dataesr/scientific-paragraphs-categorization huggingface dataset:
e. , simple constraints expressing name equalities. Example 11 (Name passing) Assume two components P and Q of a system such that P creates a local variable that must be shared with Q. This system can be modeled as: P = (local y) (x y. P ) Q = x z. Q In P Q, P sends the private name y on channel x and synchronizes with Q leading to (local x) (P Q tell(y = z)). Similar to the non-monotonic extension of scc reported in  [31] , cc-pi also introduces retraction of constraints (retract c) whose effect is to erase a previously told constraints. Furthermore, it is possible to check if a given constraint c is consistent with the current store though the prefix check c. Another line of development in this direction was the π + -calculus  [66]. This language is an extension of the π-calculus  [140]  with constraint agents that can perform tell and ask actions.
Programming Languages Based on the CCP Model Several CCP programming languages have been designed. These cover a wide spectrum going from syntactic sugar over a particular CCP calculus, to graphical representations of the calculus primitives and to full fledged general purpose multiparadigm languages. Early CCP languages took inspiration in constraint logic programming (CLP), where unification was replaced by constraint solving. An example is the language cc(F D)  [111]  that implements an efficient finite domains constraint system. The CLP model was implemented in various languages, each with a suitable constraint system (finite domains, booleans, real numbers). Nevertheless, these languages lacked flexibility since problem solving had to be tailored to the specific fix set of predefined constraints.
In contrast, cc(F D) offered general-purpose combinators, applicable to any constraint system, such as constructive disjunction and blocking implication  [111]. These, together with entailment, allow the language to be tailored to specific user domains without losing the "naturalness" of specifications. Programs in cc(F D) are written in a Prolog-like syntax and user constraints are translated into canonical forms called indexicals  [56]  that can be implemented very efficiently. Even though solving constraint problems remains an important goal of CCP languages, they have mostly evolved into powerful ways to define complex synchronization schemes in concurrent and distributed settings. In the rest of this section we describe some of the systems and programming languages built on the ideas of the CCP model.
The committed-choice feature of CHR is used to represent each when c i do P i process in a non-deterministic choice i∈I when c i do P i as a simplification rule of the form summation( (. ) ) ⇐⇒ c i | P i. The committed choice ensures that when this rule is chosen (c i holds) none of the other rules for ask constructs in the summation can be used. As mentioned, a key feature of CHR is the possibility of its embedding in many different types of programming languages (logic, functional, explicit-state), such as CHR(Prolog), CHR(Haskell), CHR(C). Various applications, ranging from Multi-Agent systems to language processing (CHR grammars) or software testing have been developed in CHR. A summary of these can be found in  [199]. The simplicity and expressivity of CHR have attracted the attention of several researchers.
Interpreters for CCP Calculi Similar to jcc, some other interpreters for the calculi described in Section 3 have been implemented. In the context of lcc, SiLCC (http://contraintes. rocq. inria. fr/ ˜tmartine/silcc/) is an implementation of the language with a module system as described in  [106]. Furthermore, ALCOVE Aeminium Linear COnstraints VErifier (http://avispa. puj. edu. co) is a lcc-based tool for the analysis of access permissions in concurrent-by-default programs written in Aeminium  [201]. The ntcc calculus has been implemented as ntccSim (http://avispa. puj. edu. co), an interpreter written in the Oz language. An important feature of this tool is that several constraint systems can be included in the same model. For instance, constraints over finite domains (FD) and real intervals (XRI) have been used to implement computational models of biological system (see Section 5.
3). The ntccrt interpreter for the ntcc calculus (http://sourceforge. net/projects/ntccrt/) is written in C++ and specifications can be made in Common Lisp or in OpenMusic (http://repmus. ircam. fr/openmusic/), and then translated to C++. This framework can be also integrated as a plugin for either Pure Data (PD) or Max/MSP  [169]  to take advantage of the facilities offered by those languages to implement, for example, sound processors. ntccrt makes use of the state of the art propagation techniques in Gecode (http://www. gecode. org/) to implement the underlying constraint system. Hence, the system is able to deal with real-time requirements for the execution of ntcc models in the context of computer-based musical improvisation (see Section 5. 2). In  [130]  an interpreter for tccp written in Maude is described (http: //users.
dsic. upv. es/ ˜villanue/tccp-func/). As for hcc, at http: //www-cs-students. stanford. edu/ ˜vgupta/hcc/ the reader may find an interpreter for this language. Finally, k-stores  [16]  is an interpreter for the epistemic and spatial calculus in Definition 17. In the context of CHR, implementations of Prolog such as SWI-Prolog (http: //www. swi-prolog. org) and SICStus Prolog (http://sicstus. sics. se) feature modules for CHR. WebCHR is a web tool that allows the execution of Prolog and CHR programs (http://chr. informatik. uni-ulm. de/ ˜webchr/). Implementations of CHR for different programming languages such as Java, C and Haskell can be found at http://chr. informatik. uni-ulm. de/. The system CHRat  [76]  implements a modular version of CHR that allows for reusing built-in constraints, defined in a constraint system, as a constraint solver in another CHR program (http: //contraintes.
g. in  [74, 32]. For instance, in  [32]  it is shown that hcc can naturally model a variety of biological phenomena, such as reaching thresholds, kinetics, genetic interaction and biological pathways. In  [46] , the authors carry out a comparative study of sCCP, hcc, and Biocham  [75]  as languages for the modeling of biochemical reactions. In  [26]  the authors compare the sCCP, ntcc, and hcc models for the blood coagulation process. Experimental results are shown when using the interpreters of hcc and ntcc to simulate the system. Finally,  [178]  makes use of a linear CCP language to model protein interaction. The work in  [160]  uses CCP techniques for the protein structure prediction problem, which consists in predicting the 3D native conformation of a protein, when its sequence of amino acids is known.
This system gives guarantees that a channel name and encrypted values are only extracted by agents that are able to infer the channel or the non-encrypted value from the store. An extension of tccp  [34]  is studied in  [129]  as a language for modeling security protocols. The authors show how the language can naturally express the behavior of the principals in the protocol and a Dolev-Yao attacker  [67]  for verification purposes. In  [118] , a policy language for role-based access control in distributed systems along the lines of Default tcc is proposed. The authors combine constraint reasoning and temporal logic model-checking to verify whether a given resource (e. g. a directory in a file system) can be accessed. Soft Concurrent Constraint Programming based languages have been used in the modeling and verification of service oriented computing systems.
The cc-pi calculus, for instance, has been used to specify Quality of Service (QoS) and to conclude Service Level Agreement (SLA) contracts  [50]. The language is equipped with mechanisms for resource allocation and for joining different SLA requirements to reach an agreement between agents (clients and servers) in a service oriented computing scenario. In  [53] , the non-deterministic choice in cc-pi is replaced by a prioritized guarded choice. Alternatives are labeled with constraints and the chosen one corresponds to the constraint with a higher priority over the constraints of the alternative branches. The prioritized calculus is then used to express richer QoS negotiations where agents may state preferences between a set of possible alternatives. See also  [52]  where an overview of cc-pi and prioritized cc-pi is given.
Type rules statically ensure that a predefined communication scheme/protocol (typically based on duality) is respected along process execution. The work in  [133]  studies an encoding of the language for structured communications proposed in  [115]  into utcc. The framework allows for the declarative analysis of sessions in network protocols. Furthermore, due to the timed nature of utcc, it is possible to reason about session duration and expiration in structured communications. In  [59] , the authors combine CCP and name passing in the style of cc-pi together with sessions. The resulting calculus aims at specifying QoS requirements where safe interactions between clients and servers are assured. The primitive used to open a session makes use of constraints whose satisfaction is necessary for starting and conducting the session interaction.
This model is then compiled into a target calculus close to the prioritized cc-pi calculus  [53]  where named constraint semirings  [50]  encode the behaviors of agents. More precisely, the choices in the compiled model are guarded by check (ask) constructs that enable the corresponding continuation only if the global store allows it. The novelty of this approach relies on the fact that constraints are used to choose the right interaction and to avoid deadlock in the execution phase. That is, the combination of the constraints of the client and the server leads only to executions of the client-service system that do not stuck. Propositional Contract Logic (PCL)  [17]  extends intuitionistic logic with a contractual form of implication. This logic aims to model SLA contracts to formalize the duties of the client and the server in a service oriented scenario.
Other Applications and Results In  [206] , a Büchi finite state automata characterization of the strongest postcondition of the local independent fragment of the ntcc calculus is given. Using this characterization, the author proves the decidability of the satisfaction problem for the restricted negation formulas without rigid variables in linear temporal logic  [135]. The work in  [209]  studies the execution of formal specifications in SPECS-C++, a model-based formal specification language designed for specifying the interfaces of C++ classes. Since this specification language was not designed to be executed, the approach proposed by the authors is to translate such a formal specifications into the CCP based language AKL  [109]. A subset of the specifications in SPECS-C++ can be then executed in AKL.
The elegant semantic characterization of CCP has been extended to its subcalculi. In  [182] , tcc processes are denoted as closure operators on sequences of constraints. Then, for instance, the sequence c 1. c 2. c 3. is quiescent for next P only if the subsequent c 2. c 3. is quiescent for P. Similarly,  [153]  gives a denotational semantics to the ntcc calculus. This idea is also present in  [157]  where processes are identified with closure operators on sequences of linear temporal logic formulas  [135]  for the case of the utcc calculus. As for tccp, in  [34]  it is shown that the full abstraction problem for this language cannot be reduced to that one of CCP. Then, a semantics based on reactive sequences is proposed to be correct with respect to the notion of observables and fully abstract.
Such judgments are valid if and only if the intersection of the denotations of the agents P 1 ,. , P n is contained in the denotation of P ; equivalently, any observation that can be made from the parallel system of agents P 1 ,. , P n can also be made from P. The results in  [33]  are extended and strengthened in  [153] , where a linear temporal logic characterization of ntcc is studied along with a proof system to verify properties. In the same lines,  [158]  gives a logic characterization for the utcc calculus. A temporal logic based on the epistemic modalities of knowledge and belief is proposed in  [35]. The assertions in the logic capture what a process assumes from the input (the environment) and what a process commits to, i. e. , the outputs in a given time-unit. Then, this logic provides a language for the specification of the reactive behavior of processes.
A sound a complete proof system to reason about the correctness of tccp programs based on this logic is reported in  [35]. Model checking techniques have been also explored in the context of temporal CCP languages. In  [3, 85] , the behavior of tccp processes is modeled by means of a so called tccp structure. Such structure is like a Kripke structure where, following the CCP philosophy, the state of the system is represented as a conjunction of constraints. This allows for the specification of the possible states and transitions the system may exhibit. Then, the modal logic in  [35]  is used to specify the property to be verified and the model checking graph is analyzed to decide if the process satisfies or not the property. A tool implementing the construction of the tccp structure is described in  [131].
The work of  [85]  was based on the ideas developed for the automatic verification of tcc programs in  [84]. In order to mitigate the state explosion problem,  [5]  considers an abstract modelchecking technique where both the model and the property to be verified are abstracted. Following a data-abstraction approach, abstract operations are defined to over approximate the behavior of the original program. The authors identify that an overapproximation is not sufficient to give an accurate approximation of the synchronization and timed mechanisms of tccp. Then, under-approximations of the semantics are considered to improve accuracy. The authors prove the total correctness of the abstract semantics which models precisely the suspension of processes. The abstract semantics is also implemented as a source-to-source transformation that compiles the abstract program back into tccp.
Abstract refinements are also proposed to improve accuracy in the verification process. The work in  [5]  is extended in  [7]  where the authors study a general framework for abstract verification and analysis of concurrent programs. The programs considered in this study are imperative (states as variable valuations) and declarative (states as conjunction of constraints as in tccp) style. The semantics is approximated and implemented as a source-to-source transformation that interprets the abstract actions into the original language. Finally, we mention the work of  [6]  that proposes a new semantics for tccp able to recognize the time instant when some piece of information is added to the store. The logic in  [35]  is also extended with discrete-time marks to model synchronous real-time properties.
CELL NUMBER QUANTIFICATION All images were acquired using a confocal microscope (Zeiss LSM 710 Quasar Carl Zeiss, Oberkochen, Germany). The total number of immunoreactive cells was estimated throughout the entire granule cell layer using stereological sampling, as previously described  (Thuret et al. , 2009) , between -1. 3 to -2. 9 mm from the Bregma. For each animal, a 1-in-6 series of sections was stained with the nucleus marker DAPI and used to measure the volume of the granule cell layer. The granule cell area was traced using Axiovision (Zeiss, Germany) software and the granule cell volume was determined by multiplying the traced granule cell layer area by the thickness of the corresponding section and the distance between the sections sampled (240 μm). For all mice analyzed in this study, no difference of volume was found between groups [One-Way ANOVA, F (3, 15) = 0.
29, p = 0. 82], (data not shown). All cells were counted blind with regard to the mouse status. The number of labeled cells was counted for each section, in the entire thickness of the granular cell layer of the DG with a 40x objective. RGL cells and cells expressing BrdU, Ki-67, DCX or Tbr2 were counted in an area containing the granule cell layer and the subgranular zone, whereas cells expressing Iba1, MHC-II and GFAP (Figures  2A, D, F ) were counted in an area including the sub-granular cell layer, the granule cell layer, the molecular layer and the hilus. Cells expressing Iba1 (Figure  2B ) were also counted in the primary somatosensory cortex (S1). For in vitro cell quantification, images were acquired using confocal microscopy. The numbers of RFP-expressing NPCs, Iba1-expressing microglia and GFAP-expressing astrocytes were counted in 4 selected fields, systematically placed in the same positions relative to the coverslips' edges.
STATISTICAL ANALYSIS Hypothesis testing was two-tailed. All analyses were performed using JMP10 software. First, Shapiro-Wilk tests were performed on each dataset to test for distribution normality. The distribution was normal for all data. To test for possible interaction between the 2 groups (Aging and Running) a Two-Way ANOVA was performed. When an interaction was found, a One-Way ANOVA test was performed, if no interaction was found, we analyzed each variable independently using a Two-Way ANOVA. All analyses were followed by a post-hoc Tukey HSD test. In order to test linear correlation, Spearman correlation test was performed. Results are expressed by the Spearman correlation coefficient (ρ) and the p-value. Data is presented as mean ± standard error of the mean (SEM).
Brains were sectioned and immunostained for BrdU and markers for adult neurogenesis and microglia. We first assessed cell proliferation in the granule cell layer of the DG. A Two-Way ANOVA test revealed that there is interaction between aging and running for Ki-67 marker In the DG, proliferative cells are divided in 2 main cell populations: the type 1, radial glia-like (RGL) stem cells and the type 2, TAPs. RGL cells were identified by the expression of GFP, their nucleus located in the subgranular zone and a radial process extending through the granule cell layer and branching into the molecular layer  (Huttmann et al. , 2003; Mignone et al. , 2004; Kriegstein and Alvarez-Buylla, 2009; Beckervordersandforth et al. , 2010). They expressed the selfrenewal factor Sox2 (data not shown). For RGL, Two-Way ANOVA test showed that there is interaction between aging and running [F NR 8 M vs.
FLOW CYTOMETRY ANALYSES For the GFPi-mRFP assays, flow cytometry data were acquired with a MoFlo (Dako Cytomation-Beckman Coulter). RFP was excited with a 561-nm CrystaLaser GCL-050-561 50 mW DPSS laser coupled to fiber optics (38 mW output) and emission detected using a 630/75-nm bandpass filter on channel 7 (FL7); GFP was excited with a 488-nm Coherent Sapphire 488-200 CDRH (140 mW output) and emission detected using a 530/40-nm filter pass on channel 1 (FL1). In some cases, experiments were reproduced with data acquired with a BD FACSAria III: RFP was measured on the PE-Texas Red/mCherry channel, excited with a Yellow Green 561 nm Laser and emission detected with a 610/20nm filter pass; GFP was measured on the FITC channel, excited with a 488-nm Blue Laser and emission detected with a 530/30-nm filter pass.
For the GFPi-CFP assay, data were acquired on a CyAn ADP (Beckman Coulter), a BD FACSAria III or on a LSR Fortessa (BD Bioscience), using a 96well-plate auto sampler. GFP was excited and detected using the same wavelengths as described above for the MoFlo when using the CyAn ADP or as described for the FAC-SAria III when using the LSR Fortessa analyzer. The CFP was either excited by a 405-nm laser using a 450/50-nm filter for detection or by a 442-nm Blue-Violet laser and measured using a 470/20-nm filter pass (LSR Fortessa) which considerably increased the mean fluorescence intensity of the CFP. Data were collected with the following programs: FACSDiva (BD Bioscience) for the LSR Fortessa and FACSAriaIII, Summit (Beckman Coulter) for the Cyan ADP and the MoFlo. In all cases, data analysis was performed using the FlowJo software (Tree Star Inc.
The apparent recombination coefficient ρ a is estimated by fitting the expression to empirical data of the relative frequency of cells without recombined plasmids, denoted F 0 (x), as a function of the x-signal intensity, i. e. , the relative frequency of GFP -cells as a function of intensity of RFP signal (illustrated in Figure  3F ). The data processing, model fitting and estimation were performed in R. Briefly, bivariate (RFP signal, GFP signal) data were exported from FlowJo as scaled values after appropriate gating and subsequently imported into the statistical software R. The function log 10 (y) = log 10 (x 0 + b 0x ) is fitted to data from samples without nominal RAG activity by minimizing least-squares and ensuring that the residuals have mean zero and no trends, and the standard deviation of the residuals S 0 computed.
This difference was not quantifiable by simple percentage analysis but revealed by a relative recombination coefficient ρ of 2. 3 × 10 -4 ± 0. 5 × 10 -4 , close but above the minimum value detectable in the controls (5 × 10 -5 ). This case also illustrates that when RAG is limiting, only cells with high RFP expression levels, hence with high copy number of GFPi, rearrange enough GFPi to emit a detectable signal. Monitoring GFP + frequency in the last percentiles of RFP intensity also enhances the sensitivity of the analysis, although this approach is more easily confounded by variation in the flow cytometry analyzer settings (not shown). Finally, we evaluated by western blot analysis that RAG1/2 expression was about 10-fold increased when driven by CMV instead of H2k, after equimolar transfection (data not shown).
ACKNOWLEDGMENTS This work was supported by The  Portuguese League Against Cancer and The Terry Fox Foundation  through a prize awarded to  Leonor M. Sarmento  as well as by the Fundação para a Ciência e a Tecnologia: grants  PTDC/BIA-BCM/108020/2008  to  Vasco M. Barreto  and  PTDC/BIA-GEN/116830/2010  to  Jocelyne Demengeot ; fellowships to  Inês Trancoso ,  Marie Bonnet  and  Leonor M. Sarmento ; contract to  Rui Gardner. We thank,  Carlos Penha Gonçalves ,  Alekos Athanasiadis , and  José Pereira Leal  for helpful discussions and  Telma Lopes  for technical assistance with FACS analysis.
Material and method The study is based on one specimen (No. CNU-ODO-NN2012004, positive imprint and negative imprint) housed in the Key Laboratory of Insect Evolution and Environmental Changes, Capital Normal University, Beijing, China. The specimen was examined with a Leica MZ12. 5 dissecting microscope and illustrated with the aid of a drawing tube attached to the microscope. Line drawings were made using Adobe Photoshop CS graphic software. We use the following standard abbreviations: AA, anal vein; AP, anal posterior; Ax0 Ax1 Ax2, primary antenodal cross-veins; CuAa, distal branch of cubitus anterior; CuAb, proximal branch of cubitus anterior; IR1, IR2, intercalary radial veins; MAa, distal branch of median anterior; MAb, posterior branch of median anterior; MP, median posterior; N, nodus; O, oblique vein; Pt, pterostigma; RA, radius anterior; and RP, radius posterior; ScP, subcosta posterior.
Acknowledgements We thank the two anonymous reviewers for their valuable comments. This research is supported by the  National Basic Research Program of China  ( 973 Program ) (2012CB821906), the  National Natural Science Foundation of China  (No. 31071964 ,  31230065 ,  41272006 ),  Key Project of Beijing Municipal Commission of Education  ( KZ201310028005 ) and  China Geological Survey  ( 1212011120116 ).