Domestifikacija riba: moraju li sve gajene vrste biti domestifikovane?

The agricultural world today is dominated by a few mammal species that were domesticated over the past 12 000 years (Diamond, 2002). In particular, the five major species (cattle, pig, sheep, goat and horse) represent nearly 94% of mammalian livestock today. As a result, a clear dichotomy now exists between the numerous wild (from hunting) and the few domesticated mammals (produced in farms) used for human consumption. Similar to agriculture, aquaculture is often viewed as the only solution that can provide more seafood given that harvesting wild marine stocks are either stabilizing or more probably declining since the late 1980s (Watson and Pauly, 2001; FAO, 2012). Indeed, it is unlikely that fisheries will be able to supply more aquatic food products than today, ca. 90 million tones per year, including both marine and inland captures (FAO, 2012). Yet, compared to agriculture, aquaculture is a considerably younger sector that relies strongly on natural sources to farm numerous species with various production levels (Bostock et al., 2010; Jobling, 2010).Among the 313 species or group of species recorded in the United Nation’s Food and Agriculture Organization (FAO) database in 2009, which have been farmed at one time since 1950, 28.4% were no longer being produced in 2009 and 17.9% produced less than 100 t. Only 12.1% produced more than 100 000 t (Teletchea and Fontaine, 2013). In addition, and more importantly, the duration of consecutive production recorded in the FAO database was very short for most species or groups of species, only one year for 10.2% and from two to five years for 15.3%; only 18.8% have been farmed for more than 40 years (Teletchea and Fontaine, 2013). To better describe the various strategies for fish production (Ottolenghi et al., 2004; Welcomme et al., 2010; Klinger et al., 2013), a new classification comprising five levels of “domestication” with 1 being the least to 5 being the most domesticated was recently proposed (Teletchea and Fontaine, 2013). Among the 250 species recorded in the FAO database in 2009 (i.e., excluding group of species), 39 belong to the level 1 (first trials of acclimatization to the culture environment, e.g., Anguilla rostrata, Scardinius erythrophthalmus, 75 to the level 2 (also known as capture-based aquaculture, e.g., Thunnus thynnus, Aspius aspius), 61 to the level 3 (entire life cycle closed in captivity with wild inputs, e.g., Solea senegalensis, Rutilus rutilus), 45 to the level 4 (entire life cycle closed in captivity without wild inputs, e.g., Pagrus pagrus, Sander lucioperca), and 30 to the level 5 (selective breeding programme is used focusing on specific goal, e.g., Salmo salar, Cyprinus carpio). As of now, 70% of the 250 species listed in the FAO belong to the first three levels of domestication thatdepend on the availability of wild resource (Ottolenghi et al., 2004). In contrast, only a few species, or more accurately populations, can be considered truly domesticated (Balon, 2004;Bilio, 2008), i.e., an animal selectively bred in captivity and modified from its wild ancestors making it more useful to humans who control the animal’s breeding and food supply (Clutton-Brock, 1999), similar to cattle or sheep. Based on this new classification, one may ask iffarmed species must be domesticated to reach a significant production, or in other terms, whether the levels of production and domestication are positively correlated.Danas u poljoprivredi dominira nekoliko vrsta sisara koje su domestifikovane pre više od 12 000 godina (Diamond, 2002). Pet najprisutnijih vrsta (goveda, svinje, ovce, koze i konji) danas predstavljaju skoro 94% stoke sisara. Kao posledica toga, danas postoji jasna razlika između brojnih divljih (iz lova) i nekoliko domestifikovanih vrsta (proizvedenih na farmama) kojima se čovek hrani. Slično poljoprivredi, na akvakulturu se često gleda kao na jedino rešenje koje može da obezbedi više hrane iz mora obzirom da je ulov marinskih vrsta ili stabilizovan ili u opadanju od kasnih osamdesetih godina prošlog veka (Watson and Pauly, 2001; FAO, 2012). I zaista, malo je verovatno da će ribarstvo biti u mogućnosti da proizvede vise morskih prehrambenih proizvoda nego danas, ca. 90 miliona tona godisnje, uključujući i mora i kopnene vode (FAO, 2012). Ipak, u poređenju sa poljoprivredom, akvakultura je značajno mlađi sektor koji se veoma oslanja na prirodne izvore u proizvodnji brojnih vrsta sa promenljivim nivoom proizvodnje (Bostock et al., 2010; Jobling, 2010). Od 313 vrsta ili grupa vrsta koje su zabeležene u bazi podataka Organizacije za hranu i poljoprivredu Ujedinjenih Nacija (FAO) iz 2009-te godine a koje su gajene od 1950te, 28.4% se više nije proizvodilo u 2009. godini a 17.9% imalo je proizvodnju nižu od 100 tona. Samo 12.1% vrsta ima proizvodnju višu od 100 000 tona (Teletchea and Fontaine, 2013). Staviše, trajanje konsekutivne proizvodnje zabeležene u FAO-voj bazi podataka bilo je veoma kratko za većinu vrsta ili grupa vrsta: samo jedna godina za 10.2% i od dve do pet godina za 15.3%. Samo je 18.8% bilo gajeno više od četrdeset godina (Teletchea and Fontaine, 2013). Da bi se bolje opisale različite strategije proizvodnje ribe (Ottolenghi et al., 2004; Welcomme et al., 2010; Klinger et al., 2013), nedavno je predložena nova klasifikacija koja se sastoji od pet nivoa “domestifikacije”, gde je 1 oznaka za najmanje a 5 oznaka za najviše domestifikovane vrste (Teletchea and Fontaine, 2013). Od 250 vrsta zabeleženih u FAO-voj bazi podataka iz 2009-te (osim isključenih vrsta), 39 pripada nivou 1 (prvi pokušaji privikavanja na uzgojnu sredinu, npr. Anguilla rostrata; Scardinius erythrophthalmus), 75 pripada nivou 2 (ovaj nivo se takođe naziva ‘akvakultura bazirana na ulovu’, npr. Thunnus thynnus, Aspius aspius), 61 vrsta pripada nivou 3 (one vrste koje su ceo zivot zatočene, sa novim vrstama iz divljine, npr Solea senegalensis, Rutilus rutilus), 45 pripada nivou 4 (one vrste koje su ceo život zatočene, bez novih vrsta iz divljine, npr. Pagrus pagrus, Sander lucioperca), i 30 pripada nivou 5 (program selektivnog gajenja koji ima određen cilj, npr. Salmo salar, Cyprinus carpio). Od danas, 70% od 250 vrsta riba koje se nalaze na FAO-voj listi spadaju u prva tri nivoa domestifikacije koja zavise od dostupnosti divljih resursa (Ottolenghi et al., 2004). Nasuprot tome, samo nekoliko vrsta, ili tačnije populacija, se mogu smatrati potpuno domestifikovanim (Balon, 2004; Bilio, 2008), npr. životinja selektivno gajena u zatočeništvu i izmenjena u odnosu na svoje pretke je veoma značajna za ljude koji kontrolišu gajenje životinja i njihovu ishranu (Clutton-Brock, 1999), slično govedima i ovcama. Zasnovano na ovoj novoj klasifikaciji, možemo se zapitati da li gajene vrste moraju biti domestifikovane da bi dostigle značajni nivo proizvodnje? Ili, drugim rečima, da li su nivoi proizvodnje i domestifikacija u pozitivnoj korelaciji

Language and Proofs for Higher-Order SMT (Work in Progress)

Satisfiability modulo theories (SMT) solvers have throughout the years been able to cope with increasingly expressive formulas, from ground logics to full first-order logic modulo theories. Nevertheless, higher-order logic within SMT is still little explored. One main goal of the Matryoshka project, which started in March 2017, is to extend the reasoning capabilities of SMT solvers and other automatic provers beyond first-order logic. In this preliminary report, we report on an extension of the SMT-LIB language, the standard input format of SMT solvers, to handle higher-order constructs. We also discuss how to augment the proof format of the SMT solver veriT to accommodate these new constructs and the solving techniques they require.Comment: In Proceedings PxTP 2017, arXiv:1712.0089

Combining Lists with Non-Stably Infinite Theories

http://www.springerlink.comIn program verification one has often to reason about lists over elements of a given nature. Thus, it becomes important to be able to combine the theory of lists with a generic theory $T$ modeling the elements. This combination can be achieved using the Nelson-Oppen method only if $T$ is stably infinite. The goal of this paper is to relax the stable-infiniteness requirement. More specifically, we provide a new method that is able to combine the theory of lists with any theory $T$ of the elements, regardless of whether $T$ is stably infinite or not. The crux of our combination method is to guess an arrangement over a set of variables that is larger than the one considered by Nelson and Oppen. Furthermore, our results entail that it is also possible to combine $T$ with the more general theory of lists with a length function

A Rewriting Approach to the Combination of Data Structures with Bridging Theories

International audienceWe introduce a combination method à la Nelson-Oppen to solve the satisfiability problem modulo a non-disjoint union of theories connected with bridging functions. The combination method is particularly useful to handle verification conditions involving functions defined over inductive data structures. We investigate the problem of determining the data structure theories for which this combination method is sound and complete. Our completeness proof is based on a rewriting approach where the bridging function is defined as a term rewrite system, and the data structure theory is given by a basic congruence relation. Our contribution is to introduce a class of data structure theories that are combinable with a disjoint target theory via an inductively defined bridging function. This class includes the theory of equality, the theory of absolutely free data structures, and all the theories in between. Hence, our non-disjoint combination method applies to many classical data structure theories admitting a rewrite-based satisfiability procedure

A Gentle Non-Disjoint Combination of Satisfiability Procedures (Extended Version)

A satisfiability problem is often expressed in a combination of theories, and a natural approach consists in solving the problem by combining the satisfiability procedures available for the component theories. This is the purpose of the combination method introduced by Nelson and Oppen. However, in its initial presentation, the Nelson-Oppen combination method requires the theories to be signature-disjoint and stably infinite (to guarantee the existence of an infinite model). The notion of gentle theory has been introduced in the last few years as one solution to go beyond the restriction of stable infiniteness, but in the case of disjoint theories. In this paper, we adapt the notion of gentle theory to the non-disjoint combination of theories sharing only unary predicates (plus constants and the equality). Like in the disjoint case, combining two theories, one of them being gentle, requires some minor assumptions on the other one. We show that major classes of theories, i.e.\ Löwenheim and Bernays-Schönfinkel-Ramsey, satisfy the appropriate notion of gentleness introduced for this particular non-disjoint combination framework

Decidability of Difference Logic over the Reals with Uninterpreted Unary Predicates

First-order logic fragments mixing quantifiers, arithmetic, and uninterpreted predicates are often undecidable, as is, for instance, Presburger arithmetic extended with a single uninterpreted unary predicate. In the SMT world, difference logic is a quite popular fragment of linear arithmetic which is less expressive than Presburger arithmetic. Difference logic on integers with uninterpreted unary predicates is known to be decidable, even in the presence of quantifiers. We here show that (quantified) difference logic on real numbers with a single uninterpreted unary predicate is undecidable, quite surprisingly. Moreover, we prove that difference logic on integers, together with order on reals, combined with uninterpreted unary predicates, remains decidable.Comment: This is the preprint for the submission published in CADE-29. It also includes an additional detailed proof in the appendix. The Version of Record of this contribution will be published in CADE-2

Description du développement épiphysaire du tarse et du grasset équin à l’IRM et au CT : un pas vers la compréhension de l’OCD

L’ostéochondrite disséquante (OCD) est un défaut focal du processus d’ossification endochondrale en des sites spécifiques au niveau épiphysaire. Elle est caractérisée par la présence de fragments ostéochondraux pouvant se détacher de la surface articulaire. Cette maladie a un impact majeur sur les performances athlétiques des chevaux. Les deux hypothèses principales présentement véhiculées quant à sa pathogénie sont une nécrose ischémique du cartilage de croissance et une altération du métabolisme de la matrice de collagène de type II au sein du cartilage de croissance. Malgré de nombreuses années de recherche sur le sujet, plusieurs aspects de cette maladie demeurent inconnus. L’objectif de cette étude était de décrire le développement épiphysaire équin au niveau du membre pelvien à l’aide de l’imagerie médicale afin de déterminer si des variations du processus de maturation à certains sites pouvaient être un facteur prédisposant au développement de lésions d’OCD. Des membres pelviens de fœtus et de jeunes poulains ont été étudiés post-mortem. L’épiphyse du fémur distal, tibia distal et du talus ont été examinées par tomodensitométrie (CT) et résonnance magnétique 1.5 Tesla (IRM) dans le but de documenter le degré et le patron d’ossification, la régularité du front d’ossification, de même que le pourcentage du diamètre épiphysaire demeurant occupé par le complexe de cartilage articulaire-épiphysaire, et ce au niveau de certains sites prédéterminés. Les centres secondaires d’ossification (SOCs) ont été détectés pour la première fois à 7 mois de gestation (MOG) au niveau de l’épiphyse fémorale distale et à 8 MOG au niveau de l’épiphyse tibiale distale et du talus. À 8-9 MOG la lèvre latérale de la trochlée fémorale, la malléole médiale du tibia (MM) et la partie crâniale de la crête intermédiaire du tibia distal (DIRT(Cr)), tous des sites prédisposés à la maladie, avaient le plus haut pourcentage de cartilage de tous les sites évalués. Post-partum, le pourcentage de cartilage de la MM et de la DIRT(Cr) sont demeurés importants. Le CT et l’IRM ont su illustrer le développement épiphysaire équin et soutenir d’avantage le fait qu’un cartilage plus épais à certains sites articulaires pourrait avoir un rôle dans le développement de lésions d’OCD.Osteochondrosis dissecans (OCD) is a focal failure of endochondral ossification of the epiphysis characterized by the presence of cartilage flaps and osteochondral fragments. This disease has a major impact on equine athletic performances. The two current principal hypotheses on etiopathogenesis are either an ischemic necrosis of growth cartilage or altered cartilage type II collagen metabolism. Despite years of research, many knowledge gaps on the etiology of this disease remain. The objective of this study was to image epiphyseal development in the equine pelvic limb to determine whether there was a variation in site maturation that could be a predisposing factor for OCD. Pelvic limbs (fetuses and foals) were studied post-mortem. The epiphyses of the distal femur, tibia and talus were scanned with computed tomography (CT) and 1.5 Tesla magnetic resonance imaging (MRI) to investigate the degree and pattern of ossification, the regularity of the ossification front and cartilage percentage (articular epiphyseal cartilage thickness as a percentage of total epiphyseal diameter) at predetermined sites. The secondary ossification centers (SOC) were first identified in the femoral epiphyses at 7 months of gestation (MOG), and both distal tibia and talus at 8 MOG. At 8-9 MOG the lateral trochlear ridge of the femur, medial malleolus of the tibia (MM), cranial part of the distal intermediate ridge of the tibia (DIRT(Cr)), all OCD susceptible sites, had the greatest cartilage percentage compared to all other sites assessed. Post-partum, the cartilage percentage of the MM and DIRT(Cr), common sites of OCD, remained high. CT and MRI images illustrate equine epiphyseal development and provide additional evidence that greater cartilage thickness at specific joint sites could play a role in the development of OCD

Elaboration of metallic compacts with high porosity for mechanical supports of SOFC

The development of third generation Solid Oxide Fuel Cells (SOFC) with metallic mechanical supports presents several advantages over that of ceramic stacks by offering a lower cost and longer lifetime of the stacks. As a consequence, it is necessary to prepare metallic porous compacts that remain stable at the operating temperature of the SOFC (700–800 C) under reductive atmosphere. This paper presents an innovative process to elaborate iron, nickel and cobalt porous compacts. The process is based on the thermal decomposition of metal oxalate precursors with controlled morphology into metallic powders with coralline shape. Uniaxial compaction of such powders (without binder addition to the powders) under low uniaxial pressures (rising from 20 to 100 MPa) gave rise to green compacts with high porosity and good mechanical properties. After annealing at 800 C under H2 atmosphere, the compacts still present interconnected porosity high enough to allow sufficient gas flow to feed a SOFC single cell in hydrogen: the porosity rises from 25 to 50% for iron compacts, from 20 to 50% for cobalt compacts, and is higher than 40% for nickel compacts. Results from physicochemical characterization (XRD, SEM, gas permeation, Hg porosimetry) corroborated the process for SOFC application

Machine Learning for Instance Selection in SMT Solving

International audienceSMT solvers are among the most suited tools for quantifier-free first-order problems, and their support for quantified formulas has been improving in recent years. To instantiate quantifiers, they rely on heuristic techniques that generate thousands of instances, most of them useless. We propose to apply state-of-the-art machine learning techniques as classifiers for instances on top of the instantiation process. We show that such techniques can indeed decrease the number of generated useless instances. We envision that this could lead to more efficient SMT solving for quantified problems. Satisfiability-modulo-theories (SMT) solvers are among the best backends for verification tools and "hammers" in proof assistants. When proof obligations contain quantified formulas, SMT solvers rely on instantiation, replacing quantified subformulas by sets of ground instances. Three main techniques have been designed: enumerative [11], trigger-based [4], and conflict-based [12] instantiation. Among these, only conflict-based instantiation computes instances that are guaranteed to be relevant, but it is incomplete and is normally used in combination with other techniques. Enumerative and trigger-based techniques are highly heuristic and generate a large number of instances, most of them useless. As a result, the search space of the solver explodes. Reducing the number of instances could improve the solver's efficiency and success rate within a given time limit. We propose to use a state-of-the-art machine learning algorithm as a predictor over the generated set of instances to filter out irrelevant instances, and thus decrease the number of instances given to the ground solver. The predictor is invoked after each instantiation round to rate the potential usefulness of each generated instance. Several strategies are then used to build a subset of potentially relevant instances that are immediately added to the ground solver. Adding the other instances is postponed. We conducted our experiment in veriT [2], an SMT solver that implements all three in-stantiation techniques described above. We chose as predictor the XGBoost gradient boosting toolkit [3] with the binary classification objective. This configuration had already been used successfully in the context of theorem proving [6, 10]. Choosing a suitable set of features is crucial for effective machine learning. The features determine how precise the representation of the problem is. Previous works already investigate features for theorem proving [1, 5, 6, 8-10]. Our features are more specifically inspired by ENIGMA [6] and RLCoP [7]. They are basically term symbols and term walks with symbol sequences projected to features using Vowpal Wabbit hashing. Term variables and Skolem constants are translated analogously to constants. The model is further enriched with abstract features such as term size, term depth, and the number of instances. To encode our problem into sparse vectors, we use three kinds of information available to the solver: the ground part of the formula (set of literals l 1 ,. .. , l m), the quantified formul

Alethe: Towards a Generic SMT Proof Format (extended abstract)

The first iteration of the proof format used by the SMT solver veriT was presented ten years ago at the first PxTP workshop. Since then the format has matured. veriT proofs are used within multiple applications, and other solvers generate proofs in the same format. We would now like to gather feedback from the community to guide future developments. Towards this, we review the history of the format, present our pragmatic approach to develop the format, and also discuss problems that might arise when other solvers use the format.Comment: In Proceedings PxTP 2021, arXiv:2107.0154