Spectral Graph Convolutions for Population-based Disease Prediction

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects' individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce performance. In this paper, we introduce the novel concept of Graph Convolutional Networks (GCN) for brain analysis in populations, combining imaging and non-imaging data. We represent populations as a sparse graph where its vertices are associated with image-based feature vectors and the edges encode phenotypic information. This structure was used to train a GCN model on partially labelled graphs, aiming to infer the classes of unlabelled nodes from the node features and pairwise associations between subjects. We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks. This has a clear impact on the quality of the predictions, leading to 69.5% accuracy for ABIDE (outperforming the current state of the art of 66.8%) and 77% for ADNI for prediction of MCI conversion, significantly outperforming standard linear classifiers where only individual features are considered.Comment: International Conference on Medical Image Computing and Computer-Assisted Interventions (MICCAI) 201

Chlamydia Hijacks ARF GTPases To Coordinate Microtubule Posttranslational Modifications and Golgi Complex Positioning.

The intracellular bacterium Chlamydia trachomatis develops in a parasitic compartment called the inclusion. Posttranslationally modified microtubules encase the inclusion, controlling the positioning of Golgi complex fragments around the inclusion. The molecular mechanisms by which Chlamydia coopts the host cytoskeleton and the Golgi complex to sustain its infectious compartment are unknown. Here, using a genetically modified Chlamydia strain, we discovered that both posttranslationally modified microtubules and Golgi complex positioning around the inclusion are controlled by the chlamydial inclusion protein CT813/CTL0184/InaC and host ARF GTPases. CT813 recruits ARF1 and ARF4 to the inclusion membrane, where they induce posttranslationally modified microtubules. Similarly, both ARF isoforms are required for the repositioning of Golgi complex fragments around the inclusion. We demonstrate that CT813 directly recruits ARF GTPases on the inclusion membrane and plays a pivotal role in their activation. Together, these results reveal that Chlamydia uses CT813 to hijack ARF GTPases to couple posttranslationally modified microtubules and Golgi complex repositioning at the inclusion.IMPORTANCEChlamydia trachomatis is an important cause of morbidity and a significant economic burden in the world. However, how Chlamydia develops its intracellular compartment, the so-called inclusion, is poorly understood. Using genetically engineered Chlamydia mutants, we discovered that the effector protein CT813 recruits and activates host ADP-ribosylation factor 1 (ARF1) and ARF4 to regulate microtubules. In this context, CT813 acts as a molecular platform that induces the posttranslational modification of microtubules around the inclusion. These cages are then used to reposition the Golgi complex during infection and promote the development of the inclusion. This study provides the first evidence that ARF1 and ARF4 play critical roles in controlling posttranslationally modified microtubules around the inclusion and that Chlamydia trachomatis hijacks this novel function of ARF to reposition the Golgi complex

Reactions of C+ + Cl-, Br-, and I--A comparison of theory and experiment.

Rate constants for the reactions of C+ + Cl-, Br-, and I- were measured at 300 K using the variable electron and neutral density electron attachment mass spectrometry technique in a flowing afterglow Langmuir probe apparatus. Upper bounds of <10-8 cm3 s-1 were found for the reaction of C+ with Br- and I-, and a rate constant of 4.2 ± 1.1 × 10-9 cm3 s-1 was measured for the reaction with Cl-. The C+ + Cl- mutual neutralization reaction was studied theoretically from first principles, and a rate constant of 3.9 × 10-10 cm3 s-1, an order of magnitude smaller than experiment, was obtained with spin-orbit interactions included using a semiempirical model. The discrepancy between the measured and calculated rate constants could be explained by the fact that in the experiment, the total loss of C+ ions was measured, while the theoretical treatment did not include the associative ionization channel. The charge transfer was found to take place at small internuclear distances, and the spin-orbit interaction was found to have a minor effect on the rate constant

Thermal electron attachment to F2

Rate constants have been measured from 300 to 700 K for thermal electron attachment to F2 using two flowing afterglow–Langmuir probe apparatuses. Dissociative attachment yielding F− is observed with a rate constant of 5.0 ± 1.3 × 10−9 cm3 s−1 at 300 K, rising to 9.6 ± 2.4 × 10−9 cm3 s−1 at 700 K, well below the previously accepted values of McCorkle et al. [D. L.McCorkle, L. G. Christophorou, A. A. Christodoulides, and L. Pichiarella, J. Chem. Phys. 85, 1966 (1986)]. The absolute concentration of F2 reaching the afterglowis verified by measuring the near-collisional rate constant (4.5 ± 1.5 × 10−10 cm3 s−1) for Ar+ + F2→ArF+ + F. Prior attempts to apply R-matrix calculations to the F2 + e− system have failed to explain previously reported thermal and nonthermal attachment rate constants along with high-resolution, low-energy attachment cross sections. The present results are reproduced exceptionally well by R-matrix calculations employing previously calculated resonance widths without adjustment

Franck-Condon Factors and Radiative Lifetime of the A^{2}\Pi_{1/2} - X^{2}\Sigma^{+} Transition of Ytterbium Monoflouride, YbF

The fluorescence spectrum resulting from laser excitation of the A^{2}\Pi_{1/2} - X^{2}\Sigma^{+} (0,0) band of ytterbium monofluoride, YbF, has been recorded and analyzed to determine the Franck-Condon factors. The measured values are compared with those predicted from Rydberg-Klein-Rees (RKR) potential energy curves. From the fluorescence decay curve the radiative lifetime of the A^{2}\Pi_{1/2} state is measured to be 28\pm2 ns, and the corresponding transition dipole moment is 4.39\pm0.16 D. The implications for laser cooling YbF are discussed.Comment: 5 pages, 5 figure

Box H/ACA snoRNAs are preferred substrates for the trimethylguanosine synthase in the divergent unicellular eukaryote Trichomonas vaginalis.

The 2,2,7-trimethylguanosine caps of eukaryal snRNAs and snoRNA are formed by the enzyme Tgs1, which catalyzes sequential guanine-N2 methylations of m7G caps. Atypically, in the divergent unicellular eukaryote Trichomonas vaginalis, spliceosomal snRNAs lack a guanosine cap and the recombinant T. vaginalis trimethylguanosine synthase (TvTgs) produces only m2,7G in vitro. Here, we show by direct metabolic labeling that endogenous T. vaginalis RNAs contain m7G, m2,7G, and m2,2,7G caps. Immunodepletion of TvTgs from cell extracts and TvTgs add-back experiments demonstrate that TvTgs produces m2,7G and m2,2,7G caps. Expression of TvTgs in yeast tgs1D cells leads to the formation of m2,7G and m2,2,7G caps and complementation of the lethality of a tgs1D mud2D strain. Whereas TvTgs is present in the nucleus and cytosol of T. vaginalis cells, TMG-containing RNAs are localized primarily in the nucleolus. Molecular cloning of anti-TMG affinity-purified T. vaginalis RNAs identified 16 box H/ACA snoRNAs, which are implicated in guiding RNA pseudouridylation. The ensemble of new T. vaginalis H/ACA snoRNAs allowed us to predict and partially validate an extensive map of pseudouridines in T. vaginalis rRNA

Label-free electrochemical monitoring of DNA ligase activity

This study presents a simple, label-free electrochemical technique for the monitoring of DNA ligase activity. DNA ligases are enzymes that catalyze joining of breaks in the backbone of DNA and are of significant scientific interest due to their essential nature in DNA metabolism and their importance to a range of molecular biological methodologies. The electrochemical behavior of DNA at mercury and some amalgam electrodes is strongly influenced by its backbone structure, allowing a perfect discrimination between DNA molecules containing or lacking free ends. This variation in electrochemical behavior has been utilized previously for a sensitive detection of DNA damage involving the sugar-phosphate backbone breakage. Here we show that the same principle can be utilized for monitoring of a reverse process, i.e., the repair of strand breaks by action of the DNA ligases. We demonstrate applications of the electrochemical technique for a distinction between ligatable and unligatable breaks in plasmid DNA using T4 DNA ligase, as well as for studies of the DNA backbone-joining activity in recombinant fragments of E. coli DNA ligase

Stark deceleration of CaF molecules in strong- and weak-field seeking states

We report the Stark deceleration of CaF molecules in the strong-field seeking ground state and in a weak-field seeking component of a rotationally-excited state. We use two types of decelerator, a conventional Stark decelerator for the weak-field seekers, and an alternating gradient decelerator for the strong-field seekers, and we compare their relative merits. We also consider the application of laser cooling to increase the phase-space density of decelerated molecules.Comment: 10 pages, 8 figure