GRAPE: a graphical pipeline environment for image analysis in adaptive magnetic resonance imaging

Purpose

We present a platform, GRAphical Pipeline Environment (GRAPE), to facilitate the development of patient-adaptive magnetic resonance imaging (MRI) protocols.

Methods

GRAPE is an open-source project implemented in the Qt C++ framework to enable graphical creation, execution, and debugging of real-time image analysis algorithms integrated with the MRI scanner. The platform provides the tools and infrastructure to design new algorithms, and build and execute an array of image analysis routines, and provides a mechanism to include existing analysis libraries, all within a graphical environment. The application of GRAPE is demonstrated in multiple MRI applications, and the software is described in detail for both the user and the developer.

Results

GRAPE was successfully used to implement and execute three applications in MRI of the brain, performed on a 3.0-T MRI scanner: (i) a multi-parametric pipeline for segmenting the brain tissue and detecting lesions in multiple sclerosis (MS), (ii) patient-specific optimization of the 3D fluid-attenuated inversion recovery MRI scan parameters to enhance the contrast of brain lesions in MS, and (iii) an algebraic image method for combining two MR images for improved lesion contrast.

Conclusions

GRAPE allows graphical development and execution of image analysis algorithms for inline, real-time, and adaptive MRI applications.

     

Diffusion tensor quantification of the macrostructure and microstructure of human midsagittal corpus callosum across the lifespan

The midsagittal cross-sectional area of the human corpus callosum (CC) has been used by many researchers as a marker of development, natural aging, and neurodegenerative and acquired pathologies. The availability of non-invasive MRI methods for quantifying the macrostructural and microstructural organization of the CC would help to clarify the CC contribution to behavior and cognition in both health and disease. In this report, we extended and validated the ability of a recently described semi-automated diffusion tensor imaging tissue segmentation method to utilize the high orientation contrast of the CC on diffusion tensor imaging. Using a cohort of healthy right-handed children and adults aged 7-59 years, we show gender-independent non-linear (quadratic) and strongly correlated growth trends in the CC area and the corresponding diffusion tensor fractional anisotropy (r = 0.67; P < 1 x 10(-10)). Our results provide preliminary evidence that diffusion tensor anisotropy in the living CC may be related to the number of small myelinated fibers.     

Lentivirus-mediated overexpression of angiotensin-(1-7) attenuated ischaemia-induced cardiac pathophysiology

Myocardial infarction (MI) results in cell death, development of interstitial fibrosis, ventricular wall thinning and ultimately, heart failure. Angiotensin-(1-7) [Ang-(1-7)] has been shown to provide cardioprotective effects. We hypothesize that lentivirus-mediated overexpression of Ang-(1-7) would protect the myocardium from ischaemic injury. A single bolus of 3.5 × 10(8) transducing units of lenti-Ang-(1-7) was injected into the left ventricle of 5-day-old male Sprague-Dawley rats. At 6 weeks of age, MI was induced by ligation of the left anterior descending coronary artery. Four weeks after the MI, echocardiography and haemodynamic parameters were measured to assess cardiac function. Postmyocardial infarction, rats showed significant decreases in fractional shortening and dP/dt (rate of rise of left ventricular pressure), increases in left ventricular end-diastolic pressure, and ventricular hypertrophy. Also, considerable upregulation of cardiac angiotensin-converting enzyme (ACE) mRNA was observed in these rats. Lentivirus-mediated cardiac overexpression of Ang-(1-7) not only prevented all these MI-induced impairments but also resulted in decreased myocardial wall thinning and an increased cardiac gene expression of ACE2 and bradykinin B2 receptor (BKR2). Furthermore, in vitro experiments using rat neonatal cardiac myocytes demonstrated protective effects of Ang-(1-7) against hypoxia-induced cell death. This beneficial effect was associated with decreased expression of inflammatory cytokines (tumour necrosis factor-α and interleukin-6) and increased gene expression of ACE2, BKR2 and interleukin-10. Our findings indicate that overexpression of Ang-(1-7) improves cardiac function and attenuates left ventricular remodelling post-MI. The protective effects of Ang-(1-7) appear to be mediated, at least in part, through modulation of the cardiac renin-angiotensin system and cytokine production.     

Primary Meningoencephalitis by Naegleria fowleri: First Reported Case from Mangalore, South India

A fatal case of primary amebic meningoencephalitis (PAM) in a 5-month-old infant is described. The disease may have been contracted during bathing. The source of water was from an artificial well. The clinical presentation, the isolation of the ameba from the cerebrospinal fluid, the poor response to amphotericin B, and the ultimate fatal outcome are all consistent with the diagnosis of PAM. On the basis of its ability to grow at temperatures above 30 degrees C, the morphology of the trophozoite, and the presence of flagellate forms, the ameba was identified as Naegleria fowleri. Pathogenic N. fowleri amebae were recovered from samples of water from the well. To our knowledge this case represents the second case of PAM in an infant in the absence of the history of swimming.     

Response of MSTd neurons to simulated 3D orientation of rotating planes.

We studied whether the dorsal division of the medial superior temporal area (MSTd) in the macaque has activity related to structure-from-motion (SFM) processing. As the simplest form of three-dimensional (3D) structure, we chose a planar stimulus and examined the relation between the neural responses and the simulated 3D orientation of the plane defined by motion cues. We recorded from 114 MSTd neurons while monkeys were performing a visual fixation task. These neurons responded to a basic set of optic flow patterns such as translation, expansion/contraction, and rotation. Responses of these neurons to rotating plane stimuli were examined to see whether the MSTd neurons exhibited selectivity to the tilt and slant that characterize the 3D orientation of the plane. We found that most MSTd neurons tested (97 of 114) responded to the plane stimuli, and many neurons (65 of 97) exhibited selectivity to tilt and/or slant. Of 97 neurons, 18% (17/97) were selective only to tilt, 24% (23/97) only to slant, and 26% (25/97) to both. Control experiments rejected the possibility that the selectivity could be explained solely by the sensitivity to local stimulus components such as local translation, local speed, and local speed gradients. These results suggest that MSTd neurons are sensitive to stimulus features specific to the perceived 3D orientation of the rotating plane stimuli and suggest that area MSTd is involved in SFM processing.     

CD8dim but not CD8bright cells positive to CD56 dominantly express KIR and are cytotoxic during visceral leishmaniasis

This study reports a structural and functional heterogeneity of CD8⁺CD56⁺NKT cells, which usually decrease quantitatively during visceral leishmaniasis. Based on fluorescence intensity of CD8 receptors on CD56⁺NKT cells, two populations of CD8⁺CD56⁺NKT cells have been identified. These cells were recognized as CD8^dimCD56⁺NKT and CD8^brightCD56⁺NKT cells. We further analyzed the functional nature of CD8^dim and CD8^bright positive CD56⁺NKT cells. In comparison to CD8^brightCD56⁺NKT cells, a significantly higher percentage of CD8^dimCD56⁺NKT cells expressed KIR during VL. The percentage of CD8^dimCD56⁺NKT cells expressing KIR was found 4 fold higher in VL as compared to healthy subjects. But, the difference was insignificant in case of CD8^brightCD56⁺NKT cells. CD8⁺CD56⁺NKT cells release granzyme B to kill the infected cells. A categorical difference was also observed in the function of CD8^dimCD56⁺NKT and CD8^brightCD56⁺NKT cells during visceral leishmaniasis. The percentage of granzyme B expressing CD8^dimCD56⁺NKT cells was 2.83 fold higher in VL compared to healthy subjects. But, there was no significant difference in granzyme B expressing CD8^brightCD56⁺NKT cells in samples from healthy and VL subjects. However, within VL subject, the percentage of granzyme B expressing CD8^dimCD56⁺NKT cells was 5.7 fold higher in comparison to CD8^brightCD56⁺NKT cells. This study concludes that CD8^dimCD56⁺NKT cells are more cytotoxic than CD8^brightCD56⁺NKT cells during VL.     

Reconstruction of goat femur segmental defects using triphasic ceramic-coated hydroxyapatite in combination with autologous cells and platelet-rich plasma

Segmental bone defects resulting from trauma or pathology represent a common and significant clinical problem. In this study, a triphasic ceramic (calcium silicate, hydroxyapatite and tricalcium phosphate)-coated hydroxyapatite (HASi) having the benefits of both HA (osteointegration, osteoconduction) and silica (degradation) was used as a bone substitute for the repair of segmental defect (2 cm) created in a goat femur model. Three experimental goat femur implant groups – (a) bare HASi, (b) osteogenic-induced goat bone marrow-derived mesenchymal stem cells cultured HASi (HASi + C) and (c) osteogenic-induced goat bone marrow-derived mesenchymal stem cells cultured HASi + platelet-rich plasma (HASi + CP) – were designed and efficacy performance in the healing of the defect was evaluated. In all the groups, the material united with host bone without any inflammation and an osseous callus formed around the implant. This reflects the osteoconductivity of HASi where the cells have migrated from the cut ends of host bone. The most observable difference between the groups appeared in the mid region of the defect. In bare HASi groups, numerous osteoblast-like cells could be seen together with a portion of material. However, in HASi + C and HASi + CP, about 60–70% of that area was occupied by woven bone, in line with material degradation. The interconnected porous nature (50–500 μm), together with the chemical composition of the HASi, facilitated the degradation of HASi, thereby opening up void spaces for cellular ingrowth and bone regeneration. The combination of HASi with cells and PRP was an added advantage that could promote the expression of many osteoinductive proteins, leading to faster bone regeneration and material degradation. Based on these results, we conclude that bare HASi can aid in bone regeneration but, with the combination of cells and PRP, the sequence of healing events are much faster in large segmental bone defects in weight-bearing areas in goats.     

Role of fine‐needle aspiration cytology and fluid cytology in extra‐pulmonary tuberculosis

Extra‐pulmonary tuberculosis is the presence of disease in an organ without obvious involvement of the lungs (World Health Organization, Tuberculosis Fact sheet, 2006). The present article focuses on the incidence of extra‐pulmonary tuberculosis as an emerging and clinically significant disease to be reckoned with in the present era. It also highlights fine‐needle aspiration cytology (FNAC) as an inexpensive, less invasive procedure for early diagnosis of such tuberculosis and timely initiation of specific therapy. All cases of proved tuberculosis presenting to the M.V.J. Medical College and Research Hospital were recorded over a period of two years (2008–2010); and categorized as pulmonary and extra‐pulmonary cases. A total of 96 cases of tuberculosis were observed; extra‐pulmonary tuberculosis was seen in 64 cases. Of these 56 cases were from lymphnodes and 8 from extra‐nodal sites which included tuberculous dactylitis (two cases), tuberculous mastitis (two cases), tuberculous synovial effusion (one case), pericardial effusion (one case), epididymo‐orchitis (one case), and cold abscess (one case). The cytology patterns observed included granulomatous inflammation and necrosis with or without acid fast bacilli. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.     

Mechanism-based Classification and Physical Therapy Management of Persons with Cancer Pain: A Prospective Case Series

Context:

Mechanism-based classification (MBC) was established with current evidence and physical therapy (PT) management methods for both cancer and for noncancer pain.

Aims:

This study aims to describe the efficacy of MBC-based PT in persons with primary complaints of cancer pain.

Settings and Design:

A prospective case series of patients who attended the physiotherapy department of a multispecialty university-affiliated teaching hospital.

Material and Methods:

A total of 24 adults (18 female, 6 male) aged 47.5 ± 10.6 years, with primary diagnosis of heterogeneous group of cancer, chief complaints of chronic disabling pain were included in the study on their consent for participation The patients were evaluated and classified on the basis of five predominant mechanisms for pain. Physical therapy interventions were recommended based on mechanisms identified and home program was prescribed with a patient log to ensure compliance. Treatments were given in five consecutive weekly sessions for five weeks each of 30 min duration.

Statistical Analysis Used:

Pre–post comparisons for pain severity (PS) and pain interference (PI) subscales of Brief pain inventory-Cancer pain (BPI-CP) and, European organization for research and treatment in cancer-quality of life questionnaire (EORTC-QLQ-C30) were done using Wilcoxon signed-rank test at 95% confidence interval using SPSS for Windows version 16.0 (SPSS Inc, Chicago, IL).

Results:

There were statistically significant (P < 0.05) reduction in pain severity, pain interference and total BPI-CP scores, and the EORTC-QLQ-C30.

Conclusion:

MBC-PT was effective for improving BPI-CP and EORTC-QLQ-C30 scores in people with cancer pain.