Occurrence of Coxiellosis in ruminants and its associated risk factors.

Coxiellosis in animals is caused by the zoonotic pathogen, Coxiella burnetii. Although the disease is of public health importance it remains underdiagnosed and underreported. The cross- sectional study was aimed to estimate the occurrence of the disease in livestock of study area and also to identify the risk factors associated with the disease in animals. Blood, serum, and vaginal swabs samples were collected from 200 ruminants (cattle, sheep, and goats), across various farms in Karnataka, India. These samples were then screened using ELISA and PCR (com1 and IS1111). A questionnaire was administered to the farm owners to collect the risk factor-related information. About 5.26 % cattle, 12.3 % sheep, and 12.5 % goats were positive by ELISA. By PCR, 9.47 % cattle, 9.3 % sheep, and 10 % goats were positive. Overall, the occurrence of 14.73 %, 18.46 % and 17.5 % was estimated in cattle, sheep and goat, respectively. PCR targeting the IS1111 gene detected higher number of samples as positive as compared to the com1 gene PCR. Higher number of vaginal swab samples were detected as positive as compared to blood. History of reproductive disorders (OR: 4.30; 95 %CI:1.95- 9.46), abortion (OR: 30.94; 95 %CI:6.30- 151.84) and repeat breeding (OR:11.36; 95 %CI:4.16- 30.99) were significantly associated with coxiellosis (p < 0.005). Multivariable analysis by logistic regression model analysis suggested retained abortion, repeat breeding and rearing of animal in semi-intensive system as factors significantly associated with the infection. Cultural identification of the PCR positive samples were cultured using embryonated egg propagation and cell culture techniques and positivity was confirmed in six samples. Phylogenetic analysis of the com1 and IS1111 gene revealed clustering based on similar geographic locations. The study estimated the occurrence of the disease in the study area and identified the potential risk factors.

Risk of radiation necrosis after stereotactic radiosurgery for melanoma brain metastasis by anatomical location.

PURPOSE: In this retrospective study, we have explored the anatomical factors that lead to the development of radiation necrosis (RN) in the setting of stereotactic radiosurgery (SRS) for melanoma brain metastases (MBM). METHODS: Between 2014 and 2018, 137 patients underwent SRS for 311 MBM. Lesions were assessed according to anatomical zones: zone 1-peripheral grey-white matter junction and cortical mantle, zone 2-deep white matter, including tumours located at base of sulci, zone 3-tumours adjacent to ependymal lining or in deep locations such as brainstem, basal ganglia and thalamus. Other anatomical factors including lobes, medial-peripheral, supra or infratentorial locations were also recorded. RESULTS: In all, 12.4% (n = 17) of patients and 6.1% (n = 20) of lesions developed RN, actuarial incidence of RN at 12 and 24 months was 10% and 14.2% respectively. Zone 2 lesions recorded the highest rate of development of RN (n = 7/19; 36%), zone 3 (N = 4/24; 16%) and zone 1 (n = 9/268; 3%). Five of 17 patients developed symptomatic RN and 7/17 patients underwent surgery for RN. CONCLUSION: This study raises awareness of the increased likelihood of deep lesions particularly in white matter structures to develop RN after SRS. Further studies including larger cohorts would be useful in identifying statistical differences in the rate of development of RN in different anatomical zones.

ITS2 characterization and Anopheles species identification of the subgenus Cellia.

In Mizoram, the origin and molecular nature of Anopheles species is poorly understood, despite the region having high malarial incidence and rich biodiversity. A diagnostic PCR assay for distinguishing the Cellia subgenera members of Anopheles species was developed based on the interspecific ITS2 variation. No intraspecific variation was found and the size (362-604bp) and GC content (48.8-58.9%) of the ITS2 were highly variable among Anophelines. The ITS2 of A. vagus is significantly longer than those of other Anopheles species. Significant relationship was observed among repeats, minimum free energy and RNA secondary structures. Different types of microsatellites were identified and among them dinucleotide, pentanucleotide and polynucleotide microsatellites were predominant. Variation in the length of the ITS2 between species was due to indels in simple repeats. Four domain types of RNA secondary structures were identified and the lowest free energy values were predicted using the computer software, RNAfold. Types I and II were observed only in Neocellia and Myzomyia series and Types III and IV were common in Neocellia and Pyretophorus series. ITS2-based PCR protocol provides a means for vector ecologists, malaria epidemiologists and control personnel to accurately identify members of the subgenera Cellia and a better understanding of their genomic status in Mizoram.

In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis.

Cell-mediated immunity is critical for the control of Mycobacterium tuberculosis infection. We hypothesized that those proteins of M. tuberculosis (MTB) that do not have homologs in humans as well as human gut flora, would mount a good antigenic response in man, and employed a bioinformatics approach to identify MTB antigens capable of inducing a robust cell-mediated immune response in humans. In the first step we identified 624 MTB proteins that had no homologs in humans. Comparison of this set of proteins with the proteome of 77 different microbes that comprise the human gut flora narrowed down the list to 180 proteins unique to MTB. Twenty nine of the 180 proteins are known to be associated with dormancy. Since dormancy associated proteins are known to harbor CTL epitopes, we selected four representative unique proteins and subjected them to epitope analysis using ProPred1. Nineteen novel promiscuous epitopes were identified in the four proteins. Population coverage for 7 of the 19 shortlisted epitopes including Rv3852 (58-KPAEAPVSL, 112-VPLIVAVTL, 118-VTLSLLALL and 123-LALLLIRQL), Rv2706c (66-RPLSGVSFL) Rv3466 (8- RIVEVFDAL and 38-RSLERLECL) was >74%. These novel promiscuous epitopes are conserved in other virulent MTB strains, and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.

Informatics resources for tuberculosis--towards drug discovery.

Integration of biological data on gene sequence, genome annotation, gene expression, metabolic pathways, protein structure, drug target prioritization and selection, has resulted in several online bioinformatics databases and tools for Mycobacterium tuberculosis. Alongside there has been a growth in the list of cheminformatics databases for small molecules and tools to facilitate drug discovery. In spite of these efforts there is a noticeable lag in the drug discovery process which is an urgent need in the case of emerging and re-emerging infectious diseases. For example, more than 25 online databases are available freely for tuberculosis and yet these resources have not been exploited optimally. Informatics-centered drug discovery based on the integration and analysis of both bioinformatics and cheminformatics data could fill in the gap and help to accelerate the process of drug discovery. This article aims to review the current standing of developments in tuberculosis-bioinformatics and highlight areas where integration of existing resources could lead to acceleration of drug discovery against tuberculosis. Such an approach could be adapted for other diseases as well.

Study of nosocomial urinary tract infections in a pediatric intensive care unit.

Nosocomial urinary tract infections (NUTI) are one of the commonest infections in a Pediatric Intensive Care Unit (PICU). This prospective study was conducted in PICU between January and December 2008 to study the incidence, organisms and risk factors for NUTI. A total of 287 consecutive patients with >48 h PICU stay and sterile admission urine culture, were enrolled and monitored for NUTI (defined as per CDC criteria 1988) till discharge or death. Patients with and without NUTI were compared with respect to demographics, PRISM scores, primary diagnosis, nutritional status and device utilization to identify risk factors. Outcome was defined as length of PICU stay and survival or death. There were 69 episodes of UTI in 60 (20.9%) patients; incidence being 18 episodes/1000 patient days. Candida (52.1%) and Enterococcus (13%) were commonest followed by Escherichia coli (11.6%) and Klebsiella pneumoniae (10.1%). Catheterization and duration of catheterization were the risk factors for NUTI (p < 0.001). The median length of PICU stay was significantly longer in NUTI group compared to non-NUTI group (19 vs. 8 days, p = 0.001). Mortality rates in both the groups were similar.

Adaptation of radiation field analyser (RFA) as optical CT scanner for gel dosimetry.

Optical scanning is one of the emerging evaluation tools used for obtaining dose distributions in gel dosimetry. A radiation field analyzer adapted into an optical CT scanner to evaluate an irradiated Fricke gel has been already reported by others. This prototype optical CT scanner functions like a first generation x-ray CT scanner in the translate-rotate fashion. A similar scanner was constructed in our department for optical scanning of irradiated FX gel. At first, an aquarium was constructed and fitted into the water phantom of the RFA with provision to place the gel phantom to be scanned along with a light source and detector. The movements of the RFA were utilized to scan the gel phantom. A scan of a cuvette filled with colored solution was carried out and the resulting images were reconstructed and profiles obtained to evaluate the working of the optical scanner. A scan of the gel phantom was then obtained to evaluate the performance of the scanner. Thus a radiation field analyzer (DYNASCAN) was successfully adapted to an optical scanner to evaluate Fricke gels in our department.

Investigation of the PAGAT polymer gel dosimeter using magnetic resonance imaging.

Investigation of the normoxic PAGAT polymer gel dosimeter has been undertaken. The concentrations of the chemical components of the gel were varied and its response to ionizing radiation evaluated. Using MRI, the formulation to give the maximum change in the transverse relaxation rate R2 was determined to be 4.5% N, N'-methylene-bis-acrylamide (bis), 4.5% acrylamide (AA), 5% gelatine, 5 mM tetrakis (hydroxymethyl) phosphonium chloride (THPC), 0.01 mM hydroquinone (HQ) and 86% H2O. The optimal post-manufacture irradiation and post-irradiation imaging times were both determined to be 12 h. The R2-dose response was linear up to 7 Gy with R2-dose sensitivities of (0.183 +/- 0.005) s(-1) Gy(-1), (0.182 +/- 0.005) s(-1) Gy(-1) and (0.192 +/- 0.005) s(-1) Gy(-1) when imaged at 12 h, 7 days and 24 days post-irradiation, respectively. The R2-dose sensitivities were within the range of previously published values for the hypoxic PAG formulations. For the imaging parameters used in this study the optimum dose resolution was achieved for low doses. The normalized R2 edge response showed a high degree of spatial stability over a 24 day period. This study has shown that the normoxic PAGAT polymer gel has the properties of a dosimetric tool, which can be used in clinical radiotherapy. The PAGAT polymer gel has been shown to have similar qualities to the PAG polymer gel, while offering the significant advantage of simplification of the manufacturing procedure.

Experimental study of attenuation properties of normoxic polymer gel dosimeters.

The change in linear attenuation coefficient with absorbed dose has been investigated for aqueous polyacrylamide, gelatine and tetrakis (PAGAT) and aqueous methacrylic acid, gelatine and tetrakis (MAGAT) normoxic polymer gel dosimeters using tetrakis (hydroxy methyl) phosphonium chloride as the antioxidant. The measured linear attenuation coefficient increased linearly with absorbed dose up to 15 Gy for PAGAT gels and 10 Gy for MAGAT gels. Computerized tomography (CT) numbers or Hounsfield units (H) were calculated from the linear attenuation coefficients and compared with values obtained using a CT scanner. Both calculated and measured CT numbers followed a similar pattern when fitted with a biexponential curve. The CT numbers obtained from linear attenuation measurements were found to be greater than that obtained with the CT scanner for both PAGAT and MAGAT polymer gels. The H-dose sensitivities of the MAGAT and PAGAT polymer gel dosimeters measured on a CT scanner were calculated to be (0.85 +/- 0.08) H Gy(-1) and (0.31 +/- 0.03) H Gy(-1), respectively. The H-dose sensitivities of the MAGAT and PAGAT polymer gel dosimeters from attenuation measurements were found to be (1.10 +/- 0.66) H Gy(-1) and (0.34 +/- 0.01) H Gy(-1), respectively.

Modified ferrous ammonium sulfate benzoic acid xyelenol orange (MFBX) and thermoluminescent dosimeters--a comparative study.

Radiation dosimetry deals with the determination of absorbed dose to the medium exposed to ionizing radiation. Chemical dosimetry depends on oxidation or reduction of chemicals by ionizing radiation. A ferrous ammonium sulfate benzoic acid xyelenol orange (FBX) dosimeter based on this principle is being used as a clinical dosimeter at present. Certain modifications were carried out in the preparation and storage of the FBX dosimeter to increase its shelf life. The resulting dosimeter was called a modified FBX (MFBX) dosimeter and has been used in our department for the past few years. An extensive study of the dose, dose rate and energy response of the dosimeter was carried out and compared with a thermoluminescent (LiF7) dosimeter. The results obtained were found to be comparable to the thermoluminescent (LiF7) dosimeter. Hence it was concluded that the MFBX dosimeter could be used for phantom dosimetry, data collection and in vivo measurements. Easier preparation and availability of the reagents are added advantages of using MFBX as a clinical dosimeter in small radiotherapy departments.

Manual multi-leaf collimator for electron beam shaping--a feasibility study.

In electron beam therapy, lead or low melting point alloy (LMA) sheet cutouts of sufficient thickness are commonly used to shape the beam. In order to avoid making cutouts for each patient, an attempt has been made to develop a manual multi-leaf collimator for electron beams (eMLC). The eMLC has been developed using LMA for a 15 x 15 cm2 applicator. Electron beam characteristics such as depth dose, beam profiles, surface dose, output factors and virtual source position with the eMLC have been studied and compared with those of an applicator electron beam. The interleaf leakage radiation has also been measured with film dosimetry. Depth dose values obtained using the eMLC were found to be identical to those with the applicator for depths larger than Dmax. However, a decrease in the size of the beam penumbra with the eMLC and increase in the values of surface dose, output factors and virtual source position with eMLC were observed. The leakage between the leaves was less than 5% and the leakage between the opposing leaves was 15%, which could be minimized further by careful positioning of the leaves. It is observed that it is feasible to use such a manual eMLC for patients and eliminate the fabrication of cutouts for each patient.

Development of collimator insert for linac based stereotactic irradiation.

The aim of this study is to develop collimator inserts of various sizes which are either not commercially available or are expensive to import. The dosimetry parameters such as tissue maximum ratio (TMR), off-axis ratio (OAR) and output factor of the developed collimator insert are compared with that of the commercial collimator insert (Radionics). In order to check the suitability of the collimator insert developed locally for clinical use and to standardize the method of development, a collimator insert of 15 mm identical to the one supplied by Radionics is developed with low-melting alloy (Cerrobend). Moreover for the clinical use of the developed collimator insert, certain acceptance tests are performed which include a collimator concentricity test, beam size check and radiation leakage test. The dose verification is carried out with a thermoluminescent dosimeter (7LiF rods) and an FBX chemical dosimeter in a human-head-shaped Perspex phantom filled with water. The variation between the calculated and measured dose is found to be within +2.4% for 7LiF rods and -2.0% for the FBX chemical dosimeter thus ensuring the suitability of the developed collimator insert for clinical use. This has encouraged us to standardize the method adapted to develop the collimator insert and to develop collimator inserts of different field sizes.

Tuberous sclerosis with interesting features.

A case of tuberous sclerosis with intracranial calcification, retinal phakoma and premature canities is reported for its interesting features.