MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license

Fractionally-addressed delay lines

While traditional implementations of variable-length digital delay lines are based on a circular buffer accessed by two pointers, we propose an implementation where a single fractional pointer is used both for read and write operations. On modern general-purpose architectures, the proposed method is nearly as efficient as the popularinterpolated circular buffer, and it behaves well for delay-length modulations commonly found in digital audio effects. The physical interpretation of the new implementation shows that it is suitable for simulating tension or density modulations in wave-propagating media.Comment: 11 pages, 19 figures, to be published in IEEE Transactions on Speech and Audio Processing Corrected ACM-clas

Agile low phase noise radio-frequency sine wave generator applied to experiments on ultracold atoms

We report on the frequency performance of a low cost (~500$) radio-frequency sine wave generator, using direct digital synthesis (DDS) and a field-programmable gate array (FPGA). The output frequency of the device may be changed dynamically to any arbitrary value ranging from DC to 10 MHz without any phase slip. Sampling effects are substantially reduced by a high sample rate, up to 1 MHz, and by a large memory length, more than 2.10^5 samples. By using a low noise external oscillator to clock the DDS, we demonstrate a phase noise as low as that of the master clock, that is at the level of -113 dB.rad^2/Hz at 1 Hz from the carrier for an output frequency of 3.75 MHz. The device is successfully used to confine an ultracold atomic cloud of rubidium 87 in a RF-based trap, and there is no extra heating from the RF source.Comment: 10 pages, 6 figure

RF applications in digital signal processing

Ever higher demands for stability, accuracy, reproducibility, and monitoring capability are being placed on Low-Level Radio Frequency (LLRF) systems of particle accelerators. Meanwhile, continuing rapid advances in digital signal processing technology are being exploited to meet these demands, thus leading to development of digital LLRF systems. The rst part of this course will begin by focusing on some of the important building-blocks of RF signal processing including mixer theory and down-conversion, I/Q (amplitude and phase) detection, digital down-conversion (DDC) and decimation, concluding with a survey of I/Q modulators. The second part of the course will introduce basic concepts of feedback systems, including examples of digital cavity eld and phase control, followed by radial loop architectures. Adaptive feed-forward systems used for the suppression of repetitive beam disturbances will be examined. Finally, applications and principles of system identi cation approaches will be summarized