Miracle-dz/UniFAR-FTUs huggingface dataset:
The 5' nontranslated region of potato virus X RNA affects both genomic and subgenomic RNA synthesis

A tobacco protoplast system was developed to analyze cis-acting sequences required for potato virus X (PVX) replication. Protoplasts inoculated with transcripts derived from a PVX cDNA clone or from clones containing mutations in their 5' nontranslated regions (NTRs) were assayed for RNA production by S1 nuclease protection assays. A time course of plus- and minus-strand-RNA accumulation indicated that both minus- and plus-strand PVX RNAs were detectable at 0.5 h postinoculation. Although minus-strand RNAs accumulated more rapidly than plus-strand RNAs, maximum levels of plus-strand RNAs were 40- to 80-fold higher. On the basis of these data, time points were chosen for determination of RNA levels in protoplasts inoculated with PVX clones containing deletions or an insertion in their 5' NTRs. Deletions of more than 12 nucleotides from the 5' end, internal deletions, and one insertion in the 5' NTR resulted in substantially decreased levels of plus-strand-RNA production. In contrast, all modified transcripts were functional for minus-strand-RNA synthesis, suggesting that elements in the 5' NTR were not essential for minus-strand-RNA synthesis. Further analysis of the 5' NTR deletion mutants indicated that all mutations that decreased genomic plus-strand-RNA synthesis also decreased synthesis of the two major subgenomic RNAs. These data indicate that cis-acting elements from different regions of the 5' NTR are required for plus-strand-RNA synthesis and that this process may be linked to synthesis of subgenomic RNAs.
Implementing and Evaluating the First German Young-Carers Project: Intentions, Pitfalls and the Need for Piloting Complex Interventions

The aim of the study was to develop, implement and evaluate a concept for the first support program for young carers and their families in Germany. This paper intends to critically review the implementation of that study and describe the problems experienced by the research team, including: the complexity of the intervention itself, the difficulty of finding host organizations, the lack of infrastructure, different values and beliefs about the project aims held between the host organization and the research team, shortage of time, identifying and recruiting families among the hidden population of young carers. These initial problems led to the re-constructuring of the original research design. In order to evaluate factors that influenced these difficulties, the original research intentions, emerging problems and their consequences will be presented.
Inhibition of the group I mGluRs reduces acute brain damage and improves long-term histological outcomes after photothrombosis-induced ischaemia

Group I mGluRs (metabotropic glutamate receptors), including mGluR1 and mGluR5, are GPCRs (G-protein coupled receptors) and play important roles in physiology and pathology. Studies on their role in cerebral ischaemia have provided controversial results. In this study, we used a PT (photothrombosis)-induced ischaemia model to investigate whether antagonists to the group I mGluRs may offer acute and long-term protective effects in adult mice. Our results demonstrated that administration with mGluR5 antagonist MPEP [2-methyl-6-(phenylethynyl)-pyridine] or mGluR1 antagonist LY367385 by intraperitoneal injection at 3 h after PT decreased brain infarct volume evaluated one day after ischaemia. Additive effects on infarct volume were observed upon co-injection with MPEP and LY367385. These antagonists also significantly alleviated neurodegeneration and apoptosis in the penumbra. In addition, when evaluated 2 weeks after PT, they reduced infarct volume and tissue loss, attenuated glial scar formation, and inhibited cell proliferation in the penumbra. Importantly, co-injection with MPEP and LY367385 reduced the expression levels of calpain, a Ca2+-activated protease known to mediate ischaemia-induced neuronal death. Injection of calpeptin, a calpain inhibitor, could inhibit neuronal death and brain damage after PT but injection of calpeptin together with MPEP and LY367385 did not further improve the protective effects mediated by MPEP and LY367385. These results suggest that inhibition of group I mGluRs is sufficient to protect ischaemic damage through the calpain pathway. Taken together, our results demonstrate that inhibition of group I mGluRs can mitigate PT-induced brain damage through attenuating the effects of calpain, and improve long-term histological outcomes.
Validation of Reported Whole-Grain Intake from a Web-Based Dietary Record against Plasma Alkylresorcinol Concentrations in 8- to 11-Year-Olds Participating in a Randomized Controlled Trial.

BACKGROUND Whole-grain (WG) intake is important for human health, but accurate intake estimation is challenging. Use of a biomarker for WG intake provides a possible way to validate dietary assessment methods. OBJECTIVE Our aim was to validate WG intake from 2 diets reported by children, using plasma alkylresorcinol (AR) concentrations, and to investigate the 3-mo reproducibility of AR concentrations and reported WG intake. METHODS AR concentrations were analyzed in fasting blood plasma samples, and WG intake was estimated in a 7-d web-based diary by 750 participants aged 8-11 y in a 2 school meal × 3 mo crossover trial. Reported WG intake and plasma AR concentrations were compared when children ate their usual bread-based lunch (UBL) and when served a hot lunch meal (HLM). Correlations and cross-classification were used to rank subjects according to intake. The intraclass correlation coefficients (ICCs) between subjects' measurements at baseline and after the UBL were used to assess reproducibility. RESULTS Correlations between reported WG wheat + rye intake and plasma AR were 0.40 and 0.37 (P < 0.001) for the UBL and the HLM diets, and 78% and 77% were classified in the same or adjacent quartiles for the UBL and HLM diets, respectively. The ICC over 3 mo was 0.47 (95% CI: 0.38, 0.55) for plasma total ARs and 0.64 (95% CI: 0.58, 0.70) for reported WG intake. Correlations were higher when using the AR C17:0 homolog as a biomarker, reflecting rye intake instead of plasma total ARs [UBL: r = 0.47; HLM: r = 0.43, P < 0.001; ICC = 0.51 (95% CI: 0.43, 0.59)]. CONCLUSIONS Self-reported WG wheat + rye intake among children showed moderate correlations with plasma AR concentrations. Substantial intraindividual variation was found in WG intake and plasma AR concentrations. The AR homolog C17:0 may be used as a biomarker for WG intake when the WG intake primarily comes from rye as in the present study. This trial was registered at clinicaltrials.gov as NCT01457794.
Unsupervised Domain Tuning to Improve Word Sense Disambiguation

The topic of a document can prove to be useful information for Word Sense Disambiguation (WSD) since certain meanings tend to be associated with particular topics. This paper presents an LDA-based approach for WSD, which is trained using any available WSD system to establish a sense per (Latent Dirichlet allocation based) topic. The technique is tested using three unsupervised and one supervised WSD algorithms within the SPORT and FINANCE domains giving a performance increase each time, suggesting that the technique may be useful to improve the performance of any available WSD system.
Everyday Morality: An Introduction to Applied Ethics

Preface. Part One: CHARACTER AND CONDUCT. 1. Morality and Self-Interest. 2. Theories of Right Action. 3. Theories of Virtue. Part Two: MULTICULTURAL ETHICS. 4. Diversity and Relativism. 5. Religious Ethics. 6. Feminism. 7. Race and Ethnic Identity. Part Three: LIFE AND DEATH. 8. Abortion. 9. Suicide and Euthanasia. 10. Animals. 11. Environment. 12. Terrorism and Evil. Part Four: MORAL AUTONOMY AND MENTAL HEALTH. 13. Self-Respect. 14. Self-Knowledge and Self-Deception. 15. Self-Control and Courage. 16. The Therapeutic Trend. 17. Drug Abuse. Part Five: SEXUAL MORALITY. 18. Sex and Love. 19. Homosexuality and Homophobia. 20. Pornography and Fantasy. 21. Marriage and Adultery. Part Six: COMMUNITY AND WEALTH. 22. Money. 23. Meaningful Work. 24. Computers and Community. 25. Community Service. Notes. Index.
Structural specification-based testing: automated support and experimental evaluation

In this paper, we describe a testing technique, called structural specification-based testing (SST), which utilizes the formal specification of a program unit as the basis for test selection and test coverage measurement. We also describe an automated testing tool, called ADLscope, which supports SST for program units specified in Sun Microsystems' Assertion Definition Language (ADL). ADLscope automatically generates coverage conditions from a program's ADL specification. While the program is tested, ADLscope determines which of these conditions are covered by the tests. An uncovered condition exhibits aspects of the specification inadequately exercised during testing. The tester uses this information to develop new test data to exercise the uncovered conditions. We provide an overview of SST's specification-based test criteria and describe the design and implementation of ADLscope. Specification-based testing is guided by a specification, whereby the testing activity is directly related to what a component under test is supposed to do, rather than what it actually does. Specification-based testing is a significant advance in testing, because it is often more straightforward to accomplish and it can reveal failures that are often missed by traditional code-based testing techniques. As an initial evaluation of the capabilities of specification-based testing, we conducted an experiment to measure defect detection capabilities, code coverage and usability of SST/ADLscope; we report here on the results.
Experiments with geographic knowledge for information extraction

Here we present work on using spatial knowledge in conjunction with information extraction (IE). Considerable volume of location data was imported in a knowledge base (KB) with entities of general importance used for semantic annotation, indexing, and retrieval of text. The Semantic Web knowledge representation standards are used, namely RDF(S). An extensive upper-level ontology with more than two hundred classes is designed. With respect to the locations, the goal was to include the most important categories considering public and tasks not specially related to geography or related areas. The locations data is derived from number of publicly available resources and combined to assure best performance for domain-independent named-entity recognition in text. An evaluation and comparison to high performance IE application is given.
Assessing the impacts of 1.5 °C global warming - simulation protocol of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b)

In Paris, France, December 2015, the Conference of the Parties (COP) to the United Nations Framework Convention on Climate Change (UNFCCC) invited the Intergovernmental Panel on Climate Change (IPCC) to provide a "special report in 2018 on the impacts of global warming of 1.5 °C above pre-industrial levels and related global greenhouse gas emission pathways". In Nairobi, Kenya, April 2016, the IPCC panel accepted the invitation. Here we describe the response devised within the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) to provide tailored, cross-sectorally consistent impact projections to broaden the scientific basis for the report. The simulation protocol is designed to allow for (1) separation of the impacts of historical warming starting from pre-industrial conditions from impacts of other drivers such as historical land-use changes (based on pre-industrial and historical impact model simulations); (2) quantification of the impacts of additional warming up to 1.5 °C, including a potential overshoot and long-term impacts up to 2299, and comparison to higher levels of global mean temperature change (based on the low-emissions Representative Concentration Pathway RCP2.6 and a no-mitigation pathway RCP6.0) with socio-economic conditions fixed at 2005 levels; and (3) assessment of the climate effects based on the same climate scenarios while accounting for simultaneous changes in socio-economic conditions following the middle-of-the-road Shared Socioeconomic Pathway (SSP2, Fricko et al., 2016) and in particular differential bioenergy requirements associated with the transformation of the energy system to comply with RCP2.6 compared to RCP6.0. With the aim of providing the scientific basis for an aggregation of impacts across sectors and analysis of cross-sectoral interactions that may dampen or amplify sectoral impacts, the protocol is designed to facilitate consistent impact projections from a range of impact models across different sectors (global and regional hydrology, lakes, global crops, global vegetation, regional forests, global and regional marine ecosystems and fisheries, global and regional coastal infrastructure, energy supply and demand, temperature-related mortality, and global terrestrial biodiversity).
Bruton's Tyrosine Kinase Links the B Cell Receptor to Nuclear Factor κb Activation

The recognition of antigen by membrane immunoglobulin M (mIgM) results in a complex series of signaling events in the cytoplasm leading to gene activation. Bruton's tyrosine kinase (BTK), a member of the Tec family of tyrosine kinases, is essential for the full repertoire of IgM signals to be transduced. We examined the ability of BTK to regulate the nuclear factor (NF)-κB/Rel family of transcription factors, as the activation of these factors is required for a B cell response to mIgM. We found greatly diminished IgM- but not CD40-mediated NF-κB/Rel nuclear translocation and DNA binding in B cells from X-linked immunodeficient (xid) mice that harbor an R28C mutation in btk, a mutation that produces a functionally inactive kinase. The defect was due, in part, to a failure to fully degrade the inhibitory protein of NF-κB, IκBα. Using a BTK-deficient variant of DT40 chicken B cells, we found that expression of wild-type or gain-of-function mutant BTK, but not the R28C mutant, reconstituted NF-κB activity. Thus, BTK is essential for activation of NF-κB via the B cell receptor.
A Framework for Cooperative Resource Management in Mobile Cloud Computing

Mobile cloud computing is an emerging technology to improve the quality of mobile services. In this paper, we consider the resource (i.e., radio and computing resources) sharing problem to support mobile applications in a mobile cloud computing environment. In such an environment, mobile cloud service providers can cooperate (i.e., form a coalition) to create a resource pool to share their own resources with each other. As a result, the resources can be better utilized and the revenue of the mobile cloud service providers can be increased. To maximize the benefit of the mobile cloud service providers, we propose a framework for resource allocation to the mobile applications, and revenue management and cooperation formation among service providers. For resource allocation to the mobile applications, we formulate and solve optimization models to obtain the optimal number of application instances that can be supported to maximize the revenue of the service providers while meeting the resource requirements of the mobile applications. For sharing the revenue generated from the resource pool (i.e., revenue management) among the cooperative mobile cloud service providers in a coalition, we apply the concepts of core and Shapley value from cooperative game theory as a solution. Based on the revenue shares, the mobile cloud service providers can decide whether to cooperate and share the resources in the resource pool or not. Also, the provider can optimize the decision on the amount of resources to contribute to the resource pool.
Sequestration and Distribution Characteristics of Cd(II) by Microcystis aeruginosa and Its Role in Colony Formation

To investigate the sequestration and distribution characteristics of Cd(II) by Microcystis aeruginosa and its role in Microcystis colony formation, M. aeruginosa was exposed to six different Cd(II) concentrations for 10 days. Cd(II) exposure caused hormesis in the growth of M. aeruginosa. Low concentrations of Cd(II) significantly induced formation of small Microcystis colonies (P < 0.05) and increased the intracellular polysaccharide (IPS) and bound extracellular polysaccharide (bEPS) contents of M. aeruginosa significantly (P < 0.05). There was a linear relationship between the amount of Cd(II) sequestrated by algal cells and the amount added to cultures in the rapid adsorption process that occurred during the first 5 min of exposure. After 10 d, M. aeruginosa sequestrated nearly 80% of 0.2 mg L−1 added Cd(II), while >93% of Cd(II) was sequestrated in the groups with lower added concentrations of Cd(II). More than 80% of the sequestrated Cd(II) was bioadsorbed by bEPS. The Pearson correlation coefficients of exterior and interior factors related to colony formation of M. aeruginosa revealed that Cd(II) could stimulate the production of IPS and bEPS via increasing Cd(II) bioaccumulation and bioadsorption. Increased levels of cross-linking between Cd(II) and bEPS stimulated algal cell aggregation, which eventually promoted the formation of Microcystis colonies.
In Silico Prediction of Drug Binding to Cytochrome P450 2D6: Identification of a new Metabolite of Metoclopramide

Patients with cancer are often taking many different classes of drugs to treat the effects of their malignancy and the side effects of treatment, as well as their co-morbidities. The potential for drug-drug interactions which may affect the efficacy of anti-cancer treatment is high and a major source of such interactions is competition for the drug-metabolising enzymes cytochromes P450. We have examined a series of 20 drugs commonly prescribed for cancer patients looking for potential interactions via cytochrome P450 2D6. We used a homology model of cytochrome P450 2D6 together with molecular docking techniques to perform an in silico screen for binding to CYP2D6. Experimental IC 50 values were determined for these compounds and compared with the model predictions to reveal a correlation with a regression coefficient of r 2 = 0.61. Importantly, the docked conformation of the commonly prescribed anti-emetic metoclopramide predicted a new site of metabolism that was further investigated through in vitro analysis with recombinant CYP2D6. An aromatic N -hydroxy metabolite of metoclopramide – consistent with predictions from our modelling studies – was identified by high performance liquid chromatography mass spectrometry. This metabolite was found to represent a major product of metabolism in human liver microsomes and CYP2D6 was identified as the main P450 isoform responsible for catalyzing its formation. In view of the prevalence of inter-individual variation in the CYP2D6 genotype and phenotype, we suggest that those experiencing adverse reactions with metoclopramide, e.g. extra-pyramidal syndrome, are likely to have a particular CYP2D6 genotype/phenotype. This warrants further investigation.
A three-stage solution for flexible vocabulary speech understanding

This paper discusses our three-stage approach to a flexible vocabulary speech understanding system, which can detect out-ofvocabulary (OOV) words, and hypothesize their phonetic and orthographic transcriptions. In the first stage, we introduce the column-bigram finite-state transducer (FST) which, while embedding ANGIE sublexical models, also supports previously unseen data from unknown words. Secondly, the ANGIE models utilize grapheme information, providing tighter linguistic constraint as well as instantaneous sound-to-letter capability during recognition. Thirdly, the syllable-level lexical units of the first stage are automatically derived via an iterative procedure to optimize performance. The second-stage recognizer employs ANGIE to output a word network which is parsed by TINA, our natural language (NL) processor, in stage three. Experiments with a JUPITER implementation of this system are described in [1].
Improving translation memory fuzzy matching by paraphrasing

Computer-assisted translation (CAT) tools have become the major language technology to support and facilitate the translation process. Those kind of programs store previously translated source texts and their equivalent target texts in a database and retrieve related segments during the translation of new texts. However, most of them are based on string or word edit distance, not allowing retrieving of matches that are similar. In this paper we present an innovative approach to match sentences having different words but the same meaning. We use NooJ to create paraphrases of Support Verb Con-structions (SVC) of all source translation units to expand the fuzzy matching capabilities when searching in the translation memory (TM). Our first results for the EN-IT language pair show consistent and significant improvements in matching over state-of-the-art CAT systems, across different text domains.
Affective Touch at a Distance

Touch is an important modality for affective communication between individuals. Here we present a system, named the TaSST (Tactile Sleeve for Social Touch), that allows two people to communicate different types of touch at a distance by touching their own forearm. In this paper we will introduce the TaSST and present a demo setup using two TaSST sleeves.
A Corpus Level MIRA Tuning Strategy for Machine Translation

MIRA based tuning methods have been widely used in statistical machine translation (SMT) system with a large number of features. Since the corpus-level BLEU is not decomposable, these MIRA approaches usually define a variety of heuristic-driven sentencelevel BLEUs in their model losses. Instead, we present a new MIRA method, which employs an exact corpus-level BLEU to compute the model loss. Our method is simpler in implementation. Experiments on Chinese-toEnglish translation show its effectiveness over two state-of-the-art MIRA implementations.