抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

https://bioinformatics.cs.vt.edu/~easychair/HusonBryant_MBE_2006.pdf

Application of Phylogenetic Networks in Evolutionary Studies

DBpedia is a community effort to extract structured information from Wikipedia and to make this information available on the Web. DBpedia allows you to ask sophisticated queries against datasets derived from Wikipedia and to link other datasets on the Web to Wikipedia data. We describe the extraction of the DBpedia datasets, and how the resulting information is published on the Web for human-andmachine-consumption. We describe some emerging applications from the DBpedia community and show how website authors can facilitate DBpedia content within their sites. Finally, we present the current status of interlinking DBpedia with other open datasets on the Web and outline how DBpedia could serve as a nucleus for an emerging Web of open data.

/pdf/dbpedia-a-nucleus-for-a-web-of-open-data-64wla3p0zr.pdf

DBpedia: a nucleus for a web of open data

This collaboratively edited knowledgebase provides a common source of data for Wikipedia, and everyone else.

https://dl.acm.org/doi/pdf/10.1145/2629489

Wikidata: a free collaborative knowledgebase

Data integration is the problem of combining data residing at different sources, and providing the user with a unified view of these data. The problem of designing data integration systems is important in current real world applications, and is characterized by a number of issues that are interesting from a theoretical point of view. This document presents on overview of the material to be presented in a tutorial on data integration. The tutorial is focused on some of the theoretical issues that are relevant for data integration. Special attention will be devoted to the following aspects: modeling a data integration application, processing queries in data integration, dealing with inconsistent data sources, and reasoning on queries.

/pdf/data-integration-a-theoretical-perspective-58aesjvhuk.pdf

Data integration: a theoretical perspective

Many rural and remote communities around the world see themselves on the wrong side of the digital divide. In particular, there is evidence to suggest that there is a growing digital divide between urban and rural areas in terms of broadband Internet access with people living in rural areas having fewer choices and pay higher prices for slower speeds. This is true even in developed countries. Motivated by the above observations, there has been an increasing interest in deploying and researching low cost rural wireless networks with active community participation. This paper presents an overview of our efforts in this direction in deploying a rural WiFibased long distance mesh network testbed in the Scottish Highlands and Islands. We highlight the unique aspects of our testbed that differentiate it from other existing rural wireless testbeds. We also outline some of the research issues that are currently being investigated in this project.

/pdf/tegola-tiered-mesh-network-testbed-in-rural-scotland-ahwi3rm2m9.pdf

Tegola tiered mesh network testbed in rural Scotland

In order to represent inheritance, several recent designs for database programming languages have made use of class construct, which can be thought of as a restricted data type with an associated set of instances. Moreover, these classes are persistent they survive from one program invocation to another. This paper examines whether it is necessary to the together type, extent and persistence in order to model inheritance and suggests that they may be separated to provide more general database programming languages. In particular we shall see that it is possible to assign a generic data type to a function that extracts all the objects of a given type in the database so that the class hierarchy can be derived from the type hierarchy. We shall also examine object-level inheritance and its relationship to data types for relational databases. A final section examines how the various forms of persistence interact with inheritance at both object and type level.

Inheritance and persistence in database programming languages

XML [7], which is emerging as an important standard for data exchange on the World Wide Web, highlights the importance of the semistructured data. Although the XML standard itself does not require any schema or type system, a number of proposals [6, 15, 18] have been developed that roughly correspond to data definition languages. These allow one to constrain the structure of XML data by imposing a schema on it. These and other proposals also advocate the need for integrity constraints, another form of constraints that should, for example, be capable of expressing inclusion constraints and inverse relationships. The latter have recently been studied as path constraints in the context of semistructured data [4, 11]. It is likely that future XML proposals will involve both forms of constraint, and it is therefore appropriate to understand the interaction between them. This paper investigates that interaction. In particular it studies constraint implication problems, which are important both in understanding the semantics of type/constraint systems and in query optimization. A number of results on path constraint implication are established in the presences and absences of type systems. These results demonstrate that adding a type systems may in some cases simplify reasoning about path constraints and in other cases make it harder. For example, it is shown that there is a path constraint implication problem that is decidable in PTIME in the untyped context, but that becomes undecidable when a type system is added. On the other hand, there is an implication problem that is undecidable in the untyped context, but becomes not only decidable in cubic time but also finitely axiomatizable when a type system is imposed. Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-98-16. This technical report is available at ScholarlyCommons: http://repository.upenn.edu/cis_reports/106

/pdf/interaction-between-path-and-type-constraints-4pui51utc9.pdf

Interaction between path and type constraints

A new definition of complex objects is introduced which provides a denotation for incomplete tuples as well as partially described sets. Set values are “sandwiched” between “complete” and “consistent” descriptions (representing the Smyth and Hoare powerdomains respectively), allowing the maximal values to be arbitrary subsets of maximal elements in the domain of the set. We also examine the use of rules in defining queries over such objects.

Peter Buneman

Papers

Tegola tiered mesh network testbed in rural Scotland

Inheritance and persistence in database programming languages

Interaction between path and type constraints

A semantics for complex objects and approximate queries

Workshop on Query Processing for Semistructured Data and Non-Standard Data Formats