Streaming interactive proofs

An interactive proof is a conversation between a powerful machine, the ‘prover’, and a ‘verifier’ with low resources. The aim of the conversation is for the prover to convince the verifier about the output of a function (that is computationally or space intensive to evaluate) over some shared data set. The concept of streaming interactive proofs (SIPs) considers a verifier with very small space, who streams the shared data, and then engages in an interactive protocol with the prover. Our work begins by looking to improve protocols for the practical verification of outsourced data analysis. We explore non-interactive and multi-round protocols for vector and matrix multiplications and analyse the real-world practicality of these approaches. We demonstrate how these protocols can be used in data analysis, considering the numerical concerns when rounding is required. We investigate the costs for the verifier, while trying to keep the overheads for the prover at a minimum, and discuss bottlenecks. Finally, we introduce the entirely new concept of Streaming Zero Knowledge for interactive proofs, which is the adaptation of regular SIPs where now the verifier learns no additional information about the data set besides the truth of the statement the prover is trying to prove. We show several examples and build up a powerful multipurpose protocol in order to showcase the strengths of this new model

Multivariate Genomic Selection and Potential of Rapid Indirect Selection with Speed Breeding in Spring Wheat

Genomic selection (GS) can be effective in breeding for quantitative traits, such as yield, by reducing the selection cycle duration. Speed breeding (SB) uses extended photoperiod and temperature control to enable rapid generation advancement. Together, GS and SB can synergistically reduce the breeding cycle by quickly producing recombinant inbred lines (RILs) and enabling indirect phenotypic selection to improve for key traits, such as height and flowering time, prior to field trials. In addition, traits measured under SB (SB traits) correlated with field-based yield could improve yield prediction in multivariate GS. A 193-line spring wheat (Triticum aestivum L.) training population (TP), tested for grain yield in the field in multiple environments, was used to predict grain yield of a 350-line selection candidate (SC) population, across multiple environments. Four SB traits measured on the TP and SC populations were used to derive principal components, which were incorporated into multivariate GS models. Predictive ability was significantly increased by multivariate GS, in some cases being twice as high as univariate GS. Based on these results, an efficient breeding strategy is proposed combining SB and multivariate GS using yield-correlated SB traits for yield prediction. The potential for early indirect SB phenotypic selection for targeted population improvement prior to trials was also investigated. Plant height and flowering time showed strong relative predicted efficiency to indirect selection, in some cases as high as direct field selection. The higher selection intensity and rate of generation turnover under SB may enable a greater rate of genetic gain than direct field phenotyping

Diffusive and ballistic current spin-polarization in magnetron-sputtered L1o-ordered epitaxial FePt

We report on the structural, magnetic, and electron transport properties of a L1o-ordered epitaxial iron-platinum alloy layer fabricated by magnetron-sputtering on a MgO(001) substrate. The film studied displayed a long range chemical order parameter of S~0.90, and hence has a very strong perpendicular magnetic anisotropy. In the diffusive electron transport regime, for temperatures ranging from 2 K to 258 K, we found hysteresis in the magnetoresistance mainly due to electron scattering from magnetic domain walls. At 2 K, we observed an overall domain wall magnetoresistance of about 0.5 %. By evaluating the spin current asymmetry alpha = sigma_up / sigma_down, we were able to estimate the diffusive spin current polarization. At all temperatures ranging from 2 K to 258 K, we found a diffusive spin current polarization of > 80%. To study the ballistic transport regime, we have performed point-contact Andreev-reflection measurements at 4.2 K. We obtained a value for the ballistic current spin polarization of ~42% (which compares very well with that of a polycrystalline thin film of elemental Fe). We attribute the discrepancy to a difference in the characteristic scattering times for oppositely spin-polarized electrons, such scattering times influencing the diffusive but not the ballistic current spin polarization.Comment: 22 pages, 13 figure

Categorizing the severity of paralytic shellfish poisoning outbreaks in the Gulf of Maine for forecasting and management

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 277-287, doi:10.1016/j.dsr2.2013.03.027.Development of forecasting systems for harmful algal blooms (HABs) has been a long-standing research and management goal. Significant progress has been made in the Gulf of Maine, where seasonal bloom forecasts are now being issued annually using Alexandrium fundyense cyst abundance maps and a population dynamics model developed for that organism. Thus far these forecasts have used terms such as “significant”, “moderately large” or “moderate” to convey the extent of forecasted paralytic shellfish poisoning (PSP) outbreaks. In this study, historical shellfish harvesting closure data along the coast of the Gulf of Maine were used to derive a series of bloom severity levels that are analogous to those used to define major storms like hurricanes or tornados. Thirty-four years of PSP-related shellfish closure data for Maine, Massachusetts and New Hampshire were collected and mapped to depict the extent of coastline closure in each year. Due to fractal considerations, different methods were explored for measuring length of coastline closed. Ultimately, a simple procedure was developed using arbitrary straight-line segments to represent specific sections of the coastline. This method was consistently applied to each year’s PSP toxicity closure map to calculate the total length of coastline closed. Maps were then clustered together statistically to yield distinct groups of years with similar characteristics. A series of categories or levels was defined (“Level 1: Limited”, “Level 2: Moderate”, and “Level 3: Extensive”) each with an associated range of expected coastline closed, which can now be used instead of vague descriptors in future forecasts. This will provide scientifically consistent and simply defined information to the public as well as resource managers who make decisions on the basis of the forecasts.Research support provided through the Woods Hole Center for Oceans and Human Health, National Science Foundation (NSF) Grants OCE-0430724, and OCE-0911031; and National Institute of Environmental Health Sciences (NIEHS) Grant 1-P50-ES012742-01, the ECOHAB Grant program through NOAA Grant NA06NOS4780245, and the PCM HAB Grant program through NOAA Grant NA11NOS4780023

Speed breeding for multiple quantitative traits in durum wheat

Plant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named 'speed breeding' was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F2 population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F3 progeny derived from 100 'selected' and 100 'unselected' F2 individuals.Transgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F2 population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between 'selected' and 'unselected' F3 families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed.The novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.Samir Alahmad, Eric Dinglasan, Kung Ming Leung, Adnan Riaz, Nora Derbal, Kai P. Voss-Fels, Jason A. Able, Filippo M. Bassi, Jack Christopher and Lee T. Hicke

Understanding the errors of SHAPE-directed RNA structure modeling

Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in modeling the helices of RNA secondary structure. Here, we benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs gave an overall false negative rate (FNR) of 17% and a false discovery rate (FDR) of 21%, with at least one helix prediction error in five of the six cases. Extensive variations of data processing, normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual structure modeling errors are explained by the insufficient information content of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping analysis. Beyond these benchmark cases, bootstrapping suggests a low level of confidence (<50%) in the majority of helices in a previously proposed SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011

Gene expression profiling of epithelium-associated FcRL4(+) B cells in primary Sjogren's syndrome reveals a pathogenic signature

In primary Sjögren's syndrome (pSS), FcRL4+ B cells are present in inflamed salivary gland tissue, within or in close proximity to ductal epithelium. FcRL4 is also expressed by nearly all pSS-related mucosa-associated lymphoid tissue (MALT) B cell lymphomas, linking FcRL4 expression to lymphomagenesis. Whether glandular FcRL4+ B cells are pathogenic, how these cells originate, and how they functionally differ from FcRL4- B cells in pSS is unclear. This study aimed to investigate the phenotype and function of FcRL4+ B cells in the periphery and parotid gland tissue of patients with pSS. First, circulating FcRL4+ B cells from 44 pSS and 54 non-SS-sicca patients were analyzed by flow cytometry. Additionally, RNA sequencing of FcRL4+ B cells sorted from parotid gland cell suspensions of 6 pSS patients was performed. B cells were sorted from cell suspensions as mini bulk (5 cells/well) based on the following definitions: CD19+CD27-FcRL4- ('naive'), CD19+CD27+FcRL4- ('memory'), and CD19+FcRL4+ B cells. We found that, although FcRL4+ B cells were not enriched in blood in pSS compared with non-SS sicca patients, these cells generally exhibited a pro-inflammatory phenotype. Genes coding for CD11c (ITGAX), T-bet (TBX21), TACI (TNFRSF13B), Src tyrosine kinases and NF-κB pathway-related genes were, among others, significantly upregulated in glandular FcRL4+ B cells versus FcRL4- B cells. Pathway analysis showed upregulation of B cell activation, cell cycle and metabolic pathways. Thus, FcRL4+ B cells in pSS exhibit many characteristics of chronically activated, pro-inflammatory B cells and their gene expression profile suggests increased risk of lymphomagenesis. We postulate that these cells contribute significantly to the epithelial damage seen in the glandular tissue and that FcRL4+ B cells are an important treatment target in pSS

The Large Zinc Finger Protein ZAS3 Is a Critical Modulator of Osteoclastogenesis

Mice deficient in the large zinc finger protein, ZAS3, show postnatal increase in bone mass suggesting that ZAS3 is critical in the regulation of bone homeostasis. Although ZAS3 has been shown to inhibit osteoblast differentiation, its role on osteoclastogenesis has not been determined. In this report we demonstrated the role of ZAS3 in bone resorption by examining the signaling mechanisms involved in osteoclastogenesis.Comparison of adult wild-type and ZAS3 knockout (ZAS3-/-) mice showed that ZAS3 deficiency led to thicker bones that are more resistant to mechanical fracture. Additionally, ZAS3-/- bones showed fewer osteoclasts and inefficient M-CSF/sRANKL-mediated osteoclastogenesis ex vivo. Utilizing RAW 264.7 pre-osteoclasts, we demonstrated that overexpression of ZAS3 promoted osteoclastogenesis and the expression of crucial osteoclastic molecules, including phospho-p38, c-Jun, NFATc1, TRAP and CTSK. Contrarily, ZAS3 silencing by siRNA inhibited osteoclastogenesis. Co-immunoprecipitation experiments demonstrated that ZAS3 associated with TRAF6, the major receptor associated molecule in RANK signaling. Furthermore, EMSA suggested that nuclear ZAS3 could regulate transcription by binding to gene regulatory elements.Collectively, the data suggested a novel role of ZAS3 as a positive regulator of osteoclast differentiation. ZAS3 deficiency caused increased bone mass, at least in part due to decreased osteoclast formation and bone resorption. These functions of ZAS3 were mediated via activation of multiple intracellular targets. In the cytoplasmic compartment, ZAS3 associated with TRAF6 to control NF-kB and MAP kinase signaling cascades. Nuclear ZAS3 acted as a transcriptional regulator for osteoclast-associated genes. Additionally, ZAS3 activated NFATc1 required for the integration of RANK signaling in the terminal differentiation of osteoclasts. Thus, ZAS3 was a crucial molecule in osteoclast differentiation, which might potentially serve as a target in the design of therapeutic interventions for the treatment of bone diseases related to increased osteoclast activity such as postmenopausal osteoporosis, Paget's disease, and rheumatoid arthritis