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Background Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. Results We developed TargetSpy , a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Conclusion Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila, suggesting that it may be applicable to a broad range of species. Moreover, we have demonstrated that the application of machine learning techniques in combination with upcoming deep sequencing data results in a powerful microRNA target site prediction tool http://www.targetspy.org .

Purpose This study evaluates the anorectal and genitourinary function of patients treated by preoperative short-term radiotherapy (RT) or chemoradiotherapy (CRT) followed by surgery and surgery alone for rectal cancer. Methods For this study, a total of 613 patients, who were identified from a prospective rectal cancer database, underwent anterior resection of the rectum between October 2001 and December 2007. Standardized questionnaires were used to determine fecal incontinence, urinary, and sexual function. Relevant clinical variables were evaluated using univariate and multivariate analyses. Independent predictors of functional outcome were identified by a binary logistic regression analysis. Results The data of 263 (43 %) patients were available for analysis. On multivariate analysis, neoadjuvant RT ( P  < 0.01) and low anterior resection (LAR) ( P  = 0.049) were associated with fecal incontinence. In univariate analysis, fecal incontinence was linked to preoperative neoadjuvant treatment (RT and/or CRT vs. LAR) ( P  < 0.01). The hazard ratio for developing fecal incontinence was 3.3 (1.6–6.8) for patients who received RT. One hundred twenty-five patients (51.2 %) experienced urinary incontinence following surgery, the majority of whom were female ( P  < 0.01). On univariate analysis, male sexual function was associated with age ( P  < 0.01), ASA class ( P  = 0.01) and LAR ( P  = 0.01). Conclusion Multimodal therapy of low rectal cancer increases the incidence of fecal incontinence and negatively affects sexual function. The potential benefits of RT or CRT need to be balanced against the risk of increased bowel dysfunction when determining the appropriate treatment for individual patients with rectal cancer.

Currently, we are implementing a lasing without inversion (LWI) scheme in mercury based on calculations by Fry et al. [1]. A recent detailed analysis predicting exact experimental parameters shows the feasibility of our LWI scheme [2]. In this paper we report on the progress of our experiment and compare its parameters with the prior analysis.

This paper explores passive switched capacitorbased RF receiver front ends for spectrum sensing. Widebandspectrum sensors remain the most challenging block in the softwaredefined radio hardware design. The use of passive switchedcapacitors provides a very low power signal conditioning front endthat enables parallel digitization and software control andcognitive capabilities in the digital domain. In this paper, existingarchitectures are reviewed followed by a discussion of high speedpassive switched capacitor designs. A passive analog FFT front enddesign is presented as an example analog conditioning circuit. Design methodology, modeling, and optimization techniques areoutlined. Measurements are presented demonstrating a 5 GHzbroadband front end that consumes only 4 mW power.

Vibrating conveyors also named bowl feeders are a common equipment for conveying goods into production systems. These systems are used for the supplying of a certain number of goods to an individual designed interface and simultaneously arranging a correct orientation of the goods conveyed by the same time. This type of conveyor is used in various industries, such as for example automotive industry, electronic industry and medical industry. The target of this article is to determine a dynamic model and mechanical parameters by means of testing, and a numerical simulation of a ready-to-operate conveyor under standard working conditions.

This thesis discusses the limitations of wideband software defined radios (SDR). Spectrum sensing is identified as an important aspect required of SDR based cognitive radios. Several architectures and implementations are reviewed. An RF sampler followed by analog signal processing is identified as a critical block enabling low-power wideband digitization. Passive switched-capacitor charge-domain processing is introduced. Its implementation simplicity and lack of active power consumption are enticing. The effect of kT/C noise is analyzed in detail. Linear and nonlinear computation errors are analyzed and modeled, and circuit techniques for their reduction are developed. Simulations are used to optimize power and computational dynamic range. For spectrum sensing, the design of CRAFT (Charge Re-use Analog Fourier Transform): an RF front-end channelizer for wideband software defined radios based on a 16-point analog-domain FFT is described. The design relies on charge re-use to process a 5GS/s input with an average output SNDR of 47dB, and consumes only 12.2pJ/FFT conversion (3.8mW). These numbers represent orders of magnitude improvement on the work reported previously in literature. The thesis also discusses the system-level modeling and mitigation of circuit non-idealities in CRAFT. These design principles enable this implementation to achieve a large dynamic range even at high speeds. Additionally, these techniques can be easily extended to improve the performance of other passive switched-capacitor designs.

Doppler-free three-photon coherence effects at a wavelength of 253.7 nm have been observed in thermal mercury vapor. The experimental results are compared to simulations based on a detailed theoretical model reproducing the measured effects. Based on these results, we show by simulations that amplification without inversion in our setup is feasible, paving the way towards lasing without inversion in mercury.

We theoretically analyze a scheme for a fast adiabatic transfer of cold atoms from the atomic limit of isolated traps to a Mott-insulator close to the superfluid phase. This gives access to the Bose-Hubbard physics without the need of a prior Bose-Einstein condensate. The initial state can be prepared by combining the deterministic assembly of atomic arrays with resolved Raman sideband cooling. In the subsequent transfer the trap depth is reduced significantly. We derive conditions for the adiabaticity of this process and calculate optimal adiabatic ramp shapes. Using available experimental parameters, we estimate the impact of heating due to photon scattering and compute the fidelity of the transfer scheme. Finally, we discuss the particle number scaling behavior of the method for preparing low-entropy states. Our findings demonstrate the feasibility of the proposed scheme with state-of-the-art technology.

We present a novel platform for the bottom-up construction of itinerant many-body systems: ultracold atoms transferred from a Bose-Einstein condensate into freely configurable arrays of micro-lens generated focused-beam dipole traps. This complements traditional optical lattices and gives a new quality to the field of two-dimensional quantum simulators. The ultimate control of topology, well depth, atom number, and interaction strength is matched by sufficient tunneling. We characterize the required light fields, derive the Bose-Hubbard parameters for several alkali species, investigate the loading procedures and heating mechanisms. To demonstrate the potential of this approach, we analyze coupled annular Josephson contacts exhibiting many-body resonances.

We investigate the feasibility of UV lasing without inversion at a wavelength of \\(253.7\\) nm utilizing interacting dark resonances in mercury vapor. Our theoretical analysis starts with radiation damped optical Bloch equations for all relevant 13 atomic levels. These master equations are generalized by considering technical phase noise of the driving lasers. From the Doppler broadened complex susceptibility we obtain the stationary output power from semiclassical laser theory. The finite overlap of the driving Gaussian laser beams defines an ellipsoidal inhomogeneous gain distribution. Therefore, we evaluate the intra-cavity field inside a ring laser self-consistently with Fourier optics. This analysis confirms the feasibility of UV lasing and reveals its dependence on experimental parameters.