Miracle-dz/UniFAR-FTUs huggingface dataset:
Proceedings of the 9 th International Workshop on Satisfiability Modulo Theories ( SMT ) 2011

s of Invited Talks Software Construction using Executable Constraints. Viktor Kuncak (EPFL) Constructing software that satisfies the desired properties can greatly benefit from solvers based on satisfiability modulo theories (SMT) paradigm. We propose a research program in which software construction and SMT technology become even more interconnected than today. Instead of checking properties of low-level legacy programs, new generations of SMT solvers could focus on constructing programs and values within compilers and run-time systems of declarative programming languages designed with constraint solving in mind. This agenda has implications on both theories and interfaces of future SMT solvers. The theories of interest come in part from functional programming languages and from data structure libraries. They include algebraic data types (term algebras), arrays, maps, sets, and multisets, extended with recursively defined functions. New interfaces for SMT solvers are driven by their extended role: in addition to yes/no satisfiability answers, we need synthesis of values and programs. To answer declarative queries at run-time, we need efficient generation and fair enumeration of models, as well as their mapping to programming language values. To support the compilation of implicit specifications, we need SMT solvers that can solve parameterized problems and perform constraint simplification. Ultimately, SMT solvers can become virtual machines for constraint programming, working with data structures directly manipulated by programs, and performing selective specialization of frequently invoked constraint solving paths. This is joint work with: Barbara Jobstmann, Ali Sinan Koeksal, Ruzica Piskac, and Philippe Suter. More information at http://lara.epfl. ch/w/impro and http://richmodels.org . When Biology Meets (Symbolic) Computing: Algebra, Biology, Computability and Diophantus. Bud Mishra (NYU) In this talk, I will introduce a new approach to compositional and hierarchical modeling of biological systems and its relations to certain problems in algebra and algorithmics: namely, decision procedures for systems of linear Diophantine equations and inequalities, whose coefficients range over algebraic numbers and intervals. The questions, addressed here, are central to the success of the emerging field of systems biology and relate to questions in decidability theory, algorithmic algebra, hybrid automata models, etc.
Identifying patterns of associated-conditions through topic models of Electronic Medical Records

Multiple adverse health conditions co-occurring in a patient are typically associated with poor prognosis and increased office or hospital visits. Developing methods to identify patterns of co-occurring conditions can assist in diagnosis. Thus, identifying patterns of association among co-occurring conditions is of growing interest. In this paper, we report preliminary results from a data-driven study, in which we apply a machine learning method, namely, topic modeling, to Electronic Medical Records (EMRs), aiming to identify patterns of associated conditions. Specifically, we use the well-established Latent Dirichlet Allocation (LDA), a method based on the idea that documents can be modeled as a mixture of latent topics, where each topic is a distribution over words. In our study, we adapt the LDA model to identify latent topics in patients' EMRs. We evaluate the performance of our method both qualitatively and quantitatively, and show that the obtained topics indeed align well with distinct medical phenomena characterized by co-occurring conditions.
Flunarizine in Alternating Hemiplegia in Childhood. An International Study in 12 Children

Twelve children with alternating hemiplegia were treated with the calcium-entry blocker flunarizine for 4 months. All but one patient responded favourably with a reduction in frequency and/or duration and severity of attacks. Interictal symptoms decreased and mental development improved in several patients. Nine of the patients entered a subsequent double-blind placebo-controlled withdrawal study lasting another 4 months. Relapses were observed in part of the placebo as well as of the flunarizine-treated patients. The reason for this is not clear, since it is unlikely that the favourable response during the initial open-label study would be due to a placebo effect, or that tolerance to the drug had developed. Feed-back from the parents rather suggests that stress and tension, which were known trigger factors in a majority of these patients, played a role when the patient was switched to the double-blind treatment. Although the present study is not fully conclusive, apparently because of the use of an inadequate trial design, flunarizine, the first truly promising drug in this disease, deserves further study. An appeal is made to join another international double-blind study.
Differential TD learning for value function approximation

Value functions arise as a component of algorithms as well as performance metrics in statistics and engineering applications. Computation of the associated Bellman equations is numerically challenging in all but a few special cases. A popular approximation technique is known as Temporal Difference (TD) learning. The algorithm introduced in this paper is intended to resolve two well-known problems with this approach: In the discounted-cost setting, the variance of the algorithm diverges as the discount factor approaches unity. Second, for the average cost setting, unbiased algorithms exist only in special cases. It is shown that the gradient of any of these value functions admits a representation that lends itself to algorithm design. Based on this result, the new differential TD method is obtained for Markovian models on Euclidean space with smooth dynamics. Numerical examples show remarkable improvements in performance. In application to speed scaling, variance is reduced by two orders of magnitude.
Fractionation of protein, RNA, and plasmid DNA in centrifugal precipitation chromatography using cationic surfactant CTAB containing inorganic salts NaCl and NH4Cl

Centrifugal precipitation chromatography (CPC) is a separation system that mainly employs a moving concentration gradient of precipitating agent along a channel and solutes of interest undergo repetitive precipitation‐dissolution, fractionate at different locations, and elute out from the channel according to their solubility in the precipitating agent solution. We report here for the first time the use of a CPC system for fractionation of protein, RNA, and plasmid DNA in clarified lysate produced from bacterial culture. The cationic surfactant cetyltrimethylammonium bromide (CTAB) was initially used as a precipitating agent; however, all biomolecules showed no differential solubility in the moving concentration gradient of this surfactant and, as a result, no separation of protein, RNA, and plasmid DNA occurred. To overcome this problem, inorganic salts such as NaCl and NH4Cl were introduced into solution of CTAB. The protein and RNA were found to have higher solubility with the addition of these salts and separated from the plasmid DNA. Decreasing surface charge density of CTAB upon addition of NaCl and NH4Cl was believed to lead to lower surfactant complexation, and therefore caused differential solubility and fractionation of these biomolecules. Addition of CaCl2 did not improve solubility and separation of RNA from plasmid DNA. © 2004 Wiley Periodicals, Inc.
Physiological characterization of strain DCB-1, a unique dehalogenating sulfidogenic bacterium

Strain DCB-1 is an obligately anaerobic bacterium which carries out the reductive dehalogenation of halobenzoates and was previously known to grow only on pyruvate plus 20% ruminal fluid. When various electron acceptors were supplied, thiosulfate and sulfite were found to stimulate growth. Sulfide was produced from thiosulfate. Cytochrome c and desulfoviridin were detected. The mol% G+C was 49 (at the thermal denaturation temperature). Of 55 carbon sources tested, only pyruvate supported growth as the sole carbon source in mineral medium. Lactate, acetate, L- and D-malate, glycerol, and L- and D-arabinose stimulated growth when supplemented with 10% ruminal fluid and 20 mM thiosulfate. In mineral medium, pyruvate was converted to acetate and lactate, with small amounts of succinate and fumarate accumulating transiently. During growth with thiosulfate, all of these products accumulated transiently. Addition of excess hydrogen to pyruvate-grown cultures resulted in diversion of carbon to formate, lactate, and butyrate, which caused a decrease in cell yield. We conclude that strain DCB-1 is a new type of sulfidogenic bacterium.
Palaeomagnetic studies of Polish rocks; III, Neogene igneous rocks of the Pieniny mountains, Carpathians

Studia paleomagnetyczne skal polskich. III. Neogenskie skaly ogniowe Pienin Oriented samples were collected from about thirty sites in the Pieniny Mountains, Carpathians. Routine measurements and stability tests indicated consistent results from the andesite dykes exposed on Wzar mount only. Only reversed magnetization was recorded. A tentative correlation of the results with the igneous rocks o f Slovakia would equate the Wzar intrusions with the first phase and lower part of the second phase andesites of the Central Slovakian province. From the sites in the region of Szczawnica and Szlachtowa there is an indication of both normal and reversed directions of magnetization in andesites older than those found on Wzar mount.
Idea Assessment via Enterprise crowdfunding: an Empirical Analysis of Decision-Making Styles

Deciding which ideas to pursue is an essential step in innovation management. Organizations increasingly open up their decision-making processes internally and externally by harnessing the collective intelligence of crowds. One mechanism for doing so is enterprise crowdfunding, i.e. inviting employees to propose and support ideas on a crowdfunding platform inside the enterprise. In this paper, we empirically analyze such an enterprise crowdfunding endeavor where hundreds of employees endowed with the discretion to spend company budget proposed dozens of ideas and decided to fund 10 of them. Based on log files and information on the employees’ roles in their enterprise, we investigate the time course of individual decision-making – i.e., whether they decide rather quickly or more time-lagged which ideas to support Factors that influence decision-making style include characteristics of proposers, supporters, ideas, supporters’ activity level, and the progress of the trial. From this, we derive suggestions for future research into crowdfunding, and we propose relevant design parameters for using crowdfunding as a tool for internal openness and Enterprise 2.0.
CNRS TELECOM ParisTech at ImageCLEF 2016 Scalable Concept Image Annotation Task: Overcoming the Scarcity of Training Data

We introduce our participation at the ImageCLEF 2016 scalable concept detection and localization task. As in ImageCLEF 2015, this edition focuses on generating not only annotations (concept detection) but also localizing concepts into a large image collection. In our runs, we focus mainly on concept detection; our solution is purely visual and based on deep features combined with standard linear support vector machines (SVMs) built on top of well enriched training sets. Starting from loosely labeled training sets, we propose an algorithm that learns the statistical dependencies between concepts and allows us to enrich the labels of these training sets, resulting into more effective SVMs for image annotation.
Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors

Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a 2-year monthly time- series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An “epidemic population structure” (dominance of asingle cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this clusters imultaneously occurred with opportunistic clusters/OTUs, e.g., Nodularia spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formeda consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocynobacteria and the bloom offilamentous/colonialclusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic Sea predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.
A Copula Based Bayesian Approach for Paid–Incurred Claims Models for Non-Life Insurance Reserving

Our article considers the class of recently developed stochastic models that combine claims payments and incurred losses information into a coherent reserving methodology. In particular, we develop a family of Heirarchical Bayesian Paid-Incurred-Claims models, combining the claims reserving models of Hertig et al. (1985) and Gogol et al. (1993). In the process we extend the independent log-normal model of Merz et al. (2010) by incorporating different dependence structures using a Data-Augmented mixture Copula Paid-Incurred claims model. The utility and influence of incorporating both payment and incurred losses into estimating of the full predictive distribution of the outstanding loss liabilities and the resulting reserves is demonstrated in the following cases: (i) an independent payment (P) data model; (ii) the independent Payment-Incurred Claims (PIC) data model of Merz et al. (2010); (iii) a novel dependent lag-year telescoping block diagonal Gaussian Copula PIC data model incorporating conjugacy via transformation; (iv) a novel data-augmented mixture Archimedean copula dependent PIC data model. Inference in such models is developed via a class of adaptive Markov chain Monte Carlo sampling algorithms. These incorporate a data-augmentation framework utilized to efficiently evaluate the likelihood for the copula based PIC model in the loss reserving triangles. The adaptation strategy is based on representing a positive definite covariance matrix by the exponential of a symmetric matrix as proposed by Leonard et al. (1992).
More complex than expected?

We read with interest the excellent article by Aass et al. [1], in which they demonstrate the beneficial effect of polarizing (or rather non-depolarizing) St. Thomas-based cardioplegia when compared with conventional depolarizing cardioplegic arrest in a large animal model. The positive impact on systolic left ventricular function during reperfusion is evident in this clinically relevant situation, while there was little difference in G-protein-coupled receptor kinase 2 phosphorylation or other cellular outcome parameters. The authors discuss the potential role of ß-adrenergic desensitization and plasma membrane ion fluxes, but we believe that another phenomenon may also play a role: contractile protein Ca2þ sensitivity. Indeed, prolonged depolarization ultimately not only leads to cytosolic Ca2þaccumulation, which is usually considered detrimental but also induces adaptive responses, such as protein kinase C (PKC) -mediated phosphorylation of troponin I and/or T. This can impair post-ischaemic systolic function but protects the contractile apparatus from relaxation deficit and contracture [2]. Non-depolarizing arrest may prevent Ca2þoverload for some time, preserving contractile protein Ca2þ sensitivity and hence post-ischaemic systolic function. However, problems arise when ischaemia is prolonged and the net Ca2þ influx during reperfusion cannot rapidly be counteracted. Then, preserved—or ‘unprotected’—Ca2þ sensitivity impairs relaxation, resulting in a stiff and failing heart [3]. The ischaemia-reperfusion protocol used by the authors reflects the typical clinical scenario in that is subcritical with 60 min cold cardioplegic arrest, where preserved or increased Ca2þ sensitivity translates in better systolic function. Non-depolarizing cardioplegia has also been tested in other experimental models with promising results, as elegantly summarized in the review article by Dobson et al. [4], but few, if any, of those used critical ischaemia-reperfusion protocols. Of course, direct measurement of Ca2þ sensitivity requires simultaneous recordings of contractile force and cytosolic Ca2þ, which is very difficult in large animals, but it would be interesting to see whether a more critical ischaemic injury would unmask the deleterious effects of preserved Ca2þ sensitization. After all, traditional Kþ -induced cardioplegic arrest works very well for our daily routine cases, but it is the more extreme situations that continue to give us trouble. If our hypothesis is true, we feel that a temporarily lower systolic function, easily treated by adrenergic stimulation, is less problematic than a stiff heart with poorly reversible contracture. Clearly, more experimentation is warranted, which is a very good thing for such an experienced group of surgical researchers and a lately somewhat neglected field.
Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423

ABSTRACT Herbaspirillum sp. strain RV1423 was isolated from a site contaminated with alkanes and aromatic compounds and harbors the complete pathway for naphthalene degradation. The new features found in RV1423 increase considerably the versatility and the catabolic potential of a genus of bacteria previously considered mainly to be diazotrophic endophytes to plants.
The Immunogenicity of a New Human Minor Histocompatibility Antigen Results from Differential Antigen Processing

Minor histocompatibility antigens (mHAgs) present a significant impediment to organ and bone marrow transplantation between HLA-identical donor and recipient pairs. Here we report the identification of a new HLA-A*0201–restricted mHAg, HA-8. Designation of this mHAg as HA-8 is based on the nomenclature of Goulmy (Goulmy, E. 1996. Curr. Opin. Immunol. 8:75–81). This peptide, RTLDKVLEV, is derived from KIAA0020, a gene of unknown function located on chromosome 9. Polymorphic alleles of KIAA0020 encode the alternative sequences PTLDKVLEV and PTLDKVLEL. Genotypic analysis demonstrated that the HA-8–specific cytotoxic T lymphocyte (CTL) clone SKH-13 recognized only cells that expressed the allele encoding R at P1. However, when PTLDKVLEV was pulsed onto cells, or when a minigene encoding this sequence was used to artificially translocate this peptide into the endoplasmic reticulum, it was recognized by CTLs nearly as well as RTLDKVLEV. This indicates that the failure of CTLs to recognize cells expressing the PTLDKVLEV-encoding allele of KIAA0020 is due to a failure of this peptide to be appropriately proteolyzed or transported. Consistent with the latter possibility, PTLDKVLEV and its longer precursors were transported poorly compared with RTLDKVLEV by transporter associated with antigen processing (TAP). These studies identify a new human mHAg and provide the first evidence that minor histocompatibility differences can result from the altered processing of potential antigens rather than differences in interaction with the relevant major histocompatibility complex molecule or T cell receptor.
Are There Independent Age-of-Acquisition Effects in Word Reading ?

Several recent studies have suggested that the age at which a word is learned (age of acquisition) has an impact on skilled visual word recognition independent of other factors such as frequency. This result raises questions about previous studies in which age of acquisition was not controlled, and about current theories in which it is not explicitly addressed. Analyses of the materials used in previous studies suggest that the observed age of acquisition effects may have been due to other correlated stimulus properties. We then examined age of acquisition effects within computational model of the orthography to phonology mapping, which permitted close control over stimulus properties and frequency. We found little evidence for an age of acquisition effect using words that exhibit normal regularities in the mapping between spelling and sound. In this case, performance was affected by cumulative frequency (the total number of times a word was trained) but not frequency trajectory (how these training trials were distributed over the course of learning). An age of acquisition effect was observed in one condition in which early and late learned words did not overlap in terms of orthography or phonology. The results suggest that age of acquisition effects depend crucially on the nature of the mapping between codes, which varies across tasks: they are larger for arbitrary mappings that are not characteristic of the spelling-sound system, but may be relevant to acquiring other types of knowledge, such as the names of objects or faces.
Substring-based unsupervised transliteration with phonetic and contextual knowledge

We propose an unsupervised approach for substring-based transliteration which incorporates two new sources of knowledge in the learning process: (i) context by learning substring mappings, as opposed to single character mappings, and (ii) phonetic features which capture cross-lingual character similarity via prior distributions. Our approach is a two-stage iterative, boot-strapping solution , which vastly outperforms Ravi and Knight (2009)’s state-of-the-art unsupervised transliteration method and outperforms a rule-based baseline by up to 50% for top-1 accuracy on multiple language pairs. We show that substring-based models are superior to character-based models, and observe that their top-10 accuracy is comparable to the top-1 accuracy of supervised systems. Our method only requires a phonemic representation of the words. This is possible for many language-script combinations which have a high grapheme-to-phoneme correspondence e.g. scripts of Indian languages derived from the Brahmi script. Hence, Indian languages were the focus of our experiments. For other languages, a grapheme-to-phoneme converter would be required.