Detection of Leishmania (Viannia) DNA in leucocytes from the blood of patients with cutaneous leishmaniasis

ABSTRACTINTRODUCTION:Cutaneous leishmaniasis (CL) is a serious and global public health issue, with the potential of developing a mucosal form, occurring as subclinical cases, and showing recurrence despite previous treatment.METHODS:Polymorphonuclear and mononuclear DNA obtained from 49 patients was subjected to polymerase chain reaction for detection of Leishmania (Viannia).RESULTS:DNA was detected in mononuclear cells from two patients with active primary lesions positive for CL, with infection periods of 3 and 6 months, respectively.CONCLUSIONS:The DNA of Leishmania (Viannia) indicates probable parasite dissemination possibly explaining subclinical case emergence, lesion recurrence, and mucosal lesion appearance.

Single-tube nested PCR assay with in-house DNA extraction for Mycobacterium tuberculosis detection in blood and urine

Abstract: INTRODUCTION : Molecular analyses are auxiliary tools for detecting Koch's bacilli in clinical specimens from patients with suspected tuberculosis (TB). However, there are still no efficient diagnostic tests that combine high sensitivity and specificity and yield rapid results in the detection of TB. This study evaluated single-tube nested polymerase chain reaction (STNPCR) as a molecular diagnostic test with low risk of cross contamination for detecting Mycobacterium tuberculosis in clinical samples. METHODS: Mycobacterium tuberculosis deoxyribonucleic acid (DNA) was detected in blood and urine samples by STNPCR followed by agarose gel electrophoresis. In this system, reaction tubes were not opened between the two stages of PCR (simple and nested). RESULTS: STNPCR demonstrated good accuracy in clinical samples with no cross contamination between microtubes. Sensitivity in blood and urine, analyzed in parallel, was 35%-62% for pulmonary and 41%-72% for extrapulmonary TB. The specificity of STNPCR was 100% in most analyses, depending on the type of clinical sample (blood or urine) and clinical form of disease (pulmonary or extrapulmonary). CONCLUSIONS: STNPCR was effective in detecting TB, especially the extrapulmonary form for which sensitivity was higher, and had the advantage of less invasive sample collection from patients for whom a spontaneous sputum sample was unavailable. With low risk of cross contamination, the STNPCR can be used as an adjunct to conventional methods for diagnosing TB.

Performance of direct immunofluorescence assay for the detection of human metapneumovirus under clinical laboratory settings

ABSTRACT INTRODUCTION: Human metapneumovirus (hMPV) is an emergent human respiratory pathogen. This study aimed to evaluate the performance of direct immunofluorescence (DIF) to detect hMPV in a clinical laboratory setting. METHODS: Nasopharyngeal aspirate samples (448) of children and adults with respiratory illness were used to detect hMPV by using DIF and real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays. RESULTS: In all, 36 (8%) samples were positive by DIF and 94 (21%) were positive by qRT-PCR. Direct immunofluorescence specificity was 99% and sensitivity was 38%. CONCLUSIONS: DIF is not very sensitive under clinical laboratory settings.

Analysis of classification algorithms for crop detection using LANDSAT 8 images

Remote sensing - the acquisition of information about an object or phenomenon without making physical contact with the object - is applied in a multitude of different areas, ranging from agriculture, forestry, cartography, hydrology, geology, meteorology, aerial traffic control, among many others. Regarding agriculture, an example of application of this information is regarding crop detection, to monitor existing crops easily and help in the region’s strategic planning. In any of these areas, there is always an ongoing search for better methods that allow us to obtain better results. For over forty years, the Landsat program has utilized satellites to collect spectral information from Earth’s surface, creating a historical archive unmatched in quality, detail, coverage, and length. The most recent one was launched on February 11, 2013, having a number of improvements regarding its predecessors. This project aims to compare classification methods in Portugal’s Ribatejo region, specifically regarding crop detection. The state of the art algorithms will be used in this region and their performance will be analyzed.

Molecular detection of Trypanosoma sp. and Blastocrithidia sp. (Trypanosomatidae) in phlebotomine sand flies (Psychodidae) in the Federal District of Brazil

Abstract: INTRODUCTION : This study describes the occurrence of trypanosomatids in phlebotomines in Brasília, Brazil. METHODS : Two hundred and ten females of 13 sand fly species were analyzed by polymerase chain reaction (PCR) using different molecular markers (D7 24Sα rRNA, kDNA, and ITS1) and sequencing. RESULTS : PCR revealed trypanosomatid-positive samples from Nyssomyia whitmani and Evandromyia evandroi, which were negative by kDNA and ITS1 Leishmania-specific PCRs. DNA sequence analysis of D7 24Sα rRNA amplicons indicated the occurrence of Blastocrithidia sp. and Trypanosoma sp. in Nyssomyia whitmani and Evandromyia evandroi, respectively. CONCLUSIONS : Two trypanosomatid species other than Leishmania sp. were found to circulate in sand flies in Central Brazil.

Detection of canine visceral leishmaniasis by conjunctival swab PCR

Abstract: INTRODUCTION: Conjunctival swab PCR was evaluated as a tool to diagnose visceral leishmaniasis in dogs. METHODS: Conjunctival swab PCR was compared to indirect immunofluorescence antibody test and blood PCR. RESULTS: Indirect immunofluorescence was significantly correlated with conjunctival swab PCR (p < 0.05), but not with blood PCR (p > 0.05). In addition, conjunctival swab PCR was significantly associated with presence of clinical symptoms (p < 0.05), whereas blood PCR was associated with absence of clinical symptoms (p < 0.05). CONCLUSIONS: Results indicate that conjunctival swab PCR is useful in epidemiological surveys of canine visceral leishmaniasis.

Detection of codon 12 mutation in the k-ras oncogene in pancreatic tumors

Mutations at codons 12, 13, or 61 of the H-ras, K-ras, and N-ras have been detected in human neoplasias by a variety of techniques. Some of these techniques are very sensitive and can detect K-ras mutation in 90% of the cases of pancreatic adenocarcinomas. We analyzed 11 samples of pancreatic adenocarcinoma, three samples of pancreatic mucinous cystadenoma, and two samples without tumors in formalin-fixed paraffin embedded tissue sections. K-ras mutations at codon 12 were detected by a two-step PCR-enriched technique in all the samples of pancreatic adenocarcinoma, but not in cystadenoma or control samples. This technique may be useful for early detection of pancreatic cancer.

Improving the early diagnostic of prostate cancer by multiple biomarker detection with new biosensing devices

Prostate cancer (PCa) is the most common form of cancer in men, in Europe (World Health Organization data). The most recent statistics, in Portuguese territory, confirm this scenario, which states that about 50% of Portuguese men may suffer from prostate cancer and 15% of these will die from this condition. Its early detection is therefore fundamental. This is currently being done by Prostate Specific Antigen (PSA) screening in urine but false positive and negative results are quite often obtained and many patients are sent to unnecessary biopsy procedures. This early detection protocol may be improved, by the development of point-of-care cancer detection devices, not only to PSA but also to other biomarkers recently identified. Thus, the present work aims to screen several biomarkers in cultured human prostate cell lines, serum and urine samples, developing low cost sensors based on new synthetic biomaterials. Biomarkers considered in this study are the following: prostate specific antigen (PSA), annexin A3 (ANXA3), microseminoprotein-beta (MSMB) and sarcosine (SAR). The biomarker recognition may occurs by means of molecularly imprinted polymers (MIP), which are a kind of plastic antibodies, and enzymatic approaches. The growth of a rigid polymer, chemically stable, using the biomarker as a template allows the synthesis of the plastic antibody. MIPs show high sensitivity/selectivity and present much longer stability and much lower price than natural antibodies. This nanostructured material was prepared on a carbon solid. The interaction between the biomarker and the sensing-material produces electrical signals generating quantitative or semi-quantitative data. These devices allow inexpensive and portable detection in point-of-care testing.

Urinary tract infection in full-term newborn infants: value of urine culture by bag specimen collection

OBJETIVE: to evaluate the efficacy of urine culture by bag specimen for the detection of neonatal urinary tract infection in full-term newborn infants. Retrospective study (1997) including full-term newborn infants having a positive urine culture (>100,000 CFU/ml) by bag specimen collection. The urinary tract infection diagnosis was confirmed by positive urine culture (suprapubic bladder aspiration method). The select cases were divided into three groups, according to newborn infant age at the bag specimen collection: GI (< 48 h, n = 17), GII (48 h to 7 d, n = 35) and GIII (> 7 d, n = 9). Sixty one full-term newborn infants were studied (5.1 % of total infants). The diagnosis was confirmed on 19/61 (31.1 %) of full-term infants born alive. Distribution among the groups was: GI = 2/17 (11.8 %), GII = 10//35 (28.6 %), and GIII = 7/9 (77.7 %). The most relevant clinical symptoms were: fever (GI - 100 %, GII - 91.4 %) and weight loss (GI - 35.3 %, GII - 45.7 %). Urine culture results for specimens collected by suprapubic aspiration were: E. coli GI (100 %), GII (40 %) and GIII (28.6 %), E. faecalis GI (30%), Staphylococcus coagulase-negative GII (20 %) and GIII (42.8 %), and Staphylococcus aureus GII (10 %). Correlation between positive urine culture collection (bag specimen method) and urinary tract infection diagnosis, using relative risk analysis, produced the following results: GI=0.30 (CI95% 0.08-1.15), GII=0.51 (CI 95% 0.25-1.06) and GIII=3.31 (CI95% 1.8-6.06) The most frequent urinary tract infection clinical signs in the first week were fever and weight loss, while non-specific symptomatology occurred later. E. coli was most frequent infectious agent, although from the 7th day of life, staphylococcus was noted. The urine culture (bag specimen method) was effective in detecting urinary tract infection only after the 7th day of life.

Intraventricular hemorrhage in very low birth weight infants: associated risk factors and outcome in the neonatal period

Intraventricular hemorrhage (IVH) is a severe complication in very low birth weight (VLBW) newborns (NB). With the purpose of studying the incidence of IVH, the associated risk factors, and the outcomes for these neonates, we studied all the VLBW infants born in our neonatal unit. Birth weight, gestational age, presence of perinatal asphyxia, mechanical ventilation, length of hospitalization, apnea crisis, hydrocephalus, and periventricular leukomalacia were analyzed. The diagnosis of IVH was based on ultrasound scan studies (Papile's classification) performed until the tenth day of life and repeated weekly in the presence of abnormalities. Sixty-seven/101 neonates were studied. The mortality rate was 30.6% (31/101) and the incidence of IVH was 29.8% (20/67) : 70% grade I, 20% grade III and 10% grade IV. The incidence of IVH in NB <1,000 g was 53.8% (p = 0.035) and for gestational age <30 weeks was 47.3% (p = 0.04), both considered risk factors for IVH. The length of hospitalization (p = 0.00015) and mechanical ventilation (p = 0.038) were longer in IHV NB. The IVH NB had a relative risk of 2.3 of developing apnea (p = 0.02), 3.7 of hydrocephalus (p = 0.0007), and 7.7 of periventricular leukomalacia (p < 0.00001). The authors emphasize the importance of knowing the risk factors related to IVH so as to introduce prevention schemes to reduce IVH and to improve outcomes of affected newborns.

Implementation of membrane processes for improvement of the detection of food contaminants

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities (http://www.em3e.eu)

Detection of testicular cancer in men presenting with infertility

PURPOSE: Infertility is one of the less common presenting features associated with testicular tumors. We evaluated the histologic and biochemical findings, and pregnancy outcome in patients presenting with infertility who were found to have testicular tumors. METHODS: Seven patients with infertility were found to have testicular cancer over a 15-year period. All patients had a testicular ultrasound evaluation. The indications for the ultrasound were testicular pain in 2 patients, suspicious palpable mass in 4, and to rule out the presence of germ cell neoplasia in a patient with carcinoma in situ detected on a previous biopsy. Physical exam, histological findings, hormonal levels, tumor markers, and pregnancy outcome results were recorded from the patients medical charts. RESULTS: Two men had elevated serum follicle stimulant hormone and luteinizing hormone levels, 1 of them had an abnormally low serum testosterone level. Tumor markers were normal in all patients. In 4 patients the tumor was on the right side and in 3 on the left. The histological diagnoses were seminoma (n = 5), Leydig cell tumor (n = 1), and carcinoma in situ (n = 1). Of the 7 patients, 5 underwent adjuvant radiation therapy. Two patients had sperm cryopreserved. Follow up on fertility status was available in 6 cases. One patient has established a pregnancy and 5 did not achieve a pregnancy after treatment for their cancer. CONCLUSIONS: Most of the men who have testicular cancer and male infertility have a seminona. Therefore, men who present with infertility should be thoroughly investigated to rule out such serious, concomitant diseases along with their infertility.

Development and validation of gold nanoprobes for human SNP detection towards commercial application

Conventional molecular techniques for detection and characterization of relevant nucleic acid (i.e. DNA) sequences are, nowadays, cumbersome, expensive and with reduced portability. The main objective of this dissertation consisted in the optimization and validation of a fast and low-cost colorimetric nanodiagnostic methodology for the detection of single nucleotide polymorphisms (SNPs). This was done considering SNPs associated to obesity of commercial interest for STAB VIDA, and subsequent evaluation of other clinically relevant targets. Also, integration of this methodology into a microfluidic platform envisaging portability and application on points-of-care (POC) was achieved. To warrant success in pursuing these objectives, the experimental work was divided in four sections: i) genetic association of SNPs to obesity in the Portuguese population; ii) optimization and validation of the non-cross-linking approach for complete genotype characterization of these SNPs; iii) incorporation into a microfluidic platform; and iv) translation to other relevant commercial targets. FTO dbSNP rs#:9939609 carriers had higher body mass index (BMI), total body fat mass, waist perimeter and 2.5 times higher risk to obesity. AuNPs functionalized with thiolated oligonucleotides (Au-nanoprobes) were used via the non-cross-linking to validate a diagnostics approach against the gold standard technique - Sanger Sequencing - with high levels of sensitivity (87.50%) and specificity (91.67%). A proof-of-concept POC microfluidic device was assembled towards incorporation of the molecular detection strategy. In conclusion a successful framework was developed and validated for the detection of SNPs with commercial interest for STAB VIDA, towards future translation into a POC device.

Methodology for WSN communication technologies automated field tests

Wireless Sensor Networks(WSN) are networks of devices used to sense and act that applies wireless radios to communicate. To achieve a successful implementation of a wireless device it is necessary to take in consideration the existence of a wide variety of radios available, a large number of communication parameters (payload, duty cycle, etc.) and environmental conditions that may affect the device’s behaviour. However, to evaluate a specific radio towards a unique application it might be necessary to conduct trial experiments, with such a vast amount of devices, communication parameters and environmental conditions to take into consideration the number of trial cases generated can be surprisingly high. Thus, making trial experiments to achieve manual validation of wireless communication technologies becomes unsuitable due to the existence of a high number of trial cases on the field. To overcome this technological issue an automated test methodology was introduced, presenting the possibility to acquire data regarding the device’s behaviour when testing several technologies and parameters that care for a specific analysis. Therefore, this method advances the validation and analysis process of the wireless radios and allows the validation to be done without the need of specific and in depth knowledge about wireless devices.