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Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans [article]

Jedidiah Carlson, Adam E. Locke, Matthew Flickinger, Matthew Zawistowski, Shawn Levy, Richard M. Myers, Michael Boehnke, Hyun Min Kang, Laura J. Scott, Jun Z. Li, Sebastian Zöllner
2017 bioRxiv   pre-print
Here we use ~36 million singleton variants from 3,560 whole-genome sequences to infer fine-scale patterns of mutation rate heterogeneity.  ...  Remarkably, GC content, DNase hypersensitivity, CpG islands, and H3K36 trimethylation are associated with both increased and decreased mutation rates depending on nucleotide context.  ...  Let K be the index across all 7-552 mer subtypes with more than 10 observed singletons ( ∈ { , … , , }).  ... 
doi:10.1101/108290 fatcat:puvydu3bajhdpnnmzgj762tuoq

A syntactic account of singleton types via hereditary substitution

Karl Crary
2009 Proceedings of the Fourth International Workshop on Logical Frameworks and Meta-Languages Theory and Practice - LFMTP '09  
We give a syntactic proof of decidability and consistency of equivalence for the singleton type calculus, which lies at the foundation of modern module systems such as that of ML.  ...  The proof works by translation of the singleton type calculus into a canonical presentation, adapted from work on logical frameworks, in which equivalent terms are written identically.  ...  Subtyping Subtyping in the EL is associated with a subsumption rule, as is typical for type systems with subtyping. However, the IL cannot support a subsumption rule.  ... 
doi:10.1145/1577824.1577829 dblp:conf/lfmtp/Crary09 fatcat:q2n5ephm3rf7pcrhbtyjsrvz3y

Coming to Terms with Your Choices: An Existential Take on Dependent Types [article]

Georg Stefan Schmid
2020 arXiv   pre-print
We propose a new dependently-typed system with subtyping and singleton types whose goal is to enable type-level programming in an accessible style.  ...  Furthermore, we show that singleton types combined with the choice operator can serve as a replacement for many type functions of interest in practice.  ...  In [Aspinall 1994 ] Aspinall introduces ≤ , a dependently-typed system with subtyping and singleton types that resembles ours in its type language.  ... 
arXiv:2011.07653v1 fatcat:cejcks5iwbb77lkcxx3ztt2gdu

A Core Calculus for Scala Type Checking [chapter]

Vincent Cremet, François Garillot, Sergueï Lenglet, Martin Odersky
2006 Lecture Notes in Computer Science  
Both calculi model a simple, purely functional core language of objects with fields and methods in a nominal class-based type system.  ...  All presented deduction rules are syntax-directed and thus lead directly to procedures for subtyping and type assignment.  ...  This rule therefore allows us to unfold a subtyping problem referring to a singleton type to a subtyping problem between non-singleton types in a single step.  ... 
doi:10.1007/11821069_1 fatcat:j4jct4vgrbel5fa7osuzdhmomq

Omni-word Feature and Soft Constraint for Chinese Relation Extraction

Yanping Chen, Qinghua Zheng, Wei Zhang
2014 Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)  
The results show a significant improvement in Chinese relation extraction, outperforming other methods in F-score by 10% in 6 relation types and 15% in 18 relation subtypes.  ...  In Row 2, with only the F ow feature, the F-score already reaches 77.74% in 6 types and 60.31% in 18 subtypes.  ...  Zhang et al. (2011) was based on the ACE 2005 corpus with 75% data for training and 25% for testing. Performances about the 7 types and 19 subtypes were given.  ... 
doi:10.3115/v1/p14-1054 dblp:conf/acl/ChenZZ14 fatcat:cga4jamk55dvdhucmb4cwubssy

Protocol Specialization [chapter]

Matthias Neubauer, Peter Thiemann
2004 Lecture Notes in Computer Science  
Each channel acts as a component connector with the interface determined by the channel's protocol.  ...  We present an analysis that determines the minimum protocol required for each process and specify the specialization of a process with respect to a desired protocol, thereby removing unnecessary code.  ...  The type system underlying our work relies on recursive types with singleton types and subtyping. The combination with singleton types is a novel contribution to session type systems.  ... 
doi:10.1007/978-3-540-30477-7_17 fatcat:dxcr3gsttfaaxdl5qmkh7lspn4

A Path To DOT: Formalizing Fully Path-Dependent Types [article]

Marianna Rapoport, Ondřej Lhoták
2019 arXiv   pre-print
This paper presents the pDOT calculus, which generalizes DOT to support types that depend on paths of arbitrary length, as well as singleton types to track path equality.  ...  The Dependent Object Types (DOT) calculus aims to formalize the Scala programming language with a focus on path-dependent types - types such as x.a_1... a_n.T that depend on the runtime value of a path  ...  Path Alias Typing. In pDOT singleton-type related typing and subtyping rules are responsible for the handling of aliased paths and equivalent types. Singleton Type Creation.  ... 
arXiv:1904.07298v4 fatcat:ufd3sxdicjdgxih2mbgius6gcy

External Dispatch: Yet Another Object-Oriented Single and Multiple Dispatch Mechanism

Miguel Oliveira e Silva
2017 Journal of Object Technology  
A more complete realization for external dispatch motivated the definition of a new singleton language mechanism that is also presented.  ...  This mechanism is compatible with existing object-oriented language constructs, and provides a simple, expressive, and universal dispatch tool.  ...  For example: Listing 7 -Import dispatch grammar If successfully compiled and run, this expression creates an object with type T<Integer> subtype of A<Integer>, and T<> is the best conforming type match  ... 
doi:10.5381/jot.2017.16.2.a1 fatcat:llei27a2gjfalfmclm3u5gblby

Recency Types for Analyzing Scripting Languages [chapter]

Phillip Heidegger, Peter Thiemann
2010 Lecture Notes in Computer Science  
Unlike with linear types, summary types may refer to singleton types and vice versa. We prove the soundness of the type system and present a constraintbased inference algorithm.  ...  With the current surge of scripting technologies, large programs are being built with dynamically typed languages.  ...  Fig. 7 (b) defines the subtyping relation. Besides the rules dealing with reflexivity and top, one summary object type is a subtype of another, if it encompasses fewer locations.  ... 
doi:10.1007/978-3-642-14107-2_10 fatcat:tn2grzmdync63dk3jasgctrgu4

Comparative Population Analysis of Klebsiella pneumoniae Strains with Extended-Spectrum β-Lactamases Colonizing Patients in Rehabilitation Centers in Four Countries

A. Baraniak, R. Izdebski, J. Fiett, E. Sadowy, A. Adler, M. Kazma, J. Salomon, C. Lawrence, A. Rossini, A. Salvia, J. Vidal Samso, J. Fierro (+9 others)
2013 Antimicrobial Agents and Chemotherapy  
High genetic diversity ofK. pneumoniaepopulations was observed, with specific characteristics at each center.  ...  Then, 100 isolates, including representatives of all PFGE types and of multiple subtypes for each larger PFGE type with subtypes, were typed by MLST (8) .  ...  An interesting exception was the Israeli CC147 isolates, split by MLST into ST147 and ST392 (SLVs differing by tonB alleles) but clustered by PFGE into 1 type with 23 subtypes.  ... 
doi:10.1128/aac.02571-12 pmid:23403417 pmcid:PMC3623323 fatcat:crt24iku2rczhnfvpkfl75yr2u

Increased HIV Subtype Diversity Reflecting Demographic Changes in the HIV Epidemic in New South Wales, Australia

Francesca Di Giallonardo, Angie Pinto, Phillip Keen, Ansari Shaik, Alex Carrera, Hanan Salem, Christine Selvey, Steven Nigro, Neil Fraser, Karen Price, Joanne Holden, Frederick Lee (+5 others)
2020 Viruses  
In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons.  ...  However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only.  ...  The proportion of sequences associated with each cluster type or singleton is shown as a pie chart for the four subtype groups analysed.  ... 
doi:10.3390/v12121402 pmid:33291330 fatcat:pbm3a3uyufar5pzbskwnkasn4i

Relating Church-Style and Curry-Style Subtyping

Adriana Compagnoni, Healfdene Goguen
2011 Electronic Proceedings in Theoretical Computer Science  
Type theories with higher-order subtyping or singleton types are examples of systems where computation rules for variables are affected by type information in the context.  ...  The algorithm for subtyping in F-Omega-Sub can then be given on types without context or kind information.  ...  Examples where this may occur are type systems with singleton types, where a variable of a singleton type is equal to the unique element of the type, or subtyping, where a type variable may be replaced  ... 
doi:10.4204/eptcs.45.1 fatcat:e75aonjtu5fi5gkfbioujqglbi

Extensional equivalence and singleton types

Christopher A. Stone, Robert Harper
2006 ACM Transactions on Computational Logic  
The system includes dependent types for pairs and functions ( and ) and a subtyping relation induced by regarding singletons as subtypes of the base type.  ...  We study the λ S ≤ calculus, which contains singleton types S(M ) classifying terms of base type provably equivalent to the term M .  ...  Later, he used an extremely simple form of singleton type (with no elimination rule or subtyping) in order to prove parametricity results [Crary 1999 ].  ... 
doi:10.1145/1166109.1166112 fatcat:wklyh5yuvvau7onwbhctjnyihu

Extensional equivalence and singleton types

Christopher A. Stone, Robert Harper
2006 ACM Transactions on Computational Logic  
The system includes dependent types for pairs and functions ( and ) and a subtyping relation induced by regarding singletons as subtypes of the base type.  ...  We study the λ S ≤ calculus, which contains singleton types S(M ) classifying terms of base type provably equivalent to the term M .  ...  Later, he used an extremely simple form of singleton type (with no elimination rule or subtyping) in order to prove parametricity results [Crary 1999 ].  ... 
doi:10.1145/1183278.1183281 fatcat:tpyi53ceujel7mvp7u5qp52fie

Obesity Subtypes and Risk of Spontaneous versus Medically Indicated Preterm Births in Singletons and Twins

H. M. Salihu, O. Lynch, A. P. Alio, J. Liu
2008 American Journal of Epidemiology  
By contrast, obese mothers with singleton gestation had about 50% greater odds of medically indicated preterm (odds ratio ¼ 1.46, 95% confidence interval: 1.39, 1.54) and very preterm (odds ratio ¼ 1.49  ...  Using data from the Missouri maternally linked files (1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997), the authors examined the association among maternal obesity, obesity subtypes, and spontaneous  ...  All tests of hypothesis were two tailed with a type 1 error rate fixed at 5 percent. SAS, version 9.1, software (SAS Institute, Inc., Cary, North Carolina) was used to perform all analyses.  ... 
doi:10.1093/aje/kwn092 pmid:18456643 fatcat:hmwjvafev5d4dkfxxtbl7vaczi
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