Analysing malaria incidence at the small area level for developing a spatial decision support system: A case study in Kalaburagi, Karnataka, India.

Spatial decision support systems have already proved their value in helping to reduce infectious diseases but to be effective they need to be designed to reflect local circumstances and local data availability. We report the first stage of a project to develop a spatial decision support system for infectious diseases for Karnataka State in India. The focus of this paper is on malaria incidence and we draw on small area data on new cases of malaria analysed in two-monthly time intervals over the period February 2012 to January 2016 for Kalaburagi taluk, a small area in Karnataka. We report the results of data mapping and cluster detection (identifying areas of excess risk) including evaluating the temporal persistence of excess risk and the local conditions with which high counts are statistically associated. We comment on how this work might feed into a practical spatial decision support system.

Optimizing gDNA extraction from fresh frozen meningioma tissue for downstream genetic analysis.

OBJECTIVE: Meningioma is the most common brain tumor. Genetic mutations in meningioma that include deletion of the neurofibromatosis type 2 gene, (NF2), offer diagnostic information on tumor behavior, recurrence and potential response to treatment. Obtaining high-grade genetic material is critical for accurate, sensitive and robust molecular testing. Currently, no standardized procedure exists for extracting gDNA from meningioma, and this problem was addressed in this report. METHOD: This study compared the yield and quality of extracted gDNA from patient meningioma specimens using an optimized phenol chloroform method and two commercial silica column-based extractions kits and tested respective performances as template in qPCR tests and multiplex ligation-dependent probe amplification (MLPA) NF2 screening. RESULTS: Mean gDNA yields were comparable for each method tested; however, phenol chloroform extraction outperformed column-based kits in all other quality assurance metrics examined. Phenol chloroform extracted gDNA was highly pure, and of a higher fragment size species when compared to column prepared gDNA. qPCR of GAPDH, B2MG, and RPL37A housekeeping genes demonstrated variance in cycle thresholds between patient samples was much lower in the phenol chloroform group. Similarly, primer efficiencies were significantly improved in this sample group which translated to a broader qPCR linear dynamic range and much improved qPCR performance at low concentrations of template. MLPA screening identified NF2 gene deletions in 6 of 12 meningioma samples. Inconsistencies in copy number data for NF2 and reference regions of the genome were observed between gDNA sample extraction groups that included both false negative and positive errors in silica column derived gDNA samples. CONCLUSIONS: This study outlines a highly robust phenol chloroform extraction method for obtaining high-quality gDNA from frozen meningioma tissue and highlights the significance of performing adequate quality assurance when using gDNA for downstream genetic analysis. Most importantly, we demonstrate using gDNA extracted with silica column based kits can lead to diagnostic errors when screening NF2 deletions in meningiomas with MLPA.

Removal ratio of gaseous toluene and xylene transported from air to root zone via the stem by indoor plants.

This work was designed to investigate the removal efficiency as well as the ratios of toluene and xylene transported from air to root zone via the stem and by direct diffusion from the air into the medium. Indoor plants (Schefflera actinophylla and Ficus benghalensis) were placed in a sealed test chamber. Shoot or root zone were sealed with a Teflon bag, and gaseous toluene and xylene were exposed. Removal efficiency of toluene and total xylene (m, p, o) was 13.3 and 7.0 µg·m(-3)·m(-2) leaf area over a 24-h period in S. actinophylla, and was 13.0 and 7.3 µg·m(-3)·m(-2) leaf area in F. benghalensis. Gaseous toluene and xylene in a chamber were absorbed through leaf and transported via the stem, and finally reached to root zone, and also transported by direct diffusion from the air into the medium. Toluene and xylene transported via the stem was decreased with time after exposure. Xylene transported via the stem was higher than that by direct diffusion from the air into the medium over a 24-h period. The ratios of toluene transported via the stem versus direct diffusion from the air into the medium were 46.3 and 53.7% in S. actinophylla, and 46.9 and 53.1% in F. benghalensis, for an average of 47 and 53% for both species. The ratios of m,p-xylene transported over 3 to 9 h via the stem versus direct diffusion from the air into the medium was 58.5 and 41.5% in S. actinophylla, and 60.7 and 39.3% in F. benghalensis, for an average of 60 and 40% for both species, whereas the ratios of o-xylene transported via the stem versus direct diffusion from the air into the medium were 61 and 39%. Both S. actinophylla and F. benghalensis removed toluene and xylene from the air. The ratios of toluene and xylene transported from air to root zone via the stem were 47 and 60 %, respectively. This result suggests that root zone is a significant contributor to gaseous toluene and xylene removal, and transported via the stem plays an important role in this process.

Factors affecting completion of laparoscopic myomectomy.

PURPOSES: This study aimed to elucidate the factors affecting completion of laparoscopic myomectomy without unintended surgery. MATERIALS AND METHODS: The medical records of 143 patients who underwent laparoscopic myomectomy desiring to retain their uterus were retrospectively reviewed. Unintended surgery was defined as the need for conversion to other surgical methods including laparotomy or laparoscopic hysterectomy at any time during the procedures. All variables associated with completion of laparoscopic myomectomy in the univariate analysis were selected at the threshold ofp < 0.25 and then tested in a multiple-logistic regression model. RESULTS: The rate of unintended surgery was 13.3%. Univariate analysis revealed that age, previous abdomino-pelvic surgery, current medical disease, transfusion, > five myomas, myoma size > 8.2 cm, posterior wall location of myoma, intramural type of myoma, and the presence of adenomyosis were statistically significant risk factors for unintended surgery. Multivariate logistic regression analysis demonstrated that completion of laparoscopic myomectomy was significantly influenced by a history of previous abdomino-pelvic surgery (odds ratio; 6.46, 95% CI, 0.03-0.41; p value 0.04). CONCLUSION: The risk of unintended surgery during laparoscopic myomectomy is associated with a history of previous abdomino-pelvic surgery.

Predictive value of obstructive voiding symptoms and objective bladder emptying tests for urinary retention.

The prevalence of voiding dysfunction was 47.4% by the question of "do you usually experience a feeling of incomplete bladder emptying" from Korean version of PFDI (pelvic floor distress inventory), 33.7% by the value of less than 10th centile of peak flow rate of uroflowmetry by Liverpool nomogram, 20.2% by the cutoff values of less than 12 ml per second of maximum flow rate and greater than 25 cmH20 of detrusor pressure at maximum flow rate in the pressure flow study and 11.6% by the elevated post-void residual urine volume more than 50 ml in 95 women who visited urogynaecology clinic with lower urinary tract symptoms. Each method had low positive predictive values for high post-void residuals (subjective symptom 0.16, uroflowmetry 0.29, pressure flow study 0.28). The prevalence of voiding dysfunction is fairly high and none of the questionnaire and objective bladder emptying tests is sufficient for the diagnosis of urinary retention.

Prevalence of overt myeloproliferative neoplasms and JAK2 V617F mutation in Korean patients with splanchnic vein thrombosis.

INTRODUCTION: Myeloproliferative neoplasm (MPN) is known to be a major risk factor of splanchnic vein thrombosis (SVT). Recent studies revealed that a significant proportion of patients with SVT harbor a gain-of-function mutation in the JAK2 gene (V617F) with or without MPN. In this study, the authors investigated the prevalence of MPN and JAK2 V617F mutation in Korean patients with SVT. METHODS: The study subjects were 26 patients diagnosed as having SVT based on Doppler ultrasound and/or computed tomography from January 2008 to January 2010 (16 men and 10 women; mean age 44 years, range 15-75 years). The clinical and laboratory data were reviewed. The JAK2 V617F mutation was detected by allele-specific polymerase chain reaction and direct sequencing analyses using DNA from peripheral blood leukocytes. RESULTS: Among 26 study patients, 12 had portal vein thrombosis, five had hepatic vein thrombosis, three had mesenteric, and two had splenic vein thrombosis. Four patients had thrombosis involving more than one splanchnic vein. Two patients (7.7%; 2/26) had overt MPN (essential thrombocythemia). JAK2 V617F was detected in three patients (11.5%) including the two patients with overt MPN. Thus, the prevalence of the JAK2 V617F mutation in patients with SVT but without overt MPN was 4.2% (1/24). CONCLUSION: The prevalence of overt MPN and that of JAK2 V617F were lower in Korean patients with SVT than in previous reports. Data from a larger number of patients with long-term follow-up are needed to reveal the clinical relevancy of JAK2 V617F in Korean patients with SVT.

Clinical and genetic analysis of Korean patients with Marfan syndrome: possible ethnic differences in clinical manifestation.

Marfan syndrome (MFS) is an autosomal dominant disorder of the fibrous connective tissue caused by mutations in the fibrillin-1 (FBN1) gene. Although clinical and genetic analyses have been performed in various populations, there have been few studies in Korea. The aim of this study was to investigate the clinical characteristics and genetic background of Korean patients with MFS. In 39 Korean patients with MFS who met the Ghent criteria, the most common clinical finding was aortic dilatation and/or dissection (94.9%), whereas only 35.9% of patients had ectopia lentis. The majority of MFS patients had fewer than four of the skeletal findings required to fulfill the major skeletal Ghent criterion for MFS. Only 21% of Korean patients had major skeletal abnormalities and most cases showed only minor skeletal involvement. FBN1 gene mutations were detected in 35 out of 39 patients (89.7%), which is similar to rates presented in the previous reports. These results suggest that some clinical features in Korean patients with MFS differed from those reported in Western MFS patients.

Aromatase and sulfatase inhibitors from Lepiota americana.

From an edible mushroom Lepiota americana Pk., (Agaricaceae), 2-aminophenoxazin-3-one that inhibited aromatase at IC50 = 5.7 microM and 3 beta-hydroxy-5,8-epidioxyergosta-6,22-diene that inhibited sulfatase at IC50 = 0.9 microM were isolated. Neither 2-aminophenoxazin-3-one was active against sulfatase nor was 3 beta-hydroxy-5,8-epidioxyergosta-6,22-diene active against aromatase.