Many currently available diagnostic tests for typhoid fever lack sensitivity and/or specificity, especially in areas of the world where the disease is endemic. In order to identify a diagnostic test that better correlates with typhoid fever, we evaluated immune responses to Salmonella enterica serovar Typhi (serovar Typhi) in individuals with suspected typhoid fever in Dhaka, Bangladesh. We enrolled 112 individuals with suspected typhoid fever, cultured day 0 blood for serovar Typhi organisms, and performed Widal assays on days 0, 5, and 20. We harvested peripheral blood lymphocytes and analyzed antibody levels in supernatants collected on days 0, 5, and 20 (using an antibody-in-lymphocyte-supernatant [ALS] assay), as well as in plasma on these days. We measured ALS reactivity to a serovar Typhi membrane preparation (MP), a formalin-inactivated whole-cell preparation, and serovar Typhi lipopolysaccharide. We measured responses in healthy Bangladeshi, as well as in Bangladeshi febrile patients with confirmed dengue fever or leptospirosis. We categorized suspected typhoid fever individuals into different groups (groups I to V) based on blood culture results, Widal titer, and clinical features. Responses to MP antigen in the immunoglobulin A isotype were detectable at the time of presentation in the plasma of 81% of patients. The ALS assay, however, tested positive in all patients with documented or highly suspicious typhoid, suggesting that such a response could be the basis of improved diagnostic pointof-care-assay for serovar Typhi infection. It can be important for use in epidemiological studies, as well as in difficult cases involving fevers of unknown origin.Salmonella enterica serovar Typhi (serovar Typhi) is the cause of typhoid fever, an illness that affects over 20,000,000 individuals worldwide each year, killing over 200, 000 (5, 8, 16). The largest burden of typhoid fever is borne by impoverished individuals in resource-poor areas of the world. Serovar Typhi is a human-restricted invasive enteric pathogen which, after ingestion, crosses the intestinal mucosa, is taken up by gutassociated lymphoreticular tissues, and enters the systemic circulation. Both mucosal and systemic host immune responses are stimulated after infection. Serovar Typhi is an intracellular pathogen, and antibody and cell-mediated immune responses occur after infection or immunization with live oral attenuated typhoid vaccines (10,25,34).Diagnostic tests for typhoid fever often lack sensitivity and/or specificity, especially in areas of the world that are endemic for typhoid fever, where clinically distinguishing typhoid fever from other febrile illnesses is difficult (5, 17, 39). Microbiologic culturing of blood is approximately 30 to 70% sensitive, with the highest sensitivity being associated with an absence of prior use of antibiotics and the culturing of larger volumes of blood, features that complicate this mode of diagnosis in young children (5,6,8,36). Microbiologic culturing of bone marrow aspirates is more sensitive than bl...

No abstract

Antimicrobial susceptibility of 120 Helicobacter pylori isolates to metronidazole, tetracycline, clarithromycin, and amoxicillin was determined, and 77.5, 15, 10, and 6.6% of the isolates, respectively, were resistant. Only rdxA inactivation and both rdxA and frxA inactivation were responsible for metronidazole resistance in 66% (8 of 12) and 33% (4 of 12) of the isolates, respectively. Eradication ofHelicobacter pylori infection by treatment with two antimicrobial agents (clarithromycin and amoxicillin or metronidazole) and a proton pump inhibitor is recommended by various consensus groups (10,16,20). Antimicrobial resistance in H. pylori is a growing problem as it is the most important factor in determining treatment outcome. The prevalence of antimicrobial resistance varies with geographical regions (3, 25). Metronidazole resistance in H. pylori has been shown to be due to mutation in rdxA; mutation in frxA has also been shown to be associated with metronidazole resistance (11,12,23). In Bangladesh, the prevalences of H. pylori infection among infants, children, and adults are 61, 84, and 92%, respectively (1, 21, 22); however, information on antimicrobial susceptibility to commonly used drugs in H. pylori treatment is lacking. This study was conducted to evaluate (i) the prevalence of primary antibiotic resistance to commonly used antimicrobial agents and (ii) the genetic basis for metronidazole resistance in H. pylori isolates from Bangladesh.Consecutive patients attending the Gastroenterology Department of Dhaka Medical College Hospital for upper gastrointestinal endoscopy were enrolled during 1999 to 2001. Diagnosis of peptic ulcer (PU) and non-ulcer dyspepsia (NUD) or gastritis was based on endoscopic examination of the stomach and duodenum. Biopsy samples were taken from each patient for culture.Bacteria were grown in brain heart infusion agar with 7% sheep blood and incubated at 37°C in 5% O 2 , 10% CO 2 , and 85% N 2 for 3 to 6 days. The MICs of amoxicillin, clarithromycin, metronidazole, and tetracycline for the isolates were determined by the agar dilution method as described elsewhere (18,19). All tests were repeated twice, and H. pylori 26695 was used as a control. ␤-Lactamase production was tested by the chromogenic cephalosporin method (6). The molecular mechanism of susceptibility and resistance to metronidazole was studied in 12 isolates. Metronidazole-susceptible (Mtz s ) isolates were further studied (by inactivation of rdxA alone or rdxA and frxA for conversion into an Mtz r phenotype) by transformation of Mtz s isolates with plasmids pBS-rdxA-cam (rdxA::cat) and pBS-frxA-kan (frxA::kan) as described earlier (11,12).A total of 278 consecutive patients between 15 and 78 years of age were enrolled, and among them, 72.7% (202 patients) were male and 27.3% (76 patients) were female. Among the patients, 162 had PU and 116 had NUD and 62.6% (174 of 278) were culture positive for H. pylori. Among the culturepositive patients, 121 (69.5%) were male and 53 (30.4%) were female and 112 (64.3%) had PU ...

No abstract

Accurate detection and classification of breast cancer is a critical task in medical imaging due to the complexity of breast tissues. Due to automatic feature extraction ability, deep learning methods have been successfully applied in different areas, especially in the field of medical imaging. In this study, a novel patchbased deep learning method called Pa-DBN-BC is proposed to detect and classify breast cancer on histopathology images using the Deep Belief Network (DBN). Features are extracted through an unsupervised pre-training and supervised fine-tuning phase. The network automatically extracts features from image patches. Logistic regression is used to classify the patches from histopathology images. The features extracted from the patches are fed to the model as input and the model presents the result as a probability matrix as either a positive sample (cancer) or a negative sample (background). The proposed model is trained and tested on the whole slide histopathology image dataset having images from four different data cohorts and achieved an accuracy of 86%. Consequently, the proposed method is better than the traditional ones, as it automatically learns the best possible features and experimental results show that the model outperformed the previously proposed deep learning methods.

The liver segmentation in CT scan images is a significant step toward the development of a quantitative biomarker for computer-aided diagnosis. In this paper, we propose an automatic feature learning algorithm based on the deep belief network (DBN) for liver segmentation. The proposed method was based on training by a DBN for unsupervised pretraining and supervised fine tuning. The whole method of pretraining and fine tuning is known as DBN-DNN. In traditional machine learning algorithms, the pixelby-pixel learning is a time-consuming task; therefore, we use blocks as a basic unit for feature learning to identify the liver, which saves memory and computational time. An automatic active contour method is applied to refine the liver in post-processing. The experiments on test images show that the proposed algorithm obtained satisfactory results on healthy and pathological liver CT images. Our algorithm achieved 94.80% Dice similarity coefficient on mixed (healthy and pathological) images while 91.83% on pathological liver images, which is better than those of the state-of-the-art methods. INDEX TERMS Liver segmentation, deep learning, deep belief network, restricted Boltzmann machine.

Twelve clarithromycin-resistant (MIC, >1 g/ml) Helicobacter pylori isolates were analyzed for point mutations in the 23S rRNA gene. Sequence analysis of all of the resistant isolates revealed a T-to-C transition mutation at position 2182. Transformation experiments confirmed that a single T-to-C transition mutation at position 2182 is associated with clarithromycin resistance. Eradication ofHelicobacter pylori infection by treatment with two antimicrobials (clarithromycin and amoxicillin or metronidazole) and a proton pump inhibitor is recommended by various consensus groups (5, 13). The prevalence of antimicrobial susceptibility of H. pylori varies with geographical regions, and clarithromycin resistance is the major cause of treatment failure (3,5,20). Alteration in either one or both copies of the H. pylori 23S rRNA gene is associated with resistance to clarithromycin, and the mechanism is a point mutation (an adenine-to-guanine transition at either position 2142 or 2143 or an adenine-to-cytosine transversion at position 2142) of the 23S rRNA (2,8,15,18,19,23). However, a T2182C mutation has also been proposed to be associated with clarithromycin resistance (10). In the present study we have examined clarithromycin-resistant (Cla r ) H. pylori (CRHP) isolates and characterized a T2182C mutation involved in clarithromycin resistance.Twelve CRHP isolates and three clarithromycin-susceptible H. pylori (CSHP) strains isolated from individual pretreatment patients attending the Dhaka Medical College hospital during 1999 to 2001 for routine endoscopy were examined. The bacteria were grown in brain heart infusion (BHIB) agar with 7% sheep blood and incubated at 37°C in 5% O 2 -10% CO 2 -85% N 2 for 3 to 6 days. A pure culture from a single colony was stored at Ϫ70°C until further study.The MICs of clarithromycin for the isolates were determined by the agar dilution method (MIC breakpoint, Ն1 g/ ml) and by the E-test strip (AB Biodisk, Solna, Sweden) as described elsewhere (11,12,16). All tests were repeated twice, and CSHP strain 26695 (MIC, 0.032 g/ml) was used as a control. Chromosomal DNA of the isolates was extracted by the cetyltrimethylammonium bromide method. A 1,300-bp fragment of the 23S rRNA (bp 1627 to 2926; GenBank accession number U27270) was amplified with primers Cla1 (5Ј-G GCTCTTTGAGTCCTTTTAGGAC-3Ј) and Cla4 (5Ј GCAT TACTGCGCTCACACAT-3Ј) as described previously (21). The PCR product was purified with a Microcon centrifugal filter device (Millipore Corporation, Bedford, Mass.), and a cycle sequencing reaction was performed with the same primers. DNA sequencing was performed under standard conditions with an ABI PRISM 310 automated sequencer (PerkinElmer Applied Biosystems, Foster City, Calif.). DNA sequence editing and analysis were performed by DNASTAR package 5.06 (DNASTAR Inc.) software. In order to confirm the role of the T2182C mutation, the 1,300-bp PCR fragment from CRHP isolate Gj50 (MIC, 4 g/ml) was transformed to CSHP strain DM26B as described earlier (19). Briefly, exponentially growing CSH...

No abstract