G’3-stable semantics and inconsistency

We present an overview on how to perform non-monotonic reasoning based on paraconsistent logics. In particular, we show that one can define a logic programming semantics based on the paraconsistent logic G’3 which is called G’3-stable semantics. This semantics defines a frame for performing non-monotonic reasoning in domains which are pervaded with vagueness and inconsistencies. In fact, we show that, by considering also a possibilistic logic point of view, one can use this extended framework for defining a possibilistic logic programming approach able to deal with reasoning, which is at the same time non-monotonic and uncertain.Peer ReviewedPostprint (published version

Design, Mathematical Modelling, Construction and Testing of Synthetic Gene Network Oscillators to Establish Roseobacter Clade Bacteria and the Protozoan Trypanosoma brucei as Synthetic Biology Chassis.

The aim of this project is to establish Roseobacter marine bacteria and Trypanosoma brucei (T. brucei) protozoa as synthetic biology chassis. This work addresses the gap within synthetic biology resulting from the limited choice of host cells available for use in practice. This was done by developing synthetic bacterial and trypanosomal genetic regulatory networks (GRNs) which function as an oscillator as well as by developing the necessary protocols and set-ups to allow for the analysis of GRN dynamics within the host. Roseobacter clade bacteria are naturally found in diverse oceanic habitats and have an important ecological role in balancing global carbon levels. This makes Roseobacter an ideal chassis for future efforts to apply synthetic biology to bioremediation and geo-engineering challenges. The aim of this investigation was to establish straight-forward molecular biology procedures in Roseobacter bacteria followed by characterisation and modelling of an E. coli oscillator in Roseobacter. Results showed that Roseobacter synthetic biology is non-trivial. Protozoa are exploited as host cells for industrial production of biotherapeutics due to fast doubling times and host proteins’ mammalian-like post-translational glycosylation. As an established model organism for studying protozoa, T. brucei provided a test case for establishing synthetic biology in this phylum for the first time. T. brucei is highly divergent from eukaryotes commonly used in synthetic biology and possesses a sophisticated genomic machinery to evade host immune systems. The establishment of standard synthetic biology approaches in mathematical modelling and gene network design in T. brucei will underpin application of synthetic biology to enhance the industrial capability of the protozoa as a chassis and to probe its pathobiology. This investigation involved design and assembly of a Goodwin oscillator, followed by characterisation and modelling of the network and the development of a novel experimental set-up for live-cell imaging of single motile trypanosomes. Results showed that T. brucei is a promising novel synthetic biology chassi

A Brief History of Updates of Answer-Set Programs

Funding Information: The authors would like to thank José Alferes, Martin Baláz, Federico Banti, Antonio Brogi, Martin Homola, Luís Moniz Pereira, Halina Przymusinska, Teodor C. Przymusinski, and Theresa Swift, with whom they worked on the topic of this paper over the years, as well as Ricardo Gonçalves and Matthias Knorr for valuable comments on an earlier draft of this paper. The authors would also like to thank the anonymous reviewers for their insightful comments and suggestions, which greatly helped us improve this paper. The authors were partially supported by Fundação para a Ciência e Tecnologia through projects FORGET (PTDC/CCI-INF/32219/2017) and RIVER (PTDC/CCI-COM/30952/2017), and strategic project NOVA LINCS (UIDB/04516/2020). Publisher Copyright: © The Author(s), 2022. Published by Cambridge University Press.Over the last couple of decades, there has been a considerable effort devoted to the problem of updating logic programs under the stable model semantics (a.k.a. answer-set programs) or, in other words, the problem of characterising the result of bringing up-to-date a logic program when the world it describes changes. Whereas the state-of-the-art approaches are guided by the same basic intuitions and aspirations as belief updates in the context of classical logic, they build upon fundamentally different principles and methods, which have prevented a unifying framework that could embrace both belief and rule updates. In this paper, we will overview some of the main approaches and results related to answer-set programming updates, while pointing out some of the main challenges that research in this topic has faced.publishersversionpublishe

Every normal logic program has a 2-valued semantics: theory, extensions, applications, implementations

Trabalho apresentado no âmbito do Doutoramento em Informática, como requisito parcial para obtenção do grau de Doutor em InformáticaAfter a very brief introduction to the general subject of Knowledge Representation and Reasoning with Logic Programs we analyse the syntactic structure of a logic program and how it can influence the semantics. We outline the important properties of a 2-valued semantics for Normal Logic Programs, proceed to define the new Minimal Hypotheses semantics with those properties and explore how it can be used to benefit some knowledge representation and reasoning mechanisms. The main original contributions of this work, whose connections will be detailed in the sequel, are: • The Layering for generic graphs which we then apply to NLPs yielding the Rule Layering and Atom Layering — a generalization of the stratification notion; • The Full shifting transformation of Disjunctive Logic Programs into (highly nonstratified)NLPs; • The Layer Support — a generalization of the classical notion of support; • The Brave Relevance and Brave Cautious Monotony properties of a 2-valued semantics; • The notions of Relevant Partial Knowledge Answer to a Query and Locally Consistent Relevant Partial Knowledge Answer to a Query; • The Layer-Decomposable Semantics family — the family of semantics that reflect the above mentioned Layerings; • The Approved Models argumentation approach to semantics; • The Minimal Hypotheses 2-valued semantics for NLP — a member of the Layer-Decomposable Semantics family rooted on a minimization of positive hypotheses assumption approach; • The definition and implementation of the Answer Completion mechanism in XSB Prolog — an essential component to ensure XSB’s WAM full compliance with the Well-Founded Semantics; • The definition of the Inspection Points mechanism for Abductive Logic Programs;• An implementation of the Inspection Points workings within the Abdual system [21] We recommend reading the chapters in this thesis in the sequence they appear. However, if the reader is not interested in all the subjects, or is more keen on some topics rather than others, we provide alternative reading paths as shown below. 1-2-3-4-5-6-7-8-9-12 Definition of the Layer-Decomposable Semantics family and the Minimal Hypotheses semantics (1 and 2 are optional) 3-6-7-8-10-11-12 All main contributions – assumes the reader is familiarized with logic programming topics 3-4-5-10-11-12 Focus on abductive reasoning and applications.FCT-MCTES (Fundação para a Ciência e Tecnologia do Ministério da Ciência,Tecnologia e Ensino Superior)- (no. SFRH/BD/28761/2006

Graph Structures for Knowledge Representation and Reasoning

This open access book constitutes the thoroughly refereed post-conference proceedings of the 6th International Workshop on Graph Structures for Knowledge Representation and Reasoning, GKR 2020, held virtually in September 2020, associated with ECAI 2020, the 24th European Conference on Artificial Intelligence. The 7 revised full papers presented together with 2 invited contributions were reviewed and selected from 9 submissions. The contributions address various issues for knowledge representation and reasoning and the common graph-theoretic background, which allows to bridge the gap between the different communities

Sustainable Agriculture and Advances of Remote Sensing (Volume 2)

Agriculture, as the main source of alimentation and the most important economic activity globally, is being affected by the impacts of climate change. To maintain and increase our global food system production, to reduce biodiversity loss and preserve our natural ecosystem, new practices and technologies are required. This book focuses on the latest advances in remote sensing technology and agricultural engineering leading to the sustainable agriculture practices. Earth observation data, in situ and proxy-remote sensing data are the main source of information for monitoring and analyzing agriculture activities. Particular attention is given to earth observation satellites and the Internet of Things for data collection, to multispectral and hyperspectral data analysis using machine learning and deep learning, to WebGIS and the Internet of Things for sharing and publication of the results, among others

Long View (41RB112): Data Recovery of Two Plains Village Period Components in Roberts County, Texas, Volume 2

This archeological data recovery investigation in Roberts County in the northeastern panhandle of Texas was necessitated by the proposed widening of State Highway 70 (CSJ: 0490-04-037) by the Texas Department of Transportation (TxDOT), Amarillo District. This proposed highway rehabilitation program will directly impact a roughly 10 meter (m, 30 ft.) wide north-south section of prehistoric site 41RB112, the Long View site. This site consists of two horizontally distinct Plains Village period occupations shallowly buried along a linear interfluvial ridge between two small tributary creeks to the Canadian River in the midslope of this broad, dissected valley. This site was initially discovered by TxDOT archeologist, Dennis Price in June 2004 during an archeological inventory of the proposed 9.7 kilometer (6 mile) section north of the Canadian River in response to the planned highway rehabilitation program. Based on Mr. Price’s discovery of multiple artifact classes in buried context he recommended this site be assessed for its eligibility for listing on the National Register of Historic Places under criterion d and possible designation as a State Archeological Landmark (SAL) per the requirements of Section 106 of the National Historic Preservation Act (NHPA) and other related legislation. Following the Texas Historical Commissions concurrence with that recommendation, TxDOT through the Environmental (ENV) Affairs Division, contracted to TRC Environmental Corporation (TRC) under an existing Scientific Services Contract No. 57XXSA006 and issued a Work Authorization to TRC of Austin to conduct the site eligibility assessment. During a site visit by TxDOT geoarcheologist James Abbott and TRC archeologist Mike Quigg in February 2005, the site boundaries were expanded to nearly 300 meters (m) along the proposed area of potential effect (APE). Investigative strategies were devised to assess the Long View site. In May 2005, TRC’s archeologists from Austin conducted archeological testing for a NRHP and SAL eligibility assessment investigation at 41RB112. The assessment along the 10-m-wide by 300-m-long APE was accomplished by hand-excavating 28 1-by-1 m units (totaling 16.8 m3), hand-excavating four narrow ca. 30 centimeter (cm) wide trenches (two in each area totaling nearly 32 linear meters), as well as cleaning and inspecting 28 m of existing road cut exposures. These investigations determined that cultural materials clustered at the northern and southern ends (Areas A and C respectively) of the site with nearly 120 m of noncultural bearing deposits (Area B) between the two concentrations. A 4-m-wide mechanically bladed fireguard paralleled the existing fenceline throughout the length of the APE and disturbed much of the near surface materials in that zone. The opposite, eastern side of the highway was investigated through the excavation of six 50-by-50 cm shovel tests, surface, and road cut inspection. Based on the results from the hand-excavations and various collections conducted during the site assessment, it became apparent that the two ends (Areas A and C) of the Long View site in TxDOT’s proposed APE contained well-defined cultural components in the top 50 cmbs. Each end appeared to represent habitation remains from single occupation episodes with potential structures, restricted to a narrow time period of less than 100 years between uncalibrated 630 and 710 B.P. of the Plains Village period. Rodent and natural disturbances had vertically displaced some small cultural objects within the sandy deposits, but the restricted period of occupation to roughly a 100 year period reduces this impact. TRC recommended the site was eligible for listing on the National Register and as a State Landmark. The Texas Historical Commissions concurred with that recommendation, and subsequently the ENV Affairs Division of TxDOT, again contracted to TRC under an existing Scientific Services Contract No. 575XXSA008 and issued a Work Authorization to TRC Austin to perform the mitigation of the proposed impacts. Data recovery investigations were conducted during August through November 2006 along the western side of the existing highway. The previously identified northern-Area A and southern–Area C areas with high concentrations of cultural materials were targeted. These investigations began with a thorough geophysical survey that employed three noninvasive electrical detective instruments across Areas A and C anticipating to detect the locations of subsurface cultural features to target by hand-excavations. Some excavations targeted the detected anomalies, whereas others targeted previously identified features. In the end, hand-excavated blocks were completed in Areas A and C. The excavations totaled 128 m2 in Area A and 93 m2 in Area C for a grand total of 221 m2 or 103.4 m3. In conjunction with the archeological excavations, geoarcheological investigations focused on defining the age and development of the natural Holocene sediments that contained the cultural materials. The geoarcheological assessment included detailed stratigraphic documentation of site and near site deposits, sediment texture characterization, soil thin sections, magnetic susceptibility, multiple chemical analyses (organic, calcium, and phosphorus). Detailed stratigraphic data was also collected at two rare pithouse structures to pursue construction and filling episodes. The excavations yielded significant and diverse cultural assemblages from the two occupations assigned Component A and C. Both components are attributed to the Plains Village period with two discrete occupations dating to uncalibrated 460 to 535 B.P. (cal A.D. 1398 to 1447) in Component A and 530 to 700 B.P. (cal A.D. 1280 to 1437) in Component C. The two assemblages are significant not only in their diversity and quality of materials but also in the information they yielded. This report represents one of the first complete documents to present the entire cultural assemblage from a single site for this time period and region. The total recovered assemblage includes 157 formal chipped and ground stone tools, 226 informal tools, 3,414 pieces of lithic debitage, over 6,400 faunal fragments (1.4 kg), some 1,541 ceramic sherds, 1,790 burned rocks, at least 116 macrobotanical samples that includes 16 maize cobs, two human burials, and remains of a third, juvenile scattered along a previously bladed fireguard, 32 intact cultural features that include two rare pithouses, and other cultural debris related to these two campsites. The human remains and associated artifacts will be repatriated in accord with the requirements of the Native American Graves Protection and Repatriation Act (NAGPRA). A suite of 10 technical analyses directed at mostly the cultural assemblages included; use-wear, phytolith, diatom, petrography, macrobotanical, starch grain, instrumental neutron activation, bison bone isotopes, obsidian sourcing, radiocarbon and optical stimulated dating. This data was used to address 11 specific research questions concerning these Plains Village period occupations. Not only does the cultural debris contribute to our understanding of the time period but the geoarcheological information obtained explains the conditions and how the materials were preserved, and inform us concerning the past depositional environment in this immediate area. The combined information contributes to a significant understanding to a specific part of the Plains Village cultures in the Texas panhandle. Following the acceptance of the final report by the TxDOT and the Texas Historical Commission these cultural materials and all the documentation from the combined investigations will be permanently curated at Texas State University in San Marcos, Texas. The curated materials will provide important data that can be researched by interested parties in the future