Mutually Uncorrelated Primers for DNA-Based Data Storage

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized and cyclic codes.Comment: 14 pages, 3 figures, 1 Table. arXiv admin note: text overlap with arXiv:1601.0817

Fostering Sustainable Collaboration within Indigenous Communities through Community Based Participatory Research

Fostering Sustainable Collaboration within Indigenous Communities through Community Based Participatory Research It is essential to support Indigenous children’s well-being in culturally responsive ways. One important approach is to collaborate with members of the community who understand the strengths of their culture, values, and language to support their children, particularly in Montana, where the rates of Native American students attempting suicide were nearly double that of their White peers (Youth Risk Behavior Survey, 2019). In this paper, we introduce community based participatory research (CBPR) and its importance in Indigenous communities, particularly for research addressing children’s mental health. In CBPR, researchers actively engage with the community, as members provide guidance and knowledge towards a solution (Walters et al., 2008). Within indigenous communities, CBPR plays a fundamental role in cultural resurgence. Tribal nations utilize self-determination to combine Indigenous knowledge and ways of being with Western research (Atalay, 2012). CBPR connects research to community sustainability by focusing on collaboration, and developing partnerships that build sustainable community models for positive change, which can help decolonize research. In CBPR, researchers create meaningful relationships with members of the community, which allow them to build trust in order to foster the relationships important for social change (Tobias, et. al., 2013). Researchers must recognize that the process will be more interactive and prolonged, yet essential to effectively provide culturally responsive programs to support Indigenous youth. In order to partner with communities to address children’s mental health, researchers should: (1) recognize privilege and empathize with the community’s struggles, (2) respect the other view, (3) acknowledge community strengths, (4) allow both parties to share ideas openly, and (5) integrate traditional views (Walters, et. al., 2008). CBPR is beneficial for children’s mental health, as it bridges their culture to the research that affects their future

A review of Smart Contract Blockchain Based on Multi-Criteria Analysis: Challenges and Motivations

A smart contract is a digital program of transaction protocol (rules of contract) based on the consensus architecture of blockchain. Smart contracts with Blockchain are modern technologies that have gained enormous attention in scientific and practical applications. A smart contract is the central aspect of a blockchain that facilitates blockchain as a platform outside the cryptocurrency spectrum. The development of blockchain technology, with a focus on smart contracts, has advanced significantly in recent years. However research on the smart contract idea has weaknesses in the implementation sectors based on a decentralized network that shares an identical state. This paper extensively reviews smart contracts based on multi criteria analysis challenges and motivations. Therefore, implementing blockchain in multi-criteria research is required to increase the efficiency of interaction between users via supporting information exchange with high trust. Implementing blockchain in the multi-criteria analysis is necessary to increase the efficiency of interaction between users via supporting information exchange and with high confidence, detecting malfunctioning, helping users with performance issues, reaching a consensus, deploying distributed solutions and allocating plans, tasks and joint missions. The smart contract with decision-making performance, planning and execution improves the implementation based on efficiency, sustainability and management. Furthermore the uncertainty and supply chain performance lead to improved users confidence in offering new solutions in exchange for problems in smart contacts. Evaluation includes code analysis and performance while development performance can be under development.Comment: Revie

Secretion of Rhoptry and Dense Granule Effector Proteins by Nonreplicating Toxoplasma Gondii Uracil Auxotrophs Controls the Development of Antitumor Immunity

Nonreplicating type I uracil auxotrophic mutants of Toxoplasma gondii possess a potent ability to activate therapeutic immunity to established solid tumors by reversing immune suppression in the tumor microenvironment. Here we engineered targeted deletions of parasite secreted effector proteins using a genetically tractable Δku80 vaccine strain to show that the secretion of specific rhoptry (ROP) and dense granule (GRA) proteins by uracil auxotrophic mutants of T. gondii in conjunction with host cell invasion activates antitumor immunity through host responses involving CD8α+ dendritic cells, the IL-12/interferon-gamma (IFN-γ) TH1 axis, as well as CD4+ and CD8+ T cells. Deletion of parasitophorous vacuole membrane (PVM) associated proteins ROP5, ROP17, ROP18, ROP35 or ROP38, intravacuolar network associated dense granule proteins GRA2 or GRA12, and GRA24 which traffics past the PVM to the host cell nucleus severely abrogated the antitumor response. In contrast, deletion of other secreted effector molecules such as GRA15, GRA16, or ROP16 that manipulate host cell signaling and transcriptional pathways, or deletion of PVM associated ROP21 or GRA3 molecules did not affect the antitumor activity. Association of ROP18 with the PVM was found to be essential for the development of the antitumor responses. Surprisingly, the ROP18 kinase activity required for resistance to IFN-γ activated host innate immunity related GTPases and virulence was not essential for the antitumor response. These data show that PVM functions of parasite secreted effector molecules, including ROP18, manipulate host cell responses through ROP18 kinase virulence independent mechanisms to activate potent antitumor responses. Our results demonstrate that PVM associated rhoptry effector proteins secreted prior to host cell invasion and dense granule effector proteins localized to the intravacuolar network and host nucleus that are secreted after host cell invasion coordinately control the development of host immune responses that provide effective antitumor immunity against established ovarian cancer

Influence of Abiotic Drivers on 1-Year Seedling Survival of Six Mangrove Species in Southeast Asia

Establishment and survival of plant species in systems with dominant environmental drivers (i.e. factors that exert disproportionate control over species establishment and survival) is often thought to be dominated by one master variable. In forested wetlands such as mangroves, hydrology is typically considered the dominant limiting driver. At the same time, light is a major driver of plant community dynamics, with some of the best understood plant life-history tradeoffs related to fast growth under high-light conditions versus survival under low-light conditions. Yet light is given relatively limited consideration in mangrove research compared to other drivers. Understanding the relative importance of abiotic drivers for seedling survival is crucial for effective management and restoration of mangrove ecosystems. Despite increasing global efforts to plant mangrove propagules at elevations appropriate for the hydrologic conditions needed at early life history stages, restoration efforts report low survival of planted propagules. Although many studies have made considerable progress to characterize the abiotic limitations of mangrove propagule establishment, fewer studies have addressed multiple abiotic drivers that limit the survival of the established seedling stage. We characterized the light and inundation conditions of more than 900 naturally established mangrove seedlings and monitored the survival of more than 2,800 seedlings (including 16 species) located on a species-rich island in tropical Southeast Asia for 1 year. Our findings suggest that light has a stronger effect than hydrology on survival following seedling establishment. We provide a conceptual visualization of shifts in the drivers of mangrove survival/loss throughout ontogeny

Effects of Fat Source and Level on Growth Performance, Carcass Characteristics, Carcass Iodine Value and Economics of Finishing Pigs in a Commercial Environment

A total of 2,011 pigs (PIC 1050 × DNA 600; initially 62.4 ± 4.6 lb) were used in a 113-d finishing trial to evaluate the effects of two different fat sources fed at two different levels on growth performance, carcass characteristics, carcass iodine value, and economics of finishing pigs raised in a commercial environment. Pigs were randomly allotted to 1 of 5 dietary treatments with 21 to 27 pigs per pen and 16 pens per treatment. Dietary treatments were arranged in a 2 × 2 + 1 factorial with main effects of fat source and fat inclusion level. Dietary treatments included a control diet containing no added fat. The other 4 dietary treatments included two different fat sources, choice white grease or corn oil, included at either 1 or 3% of the diet. Experimental diets were fed based on a feed budget from d 0 to 113 in 6 phases. For overall growth performance, pigs fed increasing dietary fat from 0 to 3% had increased (linear, P \u3c 0.001) ADG and decreased (linear, P = 0.013) ADFI, which led to an improvement (linear, P \u3c 0.001) in F/G. There was no difference in growth performance between pigs fed choice white grease or corn oil. For carcass characteristics, increasing fat increased (linear, P ≤ 0.017) HCW, carcass yield, and backfat. For carcass fat iodine value, there was a fat source × level interaction (P \u3c 0.001) where iodine value increased linearly as corn oil increased in the diet with only a small increase in iodine value when diets with choice white grease were fed. For economics, increasing fat, regardless of fat source, increased feed cost (linear, P \u3c 0.001) and revenue (linear, P = 0.003). Increasing fat reduced (linear, P \u3c 0.001) IOFC in the high feed cost, low revenue scenario, and tended to increase (P = 0.060) IOFC in the low feed cost, high revenue scenario. In conclusion, increasing fat from 0 to 3% of the diet, regardless of fat source, increased overall ADG, reduced ADFI, and improved F/G. Increasing fat also increased HCW, carcass yield, and backfat, while pigs fed diets containing corn oil had higher carcass fat iodine values. When feed costs are high and revenue is low, the improvement in growth performance does not justify the extra diet cost from increasing added fat from 0 to 3% in the diet. However, adding fat in the diet is justifiable when feed costs are low and revenue is high, regardless of fat source used

Effects of Extruded-Expelled Soybean Meal and Benzoic Acid on Growth Performance, Carcass Characteristics, and Carcass Iodine Value of Finishing Pigs

A total of 2,162 pigs (PIC 1050 × DNA 600; initially 69.2 ± 4.9 lb) were used in a 109-d finishing trial to evaluate the effects of extruded-expelled soybean meal (EESBM) and benzoic acid on growth performance, carcass characteristics, and carcass iodine value. Pigs were randomly allotted to 1 of 4 treatments with 27 to 28 pigs per pen and 20 pens per treatment. Dietary treatments were arranged in a 2 × 2 factorial with main effects of soybean meal source and benzoic acid. Diets contained either conventional soybean meal (SBM) or extruded-expelled soybean meal (EESBM; Lester Feed and Grain, Lester, IA) with or without 0.25% VevoVitall (DSM Products; Parsippany, NJ), a source of benzoic acid. The EESBM was analyzed to be 43.2% CP and 7.73% fat (acid hydrolysis). Experimental diets were not balanced for energy, but rather formulated to the same SID Lys:ME ratio and fed based on a feed budget from d 0 to 109 in 6 phases. Overall (d 0 to 109), there were no interactions between soybean meal source and benzoic acid addition. There was a main effect of soybean meal source where pigs fed conventional SBM had greater (P = 0.01) ADFI compared to pigs fed EESBM without influencing ADG, resulting in improved (P \u3c 0.001) F/G. Also, pigs fed diets without benzoic acid had greater (P = 0.02) ADFI compared to pigs fed diets that contained benzoic acid without influencing ADG, resulting in pigs fed benzoic acid having improved (P = 0.01) F/G. When evaluating caloric efficiency, pigs fed diets containing benzoic acid had improved (P \u3c 0.001) caloric efficiency compared to pigs fed diets without benzoic acid, with soybean meal source not having any impact. For carcass characteristics, pigs fed EESBM had increased (P \u3c 0.001) carcass fat iodine value compared to pigs fed conventional SBM. For economics, there was a main effect of soybean meal source where pigs fed EESBM had a higher (P ≤ 0.002) feed cost per pig placed in the low and high feed cost scenarios. There were no differences in revenue per pig placed in the low or high revenue scenarios regardless of soybean meal source or the inclusion of benzoic acid. Pigs fed conventional SBM had a higher (P ≤ 0.02) income over feed cost (IOFC) compared to pigs fed EESBM in the high feed cost, high revenue; high feed cost, low revenue; and low feed cost, low revenue scenarios. In summary, replacing conventional SBM with EESBM improved feed efficiency, but due to increased feed cost without influencing gain, it was less economical as measured by IOFC. Also, the addition of benzoic acid improved feed efficiency but did not improve IOFC