Transit Timing and Duration Variations for the Discovery and Characterization of Exoplanets

Transiting exoplanets in multi-planet systems have non-Keplerian orbits which can cause the times and durations of transits to vary. The theory and observations of transit timing variations (TTV) and transit duration variations (TDV) are reviewed. Since the last review, the Kepler spacecraft has detected several hundred perturbed planets. In a few cases, these data have been used to discover additional planets, similar to the historical discovery of Neptune in our own Solar System. However, the more impactful aspect of TTV and TDV studies has been characterization of planetary systems in which multiple planets transit. After addressing the equations of motion and parameter scalings, the main dynamical mechanisms for TTV and TDV are described, with citations to the observational literature for real examples. We describe parameter constraints, particularly the origin of the mass/eccentricity degeneracy and how it is overcome by the high-frequency component of the signal. On the observational side, derivation of timing precision and introduction to the timing diagram are given. Science results are reviewed, with an emphasis on mass measurements of transiting sub-Neptunes and super-Earths, from which bulk compositions may be inferred.Comment: Revised version. Invited review submitted to 'Handbook of Exoplanets,' Exoplanet Discovery Methods section, Springer Reference Works, Juan Antonio Belmonte and Hans Deeg, Eds. TeX and figures may be found at https://github.com/ericagol/TTV_revie

Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch

Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.Comment: 14 pages, 4 figure

Characterisation of the passive permeability barrier of nuclear pore complexes

Nuclear pore complexes (NPCs) restrict uncontrolled nucleocytoplasmic fluxes of inert macromolecules but permit facilitated translocation of nuclear transport receptors and their cargo complexes. We probed the passive barrier of NPCs and observed sieve-like properties with a dominating mesh or channel radius of 2.6 nm, which is narrower than proposed earlier. A small fraction of diffusion channels has a wider opening, explaining the very slow passage of larger molecules. The observed dominant passive diameter approximates the distance of adjacent hydrophobic clusters of FG repeats, supporting the model that the barrier is made of FG repeat domains cross-linked with a spacing of an FG repeat unit length. Wheat germ agglutinin and the dominant-negative importin β45-462 fragment were previously regarded as selective inhibitors of facilitated NPC passage. We now observed that they do not distinguish between the passive and the facilitated mode. Instead, their inhibitory effect correlates with the size of the NPC-passing molecule. They have little effect on small species, inhibit the passage of green fluorescent protein-sized objects >10-fold and virtually block the translocation of larger ones. This suggests that passive and facilitated NPC passage proceed through one and the same permeability barrier

Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X = {X_1, ..., X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs

Uterine Torsion Dystocia Complicated by Perosomus Elumbis in an Angus Calf Associated with a Consanguineous Mating

A six-year-old multiparous Angus cow was presented for dystocia. Vaginal and rectal examinations revealed an approximately 360° counterclockwise uterine torsion. The torsion was corrected by rolling the cow counterclockwise (three episodes) with the aid of a plank coupled with manual detorsion via the vagina. The placement of obstetric chains followed by manual traction ultimately delivered a stillborn male calf with evidence of vertebral aplasia, arthrogryposis, and abdominal organ herniation. Patient history and subsequent parentage verification revealed that the calf was the result of a consanguineous (mother to son) mating. Tissue samples from the affected calf and blood samples from the dam, sire, and ten half siblings were collected for genetic testing and parentage verification. Necropsy, radiographic, and computed tomography examinations all supported a diagnosis of perosomus elumbis. Perosomus elumbis is a congenital abnormality of unknown origin(s), and this is the first report of a case associated with a consanguineous mating

Diarrhoea in a large prospective cohort of European travellers to resource-limited destinations

BACKGROUND: Incidence rates of travellers' diarrhoea (TD) need to be updated and risk factors are insufficiently known. METHODS: Between July 2006 and January 2008 adult customers of our Centre for Travel Health travelling to a resource-limited country for the duration of 1 to 8 weeks were invited to participate in a prospective cohort study. They received one questionnaire pre-travel and a second one immediately post-travel. First two-week incidence rates were calculated for TD episodes and a risk assessment was made including demographic and travel-related variables, medical history and behavioural factors. RESULTS: Among the 3100 persons recruited, 2800 could be investigated, resulting in a participation rate of 89.2%. The first two-weeks incidence for classic TD was 26.2% (95%CI 24.5-27.8). The highest rates were found for Central Africa (29.6%, 95% CI 12.4-46.8), the Indian subcontinent (26.3%, 95%CI 2.3-30.2) and West Africa (21.5%, 95%CI 14.9-28.1). Median TD duration was 2 days (range 1-90). The majority treated TD with loperamide (57.6%), while a small proportion used probiotics (23.0%) and antibiotics (6.8%). Multiple logistic regression analysis on any TD to determine risk factors showed that a resolved diarrhoeal episode experienced in the 4 months pre-travel (OR 2.03, 95%CI 1.59-2.54), antidepressive comedication (OR 2.11, 95%CI 1.17-3.80), allergic asthma (OR 1.67, 95%CI 1.10-2.54), and reporting TD-independent fever (OR 6.56, 95%CI 3.06-14.04) were the most prominent risk factors of TD. CONCLUSIONS: TD remains a frequent travel disease, but there is a decreasing trend in the incidence rate. Patients with a history of allergic asthma, pre-travel diarrhoea, or of TD-independent fever were more likely to develop TD while abroad

Virtual rehabilitation for multiple sclerosis using a Kinect-based system: randomized controlled trial

©Jose-Antonio Lozano-Quilis, Hermenegildo Gil-Gómez, Jose-Antonio Gil-Gómez, Sergio Albiol-Pérez, Guillermo Palacios-Navarro, Habib M Fardoun, Abdulfattah S Mashat. Originally published in JMIR Serious Games (http://games.jmir.org), 12.11.2014. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Serious Games, is properly cited. The complete bibliographic information, a link to the original publication on http://games.jmir.org, as well as this copyright and license information must be included.Background: The methods used for the motor rehabilitation of patients with neurological disorders include a number of different rehabilitation exercises. For patients who have been diagnosed with multiple sclerosis (MS), the performance of motor rehabilitation exercises is essential. Nevertheless, this rehabilitation may be tedious, negatively influencing patients motivation and adherence to treatment. Objective: We present RemoviEM, a system based on Kinect that uses virtual reality (VR) and natural user interfaces (NUI) to offer patients with MS an intuitive and motivating way to perform several motor rehabilitation exercises. It offers therapists a new motor rehabilitation tool for the rehabilitation process, providing feedback on the patient s progress. Moreover, it is a low-cost system, a feature that can facilitate its integration in clinical rehabilitation centers. Methods: A randomized and controlled single blinded study was carried out to assess the influence of a Kinect-based virtual rehabilitation system on the balance rehabilitation of patients with MS. This study describes RemoviEM and evaluates its effectiveness compared to standard rehabilitation. To achieve this objective, a clinical trial was carried out. Eleven patients from a MS association participated in the clinical trial. The mean age was 44.82 (SD 10.44) and the mean time from diagnosis (years) was 9.77 (SD 10.40). Clinical effectiveness was evaluated using clinical balance scales. Results: Significant group-by-time interaction was detected in the scores of the Berg Balance Scale (P=.011) and the Anterior Reach Test in standing position (P=.011). Post-hoc analysis showed greater improvement in the experimental group for these variables than in the control group for these variables. The Suitability Evaluation Questionnaire (SEQ) showed good results in usability, acceptance, security, and safety for the evaluated system. Conclusions: The results obtained suggest that RemoviEM represents a motivational and effective alternative to traditional motor rehabilitation for MS patients. These results have encouraged us to improve the system with new exercises, which are currently being developed.This contribution was partially funded by the Generalitat Valenciana ("Ajudes per a la realitzacio de projectes d'I+D per a grups d'investigacion emergents", projecte GV/2012/069) and by the Fundacion Antonio Gargallo ("Ayudas financiadas por la Obra Social de Ibercaja de proyectos de investigacion 2013", proyecto 2013/B001).Lozano Quilis, JA.; Gil Gómez, H.; Gil-Gómez, J.; Albiol Pérez, S.; Palacios Navarro, G.; Fardoun, HM.; Mashat, AS. (2014). Virtual rehabilitation for multiple sclerosis using a Kinect-based system: randomized controlled trial. JMIR Serious Games. 2(2). https://doi.org/10.2196/games.2933Se1222Adamovich, S. V., Fluet, G. G., Tunik, E., & Merians, A. S. (2009). Sensorimotor training in virtual reality: A review. Neurorehabilitation, 25(1), 29-44. doi:10.3233/nre-2009-0497Lange, B., Flynn, S., Proffitt, R., Chang, C.-Y., & «Skip» Rizzo, A. (2010). Development of an Interactive Game-Based Rehabilitation Tool for Dynamic Balance Training. Topics in Stroke Rehabilitation, 17(5), 345-352. doi:10.1310/tsr1705-345Lozano, J. A., Montesa, J., Juan, M. C., Alcañiz, M., Rey, B., Gil, J., … Morganti, F. (2005). VR-Mirror: A Virtual Reality System for Mental Practice in Post-Stroke Rehabilitation. Lecture Notes in Computer Science, 241-251. doi:10.1007/11536482_23Lange, B. S., Requejo, P., Flynn, S. M., Rizzo, A. A., Valero-Cuevas, F. J., Baker, L., & Winstein, C. (2010). The Potential of Virtual Reality and Gaming to Assist Successful Aging with Disability. Physical Medicine and Rehabilitation Clinics of North America, 21(2), 339-356. doi:10.1016/j.pmr.2009.12.007Wuang, Y.-P., Chiang, C.-S., Su, C.-Y., & Wang, C.-C. (2011). Effectiveness of virtual reality using Wii gaming technology in children with Down syndrome. Research in Developmental Disabilities, 32(1), 312-321. doi:10.1016/j.ridd.2010.10.002Chang, Y.-J., Chen, S.-F., & Huang, J.-D. (2011). A Kinect-based system for physical rehabilitation: A pilot study for young adults with motor disabilities. Research in Developmental Disabilities, 32(6), 2566-2570. doi:10.1016/j.ridd.2011.07.002Da GamaAChavezTFigueiredoLTeichriebVPoster: improving motor rehabilitation process through a natural interaction based system using kinect sensor, IEEE Symposium on 3D User Interfaces 2012: 145-1462012IEEE Symposium on 3D User InterfacesMar 4-5Costa Mesa, CABaram, Y., & Miller, A. (2006). Virtual reality cues for improvement of gait in patients with multiple sclerosis. Neurology, 66(2), 178-181. doi:10.1212/01.wnl.0000194255.82542.6bFulk, G. D. (2005). Locomotor Training and Virtual Reality-based Balance Training for an Individual with Multiple Sclerosis. Journal of Neurologic Physical Therapy, 29(1), 34-42. doi:10.1097/01.npt.0000282260.59078.e4Lozano-QuilisJAAlbiol-PerezSGil-GomezHPalaciosGFardoumHMGil-GomezJAMashatASVirtual reality system for multiple sclerosis rehabilitation using KINECT2013International Conference on Pervasive Computing Technologies for Healthcare (PervasiveHealth)May 5-8Venice, Italy366369Van Hedel, H. J., Wirz, M., & Dietz, V. (2005). Assessing walking ability in subjects with spinal cord injury: Validity and reliability of 3 walking tests. Archives of Physical Medicine and Rehabilitation, 86(2), 190-196. doi:10.1016/j.apmr.2004.02.010Podsiadlo, D., & Richardson, S. (1991). The Timed «Up & Go»: A Test of Basic Functional Mobility for Frail Elderly Persons. Journal of the American Geriatrics Society, 39(2), 142-148. doi:10.1111/j.1532-5415.1991.tb01616.xSteffen, T. M., Hacker, T. A., & Mollinger, L. (2002). Age- and Gender-Related Test Performance in Community-Dwelling Elderly People: Six-Minute Walk Test, Berg Balance Scale, Timed Up & Go Test, and Gait Speeds. Physical Therapy, 82(2), 128-137. doi:10.1093/ptj/82.2.128Gil-GomezJASEQ: Suitability Evaluation Questionnaire for Virtual Rehabilitation systems2013International Conference on Pervasive Computing Technologies for Healthcare (PervasiveHealth)2013Venice, Italy33533

Preparation and Measurement of Three-Qubit Entanglement in a Superconducting Circuit

Traditionally, quantum entanglement has played a central role in foundational discussions of quantum mechanics. The measurement of correlations between entangled particles can exhibit results at odds with classical behavior. These discrepancies increase exponentially with the number of entangled particles. When entanglement is extended from just two quantum bits (qubits) to three, the incompatibilities between classical and quantum correlation properties can change from a violation of inequalities involving statistical averages to sign differences in deterministic observations. With the ample confirmation of quantum mechanical predictions by experiments, entanglement has evolved from a philosophical conundrum to a key resource for quantum-based technologies, like quantum cryptography and computation. In particular, maximal entanglement of more than two qubits is crucial to the implementation of quantum error correction protocols. While entanglement of up to 3, 5, and 8 qubits has been demonstrated among spins, photons, and ions, respectively, entanglement in engineered solid-state systems has been limited to two qubits. Here, we demonstrate three-qubit entanglement in a superconducting circuit, creating Greenberger-Horne-Zeilinger (GHZ) states with fidelity of 88%, measured with quantum state tomography. Several entanglement witnesses show violation of bi-separable bounds by 830\pm80%. Our entangling sequence realizes the first step of basic quantum error correction, namely the encoding of a logical qubit into a manifold of GHZ-like states using a repetition code. The integration of encoding, decoding and error-correcting steps in a feedback loop will be the next milestone for quantum computing with integrated circuits.Comment: 7 pages, 4 figures, and Supplementary Information (4 figures)

Loss of Dictyostelium HSPC300 causes a scar-like phenotype and loss of SCAR protein

<p>Abstract</p> <p>Background</p> <p>SCAR/WAVE proteins couple signalling to actin polymerization, and are thus fundamental to the formation of pseudopods and lamellipods. They are controlled as part of a five-membered complex that includes the tiny HSPC300 protein. It is not known why SCAR/WAVE is found in such a large assembly, but in <it>Dictyostelium </it>the four larger subunits have different, clearly delineated functions.</p> <p>Results</p> <p>We have generated <it>Dictyostelium </it>mutants in which the HSPC300 gene is disrupted. As has been seen in other regulatory complex mutants, SCAR is lost in these cells, apparently by a post-translational mechanism, though PIR121 levels do not change. HSPC300 knockouts resemble <it>scar </it>mutants in slow migration, roundness, and lack of large pseudopods. However <it>hspc300</it>-colonies on bacteria are larger and more similar to wild type, suggesting that some SCAR function can survive without HSPC300. We find no evidence for functions of HSPC300 outside the SCAR complex.</p> <p>Conclusion</p> <p>HSPC300 is essential for most SCAR complex functions. The phenotype of HSPC300 knockouts is most similar to mutants in <it>scar</it>, not the other members of the SCAR complex, suggesting that HSPC300 acts most directly on SCAR itself.</p