Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways

Improved methods for engineering sequence-specific nucleases, including zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs), have made it possible to precisely modify plant genomes. However, the success of genome modification is largely dependent on the intrinsic activity of the engineered nucleases. In this study, we sought to enhance ZFN-mediated targeted mutagenesis and gene targeting (GT) in Arabidopsis by manipulating DNA repair pathways. Using a ZFN that creates a double-strand break (DSB) at the endogenous ADH1 locus, we analyzed repair outcomes in the absence of DNA repair proteins such as KU70 and LIG4 (both involved in classic nonhomologous end-joining, NHEJ) and SMC6B (involved in sister-chromatid-based homologous recombination, HR). We achieved a fivefold to 16-fold enhancement in HR-based GT in a ku70 mutant and a threefold to fourfold enhancement in GT in the lig4 mutant. Although the NHEJ mutagenesis frequency was not significantly changed in ku70 or lig4, DNA repair was shifted to microhomology-dependent alternative NHEJ. As a result, mutations in both ku70 and lig4 were predominantly large deletions, which facilitates easy screening for mutations by PCR. Interestingly, NHEJ mutagenesis and GT at the ADH1 locus were enhanced by sixfold to eightfold and threefold to fourfold, respectively, in a smc6b mutant. The increase in NHEJ-mediated mutagenesis by loss of SMC6B was further confirmed using ZFNs that target two other Arabidopsis genes, namely, TT4 and MPK8. Considering that components of DNA repair pathways are highly conserved across species, mutations in DNA repair genes likely provide a universal strategy for harnessing repair pathways to achieve desired targeted genome modifications.
ADAPT.DCU at TREC LiveQA: A Sentence Retrieval based Approach to Live Question Answering

Abstract : This paper describes the work done by ADAPT centre at Dublin City University towards automatically answering questions for the TREC LiveQA track. The system is based on a sentence retrieval approach. In particular, we first use the title of a new question as a query so as to retrieve a ranked list of conceptually similar questions from an index of previously asked on Yahoo! Answers. We then extract the best matching sentences from the answers of the retrieved questions. In order to construct the final answer, we combine these sentences with the best answer of the top ranked (most similar to the query) question. When no pre-existing questions with sufficient similarity with the new one can be retrieved from the index, we output an answer from a candidate set of pre-generated answers based on the domain of the question.
Performance Implications of Outsourcing in the Mobile Telecommunications Industry

We examine how outsourcing of a core service affects firm performance in the context of the mobile telephony industry. We develop hypotheses based on economies of scale, transaction costs, quality advantages from specialization, and bargaining power and test these using a ten-year panel with 50 mobile network operators outsourcing their network operations. We find that operators can decrease costs, increase revenues and improve their profitability in the long run by outsourcing mobile network operation services. This effect is stronger for small than for big operators.
Adaptive output feedback control for a class of nonlinear systems with full-state constraints

This paper studies an adaptive output-feedback control for a class of nonlinear single-input and single-output (SISO) systems with the full-state constraints. A state observer is designed to estimate those unmeasured states. At present, all the results in the output-feedback area ignore the effects of the full-state constraints. The presence of these constraints results in a complicated procedure and the major difficulties in the design. The barrier Lyapunov function (BLF) and a novel design procedure are given to overcome these difficulties. The adaptation law and the controllers are obtained based on the backstepping design procedure. In addition, only one adjustable parameter needs to be updated, and thus, the online computation burden is alleviated. The stability of the closed-loop system is proven by using the Lyapunov theorem. A simulation example is given to verify the effectiveness of the approach.
Realisierung und Optimierung der Informationsbeschaffung von Internet-Suchmaschinen am Beispiel von www.crawler.de

Information inside the world wide web represented by internet pages addressable via uniform resource locators is rapidly growing. For an efficient gathering of links or pages there is a strong demand for fast and complete internet search engines which are unfortunately restricted by their own capabilities and the net bandwidth as well as by administrative boundaries given for example by the robots exclusion agreement. Therefore it is necessary to implement new page gathering algorithms mostly based on empirical data given by a net analysis. This article presents the most recent state in optimizing the well known German internet search engine www.crawler. de by integrating the results of analyzing statistical data into its collection algorithm based on modification rates and directory depth of internet links.
Co-production : A fair-weather syndrome?

An emerging perspective in marketing considers customers as actively involved in the production, delivery and consumption of services. While different terms exist for this involvement - co-production, co-creation, prosumption - the underlying assumption is that customers are able and willing to be involved in the creation of value. In this paper, we build on Prahalad's five elements of co-production (customer engagement, self- services, customer involvement, problem solving and co- designing), we investigate the assumed positive associations between these five elements and value co-production and the positive association between value co- production and behavioral intension. In line with existing research, our findings establish that customer engagement, self-services, customer involvement and co- designing are positively associated with value co-production, but the proposed positive association between problem solving and value co-production could not be supported in size and significance. It means that customers do not want to co- produce in all but one of the elements; problem solving. In other words, dissatisfied customers do not want to be involved in helping the company to find a solution to their problem. This finding is robust among high and low experienced users; neither group wants to be involved in problem solving. From this finding, we conclude that co-production is a fair-weather syndrome, i.e. only when the service functions as expected are customers willing to co-produce. The paper offers three theoretical and managerial contributions. We document that co-production is a multifaceted construct, but not all elements contribute equally to value co-production. Self-service and co-designing contribute strongly, whereas customer engagement and customer involvement contribute incrementally to value co-production. Supplementary, we disclose that co-production is not symmetric but rather asymmetric, i.e. co-production takes place only when things go right. Finally, as a side effect we provide a valid measurement scale for co-production.
The Effect Of Cooperatives On Product Innovation In The Agri-Food System

This paper develops a game-theoretic model of heterogeneous consumers to analyze the effect of cooperative involvement on quality-enhancing product innovation activity, the pricing of food products, and the welfare of the groups involved in the context of a mixed duopoly where an openmembership consumer co-op competes with an IOF. Analytical results show that the involvement of the member welfare-maximizing co-op in R&D can be quality and welfare enhancing by increasing the arrival rate of product innovations and reducing the prices of food products. The effectiveness of the coop is shown to depend on the nature of product differentiation and the relative quality of its products, the degree of consumer heterogeneity, and the size of innovation costs.
Green Building and the Organization of Development

In this paper we investigate the organizational architecture of development firms. We use the special case of green building which we expect to raise both the uncertainty of direct development costs and payoffs as well as the bargaining costs of development to investigate if and how firms change their firm's structure or contracts to accommodate green building. Previous empirical and theoretical work on the homebuilding industry tends to focus on the size of firms (for example, Somerville 1999; Helsely and Strange 1997). Our focus is more closely related to Eccles (1981) who argues that general contractors and their subcontractors constitute a quasifirms that are not quite fully integrated nor completely market based. We build a model development firm contracting. The model allows us to estimate comparative statics results related to changes in development cost uncertainty and in bargaining costs. We then use evidence from a new survey conducted in the first quarter of 2010 to investigate the predictions of our model. The survey was sent to developers likely to engage in green building, and we obtained 102 useable responses, a 10% response rate. Survey questions focus on firm experience with their first and subsequent green projects. The respondents are mostly privately-held firms well-distributed across the U.S. and engaged in the development of single family, multifamily, office, retail and industrial real estate.
Antinociceptive effects of botulinum toxin type-A in pain and headaches treatment

Summary Since its development for clinical use in 1980s botulinum toxin, the most potent biological toxin known to man has become a useful drug in various field of medicine. It was initially used to treat neurological disorders characterized by excessive muscle contractions. Since many patients report alleviation of pain before the muscle relaxing effect of botulinum toxin type-A has started, a direct analgesic action of Botulinum toxin has been discussed. There have been a number of recent investigations concerning the efficacy of botulinum toxin type-A applications for treatment of headache and chronic pain. Most of the known effect of botulinum toxin has been attributed to its ability to inhibit the release of acetylcholine from cholinergic nerve terminal. However, this effect alone does not explain the apparent antinociceptive effect of botulinum toxin. Other peripheral and central neurogenic effect should be considered. Current data suggest that Botulinum toxin is safe and effective in headache and pain treatment if used in specialist centres by experienced doctors.
A taxonomy of open government data research areas and topics

ABSTRACT The opening of government data, in order to have both social and economic value generated from them, has attracted the attention and interest of both researchers and practitioners from various disciplines, such as information systems, management sciences, political and social sciences, and law. Despite the rapid growth of this multidisciplinary research domain, which has led to the emergence and continuous evolution of technologies and management approaches for open government data (OGD), a detailed analysis of the specific areas and topics of this research is still missing. In this article, a detailed taxonomy of research areas and corresponding research topics of the OGD domain is presented: it includes four main research areas (ODG management and policies, infrastructures, interoperability and usage and value), which are further analyzed into 35 research topics. An important advantage of this taxonomy, beyond its high level of detail, is that it has been developed through extraction and a combination of relevant knowledge from three different sources: important relevant government policy documents, research literature, and experts. For each of the 35 research topics we have identified, its research literature is summarized and main research objectives and directions are highlighted. Based on the taxonomy, an extension of the extant OGD lifecycle is advanced; also, under-researched topics that require further research are identified.
Attitudes of non‐African American focus group participants toward return of results from exome and whole genome sequencing

Exome sequencing and whole genome sequencing (ES/WGS) present individuals with the opportunity to benefit from a broad scope of genetic results of clinical and personal utility. Yet, it is unclear which genetic results people want to receive (i.e., what type of genetic information they want to learn about themselves) or conversely not receive, and how they want to receive or manage results over time. Very little is known about whether and how attitudes toward receiving individual results from ES/WGS vary among racial/ethnic populations. We conducted 13 focus groups with a racially and ethnically diverse parent population (n = 76) to investigate attitudes toward return of individual results from WGS. We report on our findings for non‐African American (non‐AA) participants. Non‐AA participants were primarily interested in genetic results on which they could act or “do something about. ” They defined “actionability” broadly to include individual medical treatment and disease prevention. The ability to plan for the future was both a motivation for and an expected benefit of receiving results. Their concerns focused on the meaning of results, specifically the potential inaccuracy and uncertainty of results. Non‐AA participants expected healthcare providers to be involved in results management by helping them interpret results in the context of their own health and by providing counseling support. We compare and contrast these themes with those we previously reported from our analysis of African American (AA) perspectives to highlight the importance of varying preferences for results, characterize the central role of temporal orientation in framing expectations about the possibility of receiving ES/WGS results, and identify potential avenues by which genomic healthcare disparities may be inadvertently perpetuated. © 2014 Wiley Periodicals, Inc.
A Secure Signature Scheme with Tight Reduction to the RSA Assumption from Indistinguishability Obfuscation

We propose a new signature scheme employing an indistinguishabi obfuscator in the standard model. Our goal is to build a signature scheme that is more tightly reducible to the RSA assumption than previously reported. A key technique to achieve this property is that we adopt a probabilistic construction in a signing algorithm with a (punctured) pseudorandom function instead of deterministic one in the previous scheme. Since a signing oracle in the security proof can choose randomness for punctured points, the proposed scheme is optimally reducible to the RSA assumption.
IFN-γ stimulates osteoclast formation and bone loss in vivo via antigen-driven T cell activation

T cell–produced cytokines play a pivotal role in the bone loss caused by inflammation, infection, and estrogen deficiency. IFN-γ is a major product of activated T helper cells that can function as a pro- or antiresorptive cytokine, but the reason why IFN-γ has variable effects in bone is unknown. Here we show that IFN-γ blunts osteoclast formation through direct targeting of osteoclast precursors but indirectly stimulates osteoclast formation and promotes bone resorption by stimulating antigen-dependent T cell activation and T cell secretion of the osteoclastogenic factors RANKL and TNF-α. Analysis of the in vivo effects of IFN-γ in 3 mouse models of bone loss — ovariectomy, LPS injection, and inflammation via silencing of TGF-β signaling in T cells — reveals that the net effect of IFN-γ in these conditions is that of stimulating bone resorption and bone loss. In summary, IFN-γ has both direct anti-osteoclastogenic and indirect pro-osteoclastogenic properties in vivo. Under conditions of estrogen deficiency, infection, and inflammation, the net balance of these 2 opposing forces is biased toward bone resorption. Inhibition of IFN-γ signaling may thus represent a novel strategy to simultaneously reduce inflammation and bone loss in common forms of osteoporosis.
ADVANCING DEER REPELLENT PERFORMANCE: FINE-TUNING HINDER APPLICATIONS AND POTENTIAL USES FOR INSECTICIDAL SOAPS

Deer feed on buds, shoots, leaves and fruit (Scott and Townsend 1985), and cause substantial economic losses for many apple producers (Purdy et al. 1987). A variety of mitigation techniques are used to control such damage including deer population reduction via hunting, exclusion fencing and scare devices . However , most commercial apple producers rely on home-made or commercial repellents to control deer damage (Purdy et al. 1987) . Despite their popularity , repellents have often provided only limited or highly-variable control (Conover 1984, 1987 , Hygnstrom and Craven 1988) . There is considerable need to improve the performance of existing repellents, or to identify new materials which are effective at preventing damage.
Real-time Assistive , Adaptive and Intelligent Mobile Robotic Control for the Powered Wheelchair

Michael Gillham, MSc, Gareth Howells, PhD, Sarah Spurgeon, Prof University of Kent Canterbury Kent, UK. ABSTRACT The SYSIASS project is an Interreg IV A 2 Mers Seas Zeeën Crossborder Cooperation which aims to address the uptake of new technological advances within the healthcare professions. One aim is to develop an intelligent system for assisted navigation and control of powered wheelchairs. Autonomous indoor robotics requires accurate knowledge, tracking of objects, and self-localisation within that operating environment. While these autonomous robotic systems are suitable for workshop or factory, when human interaction becomes part of that system, it is necessary to adapt that system to allow for the additional requirements of the human passenger, both in terms of comfort of motion and additional user interaction governing the behaviour of the system.
3D implemented SRAM/DRAM hybrid cache architecture for high-performance and low power consumption

This paper introduces our research status focusing on 3D-implemented microprocessors. 3D-IC is one of the most interesting techniques to achieve high-performance, low-power VLSI systems. Stacking multiple dies makes it possible to implement microprocessor cores and large caches (or DRAM) into the same chip. Although this kind of integration has a great potential to bring a breakthrough in computer systems, its efficiency strongly depends on the characteristics of target application programs. Unfortunately, applying die stacking implementation causes performance degradation for some programs. To tackle this issue, we introduce a novel cache architecture consisting of a small but fast SRAM and a stacked large DRAM. The cache attempts to adapt to varying behavior of application programs in order to compensate for the negative impact of the die stacking approach.
Highly diverse and antimicrobial susceptible Escherichia coli display a naïve bacterial population in fruit bats from the Republic of Congo

Bats are suspected to be a reservoir of several bacterial and viral pathogens relevant to animal and human health, but studies on Escherichia coli in these animals are sparse. We investigated the presence of E. coli in tissue samples (liver, lung and intestines) collected from 50 fruit bats of five different species (Eidolon helvum, Epomops franqueti, Hypsignathus monstrosus, Myonycteris torquata, Rousettus aegyptiacus) of two different areas in the Republic of Congo between 2009 and 2010. To assess E. coli pathotypes and phylogenetic relationships, we determined the presence of 59 virulence associated genes and multilocus sequence types (STs). Isolates were further tested for their susceptibility to several antimicrobial substances by agar disk diffusion test and for the presence of an Extended-Spectrum Beta-Lactamase phenotype. E. coli was detected in 60% of the bats analysed. The diversity of E. coli strains was very high, with 37 different STs within 40 isolates. Occasionally, we detected sequence types (e.g. ST69, ST127, and ST131) and pathotypes (e.g. ExPEC, EPEC and atypical EPEC), which are known pathogens in human and/or animal infections. Although the majority of strains were assigned to phylogenetic group B2 (46.2%), which is linked with the ExPEC pathovar, occurrence of virulence-associated genes in these strains were unexpectedly low. Due to this, and as only few of the E. coli isolates showed intermediate resistance to certain antimicrobial substances, we assume a rather naïve E. coli population, lacking contact to humans or domestic animals. Future studies featuring in depth comparative whole genome sequence analyses will provide insights into the microevolution of this interesting strain collection.
Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization

Chloroplast DNA variation in the Arctic plant species Dryas integrifolia (Rosaceae) was analysed in relation to both the present‐day geographical distribution of populations and to Pleistocene fossil records of this species. The phylogeographical structure was weak but the analysis of haplotype diversity revealed several groups of haplotypes having present‐day geographical ranges that overlap locations postulated from geographical and fossil evidence to have been glacial refugia. Based on this information we infer that two important refugial sources of Arctic recolonization by this species were Beringia and the High Arctic. Two other putative refugia, located southeast of the ice sheet and along coastal regions of the eastern Arctic may have served as sources for recolonization of smaller portions of the Arctic. The genetic substructure in the species is mostly due to variation among populations regardless of the ecogeographical region in which they are found. Spatial autocorrelation at the regional scale was also detected. High levels of diversity both within populations and ecogeographical regions are probably indicative of population establishment from several sources possibly combined with recent gene flow.
Ultraviolet-microbeam irradiation of newt-cell cytoplasm: spindle destruction, false anaphase, and delay of true anaphase.

Mitotic tissue-culture cells of the newt Triturus viridescens were irradiated in various cytoplasmic regions with monochromatic or heterochromatic ultraviolet microbeams (conical, with 25° half-angle, 8 μ in diameter in focal plane). Depending on exposure, some spindles were destroyed (i.e., true anaphase was prevented), and this was sometimes followed by quasirosette formation and false anaphase. Efficiency of spindle destruction was not detectably affected by the presence of a centrosome or part of the formed metaphase spindle in the irradiated region. For 280-nm irradiation the exposure which destroyed 50% of spindles was $2\times 10^{12}$ in terms of incident photons per cell times the cell depth in microns. Direct irradiation of centrosomes did not impair their mutual attraction for kinetochores. In metaphase-irradiated cells which survived spindle destruction, delay of true anaphase was critically dependent on whether irradiation occurred before or after the arrival of the last kinetochore at the sp.