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[3] Jean-Yves Girard. The blind spot – lectures on logic. European Mathematical Society, 2011. [4] Giuseppe Longo, Kathleen Milsted, and Sergei Soloviev. Coherence and transitivity **of** subtyping
as entailment. Journal **of** Logic and Computation, 10(4):493–526, 2000.
[5] Zhaohui Luo. Contextual analysis **of** word meanings **in** type-theoretical **semantics**. **In** Sylvain Pogodalla and Jean-Philippe Prost, editors, LACL, volume 6736 **of** LNCS, pages 159–174. Springer, 2011.

mals” also apply to “human beings”). Coercive subtyping [11] sounds promising for F. Its key
property is that, if at most one subtyping map is given between any two base types, then there also is at most one subtyping map between any two complex types. Predefined (inductive) types, e.g. integers as **in** G¨ odel’s system T and finite sets **of** α-objects with their reduction schemes as **in** [10] are also welcome — encodings **in** F are cumbersome. The key points are normalisation, confluence and the absence **of** closed constant-free terms **in** any false type. We shall also illustrate the linguistic relevance **of** these extensions, which are already included **in** Moot’s semantical and semantical parser for French named Grail. [6]

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Regarding coercions, Luo [38] makes an extensive use **of** coercive subtyping, which he introduced with Soloviev [70]: as said **in** their paper this kind **of** subtyping may also work well with system F. So we can say that the system **of** Luo is very similar. Dependent types and predicative quantification may be closer to what we wish to model, but the formal diversity **of** the numerous employed rules may result **in** an obscure formalisation. The typed system at work **in** Asher’s view [3] is a simple type theory extended with type constructors and operations imported from category theory. The theory extends cartesian closed category with a few **of** the many operations that one finds **in** topos theory, like being a subobject. This approach is difficult to compare with the two above, since it does not belong to the same family: morphisms do not represent (quotiented) proofs **of** some logic, they are closer to a set theoretic interpretation.

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(18) a. The students wrote a paper. (unambiguous) b. The students wrote three papers. (covering)
Such readings are derivable **in** our model because one can define **in** F operators for handling plurals. Firstly, one can add, as a constant, a cardinality operator for predicates ||_|| : Πα. (α → t) → N where N are the internal integers **of** system F, namely N = ΠX. (X → X) → (X → X), or a predefined integer type as **in** Gödel system T – this might be problematic if infinitely many objects satisfied the predicate, but syntax and restriction **of** selection can make sure it is only applied when it makes sense. Secondly, as shown **in** Figure 5, we can have operators for handling plurals: q (turning an individual into a property/set, a curried version **of** equality), ∗ (distributivity), # (restricted distributivity from sets **of** sets to its constituent subsets), c (for coverings), etc. The important fact is that the computation **of** such readings uses exactly the same mechanisms as lexical coercion. Some combinations are blocked by their types, but optional terms coming either from the predicate or from the plural noun may allow an a priori prohibited reading. To be precise we also provide specific tools for handling groups that are singular nouns, each **of** which denoting a set. All these functions are easily implemented **in** a typed functional programming language like Haskell, **in** the style **of** [73].

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8
Usually, F N depends only on name(N). **In** this case, we also write the function F name(N ) . Consider for
instance indefinites, which are interpreted with the quantifier a. **In** most cases, F a = λ(P, Q) .λx.P x∧Q x,
but **in** some cases, such as donkey sentences, the function depends on the context **of** the vertex N. The interest **of** using semantic graphs is to facilitate the computation **of** F N . Most times, F name(N ) reduces to a

X. R ELATED W ORKS
The phenomenon **of** self-adjunction is mentioned by Kock [14] and stressed by Thielecke [30] **in** his work on continuations. The notion **of** dialogue category was inspired by the key observation by Hofmann and Streicher [9] and then Selinger [26] that every denotational model **of** classical logic (that is, **of** the λµ-calculus) boils down to a continuation model. The formulation **of** dialogue categories as dialogue chiralities was inspired by Girard’s work on polarities **in** LC [7] and its relationship to dialogue games noticed by Laurent [17], together with the correspondence between games, polarities and continuations originally investigated with Selinger [23]. Note that similar ideas **of** symmetry appeared independently **in** the work by Cockett and Seely [4]. The game-theoretic description **of** the maps f : X → Y between atoms **in** X as labelled pointers between atomic moves is reminiscent **of** the game-theoretic account **of** Girard’s geometry **of** interaction [1] and **of** **proof**-nets [2], [25] together with the graphical description **of** the free ribbon category [13] discussed **in** the introduction. On the **proof**-theoretic side, this work should be compared with similar graphical descriptions **of** the free ∗-autonomous category [10] and **of** the free symmetric monoidal closed category [5]. One main difference with the present work is that both constructions [10], [5] require to identify diagrams modulo Trimble’s rewiring equalities [3] and thus to depart from the purely topological and diagrammatic notion **of** **proof** equality underlying dialogue categories.

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The linear nature **of** resource calculus enables it to be considered as a suitable target lan- guage for the linearisation **of** ordinary λ-calculus. The graphical syntax **of** resource inter- action nets enhances such linearisation with a tight correspondence at the level **of** Linear Logic types: boxes’ content is duplicated with any arbitrary cardinality (thus also erased), promotions becomes co-contractions, boxes themselves are forgotten, and linear implica- tions just preserved. A quick look at Figure 4.1 provides the visual intuition. Each boxing- depth-recursive choice **of** those cardinalities is a simple resource net, while the (possibly infinite) series **of** all **of** them is a resource net, called the Taylor-Ehrhard-Regnier expan- sion **of** the original **proof**-net. Probably inspired by Girard ’s notion **of** approximants **of** the exponential modality [ 1987 ], the expansion was originally formulated by Ehrhard and Regnier [ 2008 ] as a map from λ-terms to differential λ-terms, and then simplified to be targeted into its linear fragment, the resource calculus, expansion was also refined **in** a typed net-like counterpart, employing not only the call-by-name **translation** that we con- sider here [ Mazza and Pagani , 2007 , Pagani and Tasson , 2009 ], but also the call-by-value discipline [ Carraro and Guerrieri , 2014 ]. Given that resource nets strongly normalise, the expansion **of** a term can be interpreted as the series **of** its finite approximations, hence the link with Taylor series and the notion **of** differentiation.

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Moreover, the fact (not much developed **in** this extended abstract) that a design may be viewed either as a kind **of** **proof** (**in** a syntactic setting **of** the framework) or as a game (**in** a semantic setting **of** it) provides us with interesting insights on Pragmatics and Wittgensteinian language games. **In** a pragmatic theory **of** presupposition, for instance, presupposing implies making an assertion where the hearer has no access to a previous step made by the speaker, if (s)he rejects this step, (s)he makes the process to diverge. Other ”games” may be explored. Wittgenstein for instance quoted elicitation, that is the way **in** which some- body may obtain an answer to a question. Every time, Fax is used to transfer a meaning from a location

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Besides sites, four combinators are provided by core calculus. The parallel composition expresses pure concurrency. **In** f |g, f and g are run **in** parallel, their events are interleaved and the expression stops when both f and g have terminated. As suggested by its name, the sequential operator expresses sequentiality. **In** the expression f > x > g, the variable x can be used **in** g. Here, f is started first, and then a new instance **of** g[v/x], where x is bounded to v, is launched as a consequence **of** each publication **of** v. The third operator, called pruning, expresses preemption. **In** f <x< g, the variable x can be used **in** f . Both f and g are started at once, but f is paused when it needs to evaluate x. When g publishes a value, it is bounded to x **in** f and g is stopped. The other events that could have been produced by g are preempted by the publication. For example, if g is supposed to publish two values a and b, only one will be selected and published **in** each execution. We say that these two events are **in** conflict. The last operator is called otherwise. **In** f ; g, f is first started alone and g is started if and only if f stops without publishing any value.

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This being said, fuzzy logics have been widely criticised ((Kamp, 1975; Williamson, 1994; Edgington, 1997) among many others). Most objections to fuzzy approaches derive from one feature **of** fuzzy systems that is hard to swallow, namely that flat contradictions receive values **in** the range [0, 0.5]. Many have reacted negatively to the idea that a flat contradiction can be anything other than completely false. Yet, things are worse for fuzzy logic than that. As we saw **in** section 3.1, there have been empirical observations that “F and not F ” responses to borderline cases **of** vague predicates are common. Perhaps, then, flat contradictions needn’t always be false as the philosophical orthodoxy would suggest. However, taking these diverging intuitions at face value, either a flat contradiction should be valued as totally false, or, **in** borderline cases, as totally acceptable/true. Unfortunately for fuzzy logic, flat contradictions made about central borderline cases receive values **of** 0.5 which satisfies neither intuition. That said, one could defend a view that intuitions regarding flat contradictions track acceptability as opposed to limit-value degrees **of** truth. If this were so, then, provided that, for example, the acceptability **of** an outright assertion **of** a flat contradiction could be, say 0 when its degree **of** truth value is 0.5, then some intuitions can be accommodated. (See e.g. Smith (2008) for such a proposal.) Ultimately, the success **of** such a position will turn on defending the view that intuitions surrounding contradictions track acceptability and not (absolute) falsity. Other challenges arise, too. For example, a sorites argument could now be formulated surrounding acceptability, namely a metasemantic HOV problem (see Wright (1975) for discussion, Smith (2008) for a reply, and Sutton (2017) for discussion **of** difficulties with proposals such as Smith’s).

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The Chen group at the National Institute **of** Biomedical Imaging and Bioengineering **of** the National Institutes **of** Health uses nanomaterials as platforms to provide imaging contrast **in** positron emission tomography (PET). **In** medical imaging, PET can provide a direct, highly sensitive, and quantitative readout **of** organ/tissue targeting efficiency and pharmacokinetics. Compared with radiolabeled antibodies, proteins, peptides, and other biologically relevant molecules, radiolabeled nanoparticles represent a new frontier **in** molecular imaging probe design because they can combine different imaging modalities and targeting ligands **in** a single vector, synergistically improving the imaging quality. 56 However, the applications **of** radiolabeled nanoparticles are based on the premise that the radioisotopes are stably attached to the nanomaterials. Chen has developed general rules for selecting appropriate isotopes for given types **of** nanoparticles as well as adjusting the labeling reaction according to specific applications. The stability (colloidal and radiochemical) **of** the radiolabeled nanoparticles as well as their biological fate must be assessed; special attention should be paid to labeling strategies as they affect the stability **of** radiolabeled nanoparticles and might cause discrepancies **in** the interpretation **of** PET data (owing to the distribution **of** nanoparticles). Wang’s group at the Chinese Academy **of** Sciences is interested **in** creating nano–bio interfaces with controllable adhesion properties. The cell-adhesive biointerfaces are based on the cooperative effects **of** multiscale structural matching and molecular recognition. 57 They explore the relationship between cell-specific adhesion and surface structure (with

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Opinion
Lost **in** post-**translation**
Olivier Putois 1 , François Villa 1 & Jonathan B Weitzman 2
S hakespeare suggested that names are **of** little importance and that “A rose, by any other name would smell as sweet” [1], but we beg to differ. The names that we choose to describe processes and concepts— biological or otherwise—profoundly influence the way we think about them. This is brought home when interdisciplinary research gathers together colleagues from diverse fields who struggle to understand what familiar words mean **in** new intellectual contexts. As biologi- cal research becomes increasingly interdisci- plinary, the use **of** “shared but different” technical terms becomes increasingly fraught. For example, biologists share many terms with computer scientists that describe both biological and digital phenomena, and communication becomes even more demand- ing when interacting with colleagues from the social sciences, for whom words can have completely different meanings. The difficul- ties are heightened with those terms that bio- logists have outright appropriated from other disciplines—albeit with good reason—but **in** doing so have stripped away their original nuance and meaning.

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Our final goal is to have both an abstract language dissociated from the concrete languages and an extensible abstract machine to process them. **In** particular this al- lows us to define parameterizable graph operators for instance to revisit classical structural metrics and adapt their definition to go beyond the pure structural calcula- tion and take into account the types **in** the graphs. **In** the longer term, we intend to perform search (e.g. homomorphism) and logical derivation (e.g. homomorphism and merge) but also approximation (e.g. distances), clustering (e.g. propagation), analysis (e.g. centrality), etc. jointly on the same graphs. We target the design **of** an abstract graph machine [35] generalizing operations needed by and sometime shared across different languages (e.g. SPARQL, RIF, POWDER, RDF/S and OWL inferences) and operations. **In** addition we also believe it is interesting to study alternatives to OWL stack and the associated DL-reasoning. For instance a rule-based semantic web with an alternative stack (RDF/S + SPARQL + Rules) provides certain advantages: rules are often more **natural** for humans, they support event-based programming and web service integration, they are usable both for domain independent and domain depen- dent inferences, etc.

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Keywords scope ambiguities, theta-roles, minimalist gram- mars, categorial grammars, λµ-calculus
1.1 Introduction
Many works have been done on Type-Theoretical Grammars since the famous books by Glyn Morrill (Morrill (1994)) and Aarne Ranta (Ranta (1994)), respectively based on the Categorial tradition (Lam- bek (1958), Moortgat (1997)) and on Martin-L¨ of’s Constructive Type Theory. More recently, much has been done, exploiting Curry’s distinc- tion between the tectogrammatical and the phenogrammatical levels, and this has led to interesting proposals like Lambda Grammars, Ab- stract Categorial Grammars and Convergent Grammars (de Groote (2001a), Muskens (2003), Pollard (2007)). Type-theoretic formulations **of** Minimalist Grammars have also been proposed (Lecomte and Retor´e (2001), Amblard (2007), Lecomte (2005), Anoun and Lecomte (2006)). All these works take care **of** problems like scope ambiguities which are traditional **in** the Montagovian perspective but they pay little attention to thematic roles and binding phenomena (except Anoun and Lecomte (2006) and Pollard (2007)). These questions have been more widely

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© Servier et EDK
430 M/S n° 4, vol. 25, avril 2009
these difficulties, numerous opportunities exist such as multiple unmet medical needs, the increasing incidence **of** certain diseases such as Alzheimer’s disease, cancer, diabetes and obesity due to demographic changes, as well as the emergence **of** evolving markets such as China, India, and Eastern Europe. Consequently, Pharma is now responding to this challenge by improving both the productivity and the innovation **in** its drug discovery and development pipelines. **In** this regard, the advent **of** new technologies and expertise such as genomics, proteomics, structural biology, and molecular informatics **in** an integrated systems biology approach also provides a powerful opportunity for Pharma to address some **of** these difficulties. The key features behind this new strategy imply a discovery process based on an improved understanding **of** the molecular mechanism **of** diseases and drugs, translational research that places the patient at the center **of** the research process, and the application **of** biomarkers throughout the discovery and development phases. Moreover, new paradigms are required to improve target validation and develop more predictive cellular and animal models **of** human pathologies, a greater capacity **in** informatics-based analysis, and, consequently, a greater access to the vast sources **of** accumulating biological data and its integrated analysis. **In** the present review, we will address some **of** these issues and **in** particular emphasize how the application **of** biomarkers could potentially lead to improved productivity, qua- lity, and innovation **in** drug discovery and ultimately better and safer medicines with improved therapeutic efficacy **in** specific pathologies

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mental properties, such as having a belief with some particular wide content, are extrinsic. properties that.do not supervene on a believer's intrinsic properties.[r]

Several structural and biochemical studies have shown that residues **of** the basic loop **of** eIF1 were important for the binding **of** the factor to the ribosome ( 14 , 15 , 17 , 18 , 57 ). Moreover, the cryo-EM structure **of** a Pa-PIC containing all initiation factors showed that aIF1 was bound to the ri- bosome **in** a manner equivalent to its eukaryotic homolog ( 24 ). Here, we show that R31, Y32 and K34 **of** the basic loop **of** Pa-aIF1 participate **in** the binding to the 30S. Moreover, some residues, such as Y32, are involved **in** the stabilization **of** the 30S:mRNA conformation (Table 1 , Supplementary Figure S6). Notably, although the basic character **of** loop 1 is conserved **in** archaea and eukaryotes, the consensus se- quences **in** the two phyla are idiosyncratic (Figure 1 C). An- other notable difference between eukaryotic and archaeal e /aIF2 and their homologues corresponds to the absence **of** the acidic loop 2 **in** the archaeal kingdom, as observed here and **in** ( 46 ). **In** eukaryotes, the acidic loop 2 was shown to participate **in** start codon selection by interacting with the D-stem-loop **of** the initiator tRNA ( 17 , 58 ). **In** addition, many archaeal aIF1 possess a zinc-binding knuckle **in** their N-terminal domain whereas this is never observed **in** eu- karyotic species. This may reflect adaptation **of** the role **of** e /aIF1 to either long-range or local scanning mechanism. Interestingly, variations **of** the loop 1 and loop 2 sequences were also noted **in** the SUI1 homologous domains **of** eIF2D and DENR implicated **in** eukaryotic re-initiation, another different mechanism for start codon selection ( 59 , 60 ).

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