Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation and Refinement of Testing Models

Writing property-based testing models is a challenging task. This article introduces a new tool, Faktory, which is capable of automatically generating an executable property-based testing model from less complicated sources: normal function type specifications, and traditional function calling contracts using pre- and post-conditions. Concretely, Faktory is an Elixir library which from an API annotated with executable calling contracts written using the Corsa contract checking library, automatically generates a property-based testing model in the form of a state machine implemented using the Makina state machine DSL. In the article we illustrate the functionalities of the Faktory tool using a number of examples. The first one shows how to test a functional data structure; the second shows how to improve test-case generation by reusing test results; and in the third example a stateful key-value storage is tested by first deriving an initial test model using Faktory, and then refining the generated model using the Makina model/state machine extension mechanism.
Advances in Protein Chemistry, Volume 65: Proteome Characterization and Proteomics

1 CombinatoRx, Incorporated, Cambridge, MA, USA, 2 Bioinformatics and Biomedical Engineering, Boston University, Boston, MA, USA and 3 Department of Biological Sciences and Department of Chemistry, Fairchild Center, Columbia University, New York, NY, USA * Corresponding author. CombinatoRx, Incorporated, 245 First St, Cambridge, MA 02142, USA. Tel. : þ 1 617 301 7151; Fax: þ 1 617 301 7110; E-mail: jlehar@combinatorx.com or jlehar@alum.mit. edu
Islands, Metapopulations, and Archipelagos: Genetic Equilibrium and Non-equilibrium Dynamics of Structured Populations in the Context of Conservation

Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent nonequilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium. I used nuclear and mitochondrial genetic data from populations of two species of reptiles from the Turks and Caicos Islands, British West Indies to test for patterns of equilibrium vs. non-equilibrium. I found unexpected shallow genetic divergence in the Turks Island boa (Epicrates chrysogaster), indicating that this
Sequential breakdown of the complex Cf-9 leaf mould resistance locus in tomato by Fulvia fulva

Leaf mould, caused by Fulvia fulva, is a devastating disease of tomato plants. In many commercial tomato cultivars, resistance to this disease is governed by the Cf-9 locus, which comprises five paralogous genes (Cf-9A–9E) that encode receptor-like proteins. Two of these proteins contribute to resistance: Cf-9C recognizes the previously identified F. fulva effector Avr9 and provides resistance during all plant growth stages, while Cf-9B recognises the yet-unidentified F. fulva effector Avr9B and provides mature plant resistance only. In recent years, F. fulva strains have emerged that have overcome the Cf-9 locus, with Cf-9C circumvented through Avr9 deletion. To understand how Cf-9B is circumvented, we set out to identify Avr9B. Comparative genomics, in planta transient expression assays and gene complementation experiments were used to identify Avr9B, while gene sequencing was used to assess Avr9B allelic variation across a worldwide strain collection. A strict correlation between Avr9 deletion and resistance-breaking mutations in Avr9B was observed in strains recently collected from Cf-9 cultivars, whereas Avr9 deletion but no mutations in Avr9B were observed in older strains. This research showcases how F. fulva has evolved to sequentially break down the two functional resistance genes of the complex Cf-9 locus and highlights that this locus now has limited value for controlling leaf mould disease in worldwide commercial tomato production.
Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules

The multilevel summation method computes an approximation to the pairwise electrostatic interaction potential and respective forces. The scalar potential is smoothly split into a short-range part computed exactly and a slowly varying long-range part approximated from a hierarchy of grids. Multilevel summation is especially appropriate for the dynamical simulation of biomolecules, because it computes continuous forces that are the gradient of a scalar potential. It provides a unified approach to computing electrostatics, in which the same method can be used for periodic and nonperiodic boundary conditions, with an amount of work that scales linearly as the size of the system. Multilevel summation is also flexible enough to be applied to other pairwise potentials. This thesis provides the most thorough investigation to date of the multilevel summation method and its use for computing electrostatic interactions. The mathematical and algorithmic details are presented along with a precise operation count. The approximation error from the method is analyzed, with error bounds formulated in terms of the fundamental method parameters. The cost and error analyses enable the determination of optimal method parameters for a desired error tolerance. Various interpolation schemes for the approximation are considered, and several alternative approaches to smoothing the electrostatic potential are examined. The use of the method with different boundary conditions is discussed, and it is shown that the application of multilevel summation to the periodic potential yields a finite sum, with the truncation expressed as bounded approximation error. The performance of multilevel summation is demonstrated to be superior to other commonly used fast methods for electrostatics, while providing comparable accuracy. The method is also shown to produce stable dynamics for cheaper, lower accuracy approximation.
Caractérisation par méthodes ultrasoniques de la zone endommagée induite par le creusement d'un tunnel en milieu argileux : cas d'étude au tunnel du Mont Terri, Suisse

L'interet croissant d'utiliser les argiles gonflantes pour des sites de stockages profonds a motive un travail de recherche sur la caracterisation des dommages induits par le processus de creusement. Il est, en effet, primordial de pouvoir qualifier la zone endommagee lors du creusement du tunnel si des matieres sensibles doivent par la suite y etre stockees et les phenomenes de diffusion controles au mieux. La recherche menee dans cette these a eu pour objectif de contribuer a qualifier et quantifier les dommages induits par des changements de contrainte sur un materiau fortement anisotrope en utilisant des techniques ultrasoniques. Deux etudes ont ete menees, en laboratoire puis sur site, afin de determiner d'eventuels facteurs d'echelle. En laboratoire, nous avons mesure l'activite des emissions acoustiques et les vitesses de propagation des ondes P en appliquant une contrainte compressive uniaxiale. Les courbes contraintes/deformations, avec l'aide des distributions d'emissions acoustiques, ont permis de discerner les differentes etapes geomecaniques des echantillons menant a la rupture. L'ecoute des emissions acoustiques a d'autre part montre que 80% de l'activite etait enregistree dans la phase de chargement precedant juste la rupture. Les mesures sur site ont ete collectees durant le creusement d'une galerie experimentale lors du projet Mont Terri. Un reseau ultrasonique a ete installe au parement d'une galerie a creuser afin de surveiller et quantifier les changements de proprietes au sein du volume limite par les sondes sismiques lors de l'excavation. En raison de forages multiples des sondages, une zone endommagee autour des sondages, qui a ete identifiee, a fortement altere la quantite et la qualite des donnees.
-1-Alteration of the Function of the UDP-Glucuronosyltransferase 1A Subfamily by Cytochrome P450 3A4: Different Susceptibility for UGT Isoforms and UGT1A1/7 Variants

-3-ABSTRACT Functional protein-protein interactions between UDP-glucuronosyltransferase (UGT)1A isoforms and cytochrome P450 (CYP)3A4 were studied. To this end, UGT1A-catalyzed glucuronidation was assayed in Sf-9 cells which simultaneously expressed UGT and CYP3A4. In the kinetics of UGT1A6-catalyzed glucuronidation of 5-HT, both K m and V max were increased by CYP3A4. When CYP3A4 was co-expressed either with UGT1A1 or 1A7, the V max for the glucuronidation of the irinotecan metabolite (SN-38) was significantly increased. The S 50 or K m was little affected by simultaneous expression of CYP3A4. This study also examined the catalytic properties of the allelic variants of UGT1A1 and 1A7, and their effects on the interaction with CYP3A4. While the UGT1A1-catalyzing activity of 4-methylumbelliferone glucuronidation was reduced in its variant, UGT1A1*6, the co-expression of CYP3A4 restored the impaired function to a level comparable with the wild-type. Similarly, simultaneous expression of CYP3A4 increased the V of UGT1A7*1 (wild-type) and *2 (N129K and R131K), whereas the same was not observed in UGT1A7*3 (N129K, R131K and W208R). In the kinetics involving different concentrations of UDP-glucuronic acid (UDP-GlcUA), the K m for UDP-GlcUA was significantly higher for UGT1A7*2 and *3 than *1. The K m of UGT1A7*1 and *3 was increased by CYP3A4, whereas *2 did in the presence of 2 mM UDP-GlcUA with 10 substrate concentrations ranging from 10 to 500 µ M (UGT1A*1) and from 20 to 800 µ M (UGT1A1*6); b ranging from 2 to 100 µ M; c ranging from 8 to 500 µ M (UGT1A*1) and from 10 to 500 µ M (UGT1A1*6). Data were fitted to a Michaelis-Menten equation. Results are the estimated value ± S.E. ( ¶¶ , p <0.001; ¶¶¶ , p <0.0001 from *1)( $ , p =0.018; $$ , p <0.001; $$$ , p <0.0001 from single expression)
Being No One : The Self-Model Theory of Subjectivity by Thomas Metzinger

The notion of consciousness has been suspected of being too vague for being a topic of scientific investigation. Recently, consciousness has become more interesting in the light of new neuroscientific imaging studies. Scientists from all over the world are searching for neural correlates of consciousness. However, finding the neural basis is not enough for a scientific explanation of conscious experience. After all, we are still facing the ‘hard problem’, as David Chalmers dubbed it: why are those neural processes accompanied by conscious experience at all? Maybe we can reformulate the question in this way: Which constraints does a system have to satisfy in order to generate conscious experience? Being No One is an attempt to give an answer to the latter question. To be more precise: it is an attempt to give an answer to the question of how information processing systems generate the conscious experience of being someone. We all experience ourselves as being someone. For example, at this moment you will have the impression that it is you who is actually reading this review. And it is you who is forming thoughts about it. Could it be otherwise? Could I be wrong about what I myself am experiencing? Our daily experiences make us think that we are someone who is experiencing the world. We commonly refer to this phenomenon by speaking of the ‘self’. Metzinger claims that no such things as ‘selves’ exist in the world. All that exists are phenomenal selfmodels, that is continuously updated dynamic self-representational processes of biological organisms. Conscious beings constantly confuse themselves with the content of their actual phenomenal self-model, thinking that they are identical with a self. According to Metzinger, this is due to the nature of the representational process generating the self-model. The selfmodel is mostly transparent – the information that it is a model is not carried on the level of content – we are looking through it, having the impression of being in direct contact with our own body and the world. If you are now thinking that this idea is at least counterintuitive, you should read Being No One and find out why it is counterintuitive, and yet that there are good reasons to believe that it is correct. The first chapter of the book is introductory in style. Here, Metzinger points to a problem in consciousness research: on the one side, scientists have been too focused on generating em-
Sync: The Emerging Science of Spontaneous Order

"Sync" is a story of a dazzling kind of order in the universe, the harmony that comes from cycles in sync. The tendency to synchronize is one of the most far-reaching drives in all of nature. It extends from people to planets, from animals to atoms. In "Sync" professor Steven Strogatz considers a range of applications - human sleep and circadian rhythms, menstrual synchrony, insect outbreaks, superconductors, Lasers, secret codes, heart arrhythmias and fads - connecting all through an exploration of the same mathematical theme: self-organization, or the spontaneous emergence of order out of chaos. Focused enough to present a coherent world unto themselves, Strogatz's chosen topics touch on several of the hottest directions in contemporary science.
Population Size and Total Estimation When Sampling From Incomplete List Frames With Heterogeneous Inclusion Probabilities

Information from list and area sampling frames is combined to obtain efficient estimates of population size and totals. We consider the case where the probabilities of inclusion on the list frames are heterogeneous and are modeled as a function of covariates. We adapt and modify the methodology of Huggins (1989) and Alho (1990) for modeling auxiliary variables in capture­recapture studies using a logistic regression model. We present the results from a simulation study which compares various estimators of frame size and population totals using the logistic regression approach to modeling heterogeneous inclusion probabilities.
Equilibrium Profile of Ice Shelves

Abstract Using expressions for ice-shelf creep derived by Weertman (1957) and Thomas (1973[b]) a general method is developed for calculating equilibrium thickness profiles, velocities, and strain-rates for any ice shelf. This is done first for an unconfined glacier tongue and the result agrees well with data for Erebus Glacier tongue (Holdsworth, 1974). Anomalies occur within the first 3 km after the hinge zone and these are too great to be the result of local bottom freezing; they are probably due to disturbance of the velocity field. Secondly, profiles are calculated for bay ice shelves. Thickness gradients are largely independent of melt-rate or flow parameters but are inversely proportional to the width of the bay. Data from Antarctic ice shelves agree with this result both qualitatively and quantitatively. The theory is readily extended to ice shelves in diverging and converging bays. An ice shelf in a diverging bay can only remain intact if it is thick enough and slow enough to creep sufficiently rapidly in the transverse direction. If it cannot, it will develop major rifts or will come adrift from the bay walls. It is then likely to break up. The presence of ice rises or areas of grounding towards the seaward margin can radically alter the size of the ice shelf which can form. The theory could be used as a starting point to study non-equilibrium behaviour.
With or Without You : Time Use Complementarities and Divorce Rates in the USA ∗

The aim of this article is to test the possibility of studying the dynamics of the American divorce rate through the explicit introduction of “consumption complementarities”within the household, as suggested by Stevenson and Wolfers (2007). The proposed empirical analysis is based on two main data sources: The extent of the changes in time consumption patterns of couples in the last forty years are analysed with the American Time Use Data; the impact of these changes on divorce probabilities is then studied making use of several datasets from the National Longitudinal Study, covering the period 1967-2004. The results tend to confirm the emergence over time of new schemes of time consumption among American families. These findings, together with the way couples share household responsibilities, might play a relevant role in shaping individuals’ marital market decisions and can be used to at least partially explain the trends in the divorce rate. JEL Classification: J12, J13, D12, D86.
Multidisciplinary process integration and design optimization of a classroom building

SUMMARY: Architecture, Engineering, and Construction (AEC) professionals typically generate and analyze very few design alternatives during the conceptual stage of a project. One primary cause is limitations in the processes and software tools used by the AEC industry. The aerospace industry has overcome similar limitations by using Process Integration and Design Optimization (PIDO) software to support Multidisciplinary Design Optimization (MDO), resulting in a significant reduction to design cycle time as well as improved product performance. This paper describes a test application of PIDO to an AEC case study: the MDO of a classroom building for structural and energy performance. We demonstrate how PIDO can enable orders of magnitude improvement in the number of design cycles typically achieved in practice, and assess PIDO’s potential to improve AEC MDO processes and products.
navigating into the binding pockets of the her family protein kinases: discovery of novel egFr inhibitor as antitumor agent

: The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10 ) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase–ligand interaction space in the PDB.
Topology optimization based on improved DoubleU-Net using 4 structured datasets

Topology optimization is widely used in the engineering design phase to maximize product performance by mathematically modeling and optimizing the distribution of materials in the design space. However, deep learning to solve the topology optimization problem suffers from insufficient data and weak adaptability of the training model boundary conditions. Therefore, a Topy library-based data sample generation method is used to generate 400,000 2D samples of four types of boundary conditions for random structures, cantilever beams, continuous beams and simply supported beams, each containing two types of resolution data, and to expose this dataset. An improved DoubleU-Net network is proposed for topology optimization with high accuracy prediction in real time. In the generated dataset, the average IoU accuracies of the models for four structures, namely, random beam, cantilever beam, continuous beam and simply supported beam, are 93.26%, 96.71%, 96.35% and 97.38, respectively, and the experimental results show that DoubleU-Net can better adapt to different resolution data. The model trained with the random structure dataset
Intellectual Property Rights, Imitation, and Foreign Direct Investment: Theory and Evidence

What is the e¤ect of a strengthening of intellectual property rights (IPR) protection by developing countries on local imitation and inows of foreign direct investment (FDI)? We address this question both theoretically and empirically. On the theoretical side, we develop a North-South product cycle model in which Northern innovation, Southern imitation, and FDI are all endogenous. This model predicts that IPR reform in the South leads to increased FDI from the North, as Northern rms shift production to Southern a¢ liates. We confront the theoretical model with evidence on the response of U.S. multinationals to a series of well-documented IPR reforms by developing countries in the 1980s and 1990s. Our results indicate that U.S.-based The statistical analysis of rm-level data on U.S. multinational enterprises was conducted at the International Investment Division of the Bureau of Economic Analysis, U.S. Department of Commerce under arrangements that maintain legal con dentiality arrangements. The views expressed herein are those of the authors and do not reect o¢ cial positions of the U.S. Department of Commerce. We wish to thank Amy Glass, Fuat Sener, and seminar participants at Columbia University for helpful comments. We are grateful to Yoshiaki Ogura and Sergei Koulayev for excellent research assistance and to the National Science Foundation for nancial support.