A template effect study on voxel-based morphometry in statistic parametric mapping

Voxel-based morphometry (VBM) is an automated method allowing identification of anatomical differences in the whole brain without the pre-specification of a region of interests. Spatial normalization is one of the major processes in VBM, which transforms all images to a standard template. A variety of templates were employed in VBM researches in the literature, including the MNI template and study-specific templates. Few studies were presented to test the effect of templates on the detection accuracy of VBM, although it is claimed in many papers that the study-specific template performs better. However, the creation of the study-specific template differs on the subjects included. In this paper, the gray matter (GM) difference of two groups (female vs male) was analyzed to evaluate the effects of templates on the VBM results. The statistic parametric mapping (SPM) package, as the standard software for VBM implementation, was used for analyses.

Morphological variation of mutant sunflowers (Helianthus annuus) induced by space flight and their genetic background detection by SSR primers

After sunflower seeds were exposed to space conditions, various mutant plants were screened from the descendent plants. The morphological characters of plants changed in flower color from golden to yellow, light yellow, or even to yellowish green. The ligulate petals of the unisexual floret broadened, or became thin, while the short tubular petals of bisexual floret elongated to some extent, or even turned into semi-ligulate petals or ligulate petals, making the phenotype of the whole inflorescence like a chrysanthemum. The shape and thickness of leaves varied in some of these plants. Absolute sterile plants in mutant plants were found to possess neither normal bisexual florets nor unisexual florets, but the "pseudo-floret" only consisted of pieces of shield-like bracts on protuberant floral disc. Thirty-five pairs of simple sequence of repeat primers were used to detect the genetic variation of the plants, and the results showed that only a variation was tested in the mutant plants from 4 primers. The different PCR products obtained were extracted for sequencing and alignment analysis, and the aligned results showed that the DNA sequence changed by deletion, insertion and replacement that occurred at some sites. The results proved the high mutagenic efficacy of space flight, and ways of DNA transformation due to space conditions.

Improving access to longitudinal patient health information within an emergency department

We designed and implemented an electronic patient tracking system with improved user authentication and patient selection. We then measured access to clinical information from previous clinical encounters before and after implementation of the system. Clinicians accessed longitudinal information for 16% of patient encounters before, and 40% of patient encounters after the intervention, indicating such a system can improve clinician access to information. We also attempted to evaluate the impact of providing this access on inpatient admissions from the emergency department, by comparing the odds of inpatient admission from an emergency department before and after the improved access was made available. Patients were 24% less likely to be admitted after the implementation of improved access. However, there were many potential confounders, based on the inherent pre-post design of the evaluation. Our experience has strong implications for current health information exchange initiatives.

TU-E-BRB-11: End-To-End Positioning Quality Assurance for Image-Guided Radiosurgery of Multiple Targets Using a Single-Isocenter

PURPOSE

Using a single isocenter significantly reduces delivery times in radiosurgery involving multiple targets. However, because not every target can be placed at isocenter with this type of treatment, a conventional Winston-Lutz test cannot be used. We describe a novel Winston-Lutz like mulitarget test (MTT) for verifying accurate positioning.

METHODS

A target phantom, comprised of an acrylic plate with recesses for three 3/4″ spheres was constructed and a high-resolution (0.5×0.5×0.8 mm) CT scan obtained with PTFE spheres placed in the recesses. The scan was imported into a commercial treatment planning system and multiple beams were prepared, having their isocenter at the centroid of the arrangement of spheres. Every beam incorporated three MLC-defined rectangular apertures that circumscribed the spheres. Custom software selected setup parameters (table, gantry and collimator angle, MLC openings) such that the spheres were centered as precisely as possible within their respective MLC fields, considering the discrete width of collimator leaves. The phantom, with the PTFE replaced by steel spheres, was placed on the treatment couch and imaged using stereoscopic x-ray beams. A 6 degree-of-freedom robotic couch applied translations and rotations to reproduce the CT position. A MV EPID rendered images of the spheres within their respective apertures, allowing identification of sphere and aperture centers. Any error upstream would manifest itself as inaccurate centering of a sphere.

RESULTS

Eight beams with table angle 0 and two beams each with table angles 49.7, 89.8, 272.3, and 310.1 were selected. The maximum calculated distance between any sphere and the respective aperture center was 0.07 mm. The median difference measured from the MV images ranged from 0.1 mm to 1.4 mm with a median of 0.8 mm.

CONCLUSIONS

The MTT is a practical end-to-end test for quality assurance of the entire positioning process in multitarget radiosurgery, from CT scanning to beam delivery.

Association of β-cell function and insulin sensitivity with fasting and 2-h plasma glucose in a large Chinese population

AIM

Our aim was to provide a quantitative analysis of the changes in the principal determinants of insulin sensitivity and secretion in relation to fasting plasma glucose (FPG) or 2-h plasma glucose (2h PG) in a Chinese population with a wide range of glucose tolerance.

METHODS

A total of 5728 adults spanning the entire range of glucose tolerance were included. Insulin sensitivity was measured by Matsuda insulin sensitivity index (ISI(M)) and homeostasis model assessment of 1/homeostasis model assessment of insulin resistance (HOMA-IR). β-Cell function adjusted by insulin sensitivity was assessed from disposition index (DI) at early-phase DI(30) and total DI(120). The exponential curve was established as the best fit for the relationship between insulin sensitivity or β-cell function and FPG or 2h PG.

RESULTS

Relative to the trend classified as increasing 2h PG, hepatic insulin sensitivity and insulin secretion showed a decreasing trend to a substantial degree as FPG increased. A 1 mmol/l increase in FPG and 2h PG concentration was associated with a -22 and -21% decline in ISI(M), -16 and -4% in 1/HOMA-IR, -38 and -35% in DI(30) and -36 and -26% in DI(120). The decay constant of ISI(M) and DI(30) in IFG or ISI(M), 1/HOMA-IR, DI(30) and DI(120) in IGT was lower than that in normal glucose tolerance. Significant interactions between sex and glucose levels determining DI were found.

CONCLUSIONS

We conclude that impairment of insulin sensitivity and insulin secretion contributes to both FPG or 2h PG hyperglycaemia in a Chinese population, but that the decline in insulin secretion is more pronounced with increasing fasting than 2h PG.

Association and dissociation of autophagy, apoptosis and necrosis by systematic chemical study

To address the question of whether established or experimental anticancer chemotherapeutics can exert their cytotoxic effects by autophagy, we performed a high-content screen on a set of cytotoxic agents. We simultaneously determined parameters of autophagy, apoptosis and necrosis on cells exposed to -1400 compounds. Many agents induced a 'pure' autophagic, apoptotic or necrotic phenotype, whereas less than 100 simultaneously induced autophagy, apoptosis and necrosis. A systematic analysis of the autophagic flux induced by the most potent 80 inducers of GFP-LC3 puncta among the NCI panel agents showed that 59 among them truly induced autophagy. The remaining 21 compounds were potent inducers of apoptosis or necrosis, yet failed to stimulate an autophagic flux, which were characterized as microtubule inhibitors. Knockdown of ATG7 was efficient in preventing GFP-LC3 puncta, yet failed to attenuate cell death by the agents that induce GFP-LC3 puncta. Thus there is not a single compound that would induce cell death by autophagy in our screening, underscoring the idea that cell death is rarely, if ever, executed by autophagy in human cells.

Trends and Developments in Bioinformatics in 2010: Prospects and Perspectives

To survey major developments and trends in the field of Bioinformatics in 2010 and their relationships to those of previous years, with emphasis on long-term trends, on best practices, on quality of the science of informatics, and on quality of science as a function of informatics.

A critical review of articles in the literature of Bioinformatics over the past year.

Our main results suggest that Bioinformatics continues to be a major catalyst for progress in Biology and Translational Medicine, as a consequence of new assaying technologies, most predominantly Next Generation Sequencing, which are changing the landscape of modern biological and medical research. These assays critically depend on bioinformatics and have led to quick growth of corresponding informatics methods development. Clinical-grade molecular signatures are proliferating at a rapid rate. However, a highly publicized incident at a prominent university showed that deficiencies in informatics methods can lead to catastrophic consequences for important scientific projects. Developing evidence-driven protocols and best practices is greatly needed given how serious are the implications for the quality of translational and basic science.

Several exciting new methods have appeared over the past 18 months, that open new roads for progress in bioinformatics methods and their impact in biomedicine. At the same time, the range of open problems of great significance is extensive, ensuring the vitality of the field for many years to come.