Reproducibility of patient setup by surface image registration system in conformal radiotherapy of prostate cancer

<p>Abstract</p> <p>Background</p> <p>The reproducibility of patient setup for radiotherapy is based on various methods including external markers, X-rays with planar or computerized image acquisition, and, more recently, surface matching imaging. We analyzed the setup reproducibility of 16 patients affected by prostate cancer who underwent conformal radiotherapy with curative intent by using a surface image registration system.</p> <p>Methods</p> <p>We analyzed the setup reproducibility of 16 patients affected by prostate cancer candidates for conformal radiotherapy by using a surface image registration system. At the initial setup, EPID images were compared with DRRs and a reference 3D surface image was obtained by the AlignRT system (Vision RT, London, UK). Surface images were acquired prior to every subsequent setup procedure. EPID acquisition was repeated when errors > 5 mm were reported.</p> <p>Results</p> <p>The mean random and systematic errors were 1.2 ± 2.3 mm and 0.3 ± 3.0 mm along the X axis, 0.0 ± 1.4 mm and 0.5 ± 2.0 mm along the Y axis, and 2.0 ± 1.8 mm and -0.7 ± 2.4 mm along the Z axis respectively. The positioning error detected by AlignRT along the 3 axes X, Y, and Z exceeded the value of 5 mm in 14.1%, 2.0%, and 5.1% measurements and the value of 3 mm in 36.9%, 13.6% and 27.8% measurements, respectively. Correlation factors calculated by linear regression between the errors measured by AlignRT and EPID ranged from 0.77 to 0.92 with a mean of 0.85 and SD of 0.13. The setup measurements by surface imaging are highly reproducible and correlate with the setup errors detected by EPID.</p> <p>Conclusion</p> <p>Surface image registration system appears to be a simple, fast, non-invasive, and reproducible method to analyze the set-up alignment in 3DCRT of prostate cancer patients.</p

New instability of non-extremal black holes: spitting out supertubes

We search for stable bound states of non-extremal rotating three-charge black holes in five dimensions (Cvetic-Youm black holes) and supertubes. We do this by studying the potential of supertube probes in the non-extremal black hole background and find that generically the marginally bound state of the supersymmetric limit becomes metastable and disappears with non-extremality (higher temperature). However near extremality there is a range of parameters allowing for stable bound states, which have lower energy than the supertube-black hole merger. Angular momentum is crucial for this effect. We use this setup in the D1-D5 decoupling limit to map a thermodynamic instability of the CFT (a new phase which is entropically dominant over the black hole phase) to a tunneling instability of the black hole towards the supertube-black hole bound state. This generalizes the results of ArXiv:1108.0411 [hep-th], which mapped an entropy enigma in the bulk to the dual CFT in a supersymmetric setup.Comment: 28 pages + appendix, 15 figures, v2: References added, typos corrected. Version published in JHE

Direct imaging of the coexistence of ferromagnetism and superconductivity at the LaAlO3/SrTiO3 interface

LaAlO3 and SrTiO3 are insulating, nonmagnetic oxides, yet the interface between them exhibits a two-dimensional electron system with high electron mobility,1 superconductivity at low temperatures,2-6 and electric-field-tuned metal-insulator and superconductorinsulator phase transitions.3,6-8 Bulk magnetization and magnetoresistance measurements also suggest some form of magnetism depending on preparation conditions5,9-11 and suggest a tendency towards nanoscale electronic phase separation.10 Here we use local imaging of the magnetization and magnetic susceptibility to directly observe a landscape of ferromagnetism, paramagnetism, and superconductivity. We find submicron patches of ferromagnetism in a uniform background of paramagnetism, with a nonuniform, weak diamagnetic superconducting susceptibility at low temperature. These results demonstrate the existence of nanoscale phase separation as suggested by theoretical predictions based on nearly degenerate interface sub-bands associated with the Ti orbitals.12,13 The magnitude and temperature dependence of the paramagnetic response suggests that the vast majority of the electrons at the interface are localized, and do not contribute to transport measurements.3,6,7 In addition to the implications for magnetism, the existence of a 2D superconductor at an interface with highly broken inversion symmetry and a ferromagnetic landscape in the background suggests the potential for exotic superconducting phenomena.Comment: Edited version to appear in Nature Physic

The Five AhMTP1 Zinc Transporters Undergo Different Evolutionary Fates towards Adaptive Evolution to Zinc Tolerance in Arabidopsis halleri

Gene duplication is a major mechanism facilitating adaptation to changing environments. From recent genomic analyses, the acquisition of zinc hypertolerance and hyperaccumulation characters discriminating Arabidopsis halleri from its zinc sensitive/non-accumulator closest relatives Arabidopsis lyrata and Arabidopsis thaliana was proposed to rely on duplication of genes controlling zinc transport or zinc tolerance. Metal Tolerance Protein 1 (MTP1) is one of these genes. It encodes a Zn2+/H+ antiporter involved in cytoplasmic zinc detoxification and thus in zinc tolerance. MTP1 was proposed to be triplicated in A. halleri, while it is present in single copy in A. thaliana and A. lyrata. Two of the three AhMTP1 paralogues were shown to co-segregate with zinc tolerance in a BC1 progeny from a cross between A. halleri and A. lyrata. In this work, the MTP1 family was characterized at both the genomic and functional levels in A. halleri. Five MTP1 paralogues were found to be present in A. halleri, AhMTP1-A1, -A2, -B, -C, and -D. Interestingly, one of the two newly identified AhMTP1 paralogues was not fixed at least in one A. halleri population. All MTP1s were expressed, but transcript accumulation of the paralogues co-segregating with zinc tolerance in the A. halleri X A. lyrata BC1 progeny was markedly higher than that of the other paralogues. All MTP1s displayed the ability to functionally complement a Saccharomyces cerevisiæ zinc hypersensitive mutant. However, the paralogue showing the least complementation of the yeast mutant phenotype was one of the paralogues co-segregating with zinc tolerance. From our results, the hypothesis that pentaplication of MTP1 could be a major basis of the zinc tolerance character in A. halleri is strongly counter-balanced by the fact that members of the MTP1 family are likely to experience different evolutionary fates, some of which not concurring to increase zinc tolerance

A high-order FEM formulation for free and forced vibration analysis of a nonlocal nonlinear graded Timoshenko nanobeam based on the weak form quadrature element method

The purpose of this paper is to provide a high-order finite element method (FEM) formulation of nonlocal nonlinear nonlocal graded Timoshenko based on the weak form quadrature element method (WQEM). This formulation offers the advantages and flexibility of the FEM without its limiting low-order accuracy. The nanobeam theory accounts for the von Kármán geometric nonlinearity in addition to Eringen’s nonlocal constitutive models. For the sake of generality, a nonlinear foundation is included in the formulation. The proposed formulation generates high-order derivative terms that cannot be accounted for using regular first- or second-order interpolation functions. Hamilton’s principle is used to derive the variational statement which is discretized using WQEM. The results of a WQEM free vibration study are assessed using data obtained from a similar problem solved by the differential quadrature method (DQM). The study shows that WQEM can offer the same accuracy as DQM with a reduced computational cost. Currently the literature describes a small number of high-order numerical forced vibration problems, the majority of which are limited to DQM. To obtain forced vibration solutions using WQEM, the authors propose two different methods to obtain frequency response curves. The obtained results indicate that the frequency response curves generated by either method closely match their DQM counterparts obtained from the literature, and this is despite the low mesh density used for the WQEM systems

Speed Controls the Amplitude and Timing of the Hippocampal Gamma Rhythm

Cortical and hippocampal gamma oscillations have been implicated in many behavioral tasks. The hippocampus is required for spatial navigation where animals run at varying speeds. Hence we tested the hypothesis that the gamma rhythm could encode the running speed of mice. We found that the amplitude of slow (20–45 Hz) and fast (45–120 Hz) gamma rhythms in the hippocampal local field potential (LFP) increased with running speed. The speed-dependence of gamma amplitude was restricted to a narrow range of theta phases where gamma amplitude was maximal, called the preferred theta phase of gamma. The preferred phase of slow gamma precessed to lower values with increasing running speed. While maximal fast and slow gamma occurred at coincident phases of theta at low speeds, they became progressively more theta-phase separated with increasing speed. These results demonstrate a novel influence of speed on the amplitude and timing of the hippocampal gamma rhythm which could contribute to learning of temporal sequences and navigation

To Be or Not to Be a Flatworm: The Acoel Controversy

Since first described, acoels were considered members of the flatworms (Platyhelminthes). However, no clear synapomorphies among the three large flatworm taxa - the Catenulida, the Acoelomorpha and the Rhabditophora - have been characterized to date. Molecular phylogenies, on the other hand, commonly positioned acoels separate from other flatworms. Accordingly, our own multi-locus phylogenetic analysis using 43 genes and 23 animal species places the acoel flatworm Isodiametra pulchra at the base of all Bilateria, distant from other flatworms. By contrast, novel data on the distribution and proliferation of stem cells and the specific mode of epidermal replacement constitute a strong synapomorphy for the Acoela plus the major group of flatworms, the Rhabditophora. The expression of a piwi-like gene not only in gonadal, but also in adult somatic stem cells is another unique feature among bilaterians. These two independent stem-cell-related characters put the Acoela into the Platyhelminthes-Lophotrochozoa clade and account for the most parsimonious evolutionary explanation of epidermal cell renewal in the Bilateria. Most available multigene analyses produce conflicting results regarding the position of the acoels in the tree of life. Given these phylogenomic conflicts and the contradiction of developmental and morphological data with phylogenomic results, the monophyly of the phylum Platyhelminthes and the position of the Acoela remain unresolved. By these data, both the inclusion of Acoela within Platyhelminthes, and their separation from flatworms as basal bilaterians are well-supported alternatives

Apoptosis-Related Gene Expression Profiling in Hematopoietic Cell Fractions of MDS Patients

Contains fulltext : 168172.pdf (publisher's version ) (Open Access)Although the vast majority of patients with a myelodysplastic syndrome (MDS) suffer from cytopenias, the bone marrow is usually normocellular or hypercellular. Apoptosis of hematopoietic cells in the bone marrow has been implicated in this phenomenon. However, in MDS it remains only partially elucidated which genes are involved in this process and which hematopoietic cells are mainly affected. We employed sensitive real-time PCR technology to study 93 apoptosis-related genes and gene families in sorted immature CD34+ and the differentiating erythroid (CD71+) and monomyeloid (CD13/33+) bone marrow cells. Unsupervised cluster analysis of the expression signature readily distinguished the different cellular bone marrow fractions (CD34+, CD71+ and CD13/33+) from each other, but did not discriminate patients from healthy controls. When individual genes were regarded, several were found to be differentially expressed between patients and controls. Particularly, strong over-expression of BIK (BCL2-interacting killer) was observed in erythroid progenitor cells of low- and high-risk MDS patients (both p = 0.001) and TNFRSF4 (tumor necrosis factor receptor superfamily 4) was down-regulated in immature hematopoietic cells (p = 0.0023) of low-risk MDS patients compared to healthy bone marrow

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al

Measuring Spirituality as a Universal Human Experience: A Review of Spirituality Questionnaires

Spirituality is an important theme in health research, since a spiritual orientation can help people to cope with the consequences of a serious disease. Knowledge on the role of spirituality is, however, limited, as most research is based on measures of religiosity rather than spirituality. A questionnaire that transcends specific beliefs is a prerequisite for quantifying the importance of spirituality among people who adhere to a religion or none at all. In this review, we discuss ten questionnaires that address spirituality as a universal human experience. Questionnaires are evaluated with regard to psychometric properties, item formulation and confusion with well-being and distress. Although none of the questionnaires fulfilled all the criteria, the multidimensional Spiritual Well-Being Questionnaire is promising