Sequencing technologies using nucleotide conversion techniques such as cytosine to thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted sequences and consolidating alignment of these technologies in one package. In this paper, we describe hierarchical indexing for spliced alignment of transcripts–3 nucleotides (HISAT-3N), which can rapidly and accurately align sequences consisting of any nucleotide conversion by leveraging the powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Tests on real and simulated data sets show that HISAT-3N is faster than other modern systems, with greater alignment accuracy, higher scalability, and smaller memory requirements. HISAT-3N therefore becomes an ideal aligner when used with converted sequence technologies.

Abstract. We present an empirical investigation into the prevalence and impact of distributed denial-of-service (DDoS) attacks on operators in the Bitcoin economy. To that end, we gather and analyze posts mentioning "DDoS" on the popular Bitcoin forum bitcointalk.org. Starting from around 3 000 different posts made between May 2011 and October 2013, we document 142 unique DDoS attacks on 40 Bitcoin services. We find that 7% of all known operators have been attacked, but that currency exchanges, mining pools, gambling operators, eWallets, and financial services are much more likely to be attacked than other services. Not coincidentally, we find currency exchanges and mining pools are much more likely to have DDoS protection such as CloudFlare, Incapsula, or Amazon Cloud. We show that those services that have been attacked are more than three times as likely to buy anti-DDoS services than operators who have not been attacked. We find that big mining pools (those with historical hashrate shares of at least 5%) are much more likely to be DDoSed than small pools. We investigate Mt. Gox as a case study for DDoS attacks on currency exchanges and find a disproportionate amount of DDoS reports made during the large spike in trading volume and exchange rates in spring 2013. We conclude by outlining future opportunities for researching DDoS attacks on Bitcoin.

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IEEE P1687 is a valuable tool for accessing on-chip instruments during test, diagnosis, debug, and board configuration. However, most of these instruments should not be available to an end user in the field. We propose a method for hiding instruments in a P1687 network that utilizes a "locking" segment insertion bit (LSIB) that can only be opened when pre-defined values, corresponding to a key, are present in particular bits in the chain. We also introduce "trap" bits, which can further reduce the effectiveness of brute force attacks by permanently locking an LSIB when an incorrect value is written to the trap's update register. Only a global reset will allow the LSIB to become operable again. In this paper, we investigate the cost and effectiveness of LSIBs and traps in several different configurations and show that these relatively small modifications to the P1687 network can make undocumented instrument access exceedingly difficult.

The minimization of power consumption is an important design constraint for circuits used in portable devices. The switching activity of a circuit node in a CMOS digital circuit directly contributes to overall power dissipation. By approximating the switching activity of circuit nodes as internal switching probabilities in Binary Decision Diagrams (BDDs), it is possible to estimate the dynamic power dissipation characteristic of circuits resulting from a structural mapping of a BDD. A technique for minimizing the overall sum of switching probabilities is presented. The method is based on efficient local operations on a BDD representing the functionality of the circuit to be realized. The resulting circuit that is obtained by mapping the BDD to CMOS Pass Transistors has in simulation (using a commercially available process model) shown reduced power dissipation characteristic. Experimental results on a set of MCNC benchmarks are given for this technique.