Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software.

ObjectiveThe purpose of this study was to evaluate the reliability and quality of radiomic features in glioblastoma multiforme (GBM) derived from tumor volumes obtained with semi-automated tumor segmentation software.Materials and methodsMR images of 45 GBM patients (29 males, 16 females) were downloaded from The Cancer Imaging Archive, in which post-contrast T1-weighted imaging and fluid-attenuated inversion recovery MR sequences were used. Two raters independently segmented the tumors using two semi-automated segmentation tools (TumorPrism3D and 3D Slicer). Regions of interest corresponding to contrast-enhancing lesion, necrotic portions, and non-enhancing T2 high signal intensity component were segmented for each tumor. A total of 180 imaging features were extracted, and their quality was evaluated in terms of stability, normalized dynamic range (NDR), and redundancy, using intra-class correlation coefficients, cluster consensus, and Rand Statistic.ResultsOur study results showed that most of the radiomic features in GBM were highly stable. Over 90% of 180 features showed good stability (intra-class correlation coefficient [ICC] ≥ 0.8), whereas only 7 features were of poor stability (ICC < 0.5). Most first order statistics and morphometric features showed moderate-to-high NDR (4 > NDR ≥1), while above 35% of the texture features showed poor NDR (< 1). Features were shown to cluster into only 5 groups, indicating that they were highly redundant.ConclusionThe use of semi-automated software tools provided sufficiently reliable tumor segmentation and feature stability; thus helping to overcome the inherent inter-rater and intra-rater variability of user intervention. However, certain aspects of feature quality, including NDR and redundancy, need to be assessed for determination of representative signature features before further development of radiomics

ICT for Development: Two Contradictory Stories of an ICT Initiative

In this study we explore two different perspectives of one ICT project. The “mainstream” believed that an educational ICT project for Taiwanese aboriginals was successful, while the local aboriginals and local teachers did not. Using ethnographic research, we investigated the possible reasons for the disparity between the views of the mainstream and the locals. Our findings indicate that the paternalistic nature of the ICT project as well as a belief in technological supremacy contributed to the discrepancy of views regarding the success of the project. We use postcolonial theory to draw attention to the (often forgotten) voice of the aboriginals

Fast Methods for Simulation of Biomolecule of Electrostatics

Biomolecular structure and interactions in aqueous environment are determined by a complicated interplay between physical and chemical forces including solvation, electrostatics, van der Waals forces, the hydrophobic effect and covalent bonding. Among them, electrostatics has been of particular interest due to its long-range nature and the tradeoff between desolvation and interaction effects [1]. In addition, electrostatic interactions play a significant role within a biomolecule as well as between biomolecules, making the balance between the two vital to the understanding of macromolecular systems. As a result, much effort has been devoted to accurate modeling and simulation of biomolecule electrostatics. One important application of this work is to compute the structure of electrostatic interactions for a biomolecule in an electrolyte solution, as well as the potential that the molecule generates in space. There are two valuable uses for these simulations. First, it provides a full picture of the electrostatic energetics of a biomolecular system, improving our understanding of how electrostatics contributes to stability, specificity, function, and molecular interaction [2]. Second, these simulations serve as a tool for molecular design, since electrostatic complementarity is an important feature of interacting molecules. Through examination of the electrostatics and potential field generated by a protein molecule, for example, it may be possible to suggest improvements to other proteins or drug molecules that interact with it, or perhaps even design new interacting molecules de novo [3]. There are two approaches in simulating a protein macromolecule in an aqueous solution with nonzero ionic strength. Discrete/atomistic approaches based on Monte-Carlo or molecular dynamics simulations treat the macromolecule and solvent explicitly at the atomic level. Therefore, an enormous number of solvent molecules are required to provide reasonable accuracy, especially when electric fields far away from macroscopic surface are of interest, leading to computational infeasibility. In this work, we adopt instead an approach based on a continuum description of the macromolecule and solvent. Although the continuum model of biomolecule electrostatics is widely used, the numerical techniques used to evaluate the model do not exploit fast solver approaches developed for analyzing integrated circuit interconnect. I will describe the formulation used for analyzing biomolecule electrostatics, and then derive an integral formulation of the problem that can be rapidly solved with precorrected-FFT method [4].Singapore-MIT Alliance (SMA

Toll-like receptor 3 activation is required for normal skin barrier repair following UV damage.

UV damage to the skin leads to the release of noncoding RNA (ncRNA) from necrotic keratinocytes that activates Toll-like receptor 3 (TLR3). This release of ncRNA triggers inflammation in the skin following UV damage. Recently, TLR3 activation was also shown to aid wound repair and increase the expression of genes associated with permeability barrier repair. Here, we sought to test whether skin barrier repair after UVB damage is dependent on the activation of TLR3. We observed that multiple ncRNAs induced expression of skin barrier repair genes, that the TLR3 ligand Poly (I:C) also induced expression and function of tight junctions, and that the ncRNA U1 acts in a TLR3-dependent manner to induce expression of skin barrier repair genes. These observations were shown to have functional relevance as Tlr3-/- mice displayed a delay in skin barrier repair following UVB damage. Combined, these data further validate the conclusion that recognition of endogenous RNA by TLR3 is an important step in the program of skin barrier repair

Prediction of stable walking for a toy that cannot stand

Previous experiments [M. J. Coleman and A. Ruina, Phys. Rev. Lett. 80, 3658 (1998)] showed that a gravity-powered toy with no control and which has no statically stable near-standing configurations can walk stably. We show here that a simple rigid-body statically-unstable mathematical model based loosely on the physical toy can predict stable limit-cycle walking motions. These calculations add to the repertoire of rigid-body mechanism behaviors as well as further implicating passive-dynamics as a possible contributor to stability of animal motions.Comment: Note: only corrections so far have been fixing typo's in these comments. 3 pages, 2 eps figures, uses epsf.tex, revtex.sty, amsfonts.sty, aps.sty, aps10.sty, prabib.sty; Accepted for publication in Phys. Rev. E. 4/9/2001 ; information about Andy Ruina's lab (including Coleman's, Garcia's and Ruina's other publications and associated video clips) can be found at: http://www.tam.cornell.edu/~ruina/hplab/index.html and more about Georg Bock's Simulation Group with whom Katja Mombaur is affiliated can be found at http://www.iwr.uni-heidelberg.de/~agboc

A Partitioned Likelihood Analysis of Swallowtail Butterfly Phylogeny (Lepidoptera: Papilionidae)

Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remained underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae)

Human Oral Mucosa Tissue-Engineered Constructs Monitored by Raman Fiber-Optic Probe

In maxillofacial and oral surgery, there is a need for the development of tissue-engineered constructs. They are used for reconstructions due to trauma, dental implants, congenital defects, or oral cancer. A noninvasive monitoring of the fabrication of tissue-engineered constructs at the production and implantation stages done in real time is extremely important for predicting the success of tissue-engineered grafts. We demonstrated a Raman spectroscopic probe system, its design and application, for real-time ex vivo produced oral mucosa equivalent (EVPOME) constructs noninvasive monitoring. We performed in vivo studies to find Raman spectroscopic indicators for postimplanted EVPOME failure and determined that Raman spectra of EVPOMEs preexposed to thermal stress during manufacturing procedures displayed correlation of the band height ratio of CH2 deformation to phenylalanine ring breathing modes, giving a Raman metric to distinguish between healthy and compromised postimplanted constructs. This study is the step toward our ultimate goal to develop a stand-alone system, to be used in a clinical setting, where the data collection and analysis are conducted on the basis of these spectroscopic indicators with minimal user intervention.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140248/1/ten.tec.2013.0622.pd

rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns

BACKGROUND: DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history--an endeavor previously impossible--will finally be feasible. In this study, we assess the discriminatory power of the core plant DNA barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA and trnL-F), across all major fern lineages. We also present plastid barcode data for two genera in the hyperdiverse polypod clade--Deparia (Woodsiaceae) and the Cheilanthes marginata group (currently being segregated as a new genus of Pteridaceae)--to further evaluate the resolving power of these loci. PRINCIPAL FINDINGS: Our results clearly demonstrate the value of matK data, previously unavailable in ferns because of difficulties in amplification due to a major rearrangement of the plastid genome. With its high sequence variation, matK complements rbcL to provide a two-locus barcode with strong resolving power. With sequence variation comparable to matK, trnL-F appears to be a suitable alternative barcode region in ferns, and perhaps should be added to the core barcode region if universal primer development for matK fails. In contrast, trnH-psbA shows dramatically reduced sequence variation for the majority of ferns. This is likely due to the translocation of this segment of the plastid genome into the inverted repeat regions, which are known to have a highly constrained substitution rate. CONCLUSIONS: Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns, and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should focus on gathering more fern matK sequence data to facilitate universal primer development