Short echo time MR spectroscopy of brain tumors: Grading of cerebral gliomas by correlation analysis of normalized spectral amplitudes

Purpose:

To process single voxel spectra of low‐ and high‐grade gliomas. To propose correlation analysis of the scatter plots of normalized spectral amplitudes as a pattern recognition tool for the classification (grading) of brain tumors. To propose a spectrum processing approach that improves the differentiation of proton spectra with dominating macromolecule and lipid peaks.

Materials and Methods:

LCModel was used to process spectra. Mean metabolite concentrations and mean normalized spectra were obtained for normal white matter and for gliomas. The mean spectra of macromolecules and lipids (ML) in the range 1.4–0.9 ppm, and mean difference spectra (DS) without ML and lactate were computed. Correlation analysis of the scatter plot of the patient and mean normalized spectral amplitudes and dispersion of the scatter plot points were used for classification and grading of tumors.

Results:

It was found advantageous to perform the classifications using DS spectra. The shape of ML spectrum and concentration of tCr seem to be a good markers for glioma grade.

Conclusion:

Combining a qualitative comparison of the patient and mean DS spectra of the tumors using correlation analysis of normalized spectra amplitudes with a quantitative comparison of metabolite concentrations is a powerful tool in studying brain lesions. J. Magn. Reson. Imaging 2010;31:39–45. © 2009 Wiley‐Liss, Inc.     

Evaluation of a traditional birth attendant training programme in Bangladesh

Background and context

the 1997 Safe Motherhood Initiative effectively eliminated support for training traditional birth attendants (TBAs) in safe childbirth. Despite this, TBAs are still active in many countries such as Bangladesh, where 88% of deliveries occur at home. Renewed interest in community-based approaches and the urgent need to improve birth care has necessitated a re-examination of how provider training should be conducted and evaluated.

Objective

to demonstrate how a simple evaluation tool can provide a quantitative measure of knowledge acquisition and intended behaviour following a TBA training program.

Design

background data were collected from 45 TBAs attending two separate training sessions conducted by Bangladeshi non-governmental organization (NGO) Gonoshasthaya Kendra (GK). A semi-structured survey was conducted before and after each training session to assess the TBAs’ knowledge and reported practices related to home-based management of childbirth.

Setting

two training sessions conducted in Vatshala and Sreepur in rural Bangladesh.

Participants

45 active TBAs were recruited for this training evaluation.

Findings

there were significant improvements following the training sessions regarding how TBAs reported they would: (a) measure blood loss, (b) handle an apneic newborn, (c) refer women with convulsions and (d) refer women who are bleeding heavily. A greater degree of improvement, and higher scores overall, were observed among TBAs with no prior training and with less birth experience.

Key conclusions and recommendations for practice

as the Safe Motherhood community strives to improve safe childbirth care, the quality of care in pregnancy and childbirth for women who rely on less-skilled providers should not be ignored. These communities need assistance from governments and NGOs to help improve the knowledge and skill levels of the providers upon which they depend. Gonoshasthaya Kendra's extensive efforts to train and involve TBAs, with the aim of improving the quality of care provided to Bangladeshi women, is a good example of how to effectively integrate TBAs into safe motherhood efforts in resource-poor settings. The evaluation methodology described in this paper demonstrates how trainees’ prior experiences and beliefs may affect knowledge acquisition, and highlights the need for more attention to course content and pedagogic style.     

Effusion‐based lymphoma with morphological regression but with clonal genetic features after aspiration

Effusion‐based lymphoma (EBL) is a rare but distinct entity of large B‐cell lymphoma in effusion without association with human herpes virus‐8 (HHV‐8). Spontaneous regression after pleurocentesis has been observed; but to our knowledge, there are no reports on the morphological and molecular features of subsequent aspirations in regressing cases. Here, we report the case of a 92‐year‐old male with chronic obstructive pulmonary disease, who presented with right pleural effusion. He had no human immunodeficiency virus, hepatitis B virus, or hepatitis C virus infection, and CT scans revealed no mass lesion. The first pleural effusion aspiration cytology revealed large lymphoma cells with vesicular nuclei, irregular nuclear contours, and prominent nucleoli, consistent with EBL. The second aspiration cytology showed a few slightly enlarged lymphocytes in a background of small lymphocytes. Immunohistochemical study on cell block of the second aspiration revealed equal amounts of CD3‐positive and CD20‐positive cells. All these cells on the section tested negative for HHV‐8 through immunohistochemistry and Epstein‐Barr virus by in situ hybridization. Our initial impression was EBL in regression. However, flow cytometric immunophenotyping showed monotypic light chain expression of the gated B‐cells. B‐cell receptor gene rearrangement study showed a clonal result. Furthermore, fluorescence in situ hybridization revealed rearrangement of IGH gene. The diagnosis of the second aspiration was EBL with morphological regression but retained clonal genetic features. The patient passed away one month after diagnosis without chemotherapy. This case illustrated the importance of ancillary studies in confirming the clonal nature of a morphologically regressing EBL.     

Study of promoter hypomethylation profiles of RAS oncogenes in hepatocellular carcinoma derived from hepatitis C virus genotype 3a in Pakistani population

Epigenetic modifications such as DNA methylation contribute to progression of hepatitis C virus (HCV) infection to life‐threatening hepatocellular carcinoma (HCC) by promoting the silencing of tumor suppressor genes through DNA hypermethylation and by causing genomic instability through global hypomethylation. However few studies have addressed the promoter region hypomethylation status of the oncogenes involved in HCV derived HCC. In this study, we analyzed the promoter region methylation pattern of RAS oncogenes (HRAS, KRAS, and NRAS) using methylation‐specific PCR for 50 chronic HCV patients infected with genotype 3a (27 HCC patients and 23 control non‐HCC patients). Methylation‐specific polymerase chain reaction analysis revealed that the NRAS oncogene promoter (P = .0025) was significantly hypomethylated in HCC patients compared to the non‐HCC patients suggesting its contribution to the progression of HCV towards HCC. To identify the agent for alteration in the RAS oncogene expression, 7 HCV genes were expressed in the Huh‐7 cell line followed by measurement of the NRAS expression level in Huh‐7 by a quantitative real‐time polymerase chain reaction. An increase in the messenger RNA level of the NRAS gene was detected when Huh‐7 were transfected with Core, NS5a, and NS2 genes. Our findings suggest the involvement of NRAS oncogene in the pathogenesis of HCV3a derived HCC in Pakistani population and also identifies the HCV genes responsible for its enhanced expression. Our study raises the hypothesis that a single HCV gene may increase the chances of malignancy. Therefore, our study may have identified a useful epigenetic biomarker of HCC progression in HCV patients and may help to develop novel diagnostic tools.     

Molecular typing and whole genome next generation sequencing of human adenovirus 8 strains recovered from four 2012 outbreaks of keratoconjunctivitis in New York State

Ocular infections caused by human adenovirus (HAdV) are highly contagious. The most severe are usually caused by members of species HAdV‐D (types HAdV8, 19, 37, 53, 54, and 56) and can manifest as epidemic keratoconjunctivitis (EKC), often resulting in prolonged impairment of vision. During the early months of 2012, EKC outbreaks occurred in neonatal intensive care units (NICUs) in 3 hospitals in New York State (New York and Suffolk Counties). A total of 32 neonates were affected. For 14 of them, HAdV8 was laboratory‐confirmed as the causative agent. Nine healthcare workers were also affected with 3 laboratory‐confirmed, HAdV‐positive EKC. A fourth EKC outbreak was documented among patients attending a private ophthalmology practice in Ulster County involving a total of 35 cases. Epidemiological linkage between the neonatal intensive care unit outbreaks was demonstrated by molecular typing of virus isolates with restriction enzyme analysis and next generation whole genome sequencing. The strain isolated from the ophthalmology clinic was easily distinguishable from the others by restriction enzyme analysis.     

Fine‐scale geographic clustering pattern of human T‐cell leukemia virus type 1 infection among blood donors in Kyushu‐Okinawa,Japan

Human T‐cell leukemia virus type I (HTLV‐1) infection is endemic in Japan, particularly clustered in the southwestern district, Kyushu‐Okinawa, which consists of eight prefectures that further consist of 274 municipalities. However, no information is available about the fine‐scale distribution of HTLV‐1 infection within Kyushu‐Okinawa. To assess the municipal‐level distribution of people with HTLV‐1 infection in Kyushu‐Okinawa, we performed a cross‐sectional study using a fine‐scale geographic information system map based on HTLV‐1 screening test results from the Japanese Red Cross database from September 2012 to February 2014. Of the 881 871 (646 914 male, 234 957 female) screened blood donors, 981 were seropositive for HTLV‐1 by confirmatory test. The seroprevalence was 0.11% (95% confidence interval [CI] 0.10%‐0.12%) for all, 0.094% (95% CI, 0.09%‐0.10%) for male, and 0.16% (95% CI, 0.14%‐0.18%) for female individuals. The sex‐ and age‐specific HTLV‐1 seroprevalence varied significantly across municipalities; particularly, the seroprevalence among women aged 50 years was significantly higher than that of men in both the mainland of Kyushu‐Okinawa and the satellite island, in all of which the seroprevalence of HTLV‐1 was more than 1.2%. These results show that, even in the Kyushu‐Okinawa district, there are endemic clusters of HTLV‐1 in small areas. This suggests that public health education programs are needed to eliminate new HTLV‐1 infection in these areas.     

Cancer‐associated somatic DICER1 hotspot mutations cause defective miRNA processing and reverse‐strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage

Our group recently described recurrent somatic mutations of the miRNA processing gene DICER1 in non‐epithelial ovarian cancer. Mutations appeared to be clustered around each of four critical metal‐binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3′ end of the 5p miRNA strand of a pre‐mRNA hairpin. To investigate the effects of these cancer‐associated 'hotspot' mutations, we engineered mouse DICER1‐deficient ES cells to express wild‐type and an allelic series of the mutant DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal‐binding site mutations were compared to each other and to wild‐type DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation‐carrying cells were distinct from both wild‐type and DICER1‐deficient cells. Further, miRNA profiles showed that mutant DICER1 results in a dramatic loss in processing of mature 5p miRNA strands but were still able to create 3p strand miRNAs. Messenger RNA (mRNA) profile changes were consistent with the loss of 5p strand miRNAs and showed enriched expression for predicted targets of the lost 5p‐derived miRNAs. We therefore conclude that cancer‐associated somatic hotspot mutations of DICER1, affecting any one of four metal‐binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p strand miRNA. We further propose that this resulting 3p strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.