REM: Resource-Efficient Mining for Blockchains

Blockchains show promise as potential infrastructure for financial transaction systems. The security of blockchains today, however, relies critically on Proof-of-Work (PoW), which forces participants to waste computational resources. We present REM (Resource-Efficient Mining), a new blockchain mining framework that uses trusted hardware (Intel SGX). REM achieves security guarantees similar to PoW, but leverages the partially decentralized trust model inherent in SGX to achieve a fraction of the waste of PoW. Its key idea, Proof-of-Useful-Work (PoUW), involves miners providing trustworthy reporting on CPU cycles they devote to inherently useful workloads. REM flexibly allows any entity to create a useful workload. REM ensures the trustworthiness of these workloads by means of a novel scheme of hierarchical attestations that may be of independent interest. To address the risk of compromised SGX CPUs, we develop a statistics-based formal security framework, also relevant to other trusted-hardware-based approaches such as Intel\u27s Proof of Elapsed Time (PoET). We show through economic analysis that REM achieves less waste than PoET and variant schemes. We implement REM and, as an example application, swap it into the consensus layer of Bitcoin core. The result is the first full implementation of an SGX-based blockchain. We experiment with four example applications as useful workloads for our implementation of REM, and report a computational overhead of $5-15\%$

Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins

DNA methylation [5-methylcytosine (5mC)] is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the action of DNA methyltransferases, which deposit 5mC, and ten-eleven translocation (TET) enzymes, which participate in its active removal through the formation of 5-hydroxymethylcytosine (5hmC). TET enzymes are essential for mammalian gastrulation and activation of vertebrate developmental enhancers; however, to date, a clear picture of 5hmC function, abundance, and genomic distribution in nonvertebrate lineages is lacking. By using base-resolution 5mC and 5hmC quantification during sea urchin and lancelet embryogenesis, we shed light on the roles of nonvertebrate 5hmC and TET enzymes. We find that these invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes and show that the complement of identified 5hmC-regulated genes is conserved to vertebrates. This work demonstrates that active 5mC removal from regulatory regions is a common feature of deuterostome embryogenesis suggestive of an unexpected deep conservation of a major gene-regulatory module

Plant Products Affect Growth and Digestive Efficiency of Cultured Florida Pompano (Trachinotus carolinus) Fed Compounded Diets

Costs of compounded diets containing fish meal as a primary protein source can be expected to rise as fish meal prices increase in response to static supply and growing demand. Alternatives to fish meal are needed to reduce production costs in many aquaculture enterprises. Some plant proteins are potential replacements for fish meal because of their amino acid composition, lower cost and wide availability. In this study, we measured utilization of soybean meal (SBM) and soy protein concentrate (SPC) by Florida pompano fed compounded diets, to determine the efficacy of these products as fish meal replacements. We also calculated apparent digestibility coefficients (ADCs) for canola meal (CM), corn gluten meal (CGM), and distillers dried grains with solubles (DDGS), following typical methods for digestibility trials. Juvenile Florida pompano were fed fish-meal-free diets containing graded levels of SBM and SPC, and weight gain was compared to a control diet that contained SBM, SPC, and fish meal. Fish fed diets that contained 25–30 percent SBM in combination with 43–39 percent SPC had weight gain equivalent to fish fed the control diet with fish meal, while weight gain of fish fed other soy combinations was significantly less than that of the control group. Apparent crude protein digestibility of CGM was significantly higher than that of DDGS but not significantly different from CM. Apparent energy digestibility of DDGS was significantly lower than CGM but significantly higher than CM. Findings suggested that composition of the reference diet used in a digestibility trial affects the values of calculated ADCs, in addition to the chemical and physical attributes of the test ingredient

Scaling Searchable and Transactional Storage Systems

Data is the lifeblood of modern computing and the systems that store it have taken a prominent place in the infrastructure of practically every modern startup, business, or research application. Not-so-recent trends in distributed storage systems have removed features---such as secondary attribute search or transactions---that applications used to take for granted. These missing features must be reimplemented at the application level, or the application must be carefully constructed to work around their absence. This thesis explores work on four systems that represent advances in reversing this trend. First, it looks at HyperDex, a system which provides efficient secondary attribute search. Second, it presents two transactional storage systems, Warp and Consus. Warp targets a single data center environment while Consus targets a geo-replicated deployment and the differences in their design reflect these two considerations. Finally, this thesis presents the Warp Transactional Filesystem that shows a positive example of how the transactional properties of Warp can be extended to provide application-level transactional guarantees. Finally, the thesis looks at the broader impact of these systems and how the evolution of the systems could be used to inform the development of future distributed systems