bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contextual equivalence for inductive definitions with binders in higher order typed functional programming
Authors: LAKIN MATTHEW R. , PITTS ANDREW M. 
Published: December 2013

AbstractCorrect handling of names and binders is an important issue in meta-programming. This paper presents an embedding of constraint logic programming into the αML functional programming language, which provides a provably correct means of implementing proof search computations over inductive definitions involving names and binders modulo α-equivalence. We show that the execution of proof search in the αML operational semantics is sound and complete with regard to the model-theoretic semantics of formulae, and develop a theory of contextual equivalence for the subclass of αML expressions which correspond to inductive definitions and formulae. In particular, we prove that αML expressions, which denote inductive definitions, are contextually equivalent precisely when those inductive definitions have the same model-theoretic semantics. This paper is a revised and extended version of the conference paper (Lakin, M. R. & Pitts, A. M. (2009) Resolving inductive definitions with binders in higher-order typed functional programming. InProceedings of the 18th European Symposium on Programming (ESOP 2009), Castagna, G. (ed), Lecture Notes in Computer Science, vol. 5502. Berlin, Germany: Springer-Verlag, pp. 47–61) and draws on material from the first author's PhD thesis (Lakin, M. R. (2010)An Executable Meta-Language for Inductive Definitions with Binders. University of Cambridge, UK).
Intralinguistic and extralinguistic variation factors in Old French negation withne-Ø, ne-mie, ne-pasandne-pointacross different text types
Authors: SCHØSLER LENE , VÖLKER HARALD 
Published: December 2013

ABSTRACTOld French sentential negation (NEG) represents an important morphosyntactic change that has been investigated by a large number of scholars from different theoretical approaches. From the 12th to the 14th (and mainly in the 13th) century, there are two variants of this variable in competition: NEG with onlyne(the older variant) and NEG withne+pas/mie/point, etc. The research presented in this paper has been motivated by the wish to find relevant factors for this variation in Old French. In order to identify factors of influence on the variable NEG with or withoutpas,mieandpoint, we analyse two subcorpora containing two different text types. The choice of the tested factors is rooted both in variational linguistics and in previous studies on Old French negation, implying (extralinguistic) diasystematic factors like diatopic and diastratic ones as well as intralinguistic factors like transitivity of the verb, word order and clause type. Main findings are the probable relevance of clause type and the influence of socially definable (diastratic) groups. Beyond this, the results across the two different text type are predominantly similar, but we found differences as well. This leads us to plead in favour of the importance of considering the factor text type while working on diachronic corpora.
The disastrous “sun ray” sign in cardiac magnetic resonance: an indicator of angiosarcoma
Authors: Akkaya Zehra , Gursoy Aysegul , Erden Ayse 
Published: December 2013

AbstractDistinguishing the benign and malignant cardiac masses is usually a diagnostic challenge, and safe, non-invasive, and reliable techniques are necessary to avoid any delay in treatment. The previously described “sun ray” appearance is an important sign in the diagnosis of cardiac angiosarcoma, and in this report we present 3-T magnetic resonance imaging findings to distinguish the rare but fatal cardiac angiosarcoma.
Design and realization of a modular architecture for textual entailment
Authors: PADÓ SEBASTIAN , NOH TAE-GIL , STERN ASHER , WANG RUI , ZANOLI ROBERTO 
Published: December 2013

AbstractA key challenge at the core of many Natural Language Processing (NLP) tasks is the ability to determine which conclusions can be inferred from a given natural language text. This problem, called theRecognition of Textual Entailment (RTE), has initiated the development of a range of algorithms, methods, and technologies. Unfortunately, research on Textual Entailment (TE), like semantics research more generally, is fragmented into studies focussing on various aspects of semantics such as world knowledge, lexical and syntactic relations, or more specialized kinds of inference. This fragmentation has problematic practical consequences. Notably, interoperability among the existing RTE systems is poor, and reuse of resources and algorithms is mostly infeasible. This also makes systematic evaluations very difficult to carry out. Finally, textual entailment presents a wide array of approaches to potential end users with little guidance on which to pick. Our contribution to this situation is the novel EXCITEMENT architecture, which was developed to enable and encourage the consolidation of methods and resources in the textual entailment area. It decomposes RTE into components with strongly typed interfaces. We specify (a) a modular linguistic analysis pipeline and (b) a decomposition of the ‘core’ RTE methods into top-level algorithms and subcomponents. We identify four major subcomponent types, including knowledge bases and alignment methods. The architecture was developed with a focus on generality, supporting all major approaches to RTE and encouraging language independence. We illustrate the feasibility of the architecture by constructing mappings of major existing systems onto the architecture. The practical implementation of this architecture forms the EXCITEMENT open platform. It is a suite of textual entailment algorithms and components which contains the three systems named above, including linguistic-analysis pipelines for three languages (English, German, and Italian), and comprises a number of linguistic resources. By addressing the problems outlined above, the platform provides a comprehensive and flexible basis for research and experimentation in textual entailment and is available as open source software under the GNU General Public License.
Dynamic Nanoimpedance Characterization of the Atomic Force Microscope Tip-Surface Contact
Authors: Tobiszewski Mateusz Tomasz , Zieliński Artur , Darowicki Kazimierz 
Published: December 2013

AbstractNanoimpedance measurements, using the dynamic impedance spectroscopy technique, were carried out during loading and unloading force of a probe on three kinds of materials of different resistivity. These materials were: gold, boron-doped diamond, and AISI 304 stainless steel. Changes of impedance spectra versus applied force were registered and differences in the tip-to-sample contact character on each material were revealed. To enable comparison between materials and phases, a new standardization method is proposed, which simulates conditions of initial contact.
An inverse theorem: When the measure of the sumset is the sum of the measures in a locally compact abelian group
Authors: Griesmer John 
Published: December 2013

We classify the pairs of subsetsAA,BBof a locally compact abelian groupGGsatisfyingm∗(A+B)=m(A)+m(B)m_*(A+B)=m(A)+m(B), wheremmis the Haar measure forGGandm∗m_*is inner Haar measure. This generalizes M. Kneser’s classification of such pairs whenGGis assumed to be connected. Recently, D. Grynkiewicz classified the pairs of setsAA,BBsatisfying|A+B|=|A|+|B||A+B|=|A|+|B|in an abelian group, and our result is complementary to that classification. Our proofs combine arguments of Kneser and Grynkiewicz.
slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array
Authors: Fernandes Francisco , Freitas Ana T. 
Published: December 2013

Abstract
Motivation: Maximal exact matches, or just MEMs, are a powerful tool in the context of multiple sequence alignment and approximate string matching. The most efficient algorithms to collect them are based on compressed indexes that rely on longest common prefix array-centered data structures. However, their space-efficient representations make use of encoding techniques that are expensive from a computational point of view. With the deluge of data generated by high-throughput sequencing, new approaches need to be developed to deal with larger genomic sequences.
Results: In this work, we have developed a new longest common prefix array-sampled representation, optimized to work with the backward search method inherently used by the FM-Index. Unlike previous implementations that sacrifice running time to have smaller space, ours lead to both a fast and a space-efficient approach. This implementation was used by the new software slaMEM, developed to efficiently retrieve MEMs. The results show that the new algorithm is competitive against existing state-of-the-art approaches.
Availability and implementation: The software is implemented in C and is operating system independent. The source code is freely available for download at http://github.com/fjdf/slaMEM/ under the GPLv3 license.
Contact: atf@inesc-id.pt
Supplementary information: Supplementary data are available at Bioinformatics online.
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
Authors: Alkan Ferhat , Erten Cesim 
Published: December 2013

Abstract
Motivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks, the informal goal is to group together related nodes. For the case of protein–protein interaction networks, such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships, in predicting the functions of proteins with unknown functions and in verifying those with estimated functions.
Results: A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity, usually determined via sequence similarities, and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein–protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show, through experiments based on biological significance tests, that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore, the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms.
Availability and implementation: Supplementary material including code implementations in LEDA C++, experimental data and the results are available at http://webprs.khas.edu.tr/∼cesim/BEAMS.tar.gz.
Contacts: ferhat.alkan@stu.khas.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Structure and sequence elements of the CR4/5 domain of medaka telomerase RNA important for telomerase function
Authors: Kim Nak-Kyoon , Zhang Qi , Feigon Juli 
Published: December 2013

Abstract
Telomerase is a unique reverse transcriptase that maintains the 3′ ends of eukaryotic chromosomes by adding tandem telomeric repeats. The RNA subunit (TR) of vertebrate telomerase provides a template for reverse transcription, contained within the conserved template/pseudoknot domain, and a conserved regions 4 and 5 (CR4/5) domain, all essential for catalytic activity. We report the nuclear magnetic resonance (NMR) solution structure of the full-length CR4/5 domain from the teleost fish medaka (Oryzias latipes). Three helices emanate from a structured internal loop, forming a Y-shaped structure, where helix P6 stacks on P5 and helix P6.1 points away from P6. The relative orientations of the three helices are Mg2+ dependent and dynamic. Although the three-way junction is structured and has unexpected base pairs, telomerase activity assays with nucleotide substitutions and deletions in CR4/5 indicate that none of these are essential for activity. The results suggest that the junction is likely to change conformation in complex with telomerase reverse transcriptase and that it provides a flexible scaffold that allows P6 and P6.1 to correctly fold and interact with telomerase reverse transcriptase.
libRoadRunner: A High Performance SBML Compliant Simulator
Authors: Somogyi E. T. , Karlsson M. T. , Swat M. , Galdzicki M. , Sauro H. M 
Published: December 2013

AbstractSummaryWe describe libRoadRunner, a cross-platform, open-source, high performance C++ library for running and analyzing SBML-compliant models. libRoadRunner was created primarily to achieve high performance, ease of use, portability and an extensible architecture. libRoadRunner includes a comprehensive API, Plugin support, Python scripting and additional functionality such as stoichio-metric and metabolic control analysis.Accessibility and ImplementationTo maximize collaboration, we made libRoadRunner open source and released it under the Apache License, Version 2.0. To facilitate reuse, we have developed comprehensive Python bindings using SWIG (swig.org) and a C API. Li-bRoadRunner uses a number of statically linked third party libraries including: LLVM [4], libSBML [1], CVODE, NLEQ2, LAPACK and Poco. LibRoadRunner is supported on Windows, Mac OS X and Linux.Supplementary informationOnline documentation, build instructions and git source repository are available athttp://www.libroadrunner.org
Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants
Authors: Ju Feng , Xia Yu , Guo Feng , Wang Zhiping , Zhang Tong 
Published: December 2013

SummaryActivated sludge (AS), which has been in use for 100 years, has been the most popular biological process in various wastewater treatment plants (WWTPs), in which bacteria plays central roles in pollutant removal. However, the potential relationship between bacteria taxa and the niches occupied by specific functional bacteria in AS are largely unknown. Here, correlation‐based network analysis was applied to a 16S rRNA gene pyrosequencing dataset containing > 760 000 sequences of 50 AS samples from globally distributed full‐scale WWTPs. The results showed that (i) bacterial assembly in AS was nonrandomly arranged by taxonomic relatedness and (ii) intra‐ and inter‐phylum/class co‐occurrence higher than expected by chance was induced by multiple deterministic processes, such as habitat filtering and competition. Moreover, based on bacterial occupancy, a prevalent core set of cosmopolitan functional bacteria (e.g. multiple nitrogen‐cycling‐related bacteria) was widely distributed in the AS of different WWTPs, showing strong ecological associations among them. Additionally, the AS network has statistical and structural characteristics similar to those of previously reported ecological networks, such as power‐law connectivity distribution and nonrandomly connected properties. Overall, this work provides novel insights into the bacterial associations within AS and sheds light on the ecological rules guiding bacterial assembly in WWTPs.
Generation of Intra‐oral‐like Images from Cone Beam Computed Tomography Volumes for Dental Forensic Image Comparison
Authors: Trochesset Denise A. , Serchuk Richard B. , Colosi Dan C. 
Published: December 2013

AbstractIdentification of unknown individuals using dental comparison is well established in the forensic setting. The identification technique can be time and resource consuming if many individuals need to be identified at once. Medical CT (MDCT) for dental profiling has had limited success, mostly due to artifact from metal‐containing dental restorations and implants. Description: The authors describe a CBCT reformatting technique that creates images, which closely approximate conventional dental images. Method: Using a i‐CAT Platinum CBCT unit and standard issue i‐CAT Vision software, a protocol is developed to reproducibly and reliably reformat CBCT volumes. The reformatted images are presented with conventional digital images from the same anatomic area for comparison. Conclusion: The authors conclude that images derived from CBCT volumes following this protocol are similar enough to conventional dental radiographs to allow for dental forensic comparison/identification and that CBCT offers a superior option over MDCT for this purpose.
Delirium Due to Intoxication from the Novel Synthetic Tryptamine 5‐MeO‐DALT
Authors: Jovel Andres , Felthous Alan , Bhattacharyya Anjan 
Published: December 2013

AbstractSynthetic tryptamines have gained popularity for their hallucinogenic properties, unscheduled status, and availability from “head shops” and through the internet. Here, we present a case of synthetic tryptamine‐induced delirium secondary to 5‐MeO‐DALT ingestion in a previously healthy young male. 5‐MeO‐DALT led to the hospitalization of our patient after ingestion of a standard dose, presenting with extreme agitation, tachycardia, diaphoresis, and combativeness leading to physical restraint and intravenous sedation. A search of PubMed, Ovid, and Google Scholar for keywords of “5‐MeO‐DALT,” “5‐methoxy‐N,N‐diallyltryptamine,” or “Lucy‐N‐Nate” found no case reports or clinical articles in the literature. Rapid emergence and commercialization of this novel synthetic tryptamine 5‐MeO‐DALT points to the importance of health care and forensic professionals keeping abreast of the latest drugs of abuse and their clinical features. The authors hope this report leads the way in disseminating the potential risks associated with unscheduled and unregulated substances, synthetic tryptamines such as 5‐MeO‐DALT in particular.
Comparison of sexual compatibility in crosses between the southern and northern populations of the cabbage beetle Colaphellus bowringi
Authors: Liu Xing‐Ping , Tu Xiao‐Yun , He Hai‐Min , Chen Chao , Xue Fang‐Sen 
Published: December 2013

Abstract It is widely accepted that the genetic divergence and reproductive incompatibility between closely related species and/or populations is often viewed as an important step toward speciation. In this study, sexual compatibility in crosses between the southern XS population and the northern TA population of the polyandrous cabbage beetle Colaphellus bowringi was investigated by testing their mating preferences, mating latency, copulation duration, and reproductive performances of post‐mating. In choice mating experiments, the percentages of matings were significantly higher in intra‐population crosses than in inter‐population crosses. Both isolation index (I) and index of pair sexual isolation (IPSI) indicated partial mating incompatibility or assortative mating in crosses between the two different geographical populations. In single pair mating experiments, XS females in inter‐population crosses mated significantly later and copulated significantly shorter than those in intra‐population crosses. However, TA females in inter‐population crosses mated significantly earlier and copulated longer than those in intra‐population crosses, suggesting that larger XS males may enhance heterotypic mating. The lifetime fecundity was highest in XS homotypic matings, lowest in TA homotypic matings, and intermediate in heterotypic matings between their parents. The inter‐population crosses resulted in significantly lower egg hatching rate and shorter female longevity than intra‐population crosses. These results demonstrated that there exist some incompatibilities in premating, postmating‑prezygotic, and postzygotic stages between the southern XS population and northern TA population of the cabbage beetle Colaphellus bowringi.
Overview of Regular Dialysis Treatment in Japan (as of 31 December 2011)
Authors: Nakai Shigeru , Watanabe Yuzo , Masakane Ikuto , Wada Atsushi , Shoji Tetsuo , Hasegawa Takeshi , Nakamoto Hidetomo , Yamagata Kunihiro , Kazama Junichiro James , Fujii Naohiko , Itami Noritomo , Shinoda Toshio , Shigematsu Takashi , Marubayashi Seiji , Morita Osamu , Hashimoto Seiji , Suzuki Kazuyuki , Kimata Naoki , Hanafusa Norio , Wakai Kenji , Hamano Takayuki , Ogata Satoshi , Tsuchida Kenji , Taniguchi Masatomo , Nishi Hiroshi , Iseki Kunitoshi , Tsubakihara Yoshiharu 
Published: December 2013

AbstractA nationwide statistical survey of 4255 dialysis facilities was conducted at the end of 2011. Responses were submitted by 4213 facilities (99.0%). The number of new patients started on dialysis was 38 613 in 2011. Although the number of new patients decreased in 2009 and 2010, it increased in 2011. The number of patients who died each year has been increasing; it was 30 743 in 2011, which exceeded 30 000 for the first time. The number of patients undergoing dialysis has also been increasing every year; it was 304 856 at the end of 2011, which exceeded 300 000 for the first time. The number of dialysis patients per million at the end of 2011 was 2385.4. The crude death rate of dialysis patients in 2011 was 10.2%, which exceeded 10% for the first time in the last 20 years. The mean age of new dialysis patients was 67.84 years and the mean age of the entire dialysis patient population was 66.55 years. The most common primary cause of renal failure among new dialysis patients was diabetic nephropathy (44.3%). Diabetic nephropathy was also the most common primary disease among the entire dialysis patient population (36.7%), exceeding chronic glomerulonephritis (34.8%) which had been the highest until last year. The survey included questions related to the Great East Japan Earthquake, which occurred on 11 March 2011. The results on items associated with the Great East Japan Earthquake were reported separately from this report. The mean uric acid levels of the male and female patients were 7.30 and 7.19 mg/dL, respectively. Certain drugs for hyperuricemia were prescribed for approximately 17% of patients. From the results of the facility survey, the number of patients who underwent peritoneal dialysis (PD) was 9642 and the number of patients who did not undergo PD despite having a peritoneal dialysis catheter was 369. A basic summary of the results on the survey items associated with PD is included in this report and the details were reported separately.