infected naturally with their own unique viruses display moderate to high levels of plasma viremia. A significant reduction in CD4+ T-cells in infected versus uninfected SMs suggests that the virus may be cytopathic to some degree. These infected animals still maintain adequate CD4+ T-cells over their entire life in captivity. A distinct characteristic of natural infection is the lack of immunopathology as demonstrated by normal lymph node morphology, lower expression of activation and proliferation markers on CD4+ T-cells, and a generally muted immune response to the virus. Naturally infected SMs and AGMs clearly mount antiviral cellular and humoral immune responses. Therefore, models suggesting immune tolerance to SIV are far too simplistic to explain the lack of disease in these animals. It is probable that a unique balance between T-cell renewal and proliferation and loss through activation-induced apoptosis, and virus-induced cell death has been achieved in SMs and AGMs. The study of the dynamics of T-cell production, proliferation and cell death in asymptomatic natural infection should, therefore, yield insights into the pathogenesis of AIDS.     

Presence of pro-opiomelanocortin peptides and corticotropin-releasing factor in human placenta

Immunoreactive adrenocorticotropin (ACTH), beta-endorphin (BEP) and corticotropin-releasing factor (CRF) were detected in human term placenta obtained from elective Caesarian surgery. The concentrations of ACTH, BEP and CRF in placenta detected by radioimmunoassay (RIA) were 2.83 +/- 0.36, 0.52 +/- 0.05 and 0.56 +/- 0.15 ng/g wet weight of tissue respectively. Pro-opiomelanocortin (POMC) peptides were also detected in the amnion and chorion membranes and in the decidua. The concentrations of ACTH were 1.72 +/- 0.20, 4.43 +/- 0.39 and 5.80 +/- 0.17 ng/g and the levels of BEP were 0.42 +/- 0.18, 0.65 +/- 0.20 and 3.66 +/- 1.10 ng/g in the amnion, chorion and decidua respectively. In contrast to placenta, immunoreactive CRF was not detected in the amnion, chorion and decidua. Immunoreactive N-acetylated BEP was also not detected in all the placental subfractions. Comparison of the amounts of both ACTH and BEP in the various placental components indicated the following distribution: decidua > chorion > placenta > amnion. In decidua, POMC peptides were present in an equi-molar ratio but in the other three placental fractions, ACTH levels were three to five-fold higher than BEP. In immunohistochemical studies, only a positive staining for ACTH was obtained for decidua. Our results confirm the presence of POMC peptides and CRF in placenta and their physiological roles in pregnancy and parturition.     

Involvement of microtubules in Kunjin virus replication

Summary Induction of microtubulin paracrystals (Pc) by Kunjin (KUN) virus occurred after 15 hours post-infection and were often associated with convoluted membranes (cm) and virus particles. Vinblastine sulphate which disrupts microtubulin, had an inhibitory effect on the virus production when added during the viral latent period. When infected samples were extracted with Triton X-100 and analysed by SDS-PAGE, four viral proteins were observed.     

The double peak-to-peak analysis for determining EMG onset of muscle contraction

PURPOSE: Identification of the onset of muscle contraction with EMG signal amplitude double of the baseline value (DP-P) has been recently reported for determining the temporal parameters of muscular activity. Due to its convenience, it is suitable for clinical application. However, there is a lack of report on the reliability and comparability of this method to other established methods. Therefore, this study examined the test-retest reliability of the DP-P method and compared it with an established method that used the mean + 3 standard deviations (mean + 3 s.d.) over the baseline value for muscles of the knee. METHODS: The onset of contraction of vastus medialis obliquus (VMO) and vastus lateralis (VL) of eleven able-bodied volunteers performing isometric knee extension at 50%, 75% and 100% of MVC in 30-minute and 7-day intervals were analyzed with both the DP-P and mean + 3 s.d. methods. RESULTS: The ICC for within-day measurements of DP-P method ranged from 0.64 to 0.86 and that for between-day measurements ranged from 0.63-0.81. The ICC values were higher with submaximal than maximal contractions. There was a consistent delay of about 3 ms in EMG onset detection with the DP-P as compared to the mean + 3 s.d method. CONCLUSION: The DP-P method is a reliable method for muscle onset determination but the absolute onset time of muscle contraction obtained from this method should not be directly compared with other methods such as the mean + 3 s.d.