International Journal of Environmental Research and Public Health, 2020
It is important to investigate temporal variations of water chemistry for the purpose of improvin... more It is important to investigate temporal variations of water chemistry for the purpose of improving water quality in karst groundwater systems. Groundwater samples were collected daily under various land uses of Guiyang. Major ions and stable carbon isotope composition of dissolved inorganic carbon (δ13CDIC) were analyzed to understand the biogeochemical processes. The water chemistry was dominated by Ca2+, Mg2+, HCO3-, and SO42-, which mainly derived from the dissolution of carbonate rocks (limestone and dolomite) and oxidation of sulfide. The groundwater was defined as of the HCO3-Ca Mg and HCO3·SO4-Ca·Mg type, according to its hydrochemical characteristics. Results suggested that hydrochemical concentrations changed quickly, in response to rainfall events. The fast response revealed that karst groundwater was easily impacted by rainfall and anthropogenic inputs according to temporal variation of water chemistry. The distribution of DIC (dissolved inorganic carbon) and δ13CDIC show...
The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due t... more The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.
Comparing genomes of closely related genotypes from populations with distinct demographic histori... more Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high-quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino-acid sequence identity of 98.8% and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ~7,000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we o...
Proceedings of the 44th annual Southeast regional conference, 2006
Without physical boundaries, a wireless network faces many more security threats than a wired net... more Without physical boundaries, a wireless network faces many more security threats than a wired network does. Therefore, in the IEEE 802.16 standard a security sublayer is specified in the MAC layer to address the privacy issues across the fixed Broadband Wireless Access (BWA). Several articles have been published to address the flaws in IEEE 802.16 security after the IEEE standard 802.16-2001 was released. However, the IEEE standard 802.16-2004 revision does not settle all the discovered problems and additional flaws remain. This paper gives an overview of the IEEE 802.16 standard, focusing on the MAC layer and especially the security sublayer. We analyze the security flaws in the standard as well as in related works, and illustrate possible attacks to the authentication and key management protocols. Possible solutions are also proposed to prevent these attacks. Finally, we propose a security handover protocol that should be supported in the future 802.16e for mobility.
2007 2nd International Symposium on Wireless Pervasive Computing, 2007
Multicast delivery of data is a powerful mechanism that has strong potential in next generation n... more Multicast delivery of data is a powerful mechanism that has strong potential in next generation networks. The increased efficiency over unicast is a definite advantage, but the use of multicast poses many security risks. Effectively adding security measures to a multicast service is an intriguing problem, especially when the service is deployed in a wireless setting. Next generation IEEE 802.16 standard WirelessMAN networks are a perfect example of this problem, and the latest draft specification of the standard includes a secure protocol solution called Multicast and Broadcast Rekeying Algorithm (MBRA). In this paper, we expose the security problems of MBRA, including non-scalability and omission of backward and forward secrecy, and propose a new approach, ELAPSE, to address these problems. We analyze the security property of ELAPSE and use Qualnet simulations to show its efficiency.
Proceedings of the National Academy of Sciences, 2013
Significance Drawing from whole-genome sequences of multiple genotypes, this study documents the ... more Significance Drawing from whole-genome sequences of multiple genotypes, this study documents the molecular-genetic consequences of the loss of recombination in a microcrustacean, demonstrating that loss of heterozygosity via gene conversion-like processes is a dramatically more powerful force than accumulation of new mutations.
Investigating the phylogenetic relationships within physiologically essential gene families acros... more Investigating the phylogenetic relationships within physiologically essential gene families across a broad range of taxa can reveal the key gene duplication events underlying their family expansion and is thus important to functional genomics studies. P-Type II ATPases represent a large family of ATP powered transporters that move ions across cellular membranes and includes Na + /K + transporters, H + /K + transporters, and plasma membrane Ca 2+ pumps. Here, we examine the evolutionary history of one such transporter, the Sarco(endo)plasmic reticulum calcium ATPase (SERCA), which maintains calcium homeostasis in the cell by actively pumping Ca 2+ into the sarco(endo)plasmic reticulum. Our protein-based phylogenetic analyses across Eukaryotes revealed two monophyletic clades of SERCA proteins, one containing animals, fungi, and plants, and the other consisting of plants and protists. Our analyses suggest that the three known SERCA proteins in vertebrates arose through two major gene duplication events after the divergence from tunicates, but before the separation of fishes and tetrapods. In plants, we recovered two SERCA clades, one being the sister group to Metazoa and the other to Apicomplexa clade, suggesting an ancient duplication in an early eukaryotic ancestor, followed by subsequent loss of one copy in Opisthokonta, the other in protists, and retention of both in plants. We also report relatively recent and independent gene duplication events within invertebrate taxa including tunicates and the leech Helobdella robusta. Thus, it appears that both ancient and recent gene duplication events have played an important role in the evolution of this ubiquitous gene family across the eukaryotic domain.
A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa hav... more A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour-joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter-and intracontinental scales. The presence of well-supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500-24 000 years ago.
Multicast enables efficient large-scale content distribution and has become more and more popular... more Multicast enables efficient large-scale content distribution and has become more and more popular in network service. Security is a critical issue for multicast because many applications require access control and privacy. This issue is more sensitive to wireless network, which is lack of physical boundaries. IEEE 802.16 is the standard for next generation wireless network, which aims to provide the last mile access for Wireless Metropolitan Area Network (WirelessMAN). Multicast is also supported in IEEE 802.16, and a Multicast and Broadcast Rekeying Algorithm (MBRA) was proposed in the standard as an optional function for secure multicast. However, this algorithm does not provide backward and forward secrecy. It is not scalable to a large group either. This paper reviews the above two deficiencies of MBRA and proposes revision to address these problems for Intra-BS multicast. We also propose algorithms for secure multicast in different scenarios of WirelessMAN besides its basic schema, including Inter-BS multicast, multicast for mesh network, and multicast during handover.
International Journal of Distributed Sensor Networks, 2015
Mobile sensor networks (MSN) in the city environment have dynamic topology and large amounts of d... more Mobile sensor networks (MSN) in the city environment have dynamic topology and large amounts of data. In order to overcome the problem of data uploading and exchange, data uploading and exchange algorithm (DUEA) is proposed. In DUEA, the three-tier network architecture composed of vehicle nodes, relay nodes and sink nodes is considered. The link estimator, routing engine, and forwarding engine are modified based on CTP (collection tree protocol). In the link estimator, beacon packet is simplified. In the routing engine, the numbers of elements in the send queue of neighbor nodes, and link quality are weighed. The new calculation formulae of ETX value and selection method of father node are proposed. In the forwarding engine, different snooping methods are used for two types of data named general data and warning data. Simulation results show that compared with CTP, DUEA increases data throughput and transmission rate and reduces energy consumption of packet transmission when data is...
Lecture Notes in Geoinformation and Cartography, 2013
In this paper, we provide an overview of research on cognitively validating qualitative calculi, ... more In this paper, we provide an overview of research on cognitively validating qualitative calculi, focusing on the region connection calculus (RCC) and Egenhofer's intersection models (IM). These topological theories are often claimed to be foundational to spatial cognition, a concept we term the Egenhofer-Cohn Hypothesis 2. We have been particularly interested in extending existing approaches into the realm of spatio-temporal representation and reasoning. We provide an overview on a series of experiments that we conducted to shed light on geographic event conceptualization and topology's role in modeling and explaining cognitive behavior. Our framework also incorporates approaches to visually analyze cognitive behavior, allowing for interactive and in-depth analyses of cognitive conceptualizations. We present tangible results that can be distilled from generalizing from several experiments. These results show that the strong version of the Egenhofer-Cohn Hypothesis is not supported by all results; we suggest amendments to topological relationship specifications that are needed to serve as a sufficient basis for bridging formal and observed human spatial cognitive processes. We term this approach: topological relativity.
ABSTRACT Spatial language, such as route directions, can be analyzed to shed light on how humans ... more ABSTRACT Spatial language, such as route directions, can be analyzed to shed light on how humans communicate and conceptualize spatial knowledge. This article details a computational linguistic approach using route directions to study regional variations in spatial language. We developed a web-sourcing approach to collect human-generated route direction documents on a geographical scale. Specifically, we built the Spatially strAtified Route Direction (SARD) Corpus through automated scraping, classifying, and georeferencing of route directions. Based on semantic categories of cardinal and relative direction terms, the analysis of the SARD Corpus reveals significant differences and patterns on both national (United States, United Kingdom, and Australia) and regional (contiguous U.S. states) levels. Combining computational linguistics and georeferencing approaches offers the potential for extending classic spatial linguistic studies.
How spatial language varies regionally? This study investigates the possibility of exploring regi... more How spatial language varies regionally? This study investigates the possibility of exploring regional linguistic variations in spatial language by collecting and analyzing a Spatially-strAtified Route Direction Corpus (SARD Corpus) from volunteered spatial language text on the Web. Because of the fast content sharing functionality of the World Wide Web, it quickly becomes a hotbed for volunteered spatial language text, such as directions on hotels' Websites. These route directions can serve as a representation of everyday spatial language usage on the WWW. The spatial coverage and abundance of the data source is appealing while collecting and analyzing large quantities of spatially distributed data is still challenging. Through automated crawling, classifying and geo-referencing web documents containing route directions from the web, the SARD Corpus has been built covering the U.S., the U.K. and Australia. We implement a semantic categorical analysis scheme to explore regional variations in cardinal versus relative direction usages. Preliminary results show both similarity and differences at national level and geographic patterns at regional level. The design and implementation of building a geo-referenced large-scale corpus from Web documents offers a methodological contribution to corpus linguistics, spatial cognition, and the GISciences.
We present first results of an analysis of a corpus of linguistic descriptions that were collecte... more We present first results of an analysis of a corpus of linguistic descriptions that were collected in controlled experiments. This corpus and its analysis add to the body of knowledge on formal models for spatial language, language interpretation and generation. The experiments are grounded in qualitative formalisms (RCC and Intersection Models, IM) that have a long standing tradition as means to bridge formal and linguistic descriptions of space and spatial relations. Our experiments address dynamically changing spatial relations (movement patterns/geographic events). By keeping the formal spatial characterizations identical across experiments but changing the semantics (that is, we used movement patterns across seven different geographic domains such as a hurricane in relation to a peninsula, plus two geometric figure domains) we contribute to disentangling spatial and domain specific aspects of spatial (event) language. We briefly discuss here two aspects: First, we hand examine the corpus by selecting participants that show the same conceptual behavior as identified through RCC/IM; second, we analyze the domain specific sub-corpora to address similarities and dissimilarities between individual domains.
This article focuses on integrating computational and visual methods in a system that supports an... more This article focuses on integrating computational and visual methods in a system that supports analysts to identify, extract, map, and relate linguistic accounts of movement. We address two objectives: (1) build the conceptual, theoretical, and empirical framework needed to represent and interpret human-generated directions; and (2) design and implement a geovisual analytics workspace for direction document analysis. We have built a set of geo-enabled, computational methods to identify documents containing movement statements, and a visual analytics environment that uses natural language processing methods iteratively with geographic database support to extract, interpret, and map geographic movement references in context. Additionally, analysts can provide feedback to improve computational results. To demonstrate the value of this integrative approach, we have realized a proof-of-concept implementation focusing on identifying and processing documents that contain human-generated route directions. Using our visual analytic interface, an analyst can explore the results, provide feedback to improve those results, pose queries against a database of route directions, and interactively represent the route on a map.
A generalization of the fast coding method for efficient data hiding has been proposed. In this w... more A generalization of the fast coding method for efficient data hiding has been proposed. In this way, each secret digit in a prime-base notational system is represented by a series of cover values. Modification on one cover value can be used to embed several secret digits, so that distortion is observably reduced. The original fast coding method can be viewed as a special case of the generalized scheme with a prime base p=2. And theoretical analysis shows that the generalized running coding with p=3 can provide the best performance.
A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa hav... more A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour-joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter- and intra-continental scales. The presence of well-supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North...
International Journal of Environmental Research and Public Health, 2020
It is important to investigate temporal variations of water chemistry for the purpose of improvin... more It is important to investigate temporal variations of water chemistry for the purpose of improving water quality in karst groundwater systems. Groundwater samples were collected daily under various land uses of Guiyang. Major ions and stable carbon isotope composition of dissolved inorganic carbon (δ13CDIC) were analyzed to understand the biogeochemical processes. The water chemistry was dominated by Ca2+, Mg2+, HCO3-, and SO42-, which mainly derived from the dissolution of carbonate rocks (limestone and dolomite) and oxidation of sulfide. The groundwater was defined as of the HCO3-Ca Mg and HCO3·SO4-Ca·Mg type, according to its hydrochemical characteristics. Results suggested that hydrochemical concentrations changed quickly, in response to rainfall events. The fast response revealed that karst groundwater was easily impacted by rainfall and anthropogenic inputs according to temporal variation of water chemistry. The distribution of DIC (dissolved inorganic carbon) and δ13CDIC show...
The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due t... more The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.
Comparing genomes of closely related genotypes from populations with distinct demographic histori... more Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high-quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino-acid sequence identity of 98.8% and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ~7,000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we o...
Proceedings of the 44th annual Southeast regional conference, 2006
Without physical boundaries, a wireless network faces many more security threats than a wired net... more Without physical boundaries, a wireless network faces many more security threats than a wired network does. Therefore, in the IEEE 802.16 standard a security sublayer is specified in the MAC layer to address the privacy issues across the fixed Broadband Wireless Access (BWA). Several articles have been published to address the flaws in IEEE 802.16 security after the IEEE standard 802.16-2001 was released. However, the IEEE standard 802.16-2004 revision does not settle all the discovered problems and additional flaws remain. This paper gives an overview of the IEEE 802.16 standard, focusing on the MAC layer and especially the security sublayer. We analyze the security flaws in the standard as well as in related works, and illustrate possible attacks to the authentication and key management protocols. Possible solutions are also proposed to prevent these attacks. Finally, we propose a security handover protocol that should be supported in the future 802.16e for mobility.
2007 2nd International Symposium on Wireless Pervasive Computing, 2007
Multicast delivery of data is a powerful mechanism that has strong potential in next generation n... more Multicast delivery of data is a powerful mechanism that has strong potential in next generation networks. The increased efficiency over unicast is a definite advantage, but the use of multicast poses many security risks. Effectively adding security measures to a multicast service is an intriguing problem, especially when the service is deployed in a wireless setting. Next generation IEEE 802.16 standard WirelessMAN networks are a perfect example of this problem, and the latest draft specification of the standard includes a secure protocol solution called Multicast and Broadcast Rekeying Algorithm (MBRA). In this paper, we expose the security problems of MBRA, including non-scalability and omission of backward and forward secrecy, and propose a new approach, ELAPSE, to address these problems. We analyze the security property of ELAPSE and use Qualnet simulations to show its efficiency.
Proceedings of the National Academy of Sciences, 2013
Significance Drawing from whole-genome sequences of multiple genotypes, this study documents the ... more Significance Drawing from whole-genome sequences of multiple genotypes, this study documents the molecular-genetic consequences of the loss of recombination in a microcrustacean, demonstrating that loss of heterozygosity via gene conversion-like processes is a dramatically more powerful force than accumulation of new mutations.
Investigating the phylogenetic relationships within physiologically essential gene families acros... more Investigating the phylogenetic relationships within physiologically essential gene families across a broad range of taxa can reveal the key gene duplication events underlying their family expansion and is thus important to functional genomics studies. P-Type II ATPases represent a large family of ATP powered transporters that move ions across cellular membranes and includes Na + /K + transporters, H + /K + transporters, and plasma membrane Ca 2+ pumps. Here, we examine the evolutionary history of one such transporter, the Sarco(endo)plasmic reticulum calcium ATPase (SERCA), which maintains calcium homeostasis in the cell by actively pumping Ca 2+ into the sarco(endo)plasmic reticulum. Our protein-based phylogenetic analyses across Eukaryotes revealed two monophyletic clades of SERCA proteins, one containing animals, fungi, and plants, and the other consisting of plants and protists. Our analyses suggest that the three known SERCA proteins in vertebrates arose through two major gene duplication events after the divergence from tunicates, but before the separation of fishes and tetrapods. In plants, we recovered two SERCA clades, one being the sister group to Metazoa and the other to Apicomplexa clade, suggesting an ancient duplication in an early eukaryotic ancestor, followed by subsequent loss of one copy in Opisthokonta, the other in protists, and retention of both in plants. We also report relatively recent and independent gene duplication events within invertebrate taxa including tunicates and the leech Helobdella robusta. Thus, it appears that both ancient and recent gene duplication events have played an important role in the evolution of this ubiquitous gene family across the eukaryotic domain.
A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa hav... more A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour-joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter-and intracontinental scales. The presence of well-supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500-24 000 years ago.
Multicast enables efficient large-scale content distribution and has become more and more popular... more Multicast enables efficient large-scale content distribution and has become more and more popular in network service. Security is a critical issue for multicast because many applications require access control and privacy. This issue is more sensitive to wireless network, which is lack of physical boundaries. IEEE 802.16 is the standard for next generation wireless network, which aims to provide the last mile access for Wireless Metropolitan Area Network (WirelessMAN). Multicast is also supported in IEEE 802.16, and a Multicast and Broadcast Rekeying Algorithm (MBRA) was proposed in the standard as an optional function for secure multicast. However, this algorithm does not provide backward and forward secrecy. It is not scalable to a large group either. This paper reviews the above two deficiencies of MBRA and proposes revision to address these problems for Intra-BS multicast. We also propose algorithms for secure multicast in different scenarios of WirelessMAN besides its basic schema, including Inter-BS multicast, multicast for mesh network, and multicast during handover.
International Journal of Distributed Sensor Networks, 2015
Mobile sensor networks (MSN) in the city environment have dynamic topology and large amounts of d... more Mobile sensor networks (MSN) in the city environment have dynamic topology and large amounts of data. In order to overcome the problem of data uploading and exchange, data uploading and exchange algorithm (DUEA) is proposed. In DUEA, the three-tier network architecture composed of vehicle nodes, relay nodes and sink nodes is considered. The link estimator, routing engine, and forwarding engine are modified based on CTP (collection tree protocol). In the link estimator, beacon packet is simplified. In the routing engine, the numbers of elements in the send queue of neighbor nodes, and link quality are weighed. The new calculation formulae of ETX value and selection method of father node are proposed. In the forwarding engine, different snooping methods are used for two types of data named general data and warning data. Simulation results show that compared with CTP, DUEA increases data throughput and transmission rate and reduces energy consumption of packet transmission when data is...
Lecture Notes in Geoinformation and Cartography, 2013
In this paper, we provide an overview of research on cognitively validating qualitative calculi, ... more In this paper, we provide an overview of research on cognitively validating qualitative calculi, focusing on the region connection calculus (RCC) and Egenhofer's intersection models (IM). These topological theories are often claimed to be foundational to spatial cognition, a concept we term the Egenhofer-Cohn Hypothesis 2. We have been particularly interested in extending existing approaches into the realm of spatio-temporal representation and reasoning. We provide an overview on a series of experiments that we conducted to shed light on geographic event conceptualization and topology's role in modeling and explaining cognitive behavior. Our framework also incorporates approaches to visually analyze cognitive behavior, allowing for interactive and in-depth analyses of cognitive conceptualizations. We present tangible results that can be distilled from generalizing from several experiments. These results show that the strong version of the Egenhofer-Cohn Hypothesis is not supported by all results; we suggest amendments to topological relationship specifications that are needed to serve as a sufficient basis for bridging formal and observed human spatial cognitive processes. We term this approach: topological relativity.
ABSTRACT Spatial language, such as route directions, can be analyzed to shed light on how humans ... more ABSTRACT Spatial language, such as route directions, can be analyzed to shed light on how humans communicate and conceptualize spatial knowledge. This article details a computational linguistic approach using route directions to study regional variations in spatial language. We developed a web-sourcing approach to collect human-generated route direction documents on a geographical scale. Specifically, we built the Spatially strAtified Route Direction (SARD) Corpus through automated scraping, classifying, and georeferencing of route directions. Based on semantic categories of cardinal and relative direction terms, the analysis of the SARD Corpus reveals significant differences and patterns on both national (United States, United Kingdom, and Australia) and regional (contiguous U.S. states) levels. Combining computational linguistics and georeferencing approaches offers the potential for extending classic spatial linguistic studies.
How spatial language varies regionally? This study investigates the possibility of exploring regi... more How spatial language varies regionally? This study investigates the possibility of exploring regional linguistic variations in spatial language by collecting and analyzing a Spatially-strAtified Route Direction Corpus (SARD Corpus) from volunteered spatial language text on the Web. Because of the fast content sharing functionality of the World Wide Web, it quickly becomes a hotbed for volunteered spatial language text, such as directions on hotels' Websites. These route directions can serve as a representation of everyday spatial language usage on the WWW. The spatial coverage and abundance of the data source is appealing while collecting and analyzing large quantities of spatially distributed data is still challenging. Through automated crawling, classifying and geo-referencing web documents containing route directions from the web, the SARD Corpus has been built covering the U.S., the U.K. and Australia. We implement a semantic categorical analysis scheme to explore regional variations in cardinal versus relative direction usages. Preliminary results show both similarity and differences at national level and geographic patterns at regional level. The design and implementation of building a geo-referenced large-scale corpus from Web documents offers a methodological contribution to corpus linguistics, spatial cognition, and the GISciences.
We present first results of an analysis of a corpus of linguistic descriptions that were collecte... more We present first results of an analysis of a corpus of linguistic descriptions that were collected in controlled experiments. This corpus and its analysis add to the body of knowledge on formal models for spatial language, language interpretation and generation. The experiments are grounded in qualitative formalisms (RCC and Intersection Models, IM) that have a long standing tradition as means to bridge formal and linguistic descriptions of space and spatial relations. Our experiments address dynamically changing spatial relations (movement patterns/geographic events). By keeping the formal spatial characterizations identical across experiments but changing the semantics (that is, we used movement patterns across seven different geographic domains such as a hurricane in relation to a peninsula, plus two geometric figure domains) we contribute to disentangling spatial and domain specific aspects of spatial (event) language. We briefly discuss here two aspects: First, we hand examine the corpus by selecting participants that show the same conceptual behavior as identified through RCC/IM; second, we analyze the domain specific sub-corpora to address similarities and dissimilarities between individual domains.
This article focuses on integrating computational and visual methods in a system that supports an... more This article focuses on integrating computational and visual methods in a system that supports analysts to identify, extract, map, and relate linguistic accounts of movement. We address two objectives: (1) build the conceptual, theoretical, and empirical framework needed to represent and interpret human-generated directions; and (2) design and implement a geovisual analytics workspace for direction document analysis. We have built a set of geo-enabled, computational methods to identify documents containing movement statements, and a visual analytics environment that uses natural language processing methods iteratively with geographic database support to extract, interpret, and map geographic movement references in context. Additionally, analysts can provide feedback to improve computational results. To demonstrate the value of this integrative approach, we have realized a proof-of-concept implementation focusing on identifying and processing documents that contain human-generated route directions. Using our visual analytic interface, an analyst can explore the results, provide feedback to improve those results, pose queries against a database of route directions, and interactively represent the route on a map.
A generalization of the fast coding method for efficient data hiding has been proposed. In this w... more A generalization of the fast coding method for efficient data hiding has been proposed. In this way, each secret digit in a prime-base notational system is represented by a series of cover values. Modification on one cover value can be used to embed several secret digits, so that distortion is observably reduced. The original fast coding method can be viewed as a special case of the generalized scheme with a prime base p=2. And theoretical analysis shows that the generalized running coding with p=3 can provide the best performance.
A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa hav... more A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour-joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter- and intra-continental scales. The presence of well-supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North...
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