Migration and diving behavior of Centrophorus squamosus in the NE Atlantic. Combining electronic tagging and Argo hydrography to infer deep ocean trajectories

NASA Astrophysics Data System (ADS)

Rodríguez-Cabello, Cristina; González-Pola, Cesar; Sánchez, Francisco

2016-09-01

A total of nine leafscale gulper sharks Centrophorus squamosus (Bonnaterre, 1788), were tagged with pop-up, satellite, archival, transmitting tags (PSAT) in the Marine Protected Area (MPA) of El Cachucho (Le Danois Bank) located in waters to the north of Spain, (NE Atlantic). Tags provided data on time, pressure and temperature that were used to examine movement patterns and diving behavior. Data collected from Argo floats in the study area have been used to devise a simple geolocation algorithm to infer the probable routes followed by this species. Tag release points revealed that C. squamosus moved both to the west (Galician waters) and to the north (Porcupine Bank) from the tagging area, suggesting well defined preferred pathways. The inferred trajectories indicated that sharks alternate periods constrained to specific geographical regions with quick and prompt movements covering large distances. Two sharks made conspicuous diurnal vertical migrations being at shallower depths around midnight and at maximum depths at midday, while other sharks did not make vertical migrations. Vertical movements were done smoothly and independently of the fish swimming long-distances or resting in the area. Overall results confirm that this species is highly migratory, supporting speeds of 20 nautical miles.day-1 and well capable to swim and make vertical migrations well above the abyssal plain.

Applying Fractal Dimensions and Energy-Budget Analysis to Characterize Fracturing Processes During Magma Migration and Eruption: 2011-2012 El Hierro (Canary Islands) Submarine Eruption

NASA Astrophysics Data System (ADS)

López, Carmen; Martí, Joan; Abella, Rafael; Tarraga, Marta

2014-07-01

The impossibility of observing magma migration inside the crust obliges us to rely on geophysical data and mathematical modelling to interpret precursors and to forecast volcanic eruptions. Of the geophysical signals that may be recorded before and during an eruption, deformation and seismicity are two of the most relevant as they are directly related to its dynamic. The final phase of the unrest episode that preceded the 2011-2012 eruption on El Hierro (Canary Islands) was characterized by local and accelerated deformation and seismic energy release indicating an increasing fracturing and a migration of the magma. Application of time varying fractal analysis to the seismic data and the characterization of the seismicity pattern and the strain and the stress rates allow us to identify different stages in the source mechanism and to infer the geometry of the path used by the magma and associated fluids to reach the Earth's surface. The results obtained illustrate the relevance of such studies to understanding volcanic unrest and the causes that govern the initiation of volcanic eruptions.

Goliath catfish spawning in the far western Amazon confirmed by the distribution of mature adults, drifting larvae and migrating juveniles

PubMed Central

Barthem, Ronaldo B.; Goulding, Michael; Leite, Rosseval G.; Cañas, Carlos; Forsberg, Bruce; Venticinque, Eduardo; Petry, Paulo; Ribeiro, Mauro L. de B.; Chuctaya, Junior; Mercado, Armando

2017-01-01

We mapped the inferred long-distance migrations of four species of Amazonian goliath catfishes (Brachyplatystoma rousseauxii, B. platynemum, B. juruense and B. vaillantii) based on the presence of individuals with mature gonads and conducted statistical analysis of the expected long-distance downstream migrations of their larvae and juveniles. By linking the distribution of larval, juvenile and mature adult size classes across the Amazon, the results showed: (i) that the main spawning regions of these goliath catfish species are in the western Amazon; (ii) at least three species—B. rousseauxii, B. platynemum, and B. juruense—spawn partially or mainly as far upstream as the Andes; (iii) the main spawning area of B. rousseauxii is in or near the Andes; and (iv) the life history migration distances of B. rousseauxii are the longest strictly freshwater fish migrations in the world. These results provide an empirical baseline for tagging experiments, life histories extrapolated from otolith microchemistry interpretations and other methods to establish goliath catfish migratory routes, their seasonal timing and possible return (homing) to western headwater tributaries where they were born. PMID:28165499

Using Nocturnal Flight Calls to Assess the Fall Migration of Warblers and Sparrows along a Coastal Ecological Barrier

PubMed Central

Smith, Adam D.; Paton, Peter W. C.; McWilliams, Scott R.

2014-01-01

Atmospheric conditions fundamentally influence the timing, intensity, energetics, and geography of avian migration. While radar is typically used to infer the influence of weather on the magnitude and spatiotemporal patterns of nocturnal bird migration, monitoring the flight calls produced by many bird species during nocturnal migration represents an alternative methodology and provides information regarding the species composition of nocturnal migration. We used nocturnal flight call (NFC) recordings of at least 22 migratory songbirds (14 warbler and 8 sparrow species) during fall migration from eight sites along the mainland and island coasts of Rhode Island to evaluate five hypotheses regarding NFC detections. Patterns of warbler and sparrow NFC detections largely supported our expectations in that (1) NFC detections associated positively and strongly with wind conditions that influence the intensity of coastal bird migration and negatively with regional precipitation; (2) NFCs increased during conditions with reduced visibility (e.g., high cloud cover); (3) NFCs decreased with higher wind speeds, presumably due mostly to increased ambient noise; and (4) coastal mainland sites recorded five to nine times more NFCs, on average, than coastal nearshore or offshore island sites. However, we found little evidence that (5) nightly or intra-night patterns of NFCs reflected the well-documented latitudinal patterns of migrant abundance on an offshore island. Despite some potential complications in inferring migration intensity and species composition from NFC data, the acoustic monitoring of NFCs provides a viable and complementary methodology for exploring the spatiotemporal patterns of songbird migration as well as evaluating the atmospheric conditions that shape these patterns. PMID:24643060

Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep.

PubMed

Lv, Feng-Hua; Peng, Wei-Feng; Yang, Ji; Zhao, Yong-Xin; Li, Wen-Rong; Liu, Ming-Jun; Ma, Yue-Hui; Zhao, Qian-Jun; Yang, Guang-Li; Wang, Feng; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Zhao, Sheng-Guo; Hehua, Eer; Gorkhali, Neena A; Farhad Vahidi, S M; Muladno, Muhammad; Naqvi, Arifa N; Tabell, Jonna; Iso-Touru, Terhi; Bruford, Michael W; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua

2015-10-01

Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep

PubMed Central

Lv, Feng-Hua; Peng, Wei-Feng; Yang, Ji; Zhao, Yong-Xin; Li, Wen-Rong; Liu, Ming-Jun; Ma, Yue-Hui; Zhao, Qian-Jun; Yang, Guang-Li; Wang, Feng; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Zhao, Sheng-Guo; Hehua, EEr; Gorkhali, Neena A.; Farhad Vahidi, S. M.; Muladno, Muhammad; Naqvi, Arifa N.; Tabell, Jonna; Iso-Touru, Terhi; Bruford, Michael W.; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua

2015-01-01

Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637–0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8–11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20–60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5–6.8 ka (lineages A and B: ∼6.4–6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West–East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a “transportation hub” in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia. PMID:26085518

Comparative osteohistology of Hesperornis with reference to pygoscelid penguins: the effects of climate and behaviour on avian bone microstructure

PubMed Central

Wilson, Laura E.; Chin, Karen

2014-01-01

The broad biogeographic distribution of Hesperornis fossils in Late Cretaceous Western Interior Seaway deposits has prompted questions about whether they endured polar winters or migrated between mid- and high latitudes. Here, we compare microstructures of hesperornithiform long bones from Kansas and the Arctic to investigate whether migration or Late Cretaceous polar climate affected bone growth. We also examine modern penguin bones to determine how migration and climate may influence bone growth in birds with known behaviours. Histological analysis of hesperornithiform samples reveals continuous bone deposition throughout the cortex, plus an outer circumferential layer in adults. No cyclic growth marks, zonation or differences in vasculature are apparent in the Hesperornis specimens. Comparatively, migratory Adélie and chinstrap penguin bones show no zonation or changes in microstructure, suggesting that migration is not necessarily recorded in avian bone microstructure. Non-migratory gentoos show evidence of rapid bone growth possibly associated with increased chick growth rates in high-latitude populations and large body size. The absence of histological evidence for migration in extinct Hesperornis and extant pygoscelid penguins may reflect that these birds reached skeletal maturity before migration or overwintering. This underscores the challenges of using bone microstructure to infer the effects of behaviour and climate on avian growth. PMID:26064560

Directional Migration of Recirculating Lymphocytes through Lymph Nodes via Random Walks

PubMed Central

Thomas, Niclas; Matejovicova, Lenka; Srikusalanukul, Wichat; Shawe-Taylor, John; Chain, Benny

2012-01-01

Naive T lymphocytes exhibit extensive antigen-independent recirculation between blood and lymph nodes, where they may encounter dendritic cells carrying cognate antigen. We examine how long different T cells may spend in an individual lymph node by examining data from long term cannulation of blood and efferent lymphatics of a single lymph node in the sheep. We determine empirically the distribution of transit times of migrating T cells by applying the Least Absolute Shrinkage & Selection Operator () or regularised to fit experimental data describing the proportion of labelled infused cells in blood and efferent lymphatics over time. The optimal inferred solution reveals a distribution with high variance and strong skew. The mode transit time is typically between 10 and 20 hours, but a significant number of cells spend more than 70 hours before exiting. We complement the empirical machine learning based approach by modelling lymphocyte passage through the lymph node . On the basis of previous two photon analysis of lymphocyte movement, we optimised distributions which describe the transit times (first passage times) of discrete one dimensional and continuous (Brownian) three dimensional random walks with drift. The optimal fit is obtained when drift is small, i.e. the ratio of probabilities of migrating forward and backward within the node is close to one. These distributions are qualitatively similar to the inferred empirical distribution, with high variance and strong skew. In contrast, an optimised normal distribution of transit times (symmetrical around mean) fitted the data poorly. The results demonstrate that the rapid recirculation of lymphocytes observed at a macro level is compatible with predominantly randomised movement within lymph nodes, and significant probabilities of long transit times. We discuss how this pattern of migration may contribute to facilitating interactions between low frequency T cells and antigen presenting cells carrying cognate antigen. PMID:23028891

Inference of population splits and mixtures from genome-wide allele frequency data.

PubMed

Pickrell, Joseph K; Pritchard, Jonathan K

2012-01-01

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

PubMed Central

Paraskevis, Dimitrios; Pybus, Oliver; Magiorkinis, Gkikas; Hatzakis, Angelos; Wensing, Annemarie MJ; van de Vijver, David A; Albert, Jan; Angarano, Guiseppe; Åsjö, Birgitta; Balotta, Claudia; Boeri, Enzo; Camacho, Ricardo; Chaix, Marie-Laure; Coughlan, Suzie; Costagliola, Dominique; De Luca, Andrea; de Mendoza, Carmen; Derdelinckx, Inge; Grossman, Zehava; Hamouda, Osama; Hoepelman, IM; Horban, Andrzej; Korn, Klaus; Kücherer, Claudia; Leitner, Thomas; Loveday, Clive; MacRae, Eilidh; Maljkovic-Berry, I; Meyer, Laurence; Nielsen, Claus; Op de Coul, Eline LM; Ormaasen, Vidar; Perrin, Luc; Puchhammer-Stöckl, Elisabeth; Ruiz, Lidia; Salminen, Mika O; Schmit, Jean-Claude; Schuurman, Rob; Soriano, Vincent; Stanczak, J; Stanojevic, Maja; Struck, Daniel; Van Laethem, Kristel; Violin, M; Yerly, Sabine; Zazzi, Maurizio; Boucher, Charles A; Vandamme, Anne-Mieke

2009-01-01

Background The prevalence and the origin of HIV-1 subtype B, the most prevalent circulating clade among the long-term residents in Europe, have been studied extensively. However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced. Results In the current study we inferred the migration history of HIV-1 subtype B by way of a phylogeography of viral sequences sampled from 16 European countries and Israel. Migration events were inferred from viral phylogenies by character reconstruction using parsimony. With regard to the spatial dispersal of the HIV subtype B sequences across viral phylogenies, in most of the countries in Europe the epidemic was introduced by multiple sources and subsequently spread within local networks. Poland provides an exception where most of the infections were the result of a single point introduction. According to the significant migratory pathways, we show that there are considerable differences across Europe. Specifically, Greece, Portugal, Serbia and Spain, provide sources shedding HIV-1; Austria, Belgium and Luxembourg, on the other hand, are migratory targets, while for Denmark, Germany, Italy, Israel, Norway, the Netherlands, Sweden, Switzerland and the UK we inferred significant bidirectional migration. For Poland no significant migratory pathways were inferred. Conclusion Subtype B phylogeographies provide a new insight about the geographical distribution of viral lineages, as well as the significant pathways of virus dispersal across Europe, suggesting that intervention strategies should also address tourists, travellers and migrants. PMID:19457244

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leitner, Thomas; Paraskevis, D; Pybus, O

2008-01-01

The prevalence and the origin of HIV-1 subtype B, the most prevalent circulating clade among the long-term residents in Europe, have been studied extensively. However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced. In the current study we inferred the migration history of HIV-1 subtype B by way of a phylogeography of viral sequences sampled from 16 European countries and Israel. Migration events were inferred from viral phylogenies by character reconstruction using parsimony. With regard to the spatial dispersal of the HIV subtype B sequences across viral phylogenies, in most ofmore » the countries in Europe the epidemic was introduced by multiple sources and subsequently spread within local networks. Poland provides an exception where most of the infections were the result of a single point introduction. According to the significant migratory pathways, we show that there are considerable differences across Europe. Specifically, Greece, Portugal, Serbia and Spain, provide sources shedding HIV-1; Austria, Belgium and Luxembourg, on the other hand, are migratory targets, while for Denmark, Germany, Italy, Israel, Norway, the Netherlands, Sweden, Switzerland and the UK we inferred significant bidirectional migration. For Poland no significant migratory pathways were inferred. Subtype B phylogeographies provide a new insight about the geographical distribution of viral lineages, as well as the significant pathways of virus dispersal across Europe, suggesting that intervention strategies should also address tourists, travellers and migrants.« less

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

PubMed Central

Gutenkunst, Ryan N.; Hernandez, Ryan D.; Williamson, Scott H.; Bustamante, Carlos D.

2009-01-01

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU). PMID:19851460

Inferring the rules of social interaction in migrating caribou.

PubMed

Torney, Colin J; Lamont, Myles; Debell, Leon; Angohiatok, Ryan J; Leclerc, Lisa-Marie; Berdahl, Andrew M

2018-05-19

Social interactions are a significant factor that influence the decision-making of species ranging from humans to bacteria. In the context of animal migration, social interactions may lead to improved decision-making, greater ability to respond to environmental cues, and the cultural transmission of optimal routes. Despite their significance, the precise nature of social interactions in migrating species remains largely unknown. Here we deploy unmanned aerial systems to collect aerial footage of caribou as they undertake their migration from Victoria Island to mainland Canada. Through a Bayesian analysis of trajectories we reveal the fine-scale interaction rules of migrating caribou and show they are attracted to one another and copy directional choices of neighbours, but do not interact through clearly defined metric or topological interaction ranges. By explicitly considering the role of social information on movement decisions we construct a map of near neighbour influence that quantifies the nature of information flow in these herds. These results will inform more realistic, mechanism-based models of migration in caribou and other social ungulates, leading to better predictions of spatial use patterns and responses to changing environmental conditions. Moreover, we anticipate that the protocol we developed here will be broadly applicable to study social behaviour in a wide range of migratory and non-migratory taxa.This article is part of the theme issue 'Collective movement ecology'. © 2018 The Authors.

Stratigraphic architecture of hydromagmatic volcanoes that have undergone vent migration: a review of Korean case studies

NASA Astrophysics Data System (ADS)

Sohn, Y.

2011-12-01

Recent studies show that the architecture of hydromagmatic volcanoes is far more complex than formerly expected. A number of external factors, such as paleohydrology and tectonics, in addition to magmatic processes are thought to play a role in controlling the overall characteristics and architecture of these volcanoes. One of the main consequences of these controls is the migration of the active vent during eruption. Case studies of hydromagmatic volcanoes in Korea show that those volcanoes that have undergone vent migration are characterized by superposition or juxtaposition of multiple rim deposits of partial tuff rings and/or tuff cones that have contrasting lithofacies characteristics, bed attitudes, and paleoflow directions. Various causes of vent migration are inferred from these volcanoes. Large-scale collapse of fragile substrate is interpreted to have caused vent migration in the Early Pleistocene volcanoes of Jeju Island, which were built upon still unconsolidated continental shelf sediments. Late Pleistocene to Holocene volcanoes, which were built upon a stack of rigid, shield-forming lava flows, lack features due to large-scale substrate collapse and have generally simple and circular morphologies either of a tuff ring or of a tuff cone. However, ~600 m shift of the eruptive center is inferred from one of these volcanoes (Ilchulbong tuff cone). The vent migration in this volcano is interpreted to have occurred because the eruption was sourced by multiple magma batches with significant eruptive pauses in between. The Yangpori diatreme in a Miocene terrestrial half-graben basin in SE Korea is interpreted to be a subsurface equivalent of a hydromagmatic volcano that has undergone vent migration. The vent migration here is inferred to have had both vertical and lateral components and have been caused by an abrupt tectonic activity near the basin margin. In all these cases, rimbeds or diatreme fills derived from different source vents are bounded by either prominent or subtle, commonly laterally extensive truncation surfaces or stratigraphic discontinuities. Careful documentation of these surfaces and discontinuities thus appears vital to proper interpretation of eruption history, morphologic evolution, and even deep-seated magmatic processes of a hydromagmatic volcano. In this respect, the technique known as 'allostratigraphy' appears useful in mapping, correlation, and interpretation of many hydrovolcanic edifices and sequences.

Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod.

PubMed

Spies, Ingrid; Hauser, Lorenz; Jorde, Per Erik; Knutsen, Halvor; Punt, André E; Rogers, Lauren A; Stenseth, Nils Chr

2018-05-08

Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator F ST , such as Wright's equation, F ST ≈ 1/(4 N e m + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the N e / N t ratio (where N e is the effective and N t is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased N e / N t and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of F ST , particularly when genetic differentiation was low, F ST ≈ 10 -3 Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations. Copyright © 2018 the Author(s). Published by PNAS.

Southeast Asian origins of five Hill Tribe populations and correlation of genetic to linguistic relationships inferred with genome-wide SNP data

PubMed Central

Listman, JB; Malison, RT; Sanichwankul, K; Ittiwut, C; Mutirangura, A; Gelernter, J

2010-01-01

In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have non-mutually intelligible languages. In order to test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results of recent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages. PMID:20979205

Southeast Asian origins of five Hill Tribe populations and correlation of genetic to linguistic relationships inferred with genome-wide SNP data.

PubMed

Listman, J B; Malison, R T; Sanichwankul, K; Ittiwut, C; Mutirangura, A; Gelernter, J

2011-02-01

In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have nonmutually intelligible languages. To test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2,445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results ofrecent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages. 2010 Wiley-Liss, Inc.

A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity.

PubMed

Rakhimberdiev, Eldar; Winkler, David W; Bridge, Eli; Seavy, Nathaniel E; Sheldon, Daniel; Piersma, Theunis; Saveliev, Anatoly

2015-01-01

Solar archival tags (henceforth called geolocators) are tracking devices deployed on animals to reconstruct their long-distance movements on the basis of locations inferred post hoc with reference to the geographical and seasonal variations in the timing and speeds of sunrise and sunset. The increased use of geolocators has created a need for analytical tools to produce accurate and objective estimates of migration routes that are explicit in their uncertainty about the position estimates. We developed a hidden Markov chain model for the analysis of geolocator data. This model estimates tracks for animals with complex migratory behaviour by combining: (1) a shading-insensitive, template-fit physical model, (2) an uncorrelated random walk movement model that includes migratory and sedentary behavioural states, and (3) spatially explicit behavioural masks. The model is implemented in a specially developed open source R package FLightR. We used the particle filter (PF) algorithm to provide relatively fast model posterior computation. We illustrate our modelling approach with analysis of simulated data for stationary tags and of real tracks of both a tree swallow Tachycineta bicolor migrating along the east and a golden-crowned sparrow Zonotrichia atricapilla migrating along the west coast of North America. We provide a model that increases accuracy in analyses of noisy data and movements of animals with complicated migration behaviour. It provides posterior distributions for the positions of animals, their behavioural states (e.g., migrating or sedentary), and distance and direction of movement. Our approach allows biologists to estimate locations of animals with complex migratory behaviour based on raw light data. This model advances the current methods for estimating migration tracks from solar geolocation, and will benefit a fast-growing number of tracking studies with this technology.

Effects of landscape composition and configuration on migrating songbirds: inference from and individual-based model

Treesearch

Emily Cohen; Scott Pearson; Frank Moore

2014-01-01

The behavior of long-distance migrants during stopover is constrained by the need to quickly and safely replenish energetic reserves. Replenishing fuel stores at stopover sites requires adjusting to unfamiliar landscapes with little to no information about the distribution of resources. Despite their critical importance to the success of songbird migration, the effects...

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci

PubMed Central

Fakhfakh, Hatem; Belkadhi, Mohamed Sadok

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest. PMID:28972992

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

PubMed

Ben Abdelkrim, Ahmed; Hattab, Tarek; Fakhfakh, Hatem; Belkadhi, Mohamed Sadok; Gorsane, Faten

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

Migration Rate Of Tidal Meanders: Inferences From The Venice Lagoon

NASA Astrophysics Data System (ADS)

Finotello, A.; D'Alpaos, A.; Ghinassi, M.; Lanzoni, S.; Marani, M.; Rinaldo, A.

2015-12-01

Meandering channels are ubiquitous features of tidal landscapes. However, despite their fundamental role on the eco-morphodynamic evolution of these landscapes, tidal meanders have received less attention when compared to their fluvial counterparts. Improving current understanding of tidal meander migration, a largely-examined topic in fluvial landscapes, is a key step to highlight analogies and differences between tidal and fluvial cases. The migration of about 400 meander bends, belonging to 40 salt-marsh channels in the Northern Venice Lagoon (Italy), from 1968 to nowadays, has been investigated by means of both a classical method in fluvial frameworks and new procedure. Similarities with fluvial meanders occur, although important difference also emerge. Meanders cutting through the San Felice marsh follow the relationship between cartesian length and channel width, typical of meanders developed within different settings. However, meander migration rates proved to be smaller than those characterizing fluvial meanders. Indeed, the analysis of meander migration suggests a mean migration rate of about 0.10 m/year, consistent with the few data available in the literature. As for the fluvial case, the maximum-potential migration rate (i.e. the envelope curve of the relationship between migration rate and bend radius, both divided by channel width) reaches a maximum for radius-over-width ratio included between 2 and 3, regardless of the considered method. Nevertheless, the new-proposed method allows us to provide a more objective and continuous characterization. By using this new procedure, the channel curvature has finally been Fourier-analyzed, confirming the importance of even harmonics along the curvature spectrum. A correlation between migration rates and dominant harmonics seems to drive the evolution of tidal meanders and might represent a key-feature to distinguish them from their fluvial counterparts.

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

PubMed

Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

2017-03-15

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Evidence for Patterns of Selective Urban Migration in the Greater Indus Valley (2600-1900 BC): A Lead and Strontium Isotope Mortuary Analysis

PubMed Central

Valentine, Benjamin; Kamenov, George D.; Kenoyer, Jonathan Mark; Shinde, Vasant; Mushrif-Tripathy, Veena; Otarola-Castillo, Erik; Krigbaum, John

2015-01-01

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people’s movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a specific and highly regulated institution of migration. Intra-individual isotopic shifts are consistent with immigration from resource-rich hinterlands during childhood. Furthermore, mortuary populations formed over hundreds of years and composed almost entirely of first-generation immigrants suggest that inhumation was the final step in a process linking certain urban Indus communities to diverse hinterland groups. Additional multi disciplinary analyses are warranted to confirm inferred patterns of Indus mobility, but the available isotopic data suggest that efforts to classify and regulate human movement in the ancient Indus region likely helped structure socioeconomic integration across an ethnically diverse landscape. PMID:25923705

Evidence for Patterns of Selective Urban Migration in the Greater Indus Valley (2600-1900 BC): A Lead and Strontium Isotope Mortuary Analysis.

PubMed

Valentine, Benjamin; Kamenov, George D; Kenoyer, Jonathan Mark; Shinde, Vasant; Mushrif-Tripathy, Veena; Otarola-Castillo, Erik; Krigbaum, John

2015-01-01

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people's movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a specific and highly regulated institution of migration. Intra-individual isotopic shifts are consistent with immigration from resource-rich hinterlands during childhood. Furthermore, mortuary populations formed over hundreds of years and composed almost entirely of first-generation immigrants suggest that inhumation was the final step in a process linking certain urban Indus communities to diverse hinterland groups. Additional multi disciplinary analyses are warranted to confirm inferred patterns of Indus mobility, but the available isotopic data suggest that efforts to classify and regulate human movement in the ancient Indus region likely helped structure socioeconomic integration across an ethnically diverse landscape.

Comments in reply: new directions in migration research.

PubMed

Shaw, R P

1986-01-01

The author comments on a review of his recent book NEW DIRECTIONS IN MIGRATION RESEARCH and reflects on theory and model specification, problems of estimation and statistical inference, realities of temporal and spatial heterogeneity, choices of explanatory variables, and the importance of broader political issues in migration studies. A core hypothesis is that market forces have declined as influences on internal migration in Canada over the last 30 years. Theoretical underpinnings include declining relevance of wage considerations in the decision to migrate on the assumption that marginal utility of money diminishes and marginal utility of leisure increases as society becomes wealthier. The author perceives the human capital model to have limitations and is especially troubled by the "as if" clause--that all migrants behave "as if" they calculate benefits and risks with equal rigor. The author has "shadowed" and not quantified the costs involved. He implies that normative frameworks for future migration research and planning should be established.

Direct observations of American eels migrating across the continental shelf to the Sargasso Sea

PubMed Central

Béguer-Pon, Mélanie; Castonguay, Martin; Shan, Shiliang; Benchetrit, José; Dodson, Julian J.

2015-01-01

Since inferring spawning areas from larval distributions in the Sargasso Sea a century ago, the oceanic migration of adult American eels has remained a mystery. No adult eel has ever been observed migrating in the open ocean or in the spawning area. Here, we track movements of maturing eels equipped with pop-up satellite archival tags from the Scotian Shelf (Canada) into the open ocean, with one individual migrating 2,400 km to the northern limit of the spawning site in the Sargasso Sea. The reconstructed routes suggest a migration in two phases: one over the continental shelf and along its edge in shallow waters; the second in deeper waters straight south towards the spawning area. This study is the first direct evidence of adult Anguilla migrating to the Sargasso Sea and represents an important step forward in the understanding of routes and migratory cues. PMID:26505325

Genetic Stratigraphy of Key Demographic Events in Arabia

PubMed Central

Fernandes, Verónica; Triska, Petr; Pereira, Joana B.; Alshamali, Farida; Rito, Teresa; Machado, Alison; Fajkošová, Zuzana; Cavadas, Bruno; Černý, Viktor; Soares, Pedro

2015-01-01

At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa. PMID:25738654

Patterns and predictors of posttraumatic stress disorder in refugees: A latent class analysis.

PubMed

Minihan, Savannah; Liddell, Belinda J; Byrow, Yulisha; Bryant, Richard A; Nickerson, Angela

2018-05-01

Although elevated rates of posttraumatic stress disorder (PTSD) have been well-documented in refugees, no study has investigated the heterogeneity of DSM-5 PTSD symptomatology in such populations. This study aimed to determine whether there are unique patterns of DSM-5 defined PTSD symptomatology in refugees, and investigate whether factors characteristic of the refugee experience, including trauma exposure and post-migration stress, predict symptom profiles. Participants were 246 refugees and asylum-seekers from an Arabic-, English-, Farsi-, or Tamil-speaking background who had been resettled in Australia. Participants completed measures of post-migration living difficulties, trauma exposure, PTSD symptoms and functional disability. Latent class analysis was used to identify PTSD symptom profiles, and predictors of class membership were elucidated via multinomial logistic regression. Four classes were identified: a high-PTSD class (21.3%), a high-re-experiencing/avoidance class (15.3%), a moderate-PTSD class (23%), and a no PTSD class (40.3%). Trauma exposure and post-migration stress significantly predicted class membership and classes differed in degree of functional disability. The current study employed a cross-sectional design, which precluded inferences regarding the stability of classes of PTSD symptomatology. This study provides evidence for distinct patterns of PTSD symptomatology in refugees. We identified a novel class, characterized by high-re-experiencing and avoidance symptoms, as well as classes characterized by pervasive, moderate, and no symptomatology. Trauma exposure and post-migration stress differentially contributed to the emergence of these profiles. Individuals with high and moderate probability of PTSD symptoms evidenced substantial disability. These results support conceptualizations of PTSD as a heterogeneous construct, and highlight the importance of considering sub-clinical symptom presentations, as well as the post-migration environment, in clinical contexts. Copyright © 2018. Published by Elsevier B.V.

Genetic stratigraphy of key demographic events in Arabia.

PubMed

Fernandes, Verónica; Triska, Petr; Pereira, Joana B; Alshamali, Farida; Rito, Teresa; Machado, Alison; Fajkošová, Zuzana; Cavadas, Bruno; Černý, Viktor; Soares, Pedro; Richards, Martin B; Pereira, Luísa

2015-01-01

At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (~8-37 generations for African input into Arabia, and 30-90 generations for "back-to-Africa" migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ~2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ~8 ka. The main "back-to-Africa" migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.

The life of a meander bend: Connecting shape and dynamics via analysis of a numerical model

NASA Astrophysics Data System (ADS)

Schwenk, Jon; Lanzoni, Stefano; Foufoula-Georgiou, Efi

2015-04-01

Analysis of bend-scale meandering river dynamics is a problem of theoretical and practical interest. This work introduces a method for extracting and analyzing the history of individual meander bends from inception until cutoff (called "atoms") by tracking backward through time the set of two cutoff nodes in numerical meander migration models. Application of this method to a simplified yet physically based model provides access to previously unavailable bend-scale meander dynamics over long times and at high temporal resolutions. We find that before cutoffs, the intrinsic model dynamics invariably simulate a prototypical cutoff atom shape we dub simple. Once perturbations from cutoffs occur, two other archetypal cutoff planform shapes emerge called long and round that are distinguished by a stretching along their long and perpendicular axes, respectively. Three measures of meander migration—growth rate, average migration rate, and centroid migration rate—are introduced to capture the dynamic lives of individual bends and reveal that similar cutoff atom geometries share similar dynamic histories. Specifically, through the lens of the three shape types, simples are seen to have the highest growth and average migration rates, followed by rounds, and finally longs. Using the maximum average migration rate as a metric describing an atom's dynamic past, we show a strong connection between it and two metrics of cutoff geometry. This result suggests both that early formative dynamics may be inferred from static cutoff planforms and that there exists a critical period early in a meander bend's life when its dynamic trajectory is most sensitive to cutoff perturbations. An example of how these results could be applied to Mississippi River oxbow lakes with unknown historic dynamics is shown. The results characterize the underlying model and provide a framework for comparisons against more complex models and observed dynamics.

Population structure and demographic history of a tropical lowland rainforest tree species Shorea parvifolia (Dipterocarpaceae) from Southeastern Asia.

PubMed

Iwanaga, Hiroko; Teshima, Kosuke M; Khatab, Ismael A; Inomata, Nobuyuki; Finkeldey, Reiner; Siregar, Iskandar Z; Siregar, Ulfah J; Szmidt, Alfred E

2012-07-01

Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S. parvifolia, as indicators of temporal changes in the distribution and extent of tropical rainforest in this region, we studied levels and patterns of nucleotide polymorphism in the following five nuclear gene regions: GapC, GBSSI, PgiC, SBE2, and SODH. Seven populations from peninsular Malaysia, Sumatra, and eastern Borneo were included in the analyses. STRUCTURE analysis revealed that the investigated populations are divided into two groups: Sumatra-Malay and Borneo. Furthermore, each group contained one admixed population. Under isolation with migration model, divergence of the two groups was estimated to occur between late Pliocene (2.6 MYA) and middle Pleistocene (0.7 MYA). The log-likelihood ratio tests of several demographic models strongly supported model with population expansion and low level of migration after divergence of the Sumatra-Malay and Borneo groups. The inferred demographic history of S. parvifolia suggested the presence of a scarcely forested land bridge on the Sunda Shelf during glacial periods in the Pleistocene and predominance of tropical lowland rainforest at least in Sumatra and eastern Borneo.

Global genetic variation and transmission dynamics of H9N2 avian influenza virus.

PubMed

Wei, K; Li, Y

2018-04-01

The H9N2 influenza viruses are extensively circulating in the poultry population, and variable genotypes can be generated through mutation, recombination and reassortment, which may be better adapted to infect a new host, resist drug treatment or escape immune pressure. The LPAI H9N2 viruses have the potential to evolve towards high levels of virulence in human. Some studies about the regional dispersal were reported, but global dissemination and the drivers of the virus are poorly understood, particularly at the genome scale. Here, we have analysed all eight gene segments of 168 H9N2 genomes sampled randomly aiming to provide a panoramic framework for better understanding the genesis and genetic variation of the viruses, and utilized phylogeography and spatial epidemiology approaches to uncover the effects of the genetic variation, predictors and spread of H9N2 viruses. We found that more frequent reassortment events involve segments PA, NP and NS, and 21 isolates have possible mosaic structure resulting from recombination events. Estimates of gene-specific global dN/dS ratios showed that all genes were subject to purifying selection. However, a total of 13 sites were detected under positive selection by at least two of three methods, which located within segments HA, NA, M2, NS1 and PA. Additionally, we inferred that NA segment has the highest rate of nucleotide substitution, and its tMRCA estimate is the youngest than the remaining segments' inference. About the spatial history, air transportation of human was identified as the predominant driver of global viral migration using GLM analysis, and economic factors and geographical distance were the modest predictors. Higher migration rates were estimated between five pairs of regions (>0.01) indicating the frequent migration of the viruses between discrete geographical locations. Further, our Markov jumps analysis showed that viral migration is more frequent between Southern China and Northern China, and high rate of gene flow was observed between America and East Asia. Moreover, the America together with Southeast Asia acted as the primary hubs of global transmission, forming the trunk of evolutionary tree. These findings suggested a complex interaction between virus evolution, epidemiology and human behaviour. © 2017 Blackwell Verlag GmbH.

Paleobiology of the Latest Tithonian (Late Jurassic) Ammonite Salinites grossicostatum Inferred from Internal and External Shell Parameters.

PubMed

Zell, Patrick; Stinnesbeck, Wolfgang

2016-01-01

Based on material from the uppermost Tithonian La Caja Formation at Puerto Piñones, northeastern Mexico, the complete ontogenetic development (protoconch to adult) of the ammonite Salinites grossicostatum is outlined by a detailed morphometrical shell analysis. The embryonic stage, consisting of a small ellipsoid protoconch and ammonitella, ends at about 0.6 mm. Four major morphological changes are differentiated throughout ontogeny based on internal features such as reduced septal spacing and siphuncle position. Sexual dimorphism is reflected by shell size, siphuncular diameter, differences in the morphology of the apophysis, and by two distinct general trends in septal spacing. In addition, macroconchs are characterized by septal crowding at different stages, followed by the return to normal septum distances. Our analysis indicates a change in the mode of life after the neanic stage. A change in habitat preference is inferred for adult individuals. While microconchs persisted at Puerto Piñones, large mature macroconchs temporarily migrated to other areas, possibly for egg deposition. Salinites grossicostatum is endemic to the ancient Gulf of Mexico and is there restricted to outer continental shelf environments.

Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana

PubMed Central

Colosimo, Giuliano; Knapp, Charles R.; Wallace, Lisa E.; Welch, Mark E.

2014-01-01

Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA) indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p0.01). These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes. PMID:25229344

Inferring Foraging Areas of Nesting Loggerhead Turtles Using Satellite Telemetry and Stable Isotopes

PubMed Central

Ceriani, Simona A.; Roth, James D.; Evans, Daniel R.; Weishampel, John F.; Ehrhart, Llewellyn M.

2012-01-01

In recent years, the use of intrinsic markers such as stable isotopes to link breeding and foraging grounds of migratory species has increased. Nevertheless, several assumptions still must be tested to interpret isotopic patterns found in the marine realm. We used a combination of satellite telemetry and stable isotope analysis to (i) identify key foraging grounds used by female loggerheads nesting in Florida and (ii) examine the relationship between stable isotope ratios and post-nesting migration destinations. We collected tissue samples for stable isotope analysis from 14 females equipped with satellite tags and an additional 57 untracked nesting females. Telemetry identified three post-nesting migratory pathways and associated non-breeding foraging grounds: (1) a seasonal continental shelf–constrained migratory pattern along the northeast U.S. coastline, (2) a non-breeding residency in southern foraging areas and (3) a residency in the waters adjacent to the breeding area. Isotopic variability in both δ13C and δ15N among individuals allowed identification of three distinct foraging aggregations. We used discriminant function analysis to examine how well δ13C and δ15N predict female post-nesting migration destination. The discriminant analysis classified correctly the foraging ground used for all but one individual and was used to predict putative feeding areas of untracked turtles. We provide the first documentation that the continental shelf of the Mid- and South Atlantic Bights are prime foraging areas for a large number (61%) of adult female loggerheads from the largest loggerhead nesting population in the western hemisphere and the second largest in the world. Our findings offer insights for future management efforts and suggest that this technique can be used to infer foraging strategies and residence areas in lieu of more expensive satellite telemetry, enabling sample sizes that are more representative at the population level. PMID:23028943

Seasonal migration of marsupial megafauna in Pleistocene Sahul (Australia-New Guinea).

PubMed

Price, Gilbert J; Ferguson, Kyle J; Webb, Gregory E; Feng, Yue-Xing; Higgins, Pennilyn; Nguyen, Ai Duc; Zhao, Jian-Xin; Joannes-Boyau, Renaud; Louys, Julien

2017-09-27

Seasonal two-way migration is an ecological phenomenon observed in a wide range of large-bodied placental mammals, but is conspicuously absent in all modern marsupials. Most extant marsupials are typically smaller in body size in comparison to their migratory placental cousins, possibly limiting their potential to undertake long-distance seasonal migrations. But what about earlier, now-extinct giant marsupial megafauna? Here we present new geochemical analyses which show that the largest of the extinct marsupial herbivores, the enormous wombat-like Diprotodon optatum , undertook seasonal, two-way latitudinal migration in eastern Sahul (Pleistocene Australia-New Guinea). Our data infer that this giant marsupial had the potential to perform round-trip journeys of as much as 200 km annually, which is reminiscent of modern East African mammal migrations. These findings provide, to our knowledge, the first evidence for repetitive seasonal migration in any metatherian (including marsupials), living or extinct, and point to an ecological phenomenon absent from the continent since the Late Pleistocene. © 2017 The Author(s).

Unraveling the electrolyte properties of Na3SbS4 through computation and experiment

NASA Astrophysics Data System (ADS)

Rush, Larry E.; Hood, Zachary D.; Holzwarth, N. A. W.

2017-12-01

Solid-state sodium electrolytes are expected to improve next-generation batteries on the basis of favorable energy density and reduced cost. Na3SbS4 represents a new solid-state ion conductor with high ionic conductivities in the mS/cm range. Here, we explore the tetragonal phase of Na3SbS4 and its interface with metallic sodium anode using a combination of experiments and first-principles calculations. The computed Na-ion vacancy migration energies of 0.1 eV are smaller than the value inferred from experiment, suggesting that grain boundaries or other factors dominate the experimental systems. Analysis of symmetric cells of the electrolyte—Na/Na 3SbS4/Na —show that a conductive solid electrolyte interphase forms. Computer simulations infer that the interface is likely to be related to Na3SbS3 , involving the conversion of the tetrahedral SbS43 - ions of the bulk electrolyte into trigonal pyramidal SbS33 - ions at the interface.

Resolving the ancestry of Austronesian-speaking populations.

PubMed

Soares, Pedro A; Trejaut, Jean A; Rito, Teresa; Cavadas, Bruno; Hill, Catherine; Eng, Ken Khong; Mormina, Maru; Brandão, Andreia; Fraser, Ross M; Wang, Tse-Yi; Loo, Jun-Hun; Snell, Christopher; Ko, Tsang-Ming; Amorim, António; Pala, Maria; Macaulay, Vincent; Bulbeck, David; Wilson, James F; Gusmão, Leonor; Pereira, Luísa; Oppenheimer, Stephen; Lin, Marie; Richards, Martin B

2016-03-01

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.

Habitat use and migratory behaviour of pikeperch Sander lucioperca in Lithuanian and Latvian waters as inferred from otolith Sr:Ca ratios

NASA Astrophysics Data System (ADS)

Ložys, Linas; Shiao, Jen-Chieh; Iizuka, Yoshiyuki; Minde, Atis; Pūtys, Žilvinas; Jakubavičiūtė, Eglė; Dainys, Justas; Gorfine, Harry; Tzeng, Wann-Nian

2017-11-01

Determination of the geographic boundaries that define a stock is a key challenge in fisheries management. Acquiring an understanding of spatial distribution and migration patterns of pikeperch Sander lucioperca populations in the south-eastern Baltic Sea region would help to delineate the stocks and contribute towards sustainable exploitation of the population. In this study, habitat use and migratory behaviour of S. lucioperca were inferred from otolith Sr:Ca ratios obtained via an Electron Probe Micro-Analyzer. S. lucioperca collected from the inland Kaunas City water reservoir, where downstream migration is precluded by a hydro-power plant, consistently showed a freshwater signature in their otoliths throughout their life history. In contrast, those collected from the Baltic Sea and Curonian Lagoon in Lithuania, and the lower reaches of the Daugava River in Latvia had ratios indicative of movement between fresh and brackish water habitats. Although S. lucioperca can inhabit brackish water bodies, they predominantly reside and reproduce in freshwater systems. It is thought that periodic post-spawning migration to the sea during spring is related to better foraging conditions and perhaps as a strategy for shedding ectoparasites. Currently, catch quotas apply only to those S. lucioperca taken from the Curonian Lagoon and not the Baltic Sea. Frequent migration between freshwater habitats and the Baltic Sea suggest that S. lucioperca stocks from a given river/estuary system should be considered as a single management unit despite individual differences in migratory behaviour. The extent to which migration into the Baltic Sea could potentially compromise the effectiveness of catch quotas was the main issue which initiated this study.

Genomic Insights into the Ancestry and Demographic History of South America

PubMed Central

Homburger, Julian R.; Moreno-Estrada, Andrés; Gignoux, Christopher R.; Nelson, Dominic; Sanchez, Elena; Ortiz-Tello, Patricia; Pons-Estel, Bernardo A.; Acevedo-Vasquez, Eduardo; Miranda, Pedro; Langefeld, Carl D.; Gravel, Simon; Alarcón-Riquelme, Marta E.; Bustamante, Carlos D.

2015-01-01

South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9–14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical genetic studies in the region. PMID:26636962

Genomic Insights into the Ancestry and Demographic History of South America.

PubMed

Homburger, Julian R; Moreno-Estrada, Andrés; Gignoux, Christopher R; Nelson, Dominic; Sanchez, Elena; Ortiz-Tello, Patricia; Pons-Estel, Bernardo A; Acevedo-Vasquez, Eduardo; Miranda, Pedro; Langefeld, Carl D; Gravel, Simon; Alarcón-Riquelme, Marta E; Bustamante, Carlos D

2015-12-01

South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9-14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical genetic studies in the region.

DEVELOPMENT AND APPLICATION OF BOREHOLE FLOWMETERS FOR ENVIRONMENTAL ASSESSMENT

EPA Science Inventory

In order to understand the origin of contaminant plumes and infer their future migration, one requires a knowledge of the hydraulic conductivity (K) distribution. n many aquifers, the borehole flowmeter offers the most direct technique available for developing a log of hydraulic ...

Using avian radar to examine relationships among avian activity, bird strikes, and meteorological factors

USGS Publications Warehouse

Coates, Peter S.; Casazza, Michael L.; Halstead, Brian J.; Fleskes, Joseph P.; Laughlin, James A.

2011-01-01

Radar systems designed to detect avian activity at airfields are useful in understanding factors that influence the risk of bird and aircraft collisions (bird strikes). We used an avian radar system to measure avian activity at Beale Air Force Base, California, USA, during 2008 and 2009. We conducted a 2-part analysis to examine relationships among avian activity, bird strikes, and meteorological and time-dependent factors. We found that avian activity around the airfield was greater at times when bird strikes occurred than on average using a permutation resampling technique. Second, we developed generalized linear mixed models of an avian activity index (AAI). Variation in AAI was first explained by seasons that were based on average migration dates of birds at the study area. We then modeled AAI by those seasons to further explain variation by meteorological factors and daily light levels within a 24-hour period. In general, avian activity increased with decreased temperature, wind, visibility, precipitation, and increased humidity and cloud cover. These effects differed by season. For example, during the spring bird migration period, most avian activity occurred before sunrise at twilight hours on clear days with low winds, whereas during fall migration, substantial activity occurred after sunrise, and birds generally were more active at lower temperatures. We report parameter estimates (i.e., constants and coefficients) averaged across models and a relatively simple calculation for safety officers and wildlife managers to predict AAI and the relative risk of bird strike based on time, date, and meteorological values. We validated model predictability and assessed model fit. These analyses will be useful for general inference of avian activity and risk assessment efforts. Further investigation and ongoing data collection will refine these inference models and improve our understanding of factors that influence avian activity, which is necessary to inform management decisions aimed at reducing risk of bird strikes.

Asteroid differentiation - Pyroclastic volcanism to magma oceans

NASA Technical Reports Server (NTRS)

Taylor, G. J.; Keil, Klaus; Mccoy, Timothy; Haack, Henning; Scott, Edward R. D.

1993-01-01

A summary is presented of theoretical and speculative research on the physics of igneous processes involved in asteroid differentiation. Partial melting processes, melt migration, and their products are discussed and explosive volcanism is described. Evidence for the existence of asteroidal magma oceans is considered and processes which may have occurred in these oceans are examined. Synthesis and inferences of asteroid heat sources are discussed under the assumption that asteroids are heated mainly by internal processes and that the role of impact heating is small. Inferences of these results for earth-forming planetesimals are suggested.

Geological controls on the occurrence of gas hydrate from core, downhole log, and seismic data in the Shenhu area, South China Sea

USGS Publications Warehouse

Xiujuan Wang,; ,; Collett, Timothy S.; Lee, Myung W.; Yang, Shengxiong; Guo, Yiqun; Wu, Shiguo

2014-01-01

Multi-channel seismic reflection data, well logs, and recovered sediment cores have been used in this study to characterize the geologic controls on the occurrence of gas hydrate in the Shenhu area of the South China Sea. The concept of the "gas hydrate petroleum system" has allowed for the systematic analysis of the impact of gas source, geologic controls on gas migration, and the role of the host sediment in the formation and stability of gas hydrates as encountered during the 2007 Guangzhou Marine Geological Survey Gas Hydrate Expedition (GMGS-1) in the Shenhu area. Analysis of seismic and bathymetric data identified seventeen sub-linear, near-parallel submarine canyons in this area. These canyons, formed in the Miocene, migrated in a northeasterly direction, and resulted in the burial and abandonment of canyons partially filled by coarse-grained sediments. Downhole wireline log (DWL) data were acquired from eight drill sites and sediment coring was conducted at five of these sites, which revealed the presence of suitable reservoirs for the occurrence of concentrated gas hydrate accumulations. Gas hydrate-bearing sediment layers were identified from well log and core data at three sites mainly within silt and silt clay sediments. Gas hydrate was also discovered in a sand reservoir at one site as inferred from the analysis of the DWL data. Seismic anomalies attributed to the presence of gas below the base of gas hydrate stability zone, provided direct evidence for the migration of gas into the overlying gas hydrate-bearing sedimentary sections. Geochemical analyses of gas samples collected from cores confirmed that the occurrence of gas hydrate in the Shenhu area is controlled by the presence thermogenic methane gas that has migrated into the gas hydrate stability zone from a more deeply buried source.

Nonlinear permanent migration response to climatic variations but minimal response to disasters

PubMed Central

Bohra-Mishra, Pratikshya; Oppenheimer, Michael; Hsiang, Solomon M.

2014-01-01

We present a microlevel study to simultaneously investigate the effects of variations in temperature and precipitation along with sudden natural disasters to infer their relative influence on migration that is likely permanent. The study is made possible by the availability of household panel data from Indonesia with an exceptional tracking rate combined with frequent occurrence of natural disasters and significant climatic variations, thus providing a quasi-experiment to examine the influence of environment on migration. Using data on 7,185 households followed over 15 y, we analyze whole-household, province-to-province migration, which allows us to understand the effects of environmental factors on permanent moves that may differ from temporary migration. The results suggest that permanent migration is influenced by climatic variations, whereas episodic disasters tend to have much smaller or no impact on such migration. In particular, temperature has a nonlinear effect on migration such that above 25 °C, a rise in temperature is related to an increase in outmigration, potentially through its impact on economic conditions. We use these results to estimate the impact of projected temperature increases on future permanent migration. Though precipitation also has a similar nonlinear effect on migration, the effect is smaller than that of temperature, underscoring the importance of using an expanded set of climatic factors as predictors of migration. These findings on the minimal influence of natural disasters and precipitation on permanent moves supplement previous findings on the significant role of these variables in promoting temporary migration. PMID:24958887

Nonlinear permanent migration response to climatic variations but minimal response to disasters.

PubMed

Bohra-Mishra, Pratikshya; Oppenheimer, Michael; Hsiang, Solomon M

2014-07-08

We present a microlevel study to simultaneously investigate the effects of variations in temperature and precipitation along with sudden natural disasters to infer their relative influence on migration that is likely permanent. The study is made possible by the availability of household panel data from Indonesia with an exceptional tracking rate combined with frequent occurrence of natural disasters and significant climatic variations, thus providing a quasi-experiment to examine the influence of environment on migration. Using data on 7,185 households followed over 15 y, we analyze whole-household, province-to-province migration, which allows us to understand the effects of environmental factors on permanent moves that may differ from temporary migration. The results suggest that permanent migration is influenced by climatic variations, whereas episodic disasters tend to have much smaller or no impact on such migration. In particular, temperature has a nonlinear effect on migration such that above 25 °C, a rise in temperature is related to an increase in outmigration, potentially through its impact on economic conditions. We use these results to estimate the impact of projected temperature increases on future permanent migration. Though precipitation also has a similar nonlinear effect on migration, the effect is smaller than that of temperature, underscoring the importance of using an expanded set of climatic factors as predictors of migration. These findings on the minimal influence of natural disasters and precipitation on permanent moves supplement previous findings on the significant role of these variables in promoting temporary migration.

DIM SUM: demography and individual migration simulated using a Markov chain.

PubMed

Brown, Jeremy M; Savidge, Kevin; McTavish, Emily Jane B

2011-03-01

An increasing number of studies seek to infer demographic history, often jointly with genetic relationships. Despite numerous analytical methods for such data, few simulations have investigated the methods' power and robustness, especially when underlying assumptions have been violated. DIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration while recording ancestor-descendant relationships. It does not employ coalescent assumptions or discrete population boundaries. It is extremely flexible, allowing the user to specify border positions, reactions of organisms to borders, local and global carrying capacities, individual dispersal kernels, rates of reproduction and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from gis software) and may vary through time. In combination with software for genetic marker simulation, DIM SUM will be useful for testing phylogeographic (e.g., nested clade phylogeographic analysis, coalescent-based tests and continuous-landscape frameworks) and landscape-genetic methods, specifically regarding violations of coalescent assumptions. It can also be used to explore the qualitative features of proposed demographic scenarios (e.g. regarding biological invasions) and as a pedagogical tool. DIM SUM (with user's manual) can be downloaded from http://code.google.com/p/bio-dimsum. © 2010 Blackwell Publishing Ltd.

Statistical characteristics of dynamics for population migration driven by the economic interests

NASA Astrophysics Data System (ADS)

Huo, Jie; Wang, Xu-Ming; Zhao, Ning; Hao, Rui

2016-06-01

Population migration typically occurs under some constraints, which can deeply affect the structure of a society and some other related aspects. Therefore, it is critical to investigate the characteristics of population migration. Data from the China Statistical Yearbook indicate that the regional gross domestic product per capita relates to the population size via a linear or power-law relation. In addition, the distribution of population migration sizes or relative migration strength introduced here is dominated by a shifted power-law relation. To reveal the mechanism that creates the aforementioned distributions, a dynamic model is proposed based on the population migration rule that migration is facilitated by higher financial gains and abated by fewer employment opportunities at the destination, considering the migration cost as a function of the migration distance. The calculated results indicate that the distribution of the relative migration strength is governed by a shifted power-law relation, and that the distribution of migration distances is dominated by a truncated power-law relation. These results suggest the use of a power-law to fit a distribution may be not always suitable. Additionally, from the modeling framework, one can infer that it is the randomness and determinacy that jointly create the scaling characteristics of the distributions. The calculation also demonstrates that the network formed by active nodes, representing the immigration and emigration regions, usually evolves from an ordered state with a non-uniform structure to a disordered state with a uniform structure, which is evidenced by the increasing structural entropy.

Evaluating methods to visualize patterns of genetic differentiation on a landscape.

PubMed

House, Geoffrey L; Hahn, Matthew W

2018-05-01

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS. © 2017 John Wiley & Sons Ltd.

ATLANTIC RAIN FOREST AND CAATINGA VEGETATION DYNAMICS EXPLAIN PHYLOGEOGRAPHICAL PATTERN OF AN ENDEMIC BRAZILIAN PALM

USDA-ARS?s Scientific Manuscript database

Technical Abstract Occurrence of a wetter and cooler climate associated with humid vegetation had been inferred for the Caatinga region during the late Pleistocene and early Holocene. The existence of rainforest migration routes in northeastern Brazil is widely recognized. Present-day rainforest nat...

Inferring the annual migration patterns of fall armyworm(Lepidoptera: Noctuidae) in the United States from mitochondrial haplotypes

USDA-ARS?s Scientific Manuscript database

1. Regions of southern Florida, USA and southern Texas, USA (extending into Mexico)provide the source populations for virtually all fall armyworm infestations affecting the continental USA. Understanding how these overwintering populations annually disperse is important to efforts to predict and con...

IMGui-A Desktop GUI Application for Isolation with Migration Analyses.

PubMed

Knoblauch, Jared; Sethuraman, Arun; Hey, Jody

2017-02-01

The Isolation with Migration (IM) programs (e.g., IMa2) have been utilized extensively by evolutionary biologists for model-based inference of demographic parameters including effective population sizes, migration rates, and divergence times. Here, we describe a graphical user interface for the latest IM program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of runs, and visualizing results. Developed using node. js and the Electron framework, IMGui is an application that runs on any desktop operating system, and is available for download at https://github.com/jaredgk/IMgui-electron-packages. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Formation of VP-Zn complexes in bulk InP(Zn) by migration of P vacancies from the (110) surface

NASA Astrophysics Data System (ADS)

Slotte, J.; Saarinen, K.; Ebert, Ph.

2006-05-01

We apply a combination of positron annihilation spectroscopy and scanning tunneling microscopy to show that thermally generated P vacancies diffuse from the InP surface toward the bulk. The defect observed in the bulk can be identified as a complex consisting of a P vacancy and a Zn impurity. We infer that this pair is formed when the diffusing positive P vacancy is trapped at the Zn dopant. A rough estimate for the migration energy of the P vacancy results in a value of 1.3eV .

Causes and consequences of rural-urban migration: The case of Juba Metropolitan, Republic of South Sudan

NASA Astrophysics Data System (ADS)

Babi Moses, Lomoro Alfred; Guogping, Xiong; Celestino Ladu John, Leju

2017-08-01

Migration is the movement of people from one ecological region to another; it may be on temporary or permanent basis. This research studies focused on the causes and consequences of rural-urban migration in Juba Metropolitan, Republic of South Sudan as a case study. The stratified random sampling method on the basis of existing payam (districts) was used to divide the study area into three zones of Juba, Kator and Munuku. Data were generated through primary and secondary sources. The data generated were analyzed using SPSS. The findings of the study show that Munuki payam covers most of the migrants. The study also reveals that males migrate more than the females in Juba and migration is high within the age cohorts of 30-39 years and 40-49 years old. Furthermore, the study revealed that the propensity to migrate is directly related to educational attainment. It can be inferred from the findings of the study that the majority of migrants in Juba Metropolitan migrated in search of employment while others migrated to continue their education while others migrated in search for basic amenities, to join relatives and get married. This means, until the imbalance or disparity in socio-economic development between the rural and urban areas are removed, no amount of persuasion or force can put a stop to rural-urban migration and its’ multiplying effects in Juba Metropolitan, Republic of South Sudan.

Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains.

PubMed

Ross, Robert J H; Yates, C A; Baker, R E

2015-06-01

A key feature of cell migration is how cell movement is affected by cell-cell interactions. Furthermore, many cell migratory processes such as neural crest stem cell migration [Thomas and Erickson, 2008; McLennan et al., 2012] occur on growing domains or in the presence of a chemoattractant. Therefore, it is important to study interactions between migrating cells in the context of domain growth and directed motility. Here we compare discrete and continuum models describing the spatial and temporal evolution of a cell population for different types of cell-cell interactions on static and growing domains. We suggest that cell-cell interactions can be inferred from population density characteristics in the presence of motility bias, and these population density characteristics for different cell-cell interactions are conserved on both static and growing domains. We also study the expected displacement of a tagged cell, and show that different types of cell-cell interactions can give rise to cell trajectories with different characteristics. These characteristics are conserved in the presence of domain growth, however, they are diminished in the presence of motility bias. Our results are relevant for researchers who study the existence and role of cell-cell interactions in biological systems, so far as we suggest that different types of cell-cell interactions could be identified from cell density and trajectory data. Copyright © 2015 Elsevier Inc. All rights reserved.

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

PubMed Central

Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno; Hey, Jody

2013-01-01

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus). PMID:23457232

Computational Models Reveal a Passive Mechanism for Cell Migration in the Crypt

PubMed Central

Dunn, Sara-Jane; Näthke, Inke S.; Osborne, James M.

2013-01-01

Cell migration in the intestinal crypt is essential for the regular renewal of the epithelium, and the continued upward movement of cells is a key characteristic of healthy crypt dynamics. However, the driving force behind this migration is unknown. Possibilities include mitotic pressure, active movement driven by motility cues, or negative pressure arising from cell loss at the crypt collar. It is possible that a combination of factors together coordinate migration. Here, three different computational models are used to provide insight into the mechanisms that underpin cell movement in the crypt, by examining the consequence of eliminating cell division on cell movement. Computational simulations agree with existing experimental results, confirming that migration can continue in the absence of mitosis. Importantly, however, simulations allow us to infer mechanisms that are sufficient to generate cell movement, which is not possible through experimental observation alone. The results produced by the three models agree and suggest that cell loss due to apoptosis and extrusion at the crypt collar relieves cell compression below, allowing cells to expand and move upwards. This finding suggests that future experiments should focus on the role of apoptosis and cell extrusion in controlling cell migration in the crypt. PMID:24260407

The Discovery of Single-Nucleotide Polymorphisms—and Inferences about Human Demographic History

PubMed Central

Wakeley, John; Nielsen, Rasmus; Liu-Cordero, Shau Neen; Ardlie, Kristin

2001-01-01

A method of historical inference that accounts for ascertainment bias is developed and applied to single-nucleotide polymorphism (SNP) data in humans. The data consist of 84 short fragments of the genome that were selected, from three recent SNP surveys, to contain at least two polymorphisms in their respective ascertainment samples and that were then fully resequenced in 47 globally distributed individuals. Ascertainment bias is the deviation, from what would be observed in a random sample, caused either by discovery of polymorphisms in small samples or by locus selection based on levels or patterns of polymorphism. The three SNP surveys from which the present data were derived differ both in their protocols for ascertainment and in the size of the samples used for discovery. We implemented a Monte Carlo maximum-likelihood method to fit a subdivided-population model that includes a possible change in effective size at some time in the past. Incorrectly assuming that ascertainment bias does not exist causes errors in inference, affecting both estimates of migration rates and historical changes in size. Migration rates are overestimated when ascertainment bias is ignored. However, the direction of error in inferences about changes in effective population size (whether the population is inferred to be shrinking or growing) depends on whether either the numbers of SNPs per fragment or the SNP-allele frequencies are analyzed. We use the abbreviation “SDL,” for “SNP-discovered locus,” in recognition of the genomic-discovery context of SNPs. When ascertainment bias is modeled fully, both the number of SNPs per SDL and their allele frequencies support a scenario of growth in effective size in the context of a subdivided population. If subdivision is ignored, however, the hypothesis of constant effective population size cannot be rejected. An important conclusion of this work is that, in demographic or other studies, SNP data are useful only to the extent that their ascertainment can be modeled. PMID:11704929

Microseismicity Linked to Gas Migration and Leakage on the Western Svalbard Shelf

NASA Astrophysics Data System (ADS)

Franek, Peter; Plaza-Faverola, Andreia; Mienert, Jürgen; Buenz, Stefan; Ferré, Bénédicte; Hubbard, Alun

2017-12-01

The continental margin off Prins Karls Forland, western Svalbard, is characterized by widespread natural gas seepage into the water column at and upslope of the gas hydrate stability zone. We deployed an ocean bottom seismometer integrated into the MASOX (Monitoring Arctic Seafloor-Ocean Exchange) automated seabed observatory at the pinch-out of this zone at 389 m water depth to investigate passive seismicity over a continuous 297 day period from 13 October 2010. An automated triggering algorithm was applied to detect over 220,000 short duration events (SDEs) defined as having a duration of less than 1 s. The analysis reveals two different types of SDEs, each with a distinctive characteristic seismic signature. We infer that the first type consists of vocal signals generated by moving mammals, likely finback whales. The second type corresponds to signals with a source within a few hundred meters of the seismometer, either due east or west, that vary on short (˜tens of days) and seasonal time scales. Based on evidence of prevalent seafloor seepage and subseafloor gas accumulations, we hypothesize that the second type of SDEs is related to subseafloor fluid migration and gas seepage. Furthermore, we postulate that the observed temporal variations in microseismicity are driven by transient fluid release and due to the dynamics of thermally forced, seasonal gas hydrate decomposition. Our analysis presents a novel technique for monitoring the duration, intensity, and periodicity of fluid migration and seepage at the seabed and can help elucidate the environmental controls on gas hydrate decomposition and release.

Risk Assessment and Prediction of Heavy Metal Pollution in Groundwater and River Sediment: A Case Study of a Typical Agricultural Irrigation Area in Northeast China

PubMed Central

Zhong, Shuang; Geng, Hui; Zhang, Fengjun; Liu, Zhaoying; Wang, Tianye; Song, Boyu

2015-01-01

The areas with typical municipal sewage discharge river and irrigation water function were selected as study sites in northeast China. The samples from groundwater and river sediment in this area were collected for the concentrations and forms of heavy metals (Cr(VI), Cd, As, and Pb) analysis. The risk assessment of heavy metal pollution was conducted based on single-factor pollution index (I) and Nemerow pollution index (NI). The results showed that only one groundwater sampling site reached a polluted level of heavy metals. There was a high potential ecological risk of Cd on the N21-2 sampling site in river sediment. The morphological analysis results of heavy metals in sediment showed that the release of heavy metals can be inferred as one of the main pollution sources of groundwater. In addition, the changes in the concentration and migration scope of As were predicted by using the Groundwater Modeling System (GMS). The predicted results showed that As will migrate downstream in the next decade, and the changing trend of As polluted areas was changed with As content districts because of some pump wells downstream to form groundwater depression cone, which made the solute transfer upstream. PMID:26366176

Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies.

PubMed

Verdu, Paul; Becker, Noémie S A; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

2013-04-01

Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter-gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history.

The conquering of North America: dated phylogenetic and biogeographic inference of migratory behavior in bee hummingbirds.

PubMed

Licona-Vera, Yuyini; Ornelas, Juan Francisco

2017-06-05

Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods. All phylogenetic analyses confirmed monophyly of the Mellisugini and the inclusion of Atthis, Calothorax, Doricha, Eulidia, Mellisuga, Microstilbon, Myrmia, Tilmatura, and Thaumastura. Mellisugini consists of two clades: (1) South American species (including Tilmatura dupontii), and (2) species distributed in North and Central America and the Caribbean islands. The second clade consists of four subclades: Mexican (Calothorax, Doricha) and Caribbean (Archilochus, Calliphlox, Mellisuga) sheartails, Calypte, and Selasphorus (incl. Atthis). Coalescent-based dating places the origin of the Mellisugini in the mid-to-late Miocene, with crown ages of most subclades in the early Pliocene, and subsequent species splits in the Pleistocene. Bee hummingbirds reached western North America by the end of the Miocene and the ancestral mellisuginid (bee hummingbirds) was reconstructed as sedentary, with four independent gains of migratory behavior during the evolution of the Mellisugini. Early colonization of North America and subsequent evolution of migration best explained biogeographic and diversification patterns within the Mellisugini. The repeated evolution of long-distance migration by different lineages was critical for the colonization of North America, contributing to the radiation of bee hummingbirds. Comparative phylogeography is needed to test whether the repeated evolution of migration resulted from northward expansion of southern sedentary populations.

Sociocultural Behavior, Sex-Biased Admixture, and Effective Population Sizes in Central African Pygmies and Non-Pygmies

PubMed Central

Verdu, Paul; Becker, Noémie S.A.; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

2013-01-01

Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter–gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history. PMID:23300254

Continental-scale, seasonal movements of a heterothermic migratory tree bat

USGS Publications Warehouse

Cryan, Paul M.; Stricker, Craig A.; Wunder, Michael B.

2014-01-01

Long-distance migration evolved independently in bats and unique migration behaviors are likely, but because of their cryptic lifestyles, many details remain unknown. North American hoary bats (Lasiurus cinereus cinereus) roost in trees year-round and probably migrate farther than any other bats, yet we still lack basic information about their migration patterns and wintering locations or strategies. This information is needed to better understand unprecedented fatality of hoary bats at wind turbines during autumn migration and to determine whether the species could be susceptible to an emerging disease affecting hibernating bats. Our aim was to infer probable seasonal movements of individual hoary bats to better understand their migration and seasonal distribution in North America. We analyzed the stable isotope values of non-exchangeable hydrogen in the keratin of bat hair and combined isotopic results with prior distributional information to derive relative probability density surfaces for the geographic origins of individuals. We then mapped probable directions and distances of seasonal movement. Results indicate that hoary bats summer across broad areas. In addition to assumed latitudinal migration, we uncovered evidence of longitudinal movement by hoary bats from inland summering grounds to coastal regions during autumn and winter. Coastal regions with nonfreezing temperatures may be important wintering areas for hoary bats. Hoary bats migrating through any particular area, such as a wind turbine facility in autumn, are likely to have originated from a broad expanse of summering grounds from which they have traveled in no recognizable order. Better characterizing migration patterns and wintering behaviors of hoary bats sheds light on the evolution of migration and provides context for conserving these migrants.

New Biogeographic insight into Bauhinia s.l. (Leguminosae): integration from fossil records and molecular analyses

PubMed Central

2014-01-01

Background Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical intercontinental disjunction among the Asian, African, and American continents. Geographic distribution patterns are better recognized when fossil records and molecular sequences are combined in the analyses. Here, we describe a new macrofossil species of Bauhinia from the Upper Miocene Xiaolongtan Formation in Wenshan County, Southeast Yunnan, China, and elucidate the biogeographic significance through the analyses of molecules and fossils. Results Morphometric analysis demonstrates that the leaf shapes of B. acuminata, B. championii, B. chalcophylla, B. purpurea, and B. podopetala closely resemble the leaf shapes of the new finding fossil. Phylogenetic relationships among the Bauhinia species were reconstructed using maximum parsimony and Bayesian inference, which inferred that species in Bauhinia species are well-resolved into three main groups. Divergence times were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method under a relaxed clock, and inferred that the stem diversification time of Bauhinia was ca. 62.7 Ma. The Asian lineage first diverged at ca. 59.8 Ma, followed by divergence of the Africa lineage starting during the late Eocene, whereas that of the neotropical lineage starting during the middle Miocene. Conclusions Hypotheses relying on vicariance or continental history to explain pantropical disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. We suggest that Bauhinia originated in the middle Paleocene in Laurasia, probably in Asia, implying a possible Tethys Seaway origin or an “Out of Tropical Asia”, and dispersal of legumes. Its present pantropical disjunction resulted from disruption of the boreotropical flora by climatic cooling after the Paleocene-Eocene Thermal Maximum (PETM). North Atlantic land bridges (NALB) seem the most plausible route for migration of Bauhinia from Asia to America; and additional aspects of the Bauhinia species distribution are explained by migration and long distance dispersal (LDD) from Eurasia to the African and American continents. PMID:25288346

New Biogeographic insight into Bauhinia s.l. (Leguminosae): integration from fossil records and molecular analyses.

PubMed

Meng, Hong-Hu; Jacques, Frédéric Mb; Su, Tao; Huang, Yong-Jiang; Zhang, Shi-Tao; Ma, Hong-Jie; Zhou, Zhe-Kun

2014-08-10

Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical intercontinental disjunction among the Asian, African, and American continents. Geographic distribution patterns are better recognized when fossil records and molecular sequences are combined in the analyses. Here, we describe a new macrofossil species of Bauhinia from the Upper Miocene Xiaolongtan Formation in Wenshan County, Southeast Yunnan, China, and elucidate the biogeographic significance through the analyses of molecules and fossils. Morphometric analysis demonstrates that the leaf shapes of B. acuminata, B. championii, B. chalcophylla, B. purpurea, and B. podopetala closely resemble the leaf shapes of the new finding fossil. Phylogenetic relationships among the Bauhinia species were reconstructed using maximum parsimony and Bayesian inference, which inferred that species in Bauhinia species are well-resolved into three main groups. Divergence times were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method under a relaxed clock, and inferred that the stem diversification time of Bauhinia was ca. 62.7 Ma. The Asian lineage first diverged at ca. 59.8 Ma, followed by divergence of the Africa lineage starting during the late Eocene, whereas that of the neotropical lineage starting during the middle Miocene. Hypotheses relying on vicariance or continental history to explain pantropical disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. We suggest that Bauhinia originated in the middle Paleocene in Laurasia, probably in Asia, implying a possible Tethys Seaway origin or an "Out of Tropical Asia", and dispersal of legumes. Its present pantropical disjunction resulted from disruption of the boreotropical flora by climatic cooling after the Paleocene-Eocene Thermal Maximum (PETM). North Atlantic land bridges (NALB) seem the most plausible route for migration of Bauhinia from Asia to America; and additional aspects of the Bauhinia species distribution are explained by migration and long distance dispersal (LDD) from Eurasia to the African and American continents.

Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

PubMed Central

Smitz, Nathalie; Berthouly, Cécile; Cornélis, Daniel; Heller, Rasmus; Van Hooft, Pim; Chardonnet, Philippe; Caron, Alexandre; Prins, Herbert; van Vuuren, Bettine Jansen; De Iongh, Hans; Michaux, Johan

2013-01-01

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today. PMID:23437100

A Genealogical Interpretation of Principal Components Analysis

PubMed Central

McVean, Gil

2009-01-01

Principal components analysis, PCA, is a statistical method commonly used in population genetics to identify structure in the distribution of genetic variation across geographical location and ethnic background. However, while the method is often used to inform about historical demographic processes, little is known about the relationship between fundamental demographic parameters and the projection of samples onto the primary axes. Here I show that for SNP data the projection of samples onto the principal components can be obtained directly from considering the average coalescent times between pairs of haploid genomes. The result provides a framework for interpreting PCA projections in terms of underlying processes, including migration, geographical isolation, and admixture. I also demonstrate a link between PCA and Wright's fst and show that SNP ascertainment has a largely simple and predictable effect on the projection of samples. Using examples from human genetics, I discuss the application of these results to empirical data and the implications for inference. PMID:19834557

Gene genealogies in geographically structured populations

Treesearch

Bryan K. Epperson

1999-01-01

Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic...

Intermittent tremor migrations beneath Guerrero, Mexico, and implications for fault healing within the slow slip zone

NASA Astrophysics Data System (ADS)

Peng, Yajun; Rubin, Allan M.

2017-01-01

Slow slip events exhibit significant complexity in slip evolution and variations in recurrence intervals. Behavior that varies systematically with recurrence interval is likely to reflect different extents of fault healing between these events. Here we use high-resolution tremor catalogs beneath Guerrero, Mexico, to investigate the mechanics of slow slip. We observe complex tremor propagation styles, including rapid tremor migrations propagating either along the main tremor front or backward, reminiscent of those in northern Cascadia. We also find many migrations that originate well behind the front and repeatedly occupy the same source region during a tremor episode, similar to those previously reported from Shikoku, Japan. These migrations could be driven by slow slip in the surrounding regions, with recurrence intervals possibly modulated by tides. The propagation speed of these migrations decreases systematically with time since the previous migration over the same source area. Tremor amplitudes seem consistent with changes in the propagation speeds being controlled primarily by changes in the slip speeds. One interpretation is that the high propagation speeds and inferred high slip speeds during the migrations with short recurrence intervals are caused by incomplete healing within the host rock adjacent to the shear zone, which could lead to high permeability and reduced dilatant strengthening of the fault gouge. Similar processes may operate in other slow slip source regions such as Cascadia.

Towards a global historical biogeography of Palms

NASA Astrophysics Data System (ADS)

Couvreur, Thomas; Baker, William J.; Frigerio, Jean-Marc; Sepulchre, Pierre; Franc, Alain

2017-04-01

Four mechanisms are at work for deciphering historical biogeography of plants : speciation, extinction, migration, and drift (a sort of neutral speciation). The first three mechanisms are under selection pressure of the environment, mainly the climate and connectivity of land masses. Hence, an accurate history of climate and connectivity or non connectivity between landmasses, as well as orogenesis processes, can shed new light on the most likely speciation events and migration routes driven by paleogeography and paleoclimatology. Currently, some models exist (like DIVA) to infer the most parsimonious history (in the number of migration events) knowing the speciation history given by phylogenies (extinction are mostly unknown), in a given setting of climate and landmass connectivity. In a previous project, we have built in collaboration with LSCE a series of paleogeographic and paleoclimatic maps since the Early Cretaceous. We have developed a program, called Aran, which enables to extend DIVA to a time series of varying paleoclimatic and paleogeogarphic conditions. We apply these new methods and data to unravel the biogeographic history of palms (Arecaceae), a pantropical family of 182 genera and >2600 species whose divergence is dated in Late Cretaceous (100 My). Based on a robust dated molecular phylogeny, novel paleoclimatic and paleogeographic maps, we will generate an updated biogeographic history of Arecaceae inferred from the most parsimonious history using Aran. We will discuss the results, and put them in context with what is known and needed to provide a global biogeographic history of tropical palms.

Home on the Range: Factors Explaining Partial Migration of African Buffalo in a Tropical Environment

PubMed Central

Naidoo, Robin; Du Preez, Pierre; Stuart-Hill, Greg; Jago, Mark; Wegmann, Martin

2012-01-01

Partial migration (when only some individuals in a population undertake seasonal migrations) is common in many species and geographical contexts. Despite the development of modern statistical methods for analyzing partial migration, there have been no studies on what influences partial migration in tropical environments. We present research on factors affecting partial migration in African buffalo (Syncerus caffer) in northeastern Namibia. Our dataset is derived from 32 satellite tracking collars, spans 4 years and contains over 35,000 locations. We used remotely sensed data to quantify various factors that buffalo experience in the dry season when making decisions on whether and how far to migrate, including potential man-made and natural barriers, as well as spatial and temporal heterogeneity in environmental conditions. Using an information-theoretic, non-linear regression approach, our analyses showed that buffalo in this area can be divided into 4 migratory classes: migrants, non-migrants, dispersers, and a new class that we call “expanders”. Multimodel inference from least-squares regressions of wet season movements showed that environmental conditions (rainfall, fires, woodland cover, vegetation biomass), distance to the nearest barrier (river, fence, cultivated area) and social factors (age, size of herd at capture) were all important in explaining variation in migratory behaviour. The relative contributions of these variables to partial migration have not previously been assessed for ungulates in the tropics. Understanding the factors driving migratory decisions of wildlife will lead to better-informed conservation and land-use decisions in this area. PMID:22570722

Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan.

PubMed

Gong, Yu-Nong; Tsao, Kuo-Chien; Chen, Guang-Wu

2018-02-20

Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades. All Taiwanese H3N2 HA1 sequences and references were downloaded from public database. A Bayesian skyline plot (BSP) and phylogenetic tree were used to analyze the evolutionary history, and Bayesian phylogeographic analysis was applied to predict the spatiotemporal migrations of influenza outbreaks. Genetic diversity was found to have peaked near the summer of 2009 in BSP, in addition to the two earlier reported ones in summer of 2005 and 2007. We predicted their spatiotemporal migrations and found the summer epidemic of 2005 from Korea, and 2007 and 2009 from the Western United States. BSP also predicted an elevated genetic diversity in 2015-2017. Quasispecies were found over approximately 20% of the strains included in this time span. In addition, a first-time seen N31S mutation was noted in Taiwan in 2016-2017. We comprehensively investigated the evolutionary history of Taiwanese strains in 1979-2017. An epidemic caution could thus be raised if genetic diversity was found to have peaked. An example showed a newly-discovered cluster in 2016-2017 strains featuring a mutation N31S together with HA-160 quasispecies. Phylogeographic analysis, moreover, provided useful insights in tracing the possible source and migrations of these epidemics around the world. We demonstrated that Asian destinations including Taiwan were the immediate followers, while U.S. continent was predicted the origin of two summer epidemics in 2007 and 2009. Copyright © 2018. Published by Elsevier B.V.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history.

PubMed

Schiffels, Stephan; Haak, Wolfgang; Paajanen, Pirita; Llamas, Bastien; Popescu, Elizabeth; Loe, Louise; Clarke, Rachel; Lyons, Alice; Mortimer, Richard; Sayer, Duncan; Tyler-Smith, Chris; Cooper, Alan; Durbin, Richard

2016-01-19

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Load Balancing Using Time Series Analysis for Soft Real Time Systems with Statistically Periodic Loads

NASA Technical Reports Server (NTRS)

Hailperin, Max

1993-01-01

This thesis provides design and analysis of techniques for global load balancing on ensemble architectures running soft-real-time object-oriented applications with statistically periodic loads. It focuses on estimating the instantaneous average load over all the processing elements. The major contribution is the use of explicit stochastic process models for both the loading and the averaging itself. These models are exploited via statistical time-series analysis and Bayesian inference to provide improved average load estimates, and thus to facilitate global load balancing. This thesis explains the distributed algorithms used and provides some optimality results. It also describes the algorithms' implementation and gives performance results from simulation. These results show that our techniques allow more accurate estimation of the global system load ing, resulting in fewer object migration than local methods. Our method is shown to provide superior performance, relative not only to static load-balancing schemes but also to many adaptive methods.

Sea Level Driven Marsh Expansion in a Coupled Model of Marsh Erosion, Forest Retreat, and Human Impacts

NASA Astrophysics Data System (ADS)

Kirwan, M. L.; Walters, D. C.; Reay, W.; Carr, J.

2016-12-01

Salt marsh ecosystem services depend nonlinearly on wetland size and are threatened by sea level rise and coastal development. Here, we present a simple model of marsh migration into adjacent uplands, and couple it with existing models of seaward edge erosion and vertical soil accretion to explore how connectivity between adjacent ecosystems influences marsh size and response to sea level rise. We find that ecogeomorphic feedbacks tend to stabilize soil elevations relative to sea level rise so that changes in marsh size are determined mostly by the competition between ecological transitions at the upland boundary, and physical erosion at the seaward boundary. Salt marsh loss and natural flood protection is nearly inevitable under rapid sea level rise rates where topographic and anthropogenic barriers limit marsh migration into uplands. Where unconstrained by barriers, however, rates of marsh migration are much more sensitive to accelerated sea level rise than rates of edge erosion. Together, this behavior suggests a counterintuitive, natural tendency for marsh expansion with sea level rise, and emphasizes the disparity between coastal response to climate change with and without human intervention. Analysis of 19th century maps and modern photographs from the Chesapeake Bay region confirm that migration rates are more sensitive to sea level rise than erosion rate, and indicate that transgression has thus far allowed marshes to survive the fastest rates of relative sea level rise on the Atlantic Coast. This work suggests that the flux of organisms and sediment across adjacent ecosystems leads to an increase in system resilience that could not be inferred from studies that consider individual components of landscape change.

Migrations and swimming capabilities of endangered pallid sturgeon (Scaphirhynchus albus) to guide passage designs in the fragmented Yellowstone River

USGS Publications Warehouse

Braaten, P. J.; Elliott, Caroline M.; Rhoten, Jason C.; Fuller, D. B.; McElroy, Brandon J.

2015-01-01

Fragmentation of the Yellowstone River is hypothesized to preclude recruitment of endangered Scaphirhynchus albus (pallid sturgeon) by impeding upstream spawning migrations and access to upstream spawning areas, thereby limiting the length of free-flowing river required for survival of early life stages. Building on this hypothesis, the reach of the Yellowstone River affected by Intake Diversion Dam (IDD) is targeted for modification. Structures including a rock ramp and by-pass channel have been proposed as restoration alternatives to facilitate passage. Limited information on migrations and swimming capabilities of pallid sturgeon is available to guide engineering design specifications for the proposed structures. Migration behavior, pathways (channel routes used during migrations), and swimming capabilities of free-ranging wild adult pallid sturgeon were examined using radiotelemetry, and complemented with hydraulic data obtained along the migration pathways. Migrations of 12–26% of the telemetered pallid sturgeon population persisted to IDD, but upstream passage over the dam was not detected. Observed migration pathways occurred primarily through main channel habitats; however, migrations through side channels up to 3.9 km in length were documented. The majority of pallid sturgeon used depths of 2.2–3.4 m and mean water velocities of 0.89–1.83 m/s while migrating. Results provide inferences on depths, velocities, and habitat heterogeneity of reaches successfully negotiated by pallid sturgeon that may be used to guide designs for structures facilitating passage at IDD. Passage will provide connectivity to potential upstream spawning areas on the Yellowstone River, thereby increasing the likelihood of recruitment for this endangered species.

Phylogeographic History and Gene Flow Among Giant Galápagos Tortoises on Southern Isabela Island

PubMed Central

Ciofi, Claudio; Wilson, Gregory A.; Beheregaray, Luciano B.; Marquez, Cruz; Gibbs, James P.; Tapia, Washington; Snell, Howard L.; Caccone, Adalgisa; Powell, Jeffrey R.

2006-01-01

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals. PMID:16387883

Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island.

PubMed

Ciofi, Claudio; Wilson, Gregory A; Beheregaray, Luciano B; Marquez, Cruz; Gibbs, James P; Tapia, Washington; Snell, Howard L; Caccone, Adalgisa; Powell, Jeffrey R

2006-03-01

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.

The rationality of prejudices.

PubMed

Chadefaux, Thomas; Helbing, Dirk

2012-01-01

We model an N-player repeated prisoner's dilemma in which players are given traits (e.g., height, age, wealth) which, we assume, affect their behavior. The relationship between traits and behavior is unknown to other players. We then analyze the performance of "prejudiced" strategies--strategies that draw inferences based on the observation of some or all of these traits, and extrapolate the inferred behavior to other carriers of these traits. Such prejudiced strategies have the advantage of learning rapidly, and hence of being well adapted to rapidly changing conditions that might result, for example, from high migration or birth rates. We find that they perform remarkably well, and even systematically outperform both Tit-For-Tat and ALLD when the population changes rapidly.

Breeding behaviour of pilot whales revealed by DNA fingerprinting.

PubMed

Amos, B; Barrett, J; Dover, G A

1991-08-01

Most species of whale spend the majority of their lives well away from land, are capable of migrating over large distances and are difficult to identify individually. However, conservation measures require a detailed understanding of their social structure, breeding behaviour and migration patterns. The advent of DNA fingerprinting permits a systematic investigation of such parameters. In the Faeroe Islands there exists a traditional harvest of long-finned pilot whales (Globicephala melas), in which intact social groups (pods) are captured. This affords a unique opportunity to study genetic relationships within and between pods. We report here on a paternity analysis, using DNA fingerprinting, of mother-fetus pairs and males sampled from complete pods. In addition, a single, highly polymorphic minisatellite locus was used to infer degrees of relatedness between groups of fetuses and females. Taken together, our results suggest that pods consist of closely related adult females and their offspring. Sexually mature males either move frequently between pods or remain in their natal pod but refrain from mating with female relatives. Whichever hypothesis is correct, the data suggest that each male spends only a few months with the female post-mating and individual males often father several fetuses within a pod.

First direct evidence of long-distance seasonal movements and hibernation in a migratory bat

Treesearch

Theodore J. Weller; Kevin T. Castle; Felix Liechti; Cris D. Hein; Michael R. Schirmacher; Paul M. Cryan

2016-01-01

Understanding of migration in small bats has been constrained by limitations of techniques that were labor-intensive, provided coarse levels of resolution, or were limited to population-level inferences. Knowledge of movements and behaviors of individual bats have been unknowable because of limitations in size of tracking devices and methods to attach them for...

Fluid source inferred from strontium isotopes in pore fluid and carbonate recovered during Expedition 337 off Shimokita, Japan

NASA Astrophysics Data System (ADS)

Hong, W.; Moen, N.; Haley, B. A.

2013-12-01

IODP Expedition 337 was designed to understand the relationship between a deep-buried (2000 meters below seafloor) hydrocarbon reservoir off the Shimokita peninsula (Japan), and the microbial community that this carbon reservoir sustains at such depth. Understanding sources and pathways of flow of fluids that carry hydrocarbons, nutrients, and other reduced components is of particular interest to fulfilling the expedition objectives, since this migrating fluid supports microbial activity not only of the deep-seated communities but also to the shallow-dwelling organisms. To this aim, the concentration and isotopic signature of Sr can be valuable due to that it is relatively free from biogenic influence and pristine in terms of drill fluid contamination. From the pore water Sr profile, concentration gradually increases from 1500 to 2400 mbsf. The depth where highest Sr concentration is observed corresponds to the depths where couple layers of carbonate were observed. Such profile suggests an upward-migrating fluid carries Sr from those deep-seated carbonate layers (>2400 mbsf) to shallower sediments. To confirm this inference, pore water, in-situ formation fluid, and carbonate samples were analyzed for Sr isotopes to investigate the fluid source.

Seasonal and diel movements of white sturgeon in the lower columbia river

USGS Publications Warehouse

Parsley, M.J.; Popoff, N.D.; Van Der Leeuw, B. K.; Wright, C.D.

2008-01-01

Continuous monitoring of the movements and depths used by white sturgeon Acipenser transmontanus with acoustic telemetry technologies in the lower Columbia River provided information on diel and seasonal migrations, local movements, and site fidelity. White sturgeon moved to shallower water at night and showed greater activity, inferred from rates of movement, than during daytime. The extent of local movement within a season was variable among fish; some fish readily moved among habitats while the movements of others were more constrained. White sturgeon were absent from the study area (river kilometers 45-52) during winter and returned from upstream during the spring, confirming an upstream seasonal migration in the fall and downstream migration in spring. The return of individual fish and reoccupation of areas previously inhabited showed that some white sturgeon exhibit site fidelity. This work shows that studies seeking to characterize habitat for white sturgeon need to be cognizant of diel migrations and site fidelity. We urge caution in the use of limited fish location data to describe habitats if diel activities and fine-scale movements are not known.

Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks

PubMed Central

Ringbauer, Harald; Coop, Graham

2017-01-01

Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These identity-by-descent (IBD) blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulas for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite-likelihood approach to fit these formulas. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block-sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the Population Reference Sample data set. We show that ancestry diffusing with a rate of σ≈50−−100 km/gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance. PMID:28108588

Neogene deformation of thrust-top Rzeszów Basin (Outer Carpathians, Poland)

NASA Astrophysics Data System (ADS)

Uroda, Joanna

2015-04-01

The Rzeszów Basin is a 220 km2 basin located in the frontal part of Polish Outer Carpathians fold-and-thrust belt. Its sedimentary succession consist of ca. 600 m- thick Miocene evaporates, litoral and marine sediments. This basin developed between Babica-Kąkolówka anticline and frontal thrust of Carpathian Orogen. Rzeszów thrust-top basin is a part of Carpathian foreland basin system- wedge-top depozone. The sediments of wedge -top depozone were syntectonic deformed, what is valuable tool to understand kinematic history of the orogen. Analysis of field and 3D seismic reflection data showed the internal structure of the basin. Seismic data reveal the presence of fault-bend-folds in the basement of Rzeszów basin. The architecture of the basin - the presence of fault-releated folds - suggest that the sediments were deformed in last compressing phase of Carpathian Orogen deformation. Evolution of Rzeszów Basin is compared with Bonini et.al. (1999) model of thrust-top basin whose development is controlled by the kinematics of two competing thrust anticlines. Analysis of seismic and well data in Rzeszów basin suggest that growth sediments are thicker in south part of the basin. During the thrusting the passive rotation of the internal thrust had taken place, what influence the basin fill architecture and depocentre migration opposite to thrust propagation. Acknowledgments This study was supported by grant No 2012/07/N/ST10/03221 of the Polish National Centre of Science "Tectonic activity of the Skole Nappe based on analysis of changes in the vertical profile and depocentre migration of Neogene sediments in Rzeszów-Strzyżów area (Outer Carpathians)". Seismic data by courtesy of the Polish Gas and Oil Company. References Bonini M., Moratti G., Sani F., 1999, Evolution and depocentre migration in thrust-top basins: inferences from the Messinian Velona Basin (Northern Apennines, Italy), Tectonophysics 304, 95-108.

High-throughput dietary exposure predictions for chemical migrants from food contact substances for use in chemical prioritization.

PubMed

Biryol, Derya; Nicolas, Chantel I; Wambaugh, John; Phillips, Katherine; Isaacs, Kristin

2017-11-01

Under the ExpoCast program, United States Environmental Protection Agency (EPA) researchers have developed a high-throughput (HT) framework for estimating aggregate exposures to chemicals from multiple pathways to support rapid prioritization of chemicals. Here, we present methods to estimate HT exposures to chemicals migrating into food from food contact substances (FCS). These methods consisted of combining an empirical model of chemical migration with estimates of daily population food intakes derived from food diaries from the National Health and Nutrition Examination Survey (NHANES). A linear regression model for migration at equilibrium was developed by fitting available migration measurements as a function of temperature, food type (i.e., fatty, aqueous, acidic, alcoholic), initial chemical concentration in the FCS (C 0 ) and chemical properties. The most predictive variables in the resulting model were C 0 , molecular weight, log K ow , and food type (R 2 =0.71, p<0.0001). Migration-based concentrations for 1009 chemicals identified via publicly-available data sources as being present in polymer FCSs were predicted for 12 food groups (combinations of 3 storage temperatures and food type). The model was parameterized with screening-level estimates of C 0 based on the functional role of chemicals in FCS. By combining these concentrations with daily intakes for food groups derived from NHANES, population ingestion exposures of chemical in mg/kg-bodyweight/day (mg/kg-BW/day) were estimated. Calibrated aggregate exposures were estimated for 1931 chemicals by fitting HT FCS and consumer product exposures to exposures inferred from NHANES biomonitoring (R 2 =0.61, p<0.001); both FCS and consumer product pathway exposures were significantly predictive of inferred exposures. Including the FCS pathway significantly impacted the ratio of predicted exposures to those estimated to produce steady-state blood concentrations equal to in-vitro bioactive concentrations. While these HT methods have large uncertainties (and thus may not be appropriate for assessments of single chemicals), they can provide critical refinement to aggregate exposure predictions used in risk-based chemical priority-setting. Published by Elsevier Ltd.

A Low Mass for Mars from Jupiter's Early Gas-Driven Migration

NASA Technical Reports Server (NTRS)

Walsh, Kevin J.; Morbidelli, Alessandro; Raymond, Sean N.; O'Brien, David P.; Mandell, Avi M.

2011-01-01

Jupiter and Saturn formed in a few million years from a gas-dominated protoplanetary disk, and were susceptible to gas-driven migration of their orbits on timescales of only approximately 100,000 years. Hydrodynamic simulations show that these giant planets can undergo a two-stage, inward-then-outward, migration. The terrestrial planets finished accreting much later and their characteristics, including Mars' small mass, are best reproduced by starting from a planetesimal disk with an outer edge at about one astronomical unit from the Sun (1 AU is the Earth-Sun distance). Here we report simulations of the early Solar System that show how the inward migration of Jupiter to 1.5 AU, and its subsequent outward migration, lead to a planetesimal disk truncated at 1 AU; the terrestrial planets then form from this disk over the next 30-50 million years, with an Earth/Mars mass ratio consistent with observations. Scattering by Jupiter initially empties but then repopulates the asteroid belt, with inner-belt bodies originating between 1 and 3 AU and outer-belt bodies originating between and beyond the giant planets. This explains the significant compositional differences across the asteroid belt. The key aspect missing from previous models of terrestrial planet formation is the substantial radial migration of the giant planets, which suggests that their behaviour is more similar to that inferred for extrasolar planets than previously thought.

Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data.

PubMed

Wooding, Stephen; Ostler, Christopher; Prasad, B V Ravi; Watkins, W Scott; Sung, Sandy; Bamshad, Mike; Jorde, Lynn B

2004-08-01

Genetic, ethnographic, and historical evidence suggests that the Hindu castes have been highly endogamous for several thousand years and that, when movement between castes does occur, it typically consists of females joining castes of higher social status. However, little is known about migration rates in these populations or the extent to which migration occurs between caste groups of low, middle, and high social status. To investigate these aspects of migration, we analyzed the largest collection of genetic markers collected to date in Hindu caste populations. These data included 45 newly typed autosomal short tandem repeat polymorphisms (STRPs), 411 bp of mitochondrial DNA sequence, and 43 Y-chromosomal single-nucleotide polymorphisms that were assayed in more than 200 individuals of known caste status sampled in Andrah Pradesh, in South India. Application of recently developed likelihood-based analyses to this dataset enabled us to obtain genetically derived estimates of intercaste migration rates. STRPs indicated migration rates of 1-2% per generation between high-, middle-, and low-status caste groups. We also found support for the hypothesis that rates of gene flow differ between maternally and paternally inherited genes. Migration rates were substantially higher in maternally than in paternally inherited markers. In addition, while prevailing patterns of migration involved movement between castes of similar rank, paternally inherited markers in the low-status castes were most likely to move into high-status castes. Our findings support earlier evidence that the caste system has been a significant, long-term source of population structuring in South Indian Hindu populations, and that patterns of migration differ between males and females. Copyright 2004 Springer-Verlag

Present-day African analogue of a pre-European Amazonian floodplain fishery shows convergence in cultural niche construction.

PubMed

McKey, Doyle B; Durécu, Mélisse; Pouilly, Marc; Béarez, Philippe; Ovando, Alex; Kalebe, Mashuta; Huchzermeyer, Carl F

2016-12-27

Erickson [Erickson CL (2000) Nature 408 (6809):190-193] interpreted features in seasonal floodplains in Bolivia's Beni savannas as vestiges of pre-European earthen fish weirs, postulating that they supported a productive, sustainable fishery that warranted cooperation in the construction and maintenance of perennial structures. His inferences were bold, because no close ethnographic analogues were known. A similar present-day Zambian fishery, documented here, appears strikingly convergent. The Zambian fishery supports Erickson's key inferences about the pre-European fishery: It allows sustained high harvest levels; weir construction and operation require cooperation; and weirs are inherited across generations. However, our comparison suggests that the pre-European system may not have entailed intensive management, as Erickson postulated. The Zambian fishery's sustainability is based on exploiting an assemblage dominated by species with life histories combining high fecundity, multiple reproductive cycles, and seasonal use of floodplains. As water rises, adults migrate from permanent watercourses into floodplains, through gaps in weirs, to feed and spawn. Juveniles grow and then migrate back to dry-season refuges as water falls. At that moment fishermen set traps in the gaps, harvesting large numbers of fish, mostly juveniles. In nature, most juveniles die during the first dry season, so that their harvest just before migration has limited impact on future populations, facilitating sustainability and the adoption of a fishery based on inherited perennial structures. South American floodplain fishes with similar life histories were the likely targets of the pre-European fishery. Convergence in floodplain fish strategies in these two regions in turn drove convergence in cultural niche construction.

Load Balancing Using Time Series Analysis for Soft Real Time Systems with Statistically Periodic Loads

NASA Technical Reports Server (NTRS)

Hailperin, M.

1993-01-01

This thesis provides design and analysis of techniques for global load balancing on ensemble architectures running soft-real-time object-oriented applications with statistically periodic loads. It focuses on estimating the instantaneous average load over all the processing elements. The major contribution is the use of explicit stochastic process models for both the loading and the averaging itself. These models are exploited via statistical time-series analysis and Bayesian inference to provide improved average load estimates, and thus to facilitate global load balancing. This thesis explains the distributed algorithms used and provides some optimality results. It also describes the algorithms' implementation and gives performance results from simulation. These results show that the authors' techniques allow more accurate estimation of the global system loading, resulting in fewer object migrations than local methods. The authors' method is shown to provide superior performance, relative not only to static load-balancing schemes but also to many adaptive load-balancing methods. Results from a preliminary analysis of another system and from simulation with a synthetic load provide some evidence of more general applicability.

Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World

PubMed Central

Meiri, Meirav; Lister, Adrian M.; Collins, Matthew J.; Tuross, Noreen; Goebel, Ted; Blockley, Simon; Zazula, Grant D.; van Doorn, Nienke; Dale Guthrie, R.; Boeskorov, Gennady G.; Baryshnikov, Gennady F.; Sher, Andrei; Barnes, Ian

2014-01-01

Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species’s current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories. PMID:24335981

Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World.

PubMed

Meiri, Meirav; Lister, Adrian M; Collins, Matthew J; Tuross, Noreen; Goebel, Ted; Blockley, Simon; Zazula, Grant D; van Doorn, Nienke; Dale Guthrie, R; Boeskorov, Gennady G; Baryshnikov, Gennady F; Sher, Andrei; Barnes, Ian

2014-02-07

Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species's current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.

Recent and rapid population growth and range expansion of the Lyme disease tick vector, Ixodes scapularis, in North America.

PubMed

Khatchikian, Camilo E; Prusinski, Melissa A; Stone, Melissa; Backenson, Peter Bryon; Wang, Ing-Nang; Foley, Erica; Seifert, Stephanie N; Levy, Michael Z; Brisson, Dustin

2015-07-01

Migration is a primary force of biological evolution that alters allele frequencies and introduces novel genetic variants into populations. Recent migration has been proposed as the cause of the emergence of many infectious diseases, including those carried by blacklegged ticks in North America. Populations of blacklegged ticks have established and flourished in areas of North America previously thought to be devoid of this species. The recent discovery of these populations of blacklegged ticks may have resulted from either in situ growth of long-established populations that were maintained at very low densities or by migration and colonization from established populations. These alternative evolutionary hypotheses were investigated using Bayesian phylogeographic approaches to infer the origin and migratory history of recently detected blacklegged tick populations in the Northeastern United States. The data and results indicate that newly detected tick populations are not the product of in situ population growth from a previously established population but from recent colonization resulting in a geographic range expansion. This expansion in the geographic range proceeded primarily through progressive and local migration events from southern populations to proximate northern locations although long-distance migration events were also detected. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839).

PubMed

Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

2008-09-17

Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data.

PubMed

Yew, Chee Wei; Hoque, Mohd Zahirul; Pugh-Kitingan, Jacqueline; Minsong, Alexander; Voo, Christopher Lok Yung; Ransangan, Julian; Lau, Sophia Tiek Ying; Wang, Xu; Saw, Woei Yuh; Ong, Rick Twee-Hee; Teo, Yik-Ying; Xu, Shuhua; Hoh, Boon-Peng; Phipps, Maude E; Kumar, S Vijay

2018-07-01

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (F ST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s). © 2018 John Wiley & Sons Ltd/University College London.

Nonparametric weighted stochastic block models

NASA Astrophysics Data System (ADS)

Peixoto, Tiago P.

2018-01-01

We present a Bayesian formulation of weighted stochastic block models that can be used to infer the large-scale modular structure of weighted networks, including their hierarchical organization. Our method is nonparametric, and thus does not require the prior knowledge of the number of groups or other dimensions of the model, which are instead inferred from data. We give a comprehensive treatment of different kinds of edge weights (i.e., continuous or discrete, signed or unsigned, bounded or unbounded), as well as arbitrary weight transformations, and describe an unsupervised model selection approach to choose the best network description. We illustrate the application of our method to a variety of empirical weighted networks, such as global migrations, voting patterns in congress, and neural connections in the human brain.

A comparison of regression methods for model selection in individual-based landscape genetic analysis.

PubMed

Shirk, Andrew J; Landguth, Erin L; Cushman, Samuel A

2018-01-01

Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression-based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression-based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PubMed Central

Jiménez, Rosa Alicia

2016-01-01

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers. PMID:26788433

Efficient Process Migration for Parallel Processing on Non-Dedicated Networks of Workstations

NASA Technical Reports Server (NTRS)

Chanchio, Kasidit; Sun, Xian-He

1996-01-01

This paper presents the design and preliminary implementation of MpPVM, a software system that supports process migration for PVM application programs in a non-dedicated heterogeneous computing environment. New concepts of migration point as well as migration point analysis and necessary data analysis are introduced. In MpPVM, process migrations occur only at previously inserted migration points. Migration point analysis determines appropriate locations to insert migration points; whereas, necessary data analysis provides a minimum set of variables to be transferred at each migration pint. A new methodology to perform reliable point-to-point data communications in a migration environment is also discussed. Finally, a preliminary implementation of MpPVM and its experimental results are presented, showing the correctness and promising performance of our process migration mechanism in a scalable non-dedicated heterogeneous computing environment. While MpPVM is developed on top of PVM, the process migration methodology introduced in this study is general and can be applied to any distributed software environment.

Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline.

PubMed

Wang, Jie; Tsang, Ling Ming; Dong, Yun-Wei

2015-06-15

Substrate, ocean current and freshwater discharge are recognized as important factors that control the larval dispersal and recruitment of intertidal species. Life history traits of individual species will determine the differential responses to these physical factors, and hence resulting in contrasting phylogeography across the same biogeographic barrier. To determine how these factors affect genetic structure of rocky shore species along the China coast, a comparative phylogeographic study of four intertidal and subtidal species was conducted using mitochondrial and nuclear DNA by combining new sequences from Siphonaria japonica with previously published sequences from three species (Cellana toreuma, Sargassum horneri and Atrina pectinata). Analysis of molecular variance and pairwise ΦST revealed significant genetic differences between the Yellow Sea (YS) and the other two marginal seas (East China Sea, ECS and South China Sea, SCS) for rocky-shore species (S. japonica, C. toreuma, S. horneri), but not for muddy-shore species Atrina pectinata. Demographic history analysis proved that the population size of all these four species were persistent though the Last Glacial Maximum (LGM, ~20 ka BP). Migration analysis revealed that gene flow differentiated northward and southward migration for these four species. However, the inferred direction of gene flow using alternatively mitochondrial or nuclear markers was contradictory in S. japonica. It is concluded that there is a phylogeographical break at the Yangtze River estuary for the rocky shore species and the causation of the barrier is mainly due to the unsuitable substratum and freshwater discharge. All four intertidal and subtidal species appear to have persisted through the LGM in China, indicating the lower impact of LGM on intertidal and subtidal species than generally anticipated. The imbalanced gene flow between YS and ESCS groups for these four species could be explained by historical refugia. The discordance between mitochondrial and nuclear markers in the MIGRATE analysis of S. japonica prove the importance of employing multi-locus data in biogeographic study. Climate change, land reclamation and dam construction, which are changing substrate and hydrological conditions around Yangtze River estuary, will consequently affect the biogeographic pattern of intertidal species.

Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears

PubMed Central

Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

2013-01-01

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA. PMID:24236053

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development.

PubMed

Parker, Heidi G; Dreger, Dayna L; Rimbault, Maud; Davis, Brian W; Mullen, Alexandra B; Carpintero-Ramirez, Gretchen; Ostrander, Elaine A

2017-04-25

There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears.

PubMed

Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

2013-01-01

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

PubMed Central

Schiffels, Stephan; Haak, Wolfgang; Paajanen, Pirita; Llamas, Bastien; Popescu, Elizabeth; Loe, Louise; Clarke, Rachel; Lyons, Alice; Mortimer, Richard; Sayer, Duncan; Tyler-Smith, Chris; Cooper, Alan; Durbin, Richard

2016-01-01

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain. PMID:26783965

Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)

PubMed Central

Bedford, Trevor; Cobey, Sarah; Beerli, Peter; Pascual, Mercedes

2010-01-01

The global migration patterns of influenza viruses have profound implications for the evolutionary and epidemiological dynamics of the disease. We developed a novel approach to reconstruct the genetic history of human influenza A (H3N2) collected worldwide over 1998 to 2009 and used it to infer the global network of influenza transmission. Consistent with previous models, we find that China and Southeast Asia lie at the center of this global network. However, we also find that strains of influenza circulate outside of Asia for multiple seasons, persisting through dynamic migration between northern and southern regions. The USA acts as the primary hub of temperate transmission and, together with China and Southeast Asia, forms the trunk of influenza's evolutionary tree. These findings suggest that antiviral use outside of China and Southeast Asia may lead to the evolution of long-term local and potentially global antiviral resistance. Our results might also aid the design of surveillance efforts and of vaccines better tailored to different geographic regions. PMID:20523898

Does metabolic rate and evaporative water loss reflect differences in migratory strategy in sexually dimorphic hoverflies?

PubMed

Tomlinson, Sean; Menz, Myles H M

2015-12-01

A typical explanation for ecologically stable strategies that apply to only a proportion of a population, is bet hedging, where increased reproductive success offsets reduced reproductive rate. One such is partial migration, where only a proportion of a population moves seasonally to avoid inclement climatic conditions. Bet hedging may overlook unseen costs to maintain broad physiological resilience, implied by encountering a breadth of environmental conditions. We investigated the physiological correlates of partial migration by measuring standard metabolic rates, and rates of evaporative water loss, and then estimating upper and lower thermal tolerance in males and females of two hoverfly species, Episyrphus balteatus and Eristalis tenax. In central Europe, females of these species may either migrate or overwinter, whereas males may migrate south to the Mediterranean, but have not been found overwintering. Both species were sexually dimorphic; female Ep. balteatus were lighter than males, but female Er. tenax were heavier than males. While allometrically- corrected metabolic rate in both species increased with temperature, the most parsimonious models included no sex-specific differences in metabolic rate for either species. Evaporative water loss of both species also increased with temperature, but was higher for females of both species than males. Assuming that resting metabolism is congruent with the activity requirements of migration, highly consistent thermal tolerance and metabolic rate suggests that any given fly could migrate, although water loss patterns suggest that females may be less well-adapted to Mediterranean climates. We infer that partial migration probably results from the imperatives of their reproductive strategies. Copyright © 2015 Elsevier Inc. All rights reserved.

The late Pleistocene colonization of South America: an interdisciplinary perspective.

PubMed

Rothhammer, Francisco; Dillehay, Tom D

2009-09-01

In this article, we briefly review scenarios for the first peopling of the New World, including the Clovis First/Single Origin, Tripartite, and Dual Migration models. We then discuss bioanthropological, molecular genetic, archaeological and biogeographic evidence for the peopling of the continent. To conclude, we draw on different lines of evidence to make inferences concerning the timing, direction, and type of early human dispersion in South America.

Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America

Treesearch

Ping Lang; Fenny Dane; Thomas L. Kubisiak; Hongwen Huang

2007-01-01

The genus Castanea (Fagaceae) is widely distributed in the deciduous forests of the Northern Hemisphere. The striking similarity between the Xoras of eastern Asia and those of eastern North America and the divergence in chestnut blight resistance among species has been of interest to botanists for a century. To infer the biogeographical history of...

A low mass for Mars from Jupiter's early gas-driven migration.

PubMed

Walsh, Kevin J; Morbidelli, Alessandro; Raymond, Sean N; O'Brien, David P; Mandell, Avi M

2011-06-05

Jupiter and Saturn formed in a few million years (ref. 1) from a gas-dominated protoplanetary disk, and were susceptible to gas-driven migration of their orbits on timescales of only ∼100,000 years (ref. 2). Hydrodynamic simulations show that these giant planets can undergo a two-stage, inward-then-outward, migration. The terrestrial planets finished accreting much later, and their characteristics, including Mars' small mass, are best reproduced by starting from a planetesimal disk with an outer edge at about one astronomical unit from the Sun (1 au is the Earth-Sun distance). Here we report simulations of the early Solar System that show how the inward migration of Jupiter to 1.5 au, and its subsequent outward migration, lead to a planetesimal disk truncated at 1 au; the terrestrial planets then form from this disk over the next 30-50 million years, with an Earth/Mars mass ratio consistent with observations. Scattering by Jupiter initially empties but then repopulates the asteroid belt, with inner-belt bodies originating between 1 and 3 au and outer-belt bodies originating between and beyond the giant planets. This explains the significant compositional differences across the asteroid belt. The key aspect missing from previous models of terrestrial planet formation is the substantial radial migration of the giant planets, which suggests that their behaviour is more similar to that inferred for extrasolar planets than previously thought. ©2011 Macmillan Publishers Limited. All rights reserved

Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

USGS Publications Warehouse

Gottscho, Andrew D.; Wood, Dustin A.; Vandergast, Amy; Lemos Espinal, Julio A.; Gatesy, John; Reeder, Tod

2017-01-01

Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of theUma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.

Present-day African analogue of a pre-European Amazonian floodplain fishery shows convergence in cultural niche construction

PubMed Central

McKey, Doyle B.; Durécu, Mélisse; Pouilly, Marc; Béarez, Philippe; Ovando, Alex; Kalebe, Mashuta; Huchzermeyer, Carl F.

2016-01-01

Erickson [Erickson CL (2000) Nature 408 (6809):190–193] interpreted features in seasonal floodplains in Bolivia’s Beni savannas as vestiges of pre-European earthen fish weirs, postulating that they supported a productive, sustainable fishery that warranted cooperation in the construction and maintenance of perennial structures. His inferences were bold, because no close ethnographic analogues were known. A similar present-day Zambian fishery, documented here, appears strikingly convergent. The Zambian fishery supports Erickson’s key inferences about the pre-European fishery: It allows sustained high harvest levels; weir construction and operation require cooperation; and weirs are inherited across generations. However, our comparison suggests that the pre-European system may not have entailed intensive management, as Erickson postulated. The Zambian fishery’s sustainability is based on exploiting an assemblage dominated by species with life histories combining high fecundity, multiple reproductive cycles, and seasonal use of floodplains. As water rises, adults migrate from permanent watercourses into floodplains, through gaps in weirs, to feed and spawn. Juveniles grow and then migrate back to dry-season refuges as water falls. At that moment fishermen set traps in the gaps, harvesting large numbers of fish, mostly juveniles. In nature, most juveniles die during the first dry season, so that their harvest just before migration has limited impact on future populations, facilitating sustainability and the adoption of a fishery based on inherited perennial structures. South American floodplain fishes with similar life histories were the likely targets of the pre-European fishery. Convergence in floodplain fish strategies in these two regions in turn drove convergence in cultural niche construction. PMID:27980030

Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia

PubMed Central

Zhao, Yong-Xin; Yang, Ji; Lv, Feng-Hua; Hu, Xiao-Ju; Xie, Xing-Long; Zhang, Min; Li, Wen-Rong; Liu, Ming-Jun; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Ren, Yan-Ling; Wang, Feng; Hehua, EEr; Kantanen, Juha; Arjen Lenstra, Johannes; Han, Jian-Lin; Li, Meng-Hua

2017-01-01

Abstract China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China. PMID:28645168

Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia.

PubMed

Zhao, Yong-Xin; Yang, Ji; Lv, Feng-Hua; Hu, Xiao-Ju; Xie, Xing-Long; Zhang, Min; Li, Wen-Rong; Liu, Ming-Jun; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Ren, Yan-Ling; Wang, Feng; Hehua, EEr; Kantanen, Juha; Arjen Lenstra, Johannes; Han, Jian-Lin; Li, Meng-Hua

2017-09-01

China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Global population structure of the tope (Galeorhinus galeus) inferred by mitochondrial control region sequence data.

PubMed

Chabot, C L; Allen, L G

2009-02-01

In order to properly manage and conserve exploited shark species, detailed analyses of their population structure is needed. Global populations of Galeorhinus galeus are in decline due to the exploitation of the fishery over the past 80 years. Currently, the genetic structure of eastern Pacific populations of G. galeus is not known and recent observations in the northeastern Pacific suggest an increase in numbers. To evaluate gene flow among populations of G. galeus, 116 samples were collected and analysed from six geographically dispersed locations: Australia, North America, South Africa, South America (Argentina and Peru), and the UK. Analysis of 968 to 1006 bp of the 1068-bp mitochondrial control region revealed 38 unique haplotypes that were largely restricted to their collecting locality. Significant genetic structure was detected among populations (Phi(ST) = 0.84; P < 0.000001) and migration estimates were low (Nm = 0.05-0.97). Due to an apparent lack of migration, populations of G. galeus appear to be isolated from each other with little to no gene flow occurring among them. As a consequence of this isolation, increasing numbers of G. galeus in the northeastern Pacific can be best explained by local recruitment and not by input from geographically distant populations.

[Systematics and genegeography of Juniperus communis inferred from isoenzyme data].

PubMed

Khantemirova, E V; Berkutenko, A N; Semerikov, V L

2012-09-01

Using isoenzyme analysis, 35 populations of Juniperus communis L. from various parts of the Russian species range and by one population from Sweden and Alaska were studied. The total sample size was 1200 plants. As a result, the existence ofJ. communis var. oblonga in North Caucasus and J. communis var. depressa in North America was confirmed, but genetic differences between J. communis var. communis and J. communis var. saxatilis were not detected in the main part of the Russian species range (European part of Russia, Ural, Siberia). These populations proved to be genetically uniform with the same predominant allelic frequencies, which may evidence recent settling of this species from one of Central or East European refugium. J. communis var. saxatilis from northeastern Russia inhabiting the region behind Verkhoyansk mountain and Russian Far East showed considerable differentiation in frequencies of alleles at three loci and geographical subdivision. These populations also exhibit high intrapopulation variation. This can be connected with the refugium in this territory. The origin of this group is probably connected with migrations from Central Asia (Tibet) in the direction to northeastern Russia along mountains connecting Central and North Asia. It is also assumed that migrations of this species previously proceeded across the Beringian land bridge.

Lateral extrusion of Tunisia : Contribution of Jeffara Fault (southern branch) and Petroleum Implications

NASA Astrophysics Data System (ADS)

Ghedhoui, R.; Deffontaines, B.; Rabia, M. C.

2012-04-01

Contrasting to the northward African plate motion toward Eurasia and due to its geographic position in the North African margin, since early cretaceous, Tunisia seems to be submitted to an eastward migration. The aim of this work is to study the southern branch of this inferred tectonic splay that may guide the Tunisian extrusion characterised to the east by the Mediterranean sea as a free eastern boundary. The Jeffara Fault zone (southern Tunisia), represent a case example of such deformation faced by Tunisia. Helped by the results of previous researchers (Bouaziz, 1995 ; Rabiaa, 1998 ; Touati et Rodgers, 1998 ; Sokoutis D. et al., 2000 ; Bouaziz et al., 2002 ; Jallouli et al., 2005 ; Deffontaines et al., 2008…), and new evidences developed in this study, we propose a geodynamic Tunisian east extrusion model, due to such the northern African plate migration to the Eurasian one. In this subject, structural geomorphology is undertaken herein based on both geomorphometric drainage network analysis (Deffontaines et al., 1990), the Digital Terrain Model photo-interpretation (SRTM) combined with photo-interpretation of detailed optical images (Landsat ETM+), and confirmed by field work and numerous seismic profiles at depth. All these informations were then integrated within a GIS (Geodatabase) (Deffontaines 1990 ; Deffontaines et al. 1994 ; Deffontaines, 2000 ; Slama, 2008 ; Deffontaines, 2008) and are coherent with the eastern extrusion of the Sahel block. We infer that the NW-SE Gafsa-Tozeur, which continue to the Jeffara major fault zone acting as a transtensive right lateral motion since early cretaceous is the southern branch of the Sahel block extrusion. Our structural analyses prove the presence of NW-SE right lateral en-echelon tension gashes, NW-SE aligned salt diapirs, numerous folds offsets, en-echelon folds, and so on that parallel this major NW-SE transtensive extrusion fault zone.These evidences confirm the fact that the NW-SE Jeffara faults correspond to the tectonic accident, located in the south of the Tunisian extrusion, in favour of the eastern migration of the Sahel block toward the free Mediterranean sea boundary. Therefore this geodynamic movement explains the presence, in offshore area, of small elongated NW-SE, N-S &NE-SW petroleum transtensive basins and grabens. To conclude, at the regional scale, the structural geomorphologic approach combined with both field work and reflexion seismic profile analyses appear to be an excellent tool to prove & confirm the east Sahel block extrusion of the central Tunisian part caused by the northward migration of African plate. _______________________________________ Keywords : Geodynamics, Neotectonics, right lateral transtensive fault, Extrusion, Petroleum exploration, Geomorphometry, Digital Elevation Model, Geographic Information System (GIS), Geodatabase, Jeffara, South Tunisia.

Gas Migration Processes through the Gas Hydrate Stability Zone at Four-Way Closure Ridge Offshore SW Taiwan

NASA Astrophysics Data System (ADS)

Kunath, P.; Chi, W. C.; Berndt, C.; Liu, C. S.

2016-12-01

We have used 3D P-Cable seismic data from Four-Way-Closure Ridge, a NW-SE trending anticlinal ridge within the lower slope domain of accretionary wedge, to investigate the geological constraints influencing the fluid migration pattern in the shallow marine sediments. In the seismic data, fluid migration feature manifests itself as high reflection layers of dipping strata, which originate underneath a bottom simulating reflector (BSR) and extend towards the seafloor. Shoaling of the BSR near fluid migration pathways indicates a focused fluid flux, perturbing the temperature field. Furthermore, seafloor video footage confirmed the presence of recent methane seepage above seismically imaged fluid migration pathways. We plan to test two hypotheses for the occurrence of these fluid migration pathways: 1) the extensional regime under the anticlinal ridge crest caused the initiation of localized fault zones, acting as fluid conduits in the gas hydrate stability zone (GHSZ). 2) sediment deformation induced by focused fluid flow and massive growth and dissolution of gas hydrate, similar to processes controlling the evolution of pockmarks on the Nigerian continental margin. We suggest that these processes may be responsible for the formation of a massive hydrate core in the crest of the anticline, as inferred from other geophysical datasets. Triggering process for fluid migration cannot be clearly defined. However, the existence of blind thrust faults may help to advect deep-seated fluids. This may be augmented by biogenic production of shallow gas underneath the ridge, where the excess of gas enables the coexistence of gas, water, and gas hydrate within the GHSZ. Fluid migration structures may exists because of the buoyancy of gas-bearing fluids. This study shows a potential model on how gas-bearing fluids migrate upward towards structural highs, which might occur in other anticlinal structures around the world. Keywords: P-Cable, gas-hydrate, fluid flow, fault-related fold, methane seepage

Contradictory genetic make-up of Dutch harbour porpoises: Response to van der Plas-Duivesteijn et al.

NASA Astrophysics Data System (ADS)

Kopps, Anna M.; Palsbøll, Per J.

2016-02-01

The assessment of the status of endangered species or populations typically draw generously on the plethora of population genetic software available to detect population genetic structuring. However, despite the many available analytical approaches, population genetic inference methods [of neutral genetic variation] essentially capture three basic processes; migration, random genetic drift and mutation. Consequently, different analytical approaches essentially capture the same basic process, and should yield consistent results.

Formation and migration of Natural Gases: gas composition and isotopes as monitors between source, reservoir and seep

NASA Astrophysics Data System (ADS)

Schoell, M.; Etiope, G.

2015-12-01

Natural gases form in tight source rocks at temperatures between 120ºC up to 200ºC over a time of 40 to 50my depending on the heating rate of the gas kitchen. Inferring from pyrolysis experiments, gases after primary migration, a pressure driven process, are rich in C2+ hydrocarbons (C2 to C5). This is consistent with gas compositions of oil-associated gases such as in the Bakken Shale which occur in immediate vicinity of the source with little migration distances. However, migration of gases along porous rocks over long distances (up to 200km in the case of the Troll field offshore Norway) changes the gas composition drastically as C2+ hydrocarbons tend to be retained/sequestered during migration of gas as case histories from Virginia and the North Sea will demonstrate. Similar "molecular fractionation" is observed between reservoirs and surface seeps. In contrast to gas composition, stable isotopes in gases are, in general, not affected by the migration process suggesting that gas migration is a steady state process. Changes in isotopic composition, from source to reservoir to surface seeps, is often the result of mixing of gases of different origins. Examples from various gas provinces will support this notion. Natural gas basins provide little opportunity of tracking and identifying gas phase separation. Future research on experimental phase separation and monitoring of gas composition and gas ratio changes e.g. various C2+ compound ratios over C1 or isomer ratios such as iso/n ratios in butane and pentane may be an avenue to develop tracers for phase separation that could possibly be applied to natural systems of retrograde natural condensate fields.

Migration: a concept analysis from a nursing perspective.

PubMed

Freeman, Michelle; Baumann, Andrea; Blythe, Jennifer; Fisher, Anita; Akhtar-Danesh, Noori

2012-05-01

  This article is a report of a concept analysis of nurse migration.   International migration is increasing and nurse migrants are active participants in this movement. Migration is a complex term and can be examined from a range of perspectives. Analysis of nurse migration is needed to guide policy, practice and research.   A literature search was undertaken using electronic literature indexes, specific journals and websites, internet search engines and hand searches. No timeframe was placed on the search. Most literature found was published between 2001 and 2009. A sample of 80 documents met the inclusion criteria.   Walker and Avant's approach guided the analysis.   Nurse migration can be defined by five attributes: the motivation and decisions of individuals; external barriers and facilitators; freedom of choice to migrate; freedom to migrate as a human right, and dynamic movement. Antecedents of migration include the political, social, economic, legal, historical and educational forces that comprise the push and pull framework. The consequences of migration are positive or negative depending on the viewpoint and its affect on the individual and other stakeholders such as the source country, destination country, healthcare systems and the nursing profession.   This concept analysis clarified the complexities surrounding nurse migration. A nursing-specific middle-range theory was proposed to guide the understanding and study of nurse migration. © 2011 Blackwell Publishing Ltd.

Climate Change: Modeling the Human Response

NASA Astrophysics Data System (ADS)

Oppenheimer, M.; Hsiang, S. M.; Kopp, R. E.

2012-12-01

Integrated assessment models have historically relied on forward modeling including, where possible, process-based representations to project climate change impacts. Some recent impact studies incorporate the effects of human responses to initial physical impacts, such as adaptation in agricultural systems, migration in response to drought, and climate-related changes in worker productivity. Sometimes the human response ameliorates the initial physical impacts, sometimes it aggravates it, and sometimes it displaces it onto others. In these arenas, understanding of underlying socioeconomic mechanisms is extremely limited. Consequently, for some sectors where sufficient data has accumulated, empirically based statistical models of human responses to past climate variability and change have been used to infer response sensitivities which may apply under certain conditions to future impacts, allowing a broad extension of integrated assessment into the realm of human adaptation. We discuss the insights gained from and limitations of such modeling for benefit-cost analysis of climate change.

Bayesian inferences suggest that Amazon Yunga Natives diverged from Andeans less than 5000 ybp: implications for South American prehistory.

PubMed

Scliar, Marilia O; Gouveia, Mateus H; Benazzo, Andrea; Ghirotto, Silvia; Fagundes, Nelson J R; Leal, Thiago P; Magalhães, Wagner C S; Pereira, Latife; Rodrigues, Maira R; Soares-Souza, Giordano B; Cabrera, Lilia; Berg, Douglas E; Gilman, Robert H; Bertorelle, Giorgio; Tarazona-Santos, Eduardo

2014-09-30

Archaeology reports millenary cultural contacts between Peruvian Coast-Andes and the Amazon Yunga, a rainforest transitional region between Andes and Lower Amazonia. To clarify the relationships between cultural and biological evolution of these populations, in particular between Amazon Yungas and Andeans, we used DNA-sequence data, a model-based Bayesian approach and several statistical validations to infer a set of demographic parameters. We found that the genetic diversity of the Shimaa (an Amazon Yunga population) is a subset of that of Quechuas from Central-Andes. Using the Isolation-with-Migration population genetics model, we inferred that the Shimaa ancestors were a small subgroup that split less than 5300 years ago (after the development of complex societies) from an ancestral Andean population. After the split, the most plausible scenario compatible with our results is that the ancestors of Shimaas moved toward the Peruvian Amazon Yunga and incorporated the culture and language of some of their neighbors, but not a substantial amount of their genes. We validated our results using Approximate Bayesian Computations, posterior predictive tests and the analysis of pseudo-observed datasets. We presented a case study in which model-based Bayesian approaches, combined with necessary statistical validations, shed light into the prehistoric demographic relationship between Andeans and a population from the Amazon Yunga. Our results offer a testable model for the peopling of this large transitional environmental region between the Andes and the Lower Amazonia. However, studies on larger samples and involving more populations of these regions are necessary to confirm if the predominant Andean biological origin of the Shimaas is the rule, and not the exception.

Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan

PubMed Central

Chiu, Chi-Te; Huang, Chao-Li; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh

2016-01-01

Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration. PMID:27561108

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

VIIRS captures phytoplankton vertical migration in the NE Gulf of Mexico.

PubMed

Qi, Lin; Hu, Chuanmin; Barnes, Brian B; Lee, Zhongping

2017-06-01

In summer 2014, a toxic Karenia brevis bloom (red tide) occurred in the NE Gulf of Mexico, during which vertical migration of K. brevis has been observed from glider measurements. The current study shows that satellite observations from the Visible Infrared Imaging Radiometer Suite (VIIRS) can capture changes in surface reflectance and chlorophyll concentration occurring within 2h, which may be attributed this K. brevis vertical migration. The argument is supported by earlier glider measurements in the same bloom, by the dramatic changes in the VIIRS-derived surface chlorophyll, and by the consistency between the short-term reflectance changes and those reported earlier from field-measured K. brevis vertical migration. Estimates using the quasi-analytical algorithm also indicate significant increases in both total absorption coefficient and backscattering coefficient in two hours. The two observations in a day from a single polar-orbiting satellite sensor are thus shown to be able to infer phytoplankton vertical movement within a short timeframe, a phenomenon difficult to capture with other sensors as each sensor can provide at most one observation per day, and cross-sensor inconsistency may make interpretation of merged-sensor data difficult. These findings strongly support geostationary satellite missions to study short-term bloom dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan.

PubMed

Huang, Chi-Chun; Hsu, Tsai-Wen; Wang, Hao-Ven; Liu, Zin-Huang; Chen, Yi-Yen; Chiu, Chi-Te; Huang, Chao-Li; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh

2016-01-01

Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences.

PubMed

Hou, Yan; Lou, Anru

2014-01-01

The phylogeographical patterns of Rhodiola dumulosa, an alpine plant species restrictedly growing in the crevices of rock piles, were investigated based on 4 fragments of the chloroplast genome. To cover the full distribution of R. dumulosa in China, 19 populations from 3 major disjunct distribution areas (northern, central, and northwestern China) were sampled. A total of 5881bp (after alignment) of chloroplast DNA (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set yielded 36 haplotypes. The total genetic diversity of R. dumulosa was remarkably high (H(T) = 0.981). The interpopulation genetic differentiation was significantly large (F(ST) = 0.8537, P < 0.001), possibly due to the long-term isolation of the natural populations. N(ST) was significantly larger than G(ST) (P < 0.001), indicating the presence of phylogeographical structure among the R. dumulosa populations. We propose 2 migration steps to explain the current distribution of R. dumulosa in China. First, this species migrated from refugia in the Qinghai-Tibetan Plateau to northern areas via the intervening highlands when temperatures increased; second, the highland populations migrated toward the mountaintops when temperatures increased further because R. dumulosa is adapted to cold environments. During the second migration step, the common ancestral haplotypes may have been gradually lost.

Water recharge and solute transport through the vadose zone of fractured chalk under desert conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nativ, R.; Dahan, O.; Adar, E.

In the present study the inferred mechanism of groundwater recharge and contamination was studied using tracer concentrations in the fractured vadose zone of the Avdat chalk. The results of this study are important for an evaluation of groundwater contamination from existing and planned facilities in the northern Negev desert in Israel. This study focused on the vicinity of the Ramat Hovav industrial chemical complex in the northern Negev, which also includes the national site for hazardous waste. Water recharge and solute migration rates were examined in five core holes and one borehole which penetrate the entire vadose zone and enabledmore » the collection of rock samples for chemical and isotopic analyses, and an observation of fracture distribution with depth. Tritium profiles were used to estimate water percolation rates through the vadose zone, chloride profiles were used to assess the migration rate of nonreactive solutes, and bromide profiles were also used to evaluate the migration rate of nonreactive contaminants. Deuterium and oxygen 18 profiles were used to assess the evaporation of the infiltrating water at and near land surface.« less

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

PubMed Central

Hettling, Hannes; Condamine, Fabien L.; Vos, Karin; Nilsson, R. Henrik; Sanderson, Michael J.; Sauquet, Hervé; Scharn, Ruud; Silvestro, Daniele; Töpel, Mats; Bacon, Christine D.; Oxelman, Bengt; Vos, Rutger A.

2017-01-01

Abstract Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable. PMID:27616324

Long-term PAH monitoring results from the Anacostia River active capping demonstration using polydimethylsiloxane (PDMS) fibers.

PubMed

Lampert, David J; Lu, Xiaoxia; Reible, Danny D

2013-03-01

In this paper, the long-term monitoring results for hydrophobic organic compounds, specifically polycyclic aromatic hydrocarbons (PAHs), from a field demonstration of capping contaminated sediments at the Anacostia River in Washington DC are presented and analyzed. In situ pore water concentrations in field-contaminated sediments in the demonstration caps were quantified using a polydimethylsiloxane (PDMS)-based passive sampling device. High resolution vertical pore water concentration profiles were measured using the device and were used to infer fate and transport of polycyclic aromatics hydrocarbons (PAHs) at the site. The derived pore water concentrations were compared with observed bioaccumulation and solid-phase concentration profiles to infer contaminant migration rates and mechanisms. Observed pore water concentrations were found to be a better predictor of bioaccumulation than solid-phase concentrations. Solid-phase concentrations were low in cores which implied containment of contamination; however pore water profiles showed that contaminant migration had occurred in the first few years after cap placement. The discrepancy is the result of the low sorption capacity of the sand. Because of surface re-contamination, low sorption capacity in the demonstration caps and strong tidal pumping effects, steady state contaminant profiles were reached in the caps several years after placement. Despite re-contamination at the surface, steady state concentrations in the capped areas showed decreased contamination levels relative to the control area.

Shaler: in situ analysis of a fluvial sedimentary deposit on Mars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edgar, Lauren A.; Gupta, Sanjeev; Rubin, David M.

This article characterizes the detailed sedimentology of a fluvial sandbody on Mars for the first time and interprets its depositional processes and palaeoenvironmental setting. Despite numerous orbital observations of fluvial landforms on the surface of Mars, ground-based characterization of the sedimentology of such fluvial deposits has not previously been possible. Results from the NASA Mars Science Laboratory Curiosity rover provide an opportunity to reconstruct at fine scale the sedimentary architecture and palaeomorphology of a fluvial environment on Mars. This work describes the grain size, texture and sedimentary facies of the Shaler outcrop, reconstructs the bedding architecture, and analyses cross-stratification tomore » determine palaeocurrents. On the basis of bedset geometry and inclination, grain-size distribution and bedform migration direction, this study concludes that the Shaler outcrop probably records the accretion of a fluvial barform. The majority of the outcrop consists of large-scale trough cross-bedding of coarse sand and granules. Palaeocurrent analyses and bedform reconstruction indicate that the beds were deposited by bedforms that migrated towards the north-east, across the surface of a bar that migrated south-east. Stacked cosets of dune cross-bedding suggest aggradation of multiple bedforms, which provides evidence for short periods of sustained flow during Shaler deposition. However, local evidence for aeolian reworking and the presence of potential desiccation cracks within the outcrop suggest that fluvial deposition may have been intermittent. The uppermost strata at Shaler are distinct in terms of texture and chemistry and are inferred to record deposition from a different sediment dispersal system with a contrasting provenance. The outcrop as a whole is a testament to the availability of liquid water on the surface of Mars in its early history.« less

Shaler: in situ analysis of a fluvial sedimentary deposit on Mars

USGS Publications Warehouse

Edgar, Lauren; Gupta, Sanjeev; Rubin, David M.; Lewis, Kevin W.; Kocurek, Gary A.; Anderson, Ryan; Bell, James F.; Dromart, Gilles; Edgett, Kenneth S.; Grotzinger, John P.; Hardgrove, Craig; Kah, Linda C.; LeVeille, Richard A.; Malin, Michael C.; Mangold, Nicholas; Milliken, Ralph E.; Minitti, Michelle; Palucis, Marisa C.; Rice, Melissa; Rowland, Scott K.; Schieber, Juergen; Stack, Kathryn M.; Sumner, Dawn Y.; Wiens, Roger C.; Williams, Rebecca M.E.; Williams, Amy J.

2018-01-01

This paper characterizes the detailed sedimentology of a fluvial sandbody on Mars for the first time, and interprets its depositional processes and palaeoenvironmental setting. Despite numerous orbital observations of fluvial landforms on the surface of Mars, ground-based characterization of the sedimentology of such fluvial deposits has not previously been possible. Results from the NASA Mars Science Laboratory Curiosity rover provide an opportunity to reconstruct at fine scale the sedimentary architecture and palaeomorphology of a fluvial environment on Mars. This work describes the grain size, texture, and sedimentary facies of the Shaler outcrop, reconstructs the bedding architecture, and analyses cross-stratification to determine palaeocurrents. On the basis of bedset geometry and inclination, grain-size distribution, and bedform migration direction, this study concludes that the Shaler outcrop likely records the accretion of a fluvial barform. The majority of the outcrop consists of large-scale trough cross-bedding of coarse sand and granules. Palaeocurrent analyses and bedform reconstruction indicate that the beds were deposited by bedforms that migrated towards the northeast, across the surface of a bar that migrated southeast. Stacked cosets of dune cross-bedding suggest aggradation of multiple bedforms, which provides evidence for short periods of sustained flow during Shaler deposition. However, local evidence for aeolian reworking and the presence of potential desiccation cracks within the outcrop suggests that fluvial deposition may have been intermittent. The uppermost strata at Shaler are distinct in terms of texture and chemistry, and are inferred to record deposition from a different sediment dispersal system with a contrasting provenance. The outcrop as a whole is a testament to the availability of liquid water on the surface of Mars in its early history.

Shaler: in situ analysis of a fluvial sedimentary deposit on Mars

DOE PAGES

Edgar, Lauren A.; Gupta, Sanjeev; Rubin, David M.; ...

2017-03-09

This article characterizes the detailed sedimentology of a fluvial sandbody on Mars for the first time and interprets its depositional processes and palaeoenvironmental setting. Despite numerous orbital observations of fluvial landforms on the surface of Mars, ground-based characterization of the sedimentology of such fluvial deposits has not previously been possible. Results from the NASA Mars Science Laboratory Curiosity rover provide an opportunity to reconstruct at fine scale the sedimentary architecture and palaeomorphology of a fluvial environment on Mars. This work describes the grain size, texture and sedimentary facies of the Shaler outcrop, reconstructs the bedding architecture, and analyses cross-stratification tomore » determine palaeocurrents. On the basis of bedset geometry and inclination, grain-size distribution and bedform migration direction, this study concludes that the Shaler outcrop probably records the accretion of a fluvial barform. The majority of the outcrop consists of large-scale trough cross-bedding of coarse sand and granules. Palaeocurrent analyses and bedform reconstruction indicate that the beds were deposited by bedforms that migrated towards the north-east, across the surface of a bar that migrated south-east. Stacked cosets of dune cross-bedding suggest aggradation of multiple bedforms, which provides evidence for short periods of sustained flow during Shaler deposition. However, local evidence for aeolian reworking and the presence of potential desiccation cracks within the outcrop suggest that fluvial deposition may have been intermittent. The uppermost strata at Shaler are distinct in terms of texture and chemistry and are inferred to record deposition from a different sediment dispersal system with a contrasting provenance. The outcrop as a whole is a testament to the availability of liquid water on the surface of Mars in its early history.« less

Historical habitat barriers prevent ring-like genetic continuity throughout the distribution of threatened Alameda Striped Racers (Coluber lateralis euryxanthus)

USGS Publications Warehouse

Richmond, Jonathan Q.; Wood, Dustin A.; Swaim, Karen; Fisher, Robert N.; Vandergast, Amy

2016-01-01

We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We used cluster assignments to characterize population genetic structuring with respect to land management units and approximate Bayesian analysis to rank the ability of five alternative evolutionary hypotheses to explain the inferred structure. Then, we estimated rates of contemporary and historical migration among the major clusters and measured the fit of different historical migration models to better understand the formation of the current population structure. Our results reveal a ring-like pattern of historical connectivity around the Tri-Valley area of the East Bay (i.e., San Ramon, Amador, and Livermore valleys), with clusters largely corresponding to different management units. We found no evidence of continuous gene flow throughout the ring, however, and that the main gap in continuity is centered across the Livermore Valley. Historical migration models support higher rates of gene flow away from the terminal ends of the ring on the north and south sides of the Valley, compared with rates into those areas from western sites that border the interior San Francisco Bay. We attribute the break in ring-like connectivity to the presence of unsuitable habitat within the Livermore Valley that has been reinforced by 20th century urbanization, and the asymmetry in gene flow rates to spatial constraints on movement and east–west environmental gradients influenced by the proximity of the San Francisco Bay.

Super-Earths as Failed Cores in Orbital Migration Traps

NASA Astrophysics Data System (ADS)

Hasegawa, Yasuhiro

2016-11-01

I explore whether close-in super-Earths were formed as rocky bodies that failed to grow fast enough to become the cores of gas giants before the natal protostellar disk dispersed. I model the failed cores’ inward orbital migration in the low-mass or type I regime to stopping points at distances where the tidal interaction with the protostellar disk applies zero net torque. The three kinds of migration traps considered are those due to the dead zone's outer edge, the ice line, and the transition from accretion to starlight as the disk's main heat source. As the disk disperses, the traps move toward final positions near or just outside 1 au. Planets at this location exceeding about 3 M ⊕ open a gap, decouple from their host traps, and migrate inward in the high-mass or type II regime to reach the vicinity of the star. I synthesize the population of planets that formed in this scenario, finding that a fraction of the observed super-Earths could have been failed cores. Most super-Earths that formed this way have more than 4 M ⊕, so their orbits when the disks dispersed were governed by type II migration. These planets have solid cores surrounded by gaseous envelopes. Their subsequent photoevaporative mass loss is most effective for masses originally below about 6 M ⊕. The failed core scenario suggests a division of the observed super-Earth mass-radius diagram into five zones according to the inferred formation history.

Evaluating predictors of local dabbling duck abundance during migration: Managing the spectrum of conditions faced by migrants

USGS Publications Warehouse

Aagaard, Kevin; Crimmins, Shawn M.; Thogmartin, Wayne E.; Tavernia, Brian G.; Lyons, James E.

2015-01-01

The development of robust modelling techniques to derive inferences from large-scale migratory bird monitoring data at appropriate scales has direct relevance to their management. The Integrated Waterbird Management and Monitoring programme (IWMM) represents one of the few attempts to monitor migrating waterbirds across entire flyways using targeted local surveys. This dataset included 13,208,785 waterfowl (eight Anas species) counted during 28,000 surveys at nearly 1,000 locations across the eastern United States between autumn 2010 and spring 2013 and was used to evaluate potential predictors of waterfowl abundance at the wetland scale. Mixed-effects, log-linear models of local abundance were built for the Atlantic and Mississippi flyways during spring and autumn migration to identify factors relating to habitat structure, forage availability, and migration timing that influence target dabbling duck species abundance. Results indicated that migrating dabbling ducks responded differently to environmental factors. While the factors identified demonstrated a high degree of importance, they were inconsistent across species, flyways and seasons. Furthermore, the direction and magnitude of the importance of each covariate group considered here varied across species. Given our results, actionable policy recommendations are likely to be most effective if they consider species-level variation within targeted taxonomic units and across management areas. The methods implemented here can easily be applied to other contexts, and serve as a novel investigation into local-level population patterns using data from broad-scale monitoring programmes.

Migration of the Pee Dee River system inferred from ancestral paleochannels underlying the South Carolina Grand Strand and Long Bay inner shelf

USGS Publications Warehouse

Baldwin, W.E.; Morton, R.A.; Putney, T.R.; Katuna, M.P.; Harris, M.S.; Gayes, P.T.; Driscoll, N.W.; Denny, J.F.; Schwab, W.C.

2006-01-01

Several generations of the ancestral Pee Dee River system have been mapped beneath the South Carolina Grand Strand coastline and adjacent Long Bay inner shelf. Deep boreholes onshore and high-resolution seismic-reflection data offshore allow for reconstruction of these paleochannels, which formed during glacial lowstands, when the Pee Dee River system incised subaerially exposed coastal-plain and continental-shelf strata. Paleochannel groups, representing different generations of the system, decrease in age to the southwest, where the modern Pee Dee River merges with several coastal-plain tributaries at Winyah Bay, the southern terminus of Long Bay. Positions of the successive generational groups record a regional, southwestward migration of the river system that may have initiated during the late Pliocene. The migration was primarily driven by barrier-island deposition, resulting from the interaction of fluvial and shoreline processes during eustatic highstands. Structurally driven, subsurface paleotopography associated with the Mid-Carolina Platform High has also indirectly assisted in forcing this migration. These results provide a better understanding of the evolution of the region and help explain the lack of mobile sediment on the Long Bay inner shelf. Migration of the river system caused a profound change in sediment supply during the late Pleistocene. The abundant fluvial source that once fed sand-rich barrier islands was cut off and replaced with a limited source, supplied by erosion and reworking of former coastal deposits exposed at the shore and on the inner shelf.

Environmental correlates of upstream migration of yellow-phase American eels in the Potomac River drainage

USGS Publications Warehouse

Welsh, Stuart A.; Heather L. Liller,

2013-01-01

Assessing the relationships between upstream migration and environmental variables is important to understanding the ecology of yellow-phase American Eels Anguilla rostrata. During an American Eel migration study within the lower Shenandoah River (Potomac River drainage), we counted and measured American Eels at the Millville Dam eel ladder for three periods: 14 May–23 July 2004, 7–30 September 2004, and 1 June–31 July 2005. Using generalized estimating equations, we modeled each time series of daily American Eel counts by fitting time-varying environmental covariates of lunar illumination (LI), river discharge (RD), and water temperature (WT), including 1-d and 2-d lags of each covariate. Information-theoretic approaches were used for model selection and inference. A total of 4,847 American Eels (19–74 cm total length) used the ladder during the three periods, including 2,622 individuals during a 2-d span following a hurricane-induced peak in river discharge. Additive-effects models of RD + WT, a 2-d lag of LI + RD, and LI + RD were supported for the three periods, respectively. Parameter estimates were positive for river discharge for each time period, negative for lunar illumination for two periods and positive for water temperature during one period. Additive-effects models supported synergistic influences of environmental variables on the upstream migration of yellow-phase American Eels, although river discharge was consistently supported as an influential correlate of upstream migration.

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA.

PubMed

DeChaine, Eric G; Martini, Andrew P

2004-01-01

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.

Persistence of the single lineage of transmissible 'social cancer' in an asexual ant.

PubMed

Dobata, S; Sasaki, T; Mori, H; Hasegawa, E; Shimada, M; Tsuji, K

2011-02-01

How cooperation can arise and persist, given the threat of cheating phenotypes, is a central problem in evolutionary biology, but the actual significance of cheating in natural populations is still poorly understood. Theories of social evolution predict that cheater lineages are evolutionarily short-lived. However, an exception comes from obligate socially parasitic species, some of which thought to have arisen as cheaters within cooperator colonies and then diverged through sympatric speciation. This process requires the cheater lineage to persist by avoiding rapid extinction that would result from the fact that the cheaters inflict fitness cost on their host. We examined whether this prerequisite is fulfilled, by estimating the persistence time of cheaters in a field population of the parthenogenetic ant Pristomyrmex punctatus. Population genetic analysis found that the cheaters belong to one monophyletic lineage which we infer has persisted for 200-9200 generations. We show that the cheaters migrate and are thus horizontally transmitted between colonies, a trait allowing the lineage to avoid rapid extinction with its host colony. Although horizontal transmission of disruptive cheaters has the potential to induce extinction of the entire population, such collapse is likely averted when there is spatially restricted migration in a structured population, a scenario that matches the observed isolation by distance pattern that we found. We compare our result with other examples of disruptive and horizontally transmissible cheater lineages in nature. © 2010 Blackwell Publishing Ltd.

HGDP and HapMap Analysis by Ancestry Mapper Reveals Local and Global Population Relationships

PubMed Central

Magalhães, Tiago R.; Casey, Jillian P.; Conroy, Judith; Regan, Regina; Fitzpatrick, Darren J.; Shah, Naisha; Sobral, João; Ennis, Sean

2012-01-01

Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set. PMID:23189146

HGDP and HapMap analysis by Ancestry Mapper reveals local and global population relationships.

PubMed

Magalhães, Tiago R; Casey, Jillian P; Conroy, Judith; Regan, Regina; Fitzpatrick, Darren J; Shah, Naisha; Sobral, João; Ennis, Sean

2012-01-01

Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set.

Sedimentology and paleoecology of an Eocene Oligocene alluvial lacustrine arid system, Southern Mexico

NASA Astrophysics Data System (ADS)

Beraldi-Campesi, Hugo; Cevallos-Ferriz, Sergio R. S.; Centeno-García, Elena; Arenas-Abad, Concepción; Fernández, Luis Pedro

2006-10-01

A depositional model of the Eocene-Oligocene Coatzingo Formation in Tepexi de Rodríguez (Puebla, Mexico) is proposed, based on facies analysis of one of the best-preserved sections, the Axamilpa Section. The sedimentary evolution is interpreted as the retrogradation of an alluvial system, followed by the progressive expansion of an alkaline lake system, with deltaic, palustrine, and evaporitic environments. The analysis suggests a change towards more arid conditions with time. Fossils from this region, such as fossil tracks of artiodactyls, aquatic birds and cat-like mammals, suggest that these animals traversed the area, ostracods populated the lake waters, and plants grew on incipient soils and riparian environments many times throughout the history of the basin. The inferred habitat for some fossil plants coincides with the sedimentological interpretation of an arid to semiarid climate for that epoch. This combined sedimentological-paleontological study of the Axamilpa Section provides an environmental context in which fossils can be placed and brings into attention important biotic episodes, like bird and camelid migrations or the origin of endemic but extinct plants in this area.

Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models

PubMed Central

Safferling, Kai; Sütterlin, Thomas; Westphal, Kathi; Ernst, Claudia; Breuhahn, Kai; James, Merlin; Jäger, Dirk; Halama, Niels

2013-01-01

Wound healing is a complex process in which a tissue’s individual cells have to be orchestrated in an efficient and robust way. We integrated multiplex protein analysis, immunohistochemical analysis, and whole-slide imaging into a novel medium-throughput platform for quantitatively capturing proliferation, differentiation, and migration in large numbers of organotypic skin cultures comprising epidermis and dermis. Using fluorescent time-lag staining, we were able to infer source and final destination of keratinocytes in the healing epidermis. This resulted in a novel extending shield reepithelialization mechanism, which we confirmed by computational multicellular modeling and perturbation of tongue extension. This work provides a consistent experimental and theoretical model for epidermal wound closure in 3D, negating the previously proposed concepts of epidermal tongue extension and highlighting the so far underestimated role of the surrounding tissue. Based on our findings, epidermal wound closure is a process in which cell behavior is orchestrated by a higher level of tissue control that 2D monolayer assays are not able to capture. PMID:24385489

Continuing Investigations of the Relationship between Fin Whales, Zooplankton Concentrations and Hydrothermal Venting on the Juan de Fuca Ridge

DTIC Science & Technology

2012-09-30

Fuca Ridge. Our goal is to understand the influences of globally distributed hydrothermal plumes on the trophic ecology of the deep ocean...a layer of increased acoustic backscatter near the top of the hydrothermal plume (Thomson et al., 1991; Burd et al., 1992), leading to the inference...shallow species which presumably migrate vertically between the upper ocean and the hydrothermal plume (Burd and Thomson, 1994, 1995). Our approach is

Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea

PubMed Central

Hill, Sarah C.; Lee, Youn-Jeong; Song, Byung-Min; Kang, Hyun-Mi; Lee, Eun-Kyoung; Hanna, Amanda; Gilbert, Marius; Brown, Ian H.; Pybus, Oliver G.

2015-01-01

Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013 provides a new opportunity to investigate HPAI emergence in greater detail. Here we investigate the origin and transmission of H5N8 in the Republic of Korea, the second country to report the new strain. We reconstruct viral spread using phylogeographic methods and interpret the results in the context of ecological data on poultry density, overwintering wild bird numbers, and bird migration patterns. Our results indicate that wild waterfowl migration and domestic duck density were important to H5N8 epidemiology. Specifically, we infer that H5N8 entered the Republic of Korea via Jeonbuk province, then spread rapidly among western provinces where densities of overwintering waterfowl and domestic ducks are higher, yet rarely persisted in eastern regions. The common ancestor of H5N8 in the Republic of Korea was estimated to have arrived during the peak of inward migration of overwintering birds. Recent virus isolations likely represent re-introductions via bird migration from an as-yet unsampled reservoir. Based on the limited data from outside the Republic of Korea, our data suggest that H5N8 may have entered Europe at least twice, and Asia at least three times from this reservoir, most likely carried by wild migrating birds. PMID:26079277

Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea.

PubMed

Hill, Sarah C; Lee, Youn-Jeong; Song, Byung-Min; Kang, Hyun-Mi; Lee, Eun-Kyoung; Hanna, Amanda; Gilbert, Marius; Brown, Ian H; Pybus, Oliver G

2015-08-01

Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013 provides a new opportunity to investigate HPAI emergence in greater detail. Here we investigate the origin and transmission of H5N8 in the Republic of Korea, the second country to report the new strain. We reconstruct viral spread using phylogeographic methods and interpret the results in the context of ecological data on poultry density, overwintering wild bird numbers, and bird migration patterns. Our results indicate that wild waterfowl migration and domestic duck density were important to H5N8 epidemiology. Specifically, we infer that H5N8 entered the Republic of Korea via Jeonbuk province, then spread rapidly among western provinces where densities of overwintering waterfowl and domestic ducks are higher, yet rarely persisted in eastern regions. The common ancestor of H5N8 in the Republic of Korea was estimated to have arrived during the peak of inward migration of overwintering birds. Recent virus isolations likely represent re-introductions via bird migration from an as-yet unsampled reservoir. Based on the limited data from outside the Republic of Korea, our data suggest that H5N8 may have entered Europe at least twice, and Asia at least three times from this reservoir, most likely carried by wild migrating birds. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Plate convergence, transcurrent faults and internal deformation adjacent to Southeast Asia and the western Pacific

NASA Technical Reports Server (NTRS)

Fitch, T. J.

1971-01-01

A model for oblique convergence between plates of lithosphere is proposed in which at least a fraction of slip parallel to the plate margin results in transcurrent movements on a nearly vertical fault which is located on the continental side of a zone of plate consumption. In an extreme case of complete decoupling only the component of slip normal to the plate margin can be inferred from underthrusting. Recent movements in the western Sunda region provide the most convincing evidence for decoupling of slip, which in this region is thought to be oblique to the plate margin. A speculative model for convergence along the margins of the Philippine Sea is constructed from an inferred direction of oblique slip in the Philippine region. This model requires that the triple point formed by the junction of the Japanese and Izu-Bonin trenches and the Nankai trough migrate along the Sagami trough.

Exploiting single-cell variability to infer the dynamics of immune responses

NASA Astrophysics Data System (ADS)

Höfer, Thomas

Cell division, differentiation, migration and death determine the dynamics of immune responses. These processes are regulated by a multitude of biochemical signals which, at present, cannot faithfully be reconstituted outside the living organism. However, quantitative measurements in living organisms have been limited. In recent years experimental techniques for the ``fate mapping'' of single immune cells have been developed that allow performing parallel single-cell experiments in an experimental animal. The resulting data are more informative about underlying biological processes than traditional measurements. I will show how the theory of stochastic dynamical systems can be used to infer the topology and dynamics of cell differentiation pathways from such data. The focus will be on joint theoretical and experimental work addressing: (i) the development of immune cells during hematopoiesis, and (ii) T cell responses to diverse pathogens. I will discuss questions on the nature of cellular variability that are posed by these new findings.

Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City.

PubMed

Harris, Stephen E; Xue, Alexander T; Alvarado-Serrano, Diego; Boehm, Joel T; Joseph, Tyler; Hickerson, Michael J; Munshi-South, Jason

2016-04-01

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice,Peromyscus leucopus,in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC. © 2016 The Author(s).

Untangling cell tracks: Quantifying cell migration by time lapse image data analysis.

PubMed

Svensson, Carl-Magnus; Medyukhina, Anna; Belyaev, Ivan; Al-Zaben, Naim; Figge, Marc Thilo

2018-03-01

Automated microscopy has given researchers access to great amounts of live cell imaging data from in vitro and in vivo experiments. Much focus has been put on extracting cell tracks from such data using a plethora of segmentation and tracking algorithms, but further analysis is normally required to draw biologically relevant conclusions. Such relevant conclusions may be whether the migration is directed or not, whether the population has homogeneous or heterogeneous migration patterns. This review focuses on the analysis of cell migration data that are extracted from time lapse images. We discuss a range of measures and models used to analyze cell tracks independent of the biological system or the way the tracks were obtained. For single-cell migration, we focus on measures and models giving examples of biological systems where they have been applied, for example, migration of bacteria, fibroblasts, and immune cells. For collective migration, we describe the model systems wound healing, neural crest migration, and Drosophila gastrulation and discuss methods for cell migration within these systems. We also discuss the role of the extracellular matrix and subsequent differences between track analysis in vitro and in vivo. Besides methods and measures, we are putting special focus on the need for openly available data and code, as well as a lack of common vocabulary in cell track analysis. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Differential unroofing within the central metasedimentary Belt of the Grenville Orogen: constraints from 40Ar/39Ar thermochronology

USGS Publications Warehouse

Cosca, M.A.; Essene, E.J.; Kunk, Michael J.; Sutter, J.F.

1992-01-01

An 40Ar/39Ar thermochronological investigation of upper greenschist to granulite facies gneiss, amphibolite and marble was conducted in the Central Metasedimentary Belt (CMB), Ontario, to constrain its cooling history. Incremental 40Ar/39Ar release spectra indicate that substantial differential unroofing occurred in the CMB between ??? 1000 and ??? 600 Ma. A consistent pattern of significantly older hornblende and phlogopite 40Ar/3Ar cooling ages on the southeast sides of major northeast striking shear zones is interpreted to reflect late displacement due to extensional deformation. Variations in hornblende 40Ar/39Ar age plateaus exceeding 200 Ma occur over distances less than 50 km with major age discontinuities occurring across the Robertson Lake shear zone and the Sharbot Lake mylonite zone which separate the Sharbot Lake terrane from the Elzevir and Frontenac terranes. Extensional displacements of up to 14 km are inferred between the Frontenac and Elzevir terranes of the CMB. No evidence for significant post argon-closure vertical displacement is indicated in the vicinity of the Perth Road mylonite within the Frontenac terrane. Variations of nearly 100 Ma in phlogopite 40Ar/39Ar plateau ages occur in undeformed marble on either side of the Bancroft Shear Zone. Phlogopites from sheared and mylonitized marble within the shear zone yield 40Ar/39Ar diffusional loss profiles, but have older geologically meaningless ages thought to reflect incorporation of excess argon. By ??? 900 Ma, southeast directed extension was occurring throughout the CMB, possibly initiated along previous zones of compressional shearing. An easterly migration of active zones of extension is inferred, possibly related to an earlier, overall easterly migration of active zones of regional thrusting and easterly migration of an ancient subduction zone. The duration of extensional shearing is not well constrained, but must have ceased before ??? 600 Ma as required by the deposition of overlying undeformed Cambrian and/or Ordovician sedimentary rocks. ?? 1992 Springer-Verlag.

Shapes and binary fractions of Jovian Trojans and Hildas through NEOWISE

NASA Astrophysics Data System (ADS)

Sonnett, S.; Mainzer, A.; Grav, T.; Bauer, J.; Masiero, J.; Stevenson, R.; Nugent, C.

2014-07-01

Jovian Trojans (hereafter, Trojans) and Hildas are indicative of planetary migration patterns since their capture and physical state must be explained by dynamical evolution models. Early models of minimal planetary migration necessitate that Trojans were dynamically captured from the giant planet region (e.g., Marzari & Scholl 1998). The Nice model instead suggests that Trojans were injected from the outer solar system during a period of significant giant planet migration (e.g., Morbidelli et al. 2005). A more recent version of the Nice model suggests that asymmetric scatterings and collisions would have taken place, producing dissimilar L4 and L5 clouds (Nesvorny et al. 2013). Each of these formation scenarios predicts a different origin and/or collisional evolution for Trojans, which can be inferred from rotation properties. Namely, the physical shape as a function of size helps determine the degree of collisional processing (Farinella et al. 1992). Also, the binary fraction as a function of separation between the two components can be used to determine the dominant binary formation mechanism and thus helps characterize the dynamical environment (e.g., Kern & Elliot 2006). Rotational variation usually corresponds to elongated shapes, but high amplitudes (> 0.9 magnitudes; Sheppard & Jewitt 2004) can only be explained by close or contact binaries. Therefore, rotational lightcurves can be used to infer both shape and the presence of a close companion. Motivated by the need for more observational constraints on solar system formation models and a poor understanding of the rotation properties and binary fraction of Trojans and Hildas, we are studying their rotational lightcurve amplitudes using infrared photometry from NEOWISE (Mainzer et al. 2011; Grav et al. 2011) in order to determine debiased rotational lightcurve amplitude distributions for various Trojan subpopulations and for Trojans compared to Hildas. Preliminary amplitude distributions show a large fraction of potential close or contact binaries (having Δ m > 0.9). These distributions can be used to constrain the collisional and dynamical history of solar system formation models.

Inferring human history in East Asia from Y chromosomes.

PubMed

Wang, Chuan-Chao; Li, Hui

2013-06-03

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.

Ionization-induced solvent migration in acetanilide-methanol clusters inferred from isomer-selective infrared spectroscopy.

PubMed

Weiler, Martin; Nakamura, Takashi; Sekiya, Hiroshi; Dopfer, Otto; Miyazaki, Mitsuhiko; Fujii, Masaaki

2012-12-07

We present the resonance-enhanced multiphoton ionization, infrared-ultraviolet hole burning (IR-UV HB), and IR dip spectra of the trans-acetanilide-methanol (AA-MeOH) cluster in the S(0), S(1), and cationic ground state (D(0)) in a supersonic jet. The IR-UV HB spectra demonstrate the co-existence of two isomers in S(0,1), in which MeOH binds either to the NH or the CO site of the peptide linkage in AA, denoted as AA(NH)-MeOH and AA(CO)-MeOH. When AA(CO)-MeOH is selectively ionized, its IR spectrum in D(0) is the same as that measured for AA(+) (NH)-MeOH. Thus, photoionization of AA(CO)-MeOH induces migration of MeOH from the CO to the NH site with 100% yield. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inferring human history in East Asia from Y chromosomes

PubMed Central

2013-01-01

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history. PMID:23731529

A Genomic View of the Peopling and Population Structure of India

PubMed Central

Majumder, Partha P.; Basu, Analabha

2015-01-01

Recent advances in molecular and statistical genetics have enabled the reconstruction of human history by studying living humans. The ability to sequence and study DNA by calibrating the rate of accumulation of changes with evolutionary time has enabled robust inferences about how humans have evolved. These data indicate that modern humans evolved in Africa about 150,000 years ago and, consistent with paleontological evidence, migrated out of Africa. And through a series of settlements, demographic expansions, and further migrations, they populated the entire world. One of the first waves of migration from Africa was into India. Subsequent, more recent, waves of migration from other parts of the world have resulted in India being a genetic melting pot. Contemporary India has a rich tapestry of cultures and ecologies. There are about 400 tribal groups and more than 4000 groups of castes and subcastes, speaking dialects of 22 recognized languages belonging to four major language families. The contemporary social structure of Indian populations is characterized by endogamy with different degrees of porosity. The social structure, possibly coupled with large ecological heterogeneity, has resulted in considerable genetic diversity and local genetic differences within India. In this essay, we provide genetic evidence of how India may have been peopled, the nature and extent of its genetic diversity, and genetic structure among the extant populations of India. PMID:25147176

Quantitative Analysis of Cell Migration Using Optical Flow

PubMed Central

Boric, Katica; Orio, Patricio; Viéville, Thierry; Whitlock, Kathleen

2013-01-01

Neural crest cells exhibit dramatic migration behaviors as they populate their distant targets. Using a line of zebrafish expressing green fluorescent protein (sox10:EGFP) in neural crest cells we developed an assay to analyze and quantify cell migration as a population, and use it here to characterize in detail the subtle defects in cell migration caused by ethanol exposure during early development. The challenge was to quantify changes in the in vivo migration of all Sox10:EGFP expressing cells in the visual field of time-lapse movies. To perform this analysis we used an Optical Flow algorithm for motion detection and combined the analysis with a fit to an affine transformation. Through this analysis we detected and quantified significant differences in the cell migrations of Sox10:EGFP positive cranial neural crest populations in ethanol treated versus untreated embryos. Specifically, treatment affected migration by increasing the left-right asymmetry of the migrating cells and by altering the direction of cell movements. Thus, by applying this novel computational analysis, we were able to quantify the movements of populations of cells, allowing us to detect subtle changes in cell behaviors. Because cranial neural crest cells contribute to the formation of the frontal mass these subtle differences may underlie commonly observed facial asymmetries in normal human populations. PMID:23936049

Efficient computation of the joint sample frequency spectra for multiple populations.

PubMed

Kamm, John A; Terhorst, Jonathan; Song, Yun S

2017-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity.

Efficient computation of the joint sample frequency spectra for multiple populations

PubMed Central

Kamm, John A.; Terhorst, Jonathan; Song, Yun S.

2016-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity. PMID:28239248

Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns.

PubMed

Ascensão, Fernando; Mata, Cristina; Malo, Juan E; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P; Santos-Reis, Margarida; Fernandes, Carlos

2016-01-01

Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species' responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals.

Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns

PubMed Central

Ascensão, Fernando; Mata, Cristina; Malo, Juan E.; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P.; Santos-Reis, Margarida; Fernandes, Carlos

2016-01-01

Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species’ responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals. PMID:26978779

[Ethnic groups and towns: an analysis of migration toward the towns of the Ivory Coast].

PubMed

Marguerat, Y

1981-01-01

An analysis of urbanization and internal migration in the Ivory Coast is presented based on unpublished data from the 1975 census. Particular attention is paid to variations in migration by ethnic group.

The navigational feats of green sea turtles migrating from Ascension Island investigated by satellite telemetry.

PubMed Central

Luschi, P; Hays, G C; Del Seppia, C; Marsh, R; Papi, F

1998-01-01

Previous tagging studies of the movements of green turtles (Chelonia mydas) nesting at Ascension Island have shown that they shuttle between this remote target in the Atlantic Ocean and their feeding grounds on the Brazilian coast, a distance of 2300 km or more. Since a knowledge of sea turtle migration routes might allow inferences on the still unknown navigational mechanisms of marine animals, we tracked the postnesting migration of six green turtle females from Ascension Island to Brazil. Five of them reached the proximity of the easternmost stretch of the Brazilian coast, covering 1777-2342 km in 33-47 days. Their courses were impressively similar for the first 1000 km, with three turtles tracked over different dates following indistinguishable paths for the first 300 km. Only the sixth turtle made some relatively short trips in different directions around Ascension. The tracks show that turtles (i) are able to maintain straight courses over long distances in the open sea; (ii) may perform exploratory movements in different directions; (iii) appropriately correct their course during the journey according to external information; and (iv) initially keep the same direction as the west-south-westerly flowing current, possibly guided by chemical cues. PMID:9881473

Global multi-layer network of human mobility

PubMed Central

Belyi, Alexander; Bojic, Iva; Sobolevsky, Stanislav; Sitko, Izabela; Hawelka, Bartosz; Rudikova, Lada; Kurbatski, Alexander; Ratti, Carlo

2017-01-01

ABSTRACT Recent availability of geo-localized data capturing individual human activity together with the statistical data on international migration opened up unprecedented opportunities for a study on global mobility. In this paper, we consider it from the perspective of a multi-layer complex network, built using a combination of three datasets: Twitter, Flickr and official migration data. Those datasets provide different, but equally important insights on the global mobility – while the first two highlight short-term visits of people from one country to another, the last one – migration – shows the long-term mobility perspective, when people relocate for good. The main purpose of the paper is to emphasize importance of this multi-layer approach capturing both aspects of human mobility at the same time. On the one hand, we show that although the general properties of different layers of the global mobility network are similar, there are important quantitative differences among them. On the other hand, we demonstrate that consideration of mobility from a multi-layer perspective can reveal important global spatial patterns in a way more consistent with those observed in other available relevant sources of international connections, in comparison to the spatial structure inferred from each network layer taken separately. PMID:28553155

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics.

PubMed

Pérez-Escobar, Oscar Alejandro; Gottschling, Marc; Chomicki, Guillaume; Condamine, Fabien L; Klitgård, Bente B; Pansarin, Emerson; Gerlach, Günter

2017-07-07

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.

A wave equation migration method for receiver function imaging: 2. Application to the Japan subduction zone

NASA Astrophysics Data System (ADS)

Chen, Ling; Wen, Lianxing; Zheng, Tianyu

2005-11-01

The newly developed wave equation poststack depth migration method for receiver function imaging is applied to study the subsurface structures of the Japan subduction zone using the Fundamental Research on Earthquakes and Earth's Interior Anomalies (FREESIA) broadband data. Three profiles are chosen in the subsurface imaging, two in northeast (NE) Japan to study the subducting Pacific plate and one in southwest (SW) Japan to study the Philippine Sea plate. The descending Pacific plate in NE Japan is well imaged within a depth range of 50-150 km. The slab image exhibits a little more steeply dipping angle (˜32°) in the south than in the north (˜27°), although the general characteristics between the two profiles in NE Japan are similar. The imaged Philippine Sea plate in eastern SW Japan, in contrast, exhibits a much shallower subduction angle (˜19°) and is only identifiable at the uppermost depths of no more than 60 km. Synthetic tests indicate that the top 150 km of the migrated images of the Pacific plate is well resolved by our seismic data, but the resolution of deep part of the slab images becomes poor due to the limited data coverage. Synthetic tests also suggest that the breakdown of the Philippine Sea plate at shallow depths reflects the real structural features of the subduction zone, rather than caused by insufficient coverage of data. Comparative studies on both synthetics and real data images show the possibility of retrieval of fine-scale structures from high-frequency contributions if high-frequency noise can be effectively suppressed and a small bin size can be used in future studies. The derived slab geometry and image feature also appear to have relatively weak dependence on overlying velocity structure. The observed seismicity in the region confirms the geometries inferred from the migrated images for both subducting plates. Moreover, the deep extent of the Pacific plate image and the shallow breakdown of the Philippine Sea plate image are observed to correlate well with the depth extent of the seismicity beneath NE and SW Japan. Such a correlation supports the inference that the specific appearance of slabs and intermediate-depth earthquakes are a consequence of temperature-dependent dehydration induced metamorphism occurring in the hydrated descending oceanic crust.

Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA

PubMed Central

2011-01-01

Background Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere. Results Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (FST = 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero). Conclusions Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration. PMID:22093799

Life history reconstruction of modern and fossil sockeye salmon ( Oncorhynchus nerka) by oxygen isotopic analysis of otoliths, vertebrae, and teeth: Implication for paleoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Zazzo, A.; Smith, G. R.; Patterson, W. P.; Dufour, E.

2006-09-01

We evaluate the use of oxygen isotope values of biogenic apatite for tracking freshwater to marine migration in modern and fossil Pacific sockeye salmon. Oxygen isotope analyses of otoliths, vertebrae, and teeth of three anadromous modern sockeye salmon from Alaska establish a basis for the interpretation of fossil vertebrae and tooth apatite from Pleistocene sockeye salmon of the Skokomish River Valley, Washington. High resolution δ18O profiles in salmon otoliths provide, at a monthly resolution, a detailed record of individual history including continental rearing, migration to sea, seasonal variation in sea surface temperatures during marine life, and spawning migration before capture. Pacific salmon teeth are constantly renewed with the last set of teeth forming under the influence of freshwater. Therefore, they do not allow inference concerning sea-run versus landlocked life history in fossil salmon. Salmon vertebrae are also ambiguous indicators of life history regarding fresh versus marine water because centra are minimally ossified in the freshwater stages of life and the outermost layer of vertebral bone might be resorbed to provide nutrients during the non-feeding phase of the spawning migration. Therefore, δ18O values of accretionary growth rings in sea-run salmon vertebrae are dominated by the marine signal only if they are not diagenetically altered in freshwater deposits. In Pleistocene sockeye reported here, neither the teeth nor vertebral apatite present clear marine δ18O values due to the combined effects of tooth replacement and diagenetic alteration of bone and dentine. δ18O(PO 4) values of fossil vertebrae are intermediate between δ18O(PO 4) values of enamel and basal tooth dentin. Assuming a similar rate of isotope exchange of vertebrae and dentine with freshwater during diagenesis, these results are interpreted to reflect formation of the teeth under the influence of freshwater, and formation of the vertebrae under the influence of oceanic water. Our approach demonstrates that when appropriate knowledge of tissue formation is available, isotopic differences between altered and unaltered tissue holds promise of distinguishing between marine and freshwater origin of the tissues.

Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis.

PubMed

Yang, Chongguang; Lu, Liping; Warren, Joshua L; Wu, Jie; Jiang, Qi; Zuo, Tianyu; Gan, Mingyu; Liu, Mei; Liu, Qingyun; DeRiemer, Kathryn; Hong, Jianjun; Shen, Xin; Colijn, Caroline; Guo, Xiaoqin; Gao, Qian; Cohen, Ted

2018-04-19

Massive internal migration from rural to urban areas poses new challenges for tuberculosis control in China. We aimed to combine genomic, spatial, and epidemiological data to describe the dynamics of tuberculosis in an urban setting with large numbers of migrants. We did a population-based study of culture-positive Mycobacterium tuberculosis isolates in Songjiang, Shanghai. We used whole-genome sequencing to discriminate apparent genetic clusters of M tuberculosis sharing identical variable-number-tandem-repeat (VNTR) patterns, and analysed the relations between proximity of residence and the risk of genomically clustered M tuberculosis. Finally, we used genomic, spatial, and epidemiological data to estimate time of infection and transmission links among migrants and residents. Between Jan 1, 2009, and Dec 31, 2015, 1620 cases of culture-positive tuberculosis were recorded, 1211 (75%) of which occurred among internal migrants. 150 (69%) of 218 people sharing identical VNTR patterns had isolates within ten single-nucleotide polymorphisms (SNPs) of at least one other strain, consistent with recent transmission of M tuberculosis. Pairs of strains collected from individuals living in close proximity were more likely to be genetically similar than those from individuals who lived far away-for every additional km of distance between patients' homes, the odds that genotypically matched strains were within ten SNPs of each other decreased by about 10% (OR 0·89 [95% CI 0·87-0·91]; p<0·0001). We inferred that transmission from residents to migrants occurs as commonly as transmission from migrants to residents, and we estimated that more than two-thirds of migrants in genomic clusters were infected locally after migration. The primary mechanism driving local incidence of tuberculosis in urban centres is local transmission between both migrants and residents. Combined analysis of epidemiological, genomic, and spatial data contributes to a richer understanding of local transmission dynamics and should inform the design of more effective interventions. National Natural Science Foundation of China, National Science and Technology Major Project of China, and US National Institutes of Health. Copyright © 2018 Elsevier Ltd. All rights reserved.

Seasonal migrations of North Atlantic minke whales: novel insights from large-scale passive acoustic monitoring networks.

PubMed

Risch, Denise; Castellote, Manuel; Clark, Christopher W; Davis, Genevieve E; Dugan, Peter J; Hodge, Lynne Ew; Kumar, Anurag; Lucke, Klaus; Mellinger, David K; Nieukirk, Sharon L; Popescu, Cristian Marian; Ramp, Christian; Read, Andrew J; Rice, Aaron N; Silva, Monica A; Siebert, Ursula; Stafford, Kathleen M; Verdaat, Hans; Van Parijs, Sofie M

2014-01-01

Little is known about migration patterns and seasonal distribution away from coastal summer feeding habitats of many pelagic baleen whales. Recently, large-scale passive acoustic monitoring networks have become available to explore migration patterns and identify critical habitats of these species. North Atlantic minke whales (Balaenoptera acutorostrata) perform seasonal migrations between high latitude summer feeding and low latitude winter breeding grounds. While the distribution and abundance of the species has been studied across their summer range, data on migration and winter habitat are virtually missing. Acoustic recordings, from 16 different sites from across the North Atlantic, were analyzed to examine the seasonal and geographic variation in minke whale pulse train occurrence, infer information about migration routes and timing, and to identify possible winter habitats. Acoustic detections show that minke whales leave their winter grounds south of 30° N from March through early April. On their southward migration in autumn, minke whales leave waters north of 40° N from mid-October through early November. In the western North Atlantic spring migrants appear to track the warmer waters of the Gulf Stream along the continental shelf, while whales travel farther offshore in autumn. Abundant detections were found off the southeastern US and the Caribbean during winter. Minke whale pulse trains showed evidence of geographic variation, with longer pulse trains recorded south of 40° N. Very few pulse trains were recorded during summer in any of the datasets. This study highlights the feasibility of using acoustic monitoring networks to explore migration patterns of pelagic marine mammals. Results confirm the presence of minke whales off the southeastern US and the Caribbean during winter months. The absence of pulse train detections during summer suggests either that minke whales switch their vocal behaviour at this time of year, are absent from available recording sites or that variation in signal structure influenced automated detection. Alternatively, if pulse trains are produced in a reproductive context by males, these data may indicate their absence from the selected recording sites. Evidence of geographic variation in pulse train duration suggests different behavioural functions or use of these calls at different latitudes.

Using SPM 12’s Second-Level Bayesian Inference Procedure for fMRI Analysis: Practical Guidelines for End Users

PubMed Central

Han, Hyemin; Park, Joonsuk

2018-01-01

Recent debates about the conventional traditional threshold used in the fields of neuroscience and psychology, namely P < 0.05, have spurred researchers to consider alternative ways to analyze fMRI data. A group of methodologists and statisticians have considered Bayesian inference as a candidate methodology. However, few previous studies have attempted to provide end users of fMRI analysis tools, such as SPM 12, with practical guidelines about how to conduct Bayesian inference. In the present study, we aim to demonstrate how to utilize Bayesian inference, Bayesian second-level inference in particular, implemented in SPM 12 by analyzing fMRI data available to public via NeuroVault. In addition, to help end users understand how Bayesian inference actually works in SPM 12, we examine outcomes from Bayesian second-level inference implemented in SPM 12 by comparing them with those from classical second-level inference. Finally, we provide practical guidelines about how to set the parameters for Bayesian inference and how to interpret the results, such as Bayes factors, from the inference. We also discuss the practical and philosophical benefits of Bayesian inference and directions for future research. PMID:29456498

The Importance of Statistical Modeling in Data Analysis and Inference

ERIC Educational Resources Information Center

Rollins, Derrick, Sr.

2017-01-01

Statistical inference simply means to draw a conclusion based on information that comes from data. Error bars are the most commonly used tool for data analysis and inference in chemical engineering data studies. This work demonstrates, using common types of data collection studies, the importance of specifying the statistical model for sound…

Individual-based analysis opens new insights into understanding population structure and animal behaviour.

PubMed

Planes, Serge; Lemer, Sarah

2011-01-01

Studying the movement of individuals in the wild has always been a challenge in ecology. However, estimating such movement is essential in life sciences as it is the base-line for evaluating connectivity, a major component in developing management and conservation plans. Furthermore, movement, or migration, is an essential parameter in population genetics, as it directly affects genetic differentiation. The development of highly variable markers has allowed genetic discrimination between individuals within populations and at larger scales, and the availability of high-throughput technologies means that many samples and hence many individuals can be screened. These advances mean that we can now use genetic identification for tracking individuals, and hence follow both survival and reproductive output through the life cycle. The paper by Morrissey & Ferguson (2011, this issue) is a demonstration of this new capability, as authors were able to infer the movement of salmonid fish initially captured as juveniles, and later as reproductively mature adults.

The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation

PubMed Central

2013-01-01

Background When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study. Results By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas. Conclusions Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling. PMID:23360301

Migration of cemented femoral components after THR. Roentgen stereophotogrammetric analysis.

PubMed

Kiss, J; Murray, D W; Turner-Smith, A R; Bithell, J; Bulstrode, C J

1996-09-01

We studied the migration of 58 cemented Hinek femoral components for total hip replacement, using roentgen stereophotogrammetric analysis over four years. The implants migrated faster during the first year than subsequently, and the pattern of migration in the second period was very different. During the first year they subsided, tilted into varus and internally rotated. After this there was slow distal migration with no change in orientation. None of the prostheses has yet failed. The early migration is probably caused by resorption of bone damaged by surgical trauma or the heat generated by the polymerisation of bone cement. Later migration may be due to creep in the bone cement or the surrounding fibrous membrane. The prosthesis which we studied allows the preservation of some of the femoral neck, and comparison with published migration studies of the Charnley stem suggests that this decreases rotation and may help to prevent loosening.

Japanese migration in contemporary Japan: economic segmentation and interprefectural migration.

PubMed

Fukurai, H

1991-01-01

This paper examines the economic segmentation model in explaining 1985-86 Japanese interregional migration. The analysis takes advantage of statistical graphic techniques to illustrate the following substantive issues of interregional migration: (1) to examine whether economic segmentation significantly influences Japanese regional migration and (2) to explain socioeconomic characteristics of prefectures for both in- and out-migration. Analytic techniques include a latent structural equation (LISREL) methodology and statistical residual mapping. The residual dispersion patterns, for instance, suggest the extent to which socioeconomic and geopolitical variables explain migration differences by showing unique clusters of unexplained residuals. The analysis further points out that extraneous factors such as high residential land values, significant commuting populations, and regional-specific cultures and traditions need to be incorporated in the economic segmentation model in order to assess the extent of the model's reliability in explaining the pattern of interprefectural migration.

Transnational nurse migration: future directions for medical anthropological research.

PubMed

Prescott, Megan; Nichter, Mark

2014-04-01

Transnational nurse migration is a serious global health issue in which inequitably distributed shortages hinder health and development goals. This article selectively reviews the literature on nurse migration that has emerged from nursing, health planning, and the social sciences and offers productive directions for future anthropological research. The literature on global nurse migration has largely focused on push/pull economic logic and the concept of brain drain to understand the causes and effects of nurse migration. These concepts obscure political-economic, historical, and cultural factors that pattern nurse migration and influence the complex effects of nurse migration. Global nurse care chain analysis helps illuminate the numerous nodes in the production and migration of nurses, and management of this transnational process. Examples are provided from the Philippines and India to illustrate ways in which this analysis may be deepened, refined and rendered more critical by anthropological research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Make the Most of the Data You've Got: Bayesian Models and a Surrogate Species Approach to Assessing Benefits of Upstream Migration Flows for the Endangered Australian Grayling

NASA Astrophysics Data System (ADS)

Webb, J. Angus; Koster, Wayne M.; Stuart, Ivor G.; Reich, Paul; Stewardson, Michael J.

2018-03-01

Environmental water managers must make best use of allocations, and adaptive management is one means of improving effectiveness of environmental water delivery. Adaptive management relies on generation of new knowledge from monitoring and evaluation, but it is often difficult to make clear inferences from available monitoring data. Alternative approaches to assessment of flow benefits may offer an improved pathway to adaptive management. We developed Bayesian statistical models to inform adaptive management of the threatened Australian grayling ( Prototroctes maraena) in the coastal Thomson River, South-East Victoria Australia. The models assessed the importance of flows in spring and early summer (migration flows) for upstream dispersal and colonization of juveniles of this diadromous species. However, Australian grayling young-of-year were recorded in low numbers, and models provided no indication of the benefit of migration flows. To overcome this limitation, we applied the same models to young-of-year of a surrogate species (tupong— Pseudaphritis urvilli)—a more common diadromous species expected to respond to flow similarly to Australian grayling—and found strong positive responses to migration flows. Our results suggest two complementary approaches to supporting adaptive management of Australian grayling. First, refine monitoring approaches to allow direct measurement of effects of migration flows, a process currently under way. Second, while waiting for improved data, further investigate the use of tupong as a surrogate species. More generally, alternative approaches to assessment can improve knowledge to inform adaptive management, and this can occur while monitoring is being revised to directly target environmental responses of interest.

Make the Most of the Data You've Got: Bayesian Models and a Surrogate Species Approach to Assessing Benefits of Upstream Migration Flows for the Endangered Australian Grayling.

PubMed

Webb, J Angus; Koster, Wayne M; Stuart, Ivor G; Reich, Paul; Stewardson, Michael J

2018-03-01

Environmental water managers must make best use of allocations, and adaptive management is one means of improving effectiveness of environmental water delivery. Adaptive management relies on generation of new knowledge from monitoring and evaluation, but it is often difficult to make clear inferences from available monitoring data. Alternative approaches to assessment of flow benefits may offer an improved pathway to adaptive management. We developed Bayesian statistical models to inform adaptive management of the threatened Australian grayling (Prototroctes maraena) in the coastal Thomson River, South-East Victoria Australia. The models assessed the importance of flows in spring and early summer (migration flows) for upstream dispersal and colonization of juveniles of this diadromous species. However, Australian grayling young-of-year were recorded in low numbers, and models provided no indication of the benefit of migration flows. To overcome this limitation, we applied the same models to young-of-year of a surrogate species (tupong-Pseudaphritis urvilli)-a more common diadromous species expected to respond to flow similarly to Australian grayling-and found strong positive responses to migration flows. Our results suggest two complementary approaches to supporting adaptive management of Australian grayling. First, refine monitoring approaches to allow direct measurement of effects of migration flows, a process currently under way. Second, while waiting for improved data, further investigate the use of tupong as a surrogate species. More generally, alternative approaches to assessment can improve knowledge to inform adaptive management, and this can occur while monitoring is being revised to directly target environmental responses of interest.

Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene.

PubMed

Lin, Li; Tang, Liang; Bai, Yun-Jun; Tang, Zhi-Yao; Wang, Wei; Chen, Zhi-Duan

2015-09-03

The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus. Oryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates. Rice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.

Comprehensive view of the population history of Arabia as inferred by mtDNA variation.

PubMed

Černý, Viktor; Čížková, Martina; Poloni, Estella S; Al-Meeri, Ali; Mulligan, Connie J

2016-04-01

Genetic and archaeological research supports the theory that Arabia was the first region traversed by modern humans as they left Africa and dispersed throughout Eurasia. However, the role of Arabia from the initial migration out of Africa until more recent times is still unclear. We have generated 379 new hypervariable segment 1 (HVS-1) sequences from a range of geographic locations throughout Yemen. We compare these data to published HVS-1 sequences representing Arabia and neighboring regions to build a unique dataset of 186 populations and 14,290 sequences. We identify 4,563 haplotypes unevenly distributed across Arabia and neighboring regions. Arabia contains higher proportions of shared haplotypes than the regions with which it shares these haplotypes, suggesting high levels of migration through the region. Populations in Arabia show higher levels of population expansion than those in East Africa, but lower levels than the Near East, Middle East or India. Arabian populations also show very high levels of genetic variation that overlaps with variation from most other regions. We take a population genetics approach to provide a comprehensive view of the relationships of Arabian and neighboring populations. We show that Arabian populations share closest links to the Near East and North Africa, but have a more ancient origin with slower demographic growth and/or lower migration rates. Our conclusions are supported by phylogenetic studies but also suggest that recent migrations have erased signals of earlier events. © 2015 Wiley Periodicals, Inc.

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.

PubMed

Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G; Drummond, Alexei J

2016-08-01

When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth-death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

How will predicted land-use change affect waterfowl spring stopover ecology? Inferences from an individual-based model

USGS Publications Warehouse

Beatty, William; Kesler, Dylan C.; Webb, Elisabeth B.; Naylor, Luke W.; Raedeke, Andrew H.; Humburg, Dale D.; Coluccy, John M.; Soulliere, Gregory J.

2017-01-01

Habitat loss, habitat fragmentation, overexploitation and climate change pose familiar and new challenges to conserving natural populations throughout the world. One approach conservation planners may use to evaluate the effects of these challenges on wildlife populations is scenario planning.We developed an individual-based model to evaluate the effects of future land use and land cover changes on spring-migrating dabbling ducks in North America. We assessed the effects of three Intergovernmental Panel on Climate Change emission scenarios (A1B, A2 and B1) on dabbling duck stopover duration, movement distances and mortality. We specifically focused on migration stopover duration because previous research has demonstrated that individuals arriving earlier on the nesting grounds exhibit increased reproductive fitness.Compared to present conditions, all three scenarios increased stopover duration and movement distances of agent ducks.Although all three scenarios presented migrating ducks with increased amounts of wetland habitat, scenarios also contained substantially less cropland, which decreased overall carrying capacity of the study area.Synthesis and applications. Land-use change may increase waterfowl spring migration stopover duration in the midcontinent region of North America due to reduced landscape energetic carrying capacity. Climate change will alter spatial patterns of crop distributions with corn and rice production areas shifting to different regions. Thus, conservation planners will have to address population-level energetic implications of shifting agricultural food resources and increased uncertainty in yearly precipitation patterns within the next 50 years.

Causal inference in nonlinear systems: Granger causality versus time-delayed mutual information

NASA Astrophysics Data System (ADS)

Li, Songting; Xiao, Yanyang; Zhou, Douglas; Cai, David

2018-05-01

The Granger causality (GC) analysis has been extensively applied to infer causal interactions in dynamical systems arising from economy and finance, physics, bioinformatics, neuroscience, social science, and many other fields. In the presence of potential nonlinearity in these systems, the validity of the GC analysis in general is questionable. To illustrate this, here we first construct minimal nonlinear systems and show that the GC analysis fails to infer causal relations in these systems—it gives rise to all types of incorrect causal directions. In contrast, we show that the time-delayed mutual information (TDMI) analysis is able to successfully identify the direction of interactions underlying these nonlinear systems. We then apply both methods to neuroscience data collected from experiments and demonstrate that the TDMI analysis but not the GC analysis can identify the direction of interactions among neuronal signals. Our work exemplifies inference hazards in the GC analysis in nonlinear systems and suggests that the TDMI analysis can be an appropriate tool in such a case.

Origin of honeybees (Apis mellifera L.) from the Yucatan peninsula inferred from mitochondrial DNA analysis.

PubMed

Clarke, K E; Oldroyd, B P; Javier, J; Quezada-Euán, G; Rinderer, T E

2001-06-01

Honeybees (Apis mellifera L.) sampled at sites in Europe, Africa and South America were analysed using a mitochondrial DNA restriction fragment length polymorphism (RFLP) marker. These samples were used to provide baseline information for a detailed analysis of the process of Africanization of bees from the neotropical Yucatan peninsula of Mexico. Radical changes in mitochondrial haplotype (mitotype) frequencies were found to have occurred in the 13-year period studied. Prior to the arrival of Africanized bees (1986) the original inhabitants of the Yucatan peninsula appear to have been essentially of southeastern European origin with a smaller proportion having northwestern European ancestry. Three years after the migration of Africanized bees into the area (1989), only very low levels of maternal gene flow from Africanized populations into the resident European populations had occurred. By 1998, however, there was a sizeable increase in the proportion of African mitotypes in domestic populations (61%) with feral populations having 87% of mitotypes classified as African derived. The results suggest that the early stages of Africanization did not involve a rapid replacement of European with African mitotypes and that earlier studies probably overestimated the prevalence of African mitotypes.

Triggering mechanism and tsunamogenic potential of the Cape Fear Slide complex, U.S. Atlantic margin

USGS Publications Warehouse

Hornbach, Matthew J.; Lavier, Luc L.; Ruppel, Carolyn D.

2007-01-01

Analysis of new multibeam bathymetry data and seismic Chirp data acquired over the Cape Fear Slide complex on the U.S. Atlantic margin suggests that at least 5 major submarine slides have likely occurred there within the past 30,000 years, indicating that repetitive, large-scale mass wasting and associated tsunamis may be more common in this area than previously believed. Gas hydrate deposits and associated free gas as well as salt tectonics have been implicated in previous studies as triggers for the major Cape Fear slide events. Analysis of the interaction of the gas hydrate phase boundary and the various generations of slides indicates that only the most landward slide likely intersected the phase boundary and inferred high gas pressures below it. For much of the region, we believe that displacement along a newly recognized normal fault led to upward migration of salt, oversteepening of slopes, and repeated slope failures. Using new constraints on slide morphology, we develop the first tsunami model for the Cape Fear Slide complex. Our results indicate that if the most seaward Cape Fear slide event occurred today, it could produce waves in excess of 2 m at the present-day 100 m bathymetric contour.

What can we infer about the origin of sex in early eukaryotes?

PubMed Central

2016-01-01

Current analysis shows that the last eukaryotic common ancestor (LECA) was capable of full meiotic sex. The original eukaryotic life cycle can probably be described as clonal, interrupted by episodic sex triggered by external or internal stressors. The cycle could have started in a highly flexible form, with the interruption of either diploid or haploid clonal growth determined by stress signals only. Eukaryotic sex most likely evolved in response to a high mutation rate, arising from the uptake of the endosymbiont, as this (proto) mitochondrion generated internal reactive oxygen species. This is consistent with the likely development of full meiotic sex from a diverse set of existing archaeal (the host of the endosymbiont) repair and signalling mechanisms. Meiotic sex could thus have been one of the fruits of symbiogenesis at the basis of eukaryotic origins: a product of the merger by which eukaryotic cells arose. Symbiogenesis also explains the large-scale migration of organellar DNA to the nucleus. I also discuss aspects of uniparental mitochondrial inheritance and mitonuclear interactions in the light of the previous analysis. This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’. PMID:27619694

What can we infer about the origin of sex in early eukaryotes?

PubMed

Speijer, Dave

2016-10-19

Current analysis shows that the last eukaryotic common ancestor (LECA) was capable of full meiotic sex. The original eukaryotic life cycle can probably be described as clonal, interrupted by episodic sex triggered by external or internal stressors. The cycle could have started in a highly flexible form, with the interruption of either diploid or haploid clonal growth determined by stress signals only. Eukaryotic sex most likely evolved in response to a high mutation rate, arising from the uptake of the endosymbiont, as this (proto) mitochondrion generated internal reactive oxygen species. This is consistent with the likely development of full meiotic sex from a diverse set of existing archaeal (the host of the endosymbiont) repair and signalling mechanisms. Meiotic sex could thus have been one of the fruits of symbiogenesis at the basis of eukaryotic origins: a product of the merger by which eukaryotic cells arose. Symbiogenesis also explains the large-scale migration of organellar DNA to the nucleus. I also discuss aspects of uniparental mitochondrial inheritance and mitonuclear interactions in the light of the previous analysis.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

PubMed Central

Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P.

2016-01-01

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

Gender and migration from Albania.

PubMed

Stecklov, Guy; Carletto, Calogero; Azzarri, Carlo; Davis, Benjamin

2010-11-01

This article examines the dynamics and causes of the shift in the gender composition of migration, and more particularly, in women's access to migration opportunities and decision-making. Our analysis focuses on Albania, a natural laboratory for studying international migration where out-migration was essentially nonexistent from the end of World War II to the end of the 1980s. Interest in the Albanian case is heightened because of the complex layers of inequality existing at the time when migration began: relatively low levels of inequality within the labor market and educational system-a product of the Communist era-while household relations remained heavily steeped in tradition and patriarchy. We use micro-level data from the Albania 2005 Living Standards Measurement Study, including migration histories for family members since migration began. Based on discrete-time hazard models, the analysis shows a dramatic increase in male migration and a gradual and uneven expansion of the female proportion of this international migration. Female migration, which is shown to be strongly associated with education, wealth, and social capital, appears responsive to economic incentives and constraints. Using information on the dependency of female migration to the household demographic structure as well as the sensitivity of female migration to household-level shocks, we show how household-level constraints and incentives affect male and female migration differently. Throughout this period, however, women's migration behavior appears more directly aligned with household-level factors, and there is little evidence to suggest that increased female migration signals rising behavioral independence among Albanian women.

Gender and Migration from Albania

PubMed Central

STECKLOV, GUY; CARLETTO, CALOGERO; AZZARRI, CARLO; DAVIS, BENJAMIN

2010-01-01

This article examines the dynamics and causes of the shift in the gender composition of migration, and more particularly, in women’s access to migration opportunities and decision-making. Our analysis focuses on Albania, a natural laboratory for studying international migration where out-migration was essentially nonexistent from the end of World War II to the end of the 1980s. Interest in the Albanian case is heightened because of the complex layers of inequality existing at the time when migration began: relatively low levels of inequality within the labor market and educational system—a product of the Communist era—while household relations remained heavily steeped in tradition and patriarchy. We use micro-level data from the Albania 2005 Living Standards Measurement Study, including migration histories for family members since migration began. Based on discrete-time hazard models, the analysis shows a dramatic increase in male migration and a gradual and uneven expansion of the female proportion of this international migration. Female migration, which is shown to be strongly associated with education, wealth, and social capital, appears responsive to economic incentives and constraints. Using information on the dependency of female migration to the household demographic structure as well as the sensitivity of female migration to household-level shocks, we show how household-level constraints and incentives affect male and female migration differently. Throughout this period, however, women’s migration behavior appears more directly aligned with household-level factors, and there is little evidence to suggest that increased female migration signals rising behavioral independence among Albanian women. PMID:21308565

Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story

PubMed Central

Pagán, Israel; Holguín, África

2013-01-01

The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations. PMID:23874917

Examining the Impact of Inference Instruction on the Literal and Inferential Comprehension of Skilled and Less Skilled Readers: A Meta-Analytic Review

ERIC Educational Resources Information Center

Elleman, Amy M.

2017-01-01

Inference ability is considered central to discourse processing and has been shown to be important across models of reading comprehension. To evaluate the impact of inference instruction, a meta-analysis of 25 inference studies in Grades K-12 was conducted. Results showed that inference instruction was effective for increasing students' general…

Globalization, Development and International Migration: A Cross-National Analysis of Less-Developed Countries, 1970-2000

ERIC Educational Resources Information Center

Sanderson, Matthew R.; Kentor, Jeffrey D.

2009-01-01

It is widely argued that globalization and economic development are associated with international migration. However, these relationships have not been tested empirically. We use a cross-national empirical analysis to assess the impact of global and national factors on international migration from less-developed countries. An interdisciplinary…

Size-conditional smolting and the response of Carmel River steelhead to two decades of conservation efforts

PubMed Central

Lopez Arriaza, Juan; Urquhart, Kevan; Mangel, Marc

2017-01-01

Threshold effects are common in ecosystems and can generate counterintuitive outcomes in management interventions. A threshold effect proposed for steelhead trout (Oncorhynchus mykiss) is size-conditional smolting and marine survival. Steelhead are anadromous, maturing in the ocean but migrating to freshwater to spawn, where their offspring reside for one or more years before smolting—physiologically transforming to a saltwater form—and migrating to the ocean. In conditional smolting, juveniles transform only if growth exceeds a threshold body size prior to migration season, and subsequent marine survival correlates with size at ocean entry. Conditional smolting suggests that efforts to improve freshwater survival of juveniles may reduce smolt success if they increase competition and reduce growth. Using model-selection techniques, we asked if this effect explained declining numbers of adult Carmel River steelhead. This threatened population has been the focus of two decades of habitat restoration, as well as active translocation and captive-rearing of juveniles stranded in seasonally dewatered channels. In the top-ranked model selected by information-theoretic criteria, adult decline was linked to reduced juvenile growth rates in the lower river, consistent with the conditional smolting hypothesis. According to model inference, since 2005 most returning adult steelhead were captively-reared. However, a lower-ranked model without conditional smolting also had modest support, and suggested a negative effect of captive rearing. Translocations of juvenile fish to perennial reaches may have reduced the steelhead run slightly by raising competition, but this effect is confounded in the data with effects of river flow on growth. Efforts to recover Carmel River steelhead will probably be more successful if they focus on conditions promoting rapid growth in the river. Our analysis clearly favored a role for size-conditional smolting and marine survival in the decline of the population, but did not definitively rule out alternative explanations. PMID:29190806

Envisioning migration: Mathematics in both experimental analysis and modeling of cell behavior

PubMed Central

Zhang, Elizabeth R.; Wu, Lani F.; Altschuler, Steven J.

2013-01-01

The complex nature of cell migration highlights the power and challenges of applying mathematics to biological studies. Mathematics may be used to create model equations that recapitulate migration, which can predict phenomena not easily uncovered by experiments or intuition alone. Alternatively, mathematics may be applied to interpreting complex data sets with better resolution—potentially empowering scientists to discern subtle patterns amid the noise and heterogeneity typical of migrating cells. Iteration between these two methods is necessary in order to reveal connections within the cell migration signaling network, as well as to understand the behavior that arises from those connections. Here, we review recent quantitative analysis and mathematical modeling approaches to the cell migration problem. PMID:23660413

Envisioning migration: mathematics in both experimental analysis and modeling of cell behavior.

PubMed

Zhang, Elizabeth R; Wu, Lani F; Altschuler, Steven J

2013-10-01

The complex nature of cell migration highlights the power and challenges of applying mathematics to biological studies. Mathematics may be used to create model equations that recapitulate migration, which can predict phenomena not easily uncovered by experiments or intuition alone. Alternatively, mathematics may be applied to interpreting complex data sets with better resolution--potentially empowering scientists to discern subtle patterns amid the noise and heterogeneity typical of migrating cells. Iteration between these two methods is necessary in order to reveal connections within the cell migration signaling network, as well as to understand the behavior that arises from those connections. Here, we review recent quantitative analysis and mathematical modeling approaches to the cell migration problem. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interpretation of Ground Temperature Anomalies in Hydrothermal Discharge Areas

NASA Astrophysics Data System (ADS)

Price, A. N.; Lindsey, C.; Fairley, J. P., Jr.

2017-12-01

Researchers have long noted the potential for shallow hydrothermal fluids to perturb near-surface temperatures. Several investigators have made qualitative or semi-quantitative use of elevated surface temperatures; for example, in snowfall calorimetry, or for tracing subsurface flow paths. However, little effort has been expended to develop a quantitative framework connecting surface temperature observations with conditions in the subsurface. Here, we examine an area of shallow subsurface flow at Burgdorf Hot Springs, in the Payette National Forest, north of McCall, Idaho USA. We present a simple analytical model that uses easily-measured surface data to infer the temperatures of laterally-migrating shallow hydrothermal fluids. The model is calibrated using shallow ground temperature measurements and overburden thickness estimates from seismic refraction studies. The model predicts conditions in the shallow subsurface, and suggests that the Biot number may place a more important control on the expression of near-surface thermal perturbations than previously thought. In addition, our model may have application in inferring difficult-to-measure parameters, such as shallow subsurface discharge from hydrothermal springs.

Possible deep fault slip preceding the 2004 Parkfield earthquake, inferred from detailed observations of tectonic tremor

USGS Publications Warehouse

Shelly, David R.

2009-01-01

Earthquake predictability depends, in part, on the degree to which sudden slip is preceded by slow aseismic slip. Recently, observations of deep tremor have enabled inferences of deep slow slip even when detection by other means is not possible, but these data are limited to certain areas and mostly the last decade. The region near Parkfield, California, provides a unique convergence of several years of high-quality tremor data bracketing a moderate earthquake, the 2004 magnitude 6.0 event. Here, I present detailed observations of tectonic tremor from mid-2001 through 2008 that indicate deep fault slip both before and after the Parkfield earthquake that cannot be detected with surface geodetic instruments. While there is no obvious short-term precursor, I find unidirectional tremor migration accompanied by elevated tremor rates in the 3 months prior to the earthquake, which suggests accelerated creep on the fault ∼16 km beneath the eventual earthquake hypocenter.

Post-breeding migration and connectivity of red knots in the Western Atlantic

USGS Publications Warehouse

Lyons, James E.; Winn, Bradford; Keyes, Timothy; Kalasz, Kevin S.

2018-01-01

Red knots (Calidris canutus rufa) have 3 distinct nonbreeding regions: 1 in the southeastern United States and Caribbean, another on the northeast coast of Brazil in the Maranhão region, and a third along the Patagonian coasts of Chile and Argentina. Effective conservation and recovery of this threatened long-distance migrant will require knowledge of population structure, migration ecology, and abundance and distribution throughout the annual cycle. We conducted a stopover population and biogeographic assessment of knots at the Altamaha River Delta, Georgia, an important stopover area in the southeastern United States. We estimated stopover population size and stopover duration during post-breeding migration in 2011 at the Altamaha study area using mark-resight data, and we inferred nonbreeding regions for this stopover population using stable isotope ratios of carbon and nitrogen in feathers, and observations (sightings and captures) during boreal winter from across the hemisphere. With an integrated Bayesian analysis of all these data, we also estimated the number of birds in the southeastern United States and northern Brazil during boreal winter. For mark-resight analyses in Georgia, we made observations of marked individuals during 14 weeks from early August to early November 2011 and detected 814 individually marked birds. We used the Jolly-Seber mark-recapture model and estimated the southbound passage population at approximately 23,400 red knots. In ongoing studies elsewhere, isotope samples were collected from 175 (21%) of the 814 birds detected in our study, and ≥1 sighting or capture record during boreal winter was located in data repositories for 659 birds (81%). Isotopic signatures and boreal winter records indicate that the majority (82–96%) of the birds that stopped at the Altamaha Delta spend the boreal winter in the northern part of the nonbreeding range (southeast USA, Caribbean, and northern Brazil). Knots migrating to the southeastern United States, Caribbean, or Brazil remained on the Altamaha Delta for 42 days, whereas birds migrating to Tierra del Fuego remained only 21 days. Combining our estimate of the Altamaha stopover population size (23,400 birds) and the estimated proportion in the northern nonbreeding region (82–96%), we derived a minimum estimate of the number of knots in the southeastern United States, Caribbean, and northern South America during the boreal winter: approximately 20,800 knots, of which approximately 10,400 knots occupy the southeastern United States and 5,400 occupy Brazil. Our results provide additional evidence that coastal Georgia is an important migration area for red knots, and provide information about population structure and migratory connectivity that will be valuable for conservation planning. 

First wide-angle view of channelized turbidity currents links migrating cyclic steps to flow characteristics

PubMed Central

Hughes Clarke, John E.

2016-01-01

Field observations of turbidity currents remain scarce, and thus there is continued debate about their internal structure and how they modify underlying bedforms. Here, I present the results of a new imaging method that examines multiple surge-like turbidity currents within a delta front channel, as they pass over crescent-shaped bedforms. Seven discrete flows over a 2-h period vary in speed from 0.5 to 3.0 ms−1. Only flows that exhibit a distinct acoustically attenuating layer at the base, appear to cause bedform migration. That layer thickens abruptly downstream of the bottom of the lee slope of the bedform, and the upper surface of the layer fluctuates rapidly at that point. The basal layer is inferred to reflect a strong near-bed gradient in density and the thickening is interpreted as a hydraulic jump. These results represent field-scale flow observations in support of a cyclic step origin of crescent-shaped bedforms. PMID:27283503

Relic magma chamber structures preserved within the Mesozoic North Atlantic crust?

USGS Publications Warehouse

McCarthy, J.; Mutter, J.C.; Morton, J.L.; Sleep, Norman H.; Thompson, G.A.

1988-01-01

The North Atlantic Transect seismic reflection data, collected southwest of Bermuda, have been reinterpreted following post-stack migration and reveal two major intracrustal reflections. The shallower of these two events, located ~1 s below the igneous basement, is a subhorizontal, undulating surface that in some places is continuous for as much as 10 km. This upper crustal reflection corresponds to the intermittently sharp contact between the sheeted dikes and the underlying isotropic gabbro. A second set of lower crustal reflections, dipping ~20??-40?? eastward, is also prominent on the migrated profile and terminates downdip against the subhorizontal reflection Moho. Their presence may be ascribed to mafic-ultramafic cumulate layers frozen into the oceanic crust at the time of formation at the paleo-spreading center. The gradual thinning in the crust approaching the fracture zones is shown to be more complex than was originally inferred. An intepretation advocating crustal thickening in this narrow zone is proposed as an alternative to the crustal-thinning model of Mutter and others. -from Authors

The shaping of genetic variation in edge-of-range populations under past and future climate change

PubMed Central

Razgour, Orly; Juste, Javier; Ibáñez, Carlos; Kiefer, Andreas; Rebelo, Hugo; Puechmaille, Sébastien J; Arlettaz, Raphael; Burke, Terry; Dawson, Deborah A; Beaumont, Mark; Jones, Gareth; Wiens, John

2013-01-01

With rates of climate change exceeding the rate at which many species are able to shift their range or adapt, it is important to understand how future changes are likely to affect biodiversity at all levels of organisation. Understanding past responses and extent of niche conservatism in climatic tolerance can help predict future consequences. We use an integrated approach to determine the genetic consequences of past and future climate changes on a bat species, Plecotus austriacus. Glacial refugia predicted by palaeo-modelling match those identified from analyses of extant genetic diversity and model-based inference of demographic history. Former refugial populations currently contain disproportionately high genetic diversity, but niche conservatism, shifts in suitable areas and barriers to migration mean that these hotspots of genetic diversity are under threat from future climate change. Evidence of population decline despite recent northward migration highlights the need to conserve leading-edge populations for spearheading future range shifts. PMID:23890483

The Role of Genetic Drift in Shaping Modern Human Cranial Evolution: A Test Using Microevolutionary Modeling

PubMed Central

Smith, Heather F.

2011-01-01

The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world. PMID:21461369

Methanesulfonic acid (MSA) migration in polar ice: data synthesis and theory

NASA Astrophysics Data System (ADS)

Osman, Matthew; Das, Sarah B.; Marchal, Olivier; Evans, Matthew J.

2017-11-01

Methanesulfonic acid (MSA; CH3SO3H) in polar ice is a unique proxy of marine primary productivity, synoptic atmospheric transport, and regional sea-ice behavior. However, MSA can be mobile within the firn and ice matrix, a post-depositional process that is well known but poorly understood and documented, leading to uncertainties in the integrity of the MSA paleoclimatic signal. Here, we use a compilation of 22 ice core MSA records from Greenland and Antarctica and a model of soluble impurity transport in order to comprehensively investigate the vertical migration of MSA from summer layers, where MSA is originally deposited, to adjacent winter layers in polar ice. We find that the shallowest depth of MSA migration in our compilation varies over a wide range (˜ 2 to 400 m) and is positively correlated with snow accumulation rate and negatively correlated with ice concentration of Na+ (typically the most abundant marine cation). Although the considered soluble impurity transport model provides a useful mechanistic framework for studying MSA migration, it remains limited by inadequate constraints on key physico-chemical parameters - most notably, the diffusion coefficient of MSA in cold ice (DMS). We derive a simplified version of the model, which includes DMS as the sole parameter, in order to illuminate aspects of the migration process. Using this model, we show that the progressive phase alignment of MSA and Na+ concentration peaks observed along a high-resolution West Antarctic core is most consistent with 10-12 m2 s-1 < DMS < 10-11 m2 s-1, which is 1 order of magnitude greater than the DMS values previously estimated from laboratory studies. More generally, our data synthesis and model results suggest that (i) MSA migration may be fairly ubiquitous, particularly at coastal and (or) high-accumulation regions across Greenland and Antarctica; and (ii) can significantly change annual and multiyear MSA concentration averages. Thus, in most cases, caution should be exercised when interpreting polar ice core MSA records, although records that have undergone severe migration could still be useful for inferring decadal and lower-frequency climate variability.

Migration without migraines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lines, L.; Burton, A.; Lu, H.X.

Accurate velocity models are a necessity for reliable migration results. Velocity analysis generally involves the use of methods such as normal moveout analysis (NMO), seismic traveltime tomography, or iterative prestack migration. These techniques can be effective, and each has its own advantage or disadvantage. Conventional NMO methods are relatively inexpensive but basically require simplifying assumptions about geology. Tomography is a more general method but requires traveltime interpretation of prestack data. Iterative prestack depth migration is very general but is computationally expensive. In some cases, there is the opportunity to estimate vertical velocities by use of well information. The well informationmore » can be used to optimize poststack migrations, thereby eliminating some of the time and expense of iterative prestack migration. The optimized poststack migration procedure defined here computes the velocity model which minimizes the depth differences between seismic images and formation depths at the well by using a least squares inversion method. The optimization methods described in this paper will hopefully produce ``migrations without migraines.``« less

Archaeopedological analysis of land use dynamics in marginal areas in SW Germany

NASA Astrophysics Data System (ADS)

Henkner, Jessica; Ahlrichs, Jan; Scholten, Thomas; Knopf, Thomas; Kühn, Peter

2016-04-01

A common theory to explain human migration is climate change triggering migration and the shift of farming places. Populated areas might have been relocated or extended because of changing resources like a warming climate, soil erosion or a change in demands. But it also has to be taken into account that altered trading relations or changing religious attitudes might have caused migration into and settlement of formerly not used areas. In the case of Southwest Germany it is assumed that people migrated from the favorable Baar (more even areas, soils on loess, lower elevations) to the unfavorable Black Forest and the Swabian Jura with harsher environmental conditions (small valleys, acidic soils, steep slopes, higher elevation). Soils are generally considered as being an important resource related to human activities, especially farming, but also for using wood, water or iron ore. Colluvial deposits as geoarchives reveal the formative impact of humans on their environment: on the development of soil, relief, vegetation, and land use. Land use and therefore settlement history are inscribed in colluvial deposits, which we use as proxies for the kind and intensity of human activities. Especially in marginal areas land use and settlement dynamics are not well investigated. Important questions are how and why did people use the unfavorable land during different times? Which resources were important for different phases of settlement? In this project, soil science methods are used together with archaeological approaches, which is an essential part of archaeopedology. Using colluvial deposits from three study areas it is possible to create pedological and chronological stratigraphies reflecting land use dynamics in favorable and unfavorable areas. First AMS radiocarbon dates from the western Baar in transition to the Black Forest point to human land use with different intensity for 5500 years. Thick lower colluvial layers date back to the third millennium BC. Above-lying colluvial layers date to the 11-12th and to the 13-14th Century. Around Villingen colluvial deposits could be found in approximately 60-80 cm depth dating to 1620-1500 cal BC and in about 50 cm depth dating to 427-543 cal AD. So the age of the lowest colluvial layers are older than the widely accepted beginning of intense settlement in Southwest Germany. Inferred from the periods of intensified colluvial deposition events other reasons than warmer climate may be responsible for migration from favorable to unfavorable regions.

Bedform migration in steep channels: from local avalanches to large scale changes

NASA Astrophysics Data System (ADS)

Mettra, F.; Heyman, J.; Ancey, C.

2013-12-01

Many studies have emphasized the strength of bedload transport fluctuations in steep streams, especially at low and intermediate transport conditions (relative to the threshold of incipient motion). The origins of these fluctuations, which appear on a wide range of time scales, are still not well understood. In this study, we present the data obtained from a 2D idealized laboratory experiment with the objective of simultaneously recording the channel bed evolution and bedload transport rate at a high temporal resolution. A 3-m long by 8-cm wide transparent flume filled with well-sorted natural gravel (d50=6.5 mm) was used. An efficient technique using accelerometers has been developed to record the arrival time of every particle at the outlet of the flume for long experimental durations (up to a few days). In addition, bed elevation was monitored using cameras filming from the side of the channel, allowing the observation of global aggradation/degradation as well as bedform migration. The experimental parameters were the water discharge, the flume inclination (from 2° to 5°) and the constant feeding rate of sediments. Large-scale bed evolution showed successive aggradation and rapid degradation periods. Indeed, the measured global channel slope, i.e. mean slope over the flume length, fluctuated continuously within a range sometimes wider than 1° (experimental parameters were constant over the entire run). The analysis of these fluctuations provides evidence that steep channels behave like metastable systems, similarly to grain piles. The metastable effects increased for steeper channels and lower transport conditions. In this measurement campaign, we mainly observed upstream-migrating antidunes. For each run, various antidune heights and celerities were measured. On average, the mean antidune migration rate increased with decreasing channel slope and increasing sediment feeding rate. Relatively rare tall and fast-moving antidunes appeared more frequently at high flume angles and produced intense solid discharge pulses. Moreover, small avalanches occurred on the steep lee sides of antidunes. From these results, we infer a mechanism of steep channel evolution. The time- and space-averaged profile of the bed in the streamwise direction depends on the experimental parameters. Variations in the profile result mainly from bedform migration. The instantaneous global state of the bed (which can be characterized by the global channel slope) controls the growth of bedforms, which can be seen as local instabilities. When the global channel slope approaches its critical value, local instabilities of higher amplitude can develop and create intense bedload transport pulses, leading to a less steep, but more stable bed profile.

Mid-term migration analysis of a femoral short-stem prosthesis: a five-year EBRA-FCA-study.

PubMed

Freitag, Tobias; Fuchs, Michael; Woelfle-Roos, Julia V; Reichel, Heiko; Bieger, Ralf

2018-05-01

The objective of this study was to evaluate the mid-term migration pattern of a femoral short stem. Implant migration of 73 femoral short-stems was assessed by Ein-Bild-Roentgen-Analysis Femoral-Component-Analysis (EBRA-FCA) 5 years after surgery. Migration pattern of the whole group was analysed and compared to the migration pattern of implants "at risk" with a subsidence of more than 1.5 mm 2 years postoperative. Mean axial subsidence was 1.1 mm (-5.0 mm to 1.5 mm) after 60 months. There was a statistical significant axial migration until 2 years postoperative with settling thereafter. 2 years after surgery 18 of 73 Implants were classified "at risk." Nevertheless, all stems showed secondary stabilisation in the following period with no implant failure neither in the group of implants with early stabilisation nor the group with extensive early onset migration. In summary, even in the group of stems with more pronounced early subsidence, delayed settling occurred in all cases. The determination of a threshold of critical early femoral short stem subsidence is necessary because of the differing migration pattern described in this study with delayed settling of the Fitmore stem 2 years postoperatively compared to early settling within the first postoperative year described for conventional stems.

GPR Imaging of Fault Related Folds in a Gold-Bearing Metasedimentary Sequence, Carolina Terrane, Southern Appalachian Mountains

NASA Astrophysics Data System (ADS)

Diemer, J. A.; Bobyarchick, A. R.

2015-12-01

The Carolina terrane comprises Ediacaran to earliest Paleozoic mixed magmatic and sedimentary assemblages in the central and eastern Piedmont of the Southern Appalachian Mountains. The terrane was primarily deformed during the Late Ordovician Cherokee orogeny, that reached greenschist facies metamorphism. The Albemarle arc, a younger component of the Carolina terrane, contains volcanogenic metasedimentary rocks with intercalated mainly rhyolitic volcanic rocks. Regional inclined to overturned folds with axial planar cleavage verge southeast. At mesoscopic scales (exposures of a few square meters), folds sympathetic with regional folds are attenuated or truncated by ductile shear zones or contractional faults. Shear and fault zones are most abundant near highly silicified strataform zones in metagraywacke of the Tillery Formation; these zones are also auriferous. GPR profiles were collected across strike of two silicified, gold-bearing zones and enclosing metagraywacke to characterize the scale and extent of folding in the vicinity of ore horizons. Several GSSI SIR-3000 / 100 MHz monostatic GPR profiles were collected in profiles up to 260 meters long. In pre-migration lines processed for time zero and background removal, several clusters of shallow, rolling sigmoidal reflectors appeared separated by sets of parallel, northwest-dipping reflective discontinuities. These features are inferred to be reverse faults carrying contractional folds. After migration with an average velocity of 0.105 m/ns, vertical heights of the inferred folds became attenuated but not removed, and contractional fault reflections remained prominent. After migration, a highly convex-up cluster of reflections initially assumed to be a fold culmination resolved to an elliptical patch of high amplitudes. The patch is likely an undisclosed shaft or covered trench left by earlier gold prospecting. In this survey, useful detail appeared to a depth of 7.5 meters, and only a few gently inclined, laterally extensive reflectors are present inside the noise blanket. Also, convex-up planar reflectors greater than about 8 meters deep and tens of meters long suggest fold culminations much longer in wavelength than the shallow imaged folds. For these metasedimentary rocks GPR provides a valuable tool for imaging sub-surface structure.

Loop Evolution Observed with AIA and Hi-C

NASA Technical Reports Server (NTRS)

Mulu-Moore, Fana; Winebarger, Amy R.; Cirtain, Jonathan W.; Kobayashi, Ken; Korreck, Kelly E.; Golub, Leon; Kuzin, Sergei; Walsh, Robert William; DeForest, Craig E.; De Pontieu, Bart;

Across language families: Genome diversity mirrors linguistic variation within Europe

PubMed Central

Longobardi, Giuseppe; Ghirotto, Silvia; Guardiano, Cristina; Tassi, Francesca; Benazzo, Andrea; Ceolin, Andrea

2015-01-01

ABSTRACT Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo‐European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic distances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Linguistic and genomic trees were also estimated and compared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and linguistic diversity, the latter inferred from data on both Indo‐European and non‐Indo‐European languages. Contrary to previous observations, on the European scale, language proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture following the main population splits found convincing correlates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross‐disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 157:630–640, 2015. © 2015 Wiley Periodicals, Inc. PMID:26059462

Forming Super-Puffs Beyond 1 AU

NASA Astrophysics Data System (ADS)

Lee, Eve J.; Chiang, Eugene

2017-06-01

Super-puffs are an uncommon class of short-period planets seemingly too voluminous for their small masses (4-10 Rearth, 2-6 Mearth). Super-puffs most easily acquire their thick atmospheres as dust-free, rapidly cooling worlds outside ˜1AU where nebular gas is colder, less dense, and therefore less opaque. These puffy planets probably migrated in to their current orbits; they are expected to form the outer links of mean-motion resonant chains, and to exhibit atmospheric characteristics consistent with formation at large distances. I will also discuss, in general, how densities of planets can be used to infer their formation locations.

Optical and X-ray studies of chromospherically active stars: FR Cancri, HD 95559 and LO Pegasi

NASA Technical Reports Server (NTRS)

Pandey, J. C.; Singh, K. P.; Drake, S. A.; Sagar, R.

2005-01-01

We present a multiwavelength study of three chromospherically active stars, namely FR Cnc (= BD +16 degrees 1753), HD 95559 and LO Peg (=BD +22 degrees 4409), including newly obtained optical photometry, (for FR Cnc) low-resolution optical spectroscopy, as well as archival IR and X-ray observations. The BVR photometry carried out during the years 2001 - 2004 has found significant photometric variability to be present in all three stars. For FR Cnc, a photometric period 0.826685 +/- 0.000034 d has been established. The strong variation in the phase and amplitude of the FR Cnc light curves when folded on this period implies the presence of evolving and migrating spots or spot groups on its surface. Two independent spots with migration periods of 0.97 and 0.93 years respectively are inferred. The photometry of HD 95559 suggests the formation of a spot (group) during the interval of our observations. We infer the existence of two independent spots or groups in the photosphere of LO Peg, one of which has a migration period of 1.12 years. The optical spectroscopy of FR Cnc carried out during 2002-2003, reveals the presence of strong and variable Ca I1 H and K, H(sub beta) and H(sub alpha) emission features indicative of high level of chromospheric activity. The value of 5.3 for the ratio of the excess emission in H(sub alpha) to H(sub beta), EH(sub alpha)/EH(sub beta), suggests that the chromospheric emission may arise from an extended off-limb region. We have searched for the presence of color excesses in the near-IR JHK bands of these stars using 2MASS data, but none of them appear to have any significant color excess. We have also analyzed archival X-ray observations of HD 95559 and LO Peg carried out by with the ROSAT observatory. The best fit models to their X-ray spectra imply the presence of two coronal plasma components of differing temperatures and with sub-solar metal abundances. The inferred emission measures and temperatures of these systems are similar to those found for other active dwarf stars. The kinematics of FR Cnc suggest that it is a very young (35 - 55 Myrs) main-sequence star and a possible member of the IC 2391 supercluster. LO Peg also has young disk-type kinematics and has been previously suggested to be a member of the 100 Mys old Local Association (Pleiades Moving Group). The kinematics of HD 95559 indicate it is a possible member of the 600 Myrs old Hyades supercluster.

Migration in Vulnerable Deltas: A Research Strategy

NASA Astrophysics Data System (ADS)

Hutton, C.; Nicholls, R. J.; Allan, A.

2015-12-01

C. Hutton1, & R. J. Nicholls1, , 1 University of Southampton, University Road, Southampton, Hampshire, United Kingdom, SO17 1BJ. cwh@geodata. soton.ac.ukAbstractGlobally, deltas contain 500 million people and with rising sea levels often linked to large number of forced migrants are expected in the coming century. However, migration is already a major process in deltas, such as the growth of major cities such as Dhaka and Kolkata. Climate and environmental change interacts with a range of catchment and delta level drivers, which encompass a nexus of sea-level rise, storms, freshwater and sediment supply from the catchment, land degradation, subsidence, agricultural loss and socio-economic stresses. DECCMA (Deltas, Vulnerability and Climate Change: Migration and Adaptation/CARRIA) is investigating migration in the Ganges-Brahmaputra-Meghna (GBM), Mahanadi and Volta Deltas, including the influence of climate change. The research will explore migration from a range of perspectives including governance and stakeholder analysis, demographic analysis, household surveys of sending and receiving areas, macro-economic analysis, and hazards and hotspot analysis both historically and into the future. Migration under climate change will depend on other adaptation in the deltas and this will be examined. Collectively, integrated analysis will be developed to examine migration, other adaptation and development pathways with a particular focus on the implications for the poorest. This will require the development of input scenarios, including expert-derived exogenous scenarios (e.g., climate change) and endogenous scenarios of the delta developed in a participatory manner. This applied research will facilitate decision support methods for the development of deltas under climate change, with a focus on migration and other adaptation strategies.

Migration as a form of workforce attrition: a nine-country study of pharmacists

PubMed Central

Wuliji, Tana; Carter, Sarah; Bates, Ian

2009-01-01

Background There is a lack of evidence to inform policy development on the reasons why health professionals migrate. Few studies have sought to empirically determine factors influencing the intention to migrate and none have explored the relationship between factors. This paper reports on the first international attempt to investigate the migration intentions of pharmacy students and identify migration factors and their relationships. Methods Responses were gathered from 791 final-year pharmacy students from nine countries: Australia, Bangladesh, Croatia, Egypt, Portugal, Nepal, Singapore, Slovenia and Zimbabwe. Data were analysed by means of Principal Components Analysis (PCA) and two-step cluster analysis to determine the relationships between factors influencing migration and the characteristics of subpopulations most likely and least likely to migrate. Results Results showed a significant difference in attitudes towards the professional and sociopolitical environment of the home country and perceptions of opportunities abroad between those who have no intention of migrating and those who intend to migrate on a long-term basis. Attitudes of students planning short-term migration were not significantly different from those of students who did not intend to migrate. These attitudes, together with gender, knowledge of other migrant pharmacists and past experiences abroad, are associated with an increased propensity for migration. Conclusion Given the influence of the country context and environment on migration intentions, research and policy should frame the issue of migration in the context of the wider human resource agenda, thus viewing migration as one form of attrition and a symptom of other root causes. Remuneration is not an independent stand-alone factor influencing migration intentions and cannot be decoupled from professional development factors. Comprehensive human resource policy development that takes into account the issues of both remuneration and professional development are necessary to encourage retention. PMID:19358704

Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

PubMed Central

2012-01-01

Background The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. Results The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma). Conclusions The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants. PMID:22316163

Risk factors for covered metallic stent migration in patients with distal malignant biliary obstruction due to pancreatic cancer.

PubMed

Nakai, Yousuke; Isayama, Hiroyuki; Kogure, Hirofumi; Hamada, Tsuyoshi; Togawa, Osamu; Ito, Yukiko; Matsubara, Saburo; Arizumi, Toshihiko; Yagioka, Hiroshi; Mizuno, Suguru; Sasaki, Takashi; Yamamoto, Natsuyo; Hirano, Kenji; Tada, Minoru; Koike, Kazuhiko

2014-09-01

Covered metallic stents (CMSs) were developed to overcome tumor ingrowth in uncovered metallic stents (UMSs) for malignant biliary obstruction, but superiority of CMSs over UMSs is still controversial due to the high migration rate in CMS. Therefore, we conducted this retrospective analysis to clarify risk factors for stent migration, including mechanical properties of CMSs. Patients with unresectable pancreatic cancer, receiving CMS for distal malignant biliary obstruction in five tertiary care centers, were retrospectively studied. Univariate and multivariate analyses to identify prognostic factors for early (< 6 months) stent migration were performed using a proportional hazards model with death or stent occlusion without stent migration as a competing risk. Two mechanical properties were included in the analysis: axial force, the recovery force that leads to a CMS straightening, and radial force (RF), the expansion force against the stricture. Among 290 patients who received CMS placement for distal malignant biliary obstruction, stent migration rate was 15.2%. CMS migrated early (< 6 months) in 10.0% and distally in 11.7%, respectively. In the multivariate analysis, significant risk factors for early stent migration were chemotherapy (subdistribution hazard ratios [SHR] 4.46, P = 0.01), CMS with low RF (SHR 2.23, P = 0.03), and duodenal invasion (SHR 2.25, P = 0.02). CMS with low RF, chemotherapy, and duodenal invasion were associated with CMS migration from our study. © 2014 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

Proximate cues for a short-distance migratory species: An application of survival analysis

USGS Publications Warehouse

Meunier, J.; Song, R.; Lutz, R.S.; Andersen, D.E.; Doherty, K.E.; Bruggink, J.G.; Oppelt, E.

2008-01-01

Investigation of bird migration has often highlighted the importance of external factors in determining timing of migration However, little distinction has been made between short- and long-distance migrants and between local and flight birds (passage migrants) in describing migration chronology. In addition, measures of food abundance as a proximate factor influencing timing of migration are lacking in studies of migration chronology. To address the relationship between environmental variables and timing of migration we quantified the relative importance of proximate external factors on migration chronology of local American woodcock (Scolopax minor), a short distance migrant, using event-time analysis methods (survival analysis). We captured 1,094 woodcock local to our study sites in Michigan, Minnesota and Wisconsin (USA) during autumn 2002-2004 and documented 786 departure dates for these birds. Photoperiod appeared to provide an initial proximate cue for timing of departure. Moon phase was important in modifying timing of departure, which may serve as a navigational aid in piloting and possibly orientation. Local synoptic weather variables also contributed to timing of departure by changing the rate of departure from our study sites. We found no evidence that food availability influenced timing of woodcock departure. Our results suggest that woodcock use a conservative photoperiod-controlled strategy with proximate modifiers for timing of migration rather than relying on abundance of their primary food, earthworms. Managing harvest pressure on local birds by adjusting season lengths may be an effective management tool with consistent migration patterns from year to year based on photoperiod.

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreland, Kenneth; Geveci, Berk

2014-11-01

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipelinemore » model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.« less

Phylogeographic dispersion and diversification of rabies virus lineages associated with dogs and crab-eating foxes (Cerdocyon thous) in Brazil.

PubMed

Carnieli, Pedro; Ruthner Batista, Helena B C; de Novaes Oliveira, Rafael; Castilho, Juliana Galera; Vieira, Luiz Fernando Pereira

2013-11-01

Genetic lineages of dog-associated RABV still circulate in some areas of the North and Northeast of Brazil. In parallel, another RABV lineage circulates among wild canids in the Northeast, particularly the crab-eating fox (Cerdocyon thous). Although previous studies and phylogenetic analyses have been carried out, the way in which these lineages are dispersed temporally and spatially remained to be elucidated. In this study, RABV N gene sequences isolated from canids in North and Northeast Brazil were analyzed by the Bayesian Markov Chain Monte Carlo Method, and the results were then used in a phylogeographic study. It was inferred from the findings that the most recent common ancestor became established at the end of the nineteenth century on the border of the Brazilian states of Paraíba and Pernambuco and diversified into the lineages associated with dogs and C. thous. Around 1910, the original C. thous lineage diversified into two main sublineages in the same area, one of which migrated to the south and the other to the north. The dog-associated lineage diversified around 1945 and moved toward the north and south. From the phylogeographic analysis it was possible to infer not only the movement of the virus lineages but also the probable location where dispersion and diversification occurred. The methodology used here enabled the phylogeographic history of RABV in the region to be reconstructed, and the dispersion pattern of the virus can be used to predict its movements, making it easier to stop the advance of a rabies epidemic.

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

PubMed Central

2011-01-01

Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression. PMID:21939538

MIGRATION OF COLLEGE AND UNIVERSITY STUDENTS, STATE OF WASHINGTON.

ERIC Educational Resources Information Center

GOSSMAN, CHARLES S.; AND OTHERS

TWO GENERAL ASPECTS OF COLLEGE AND UNIVERSITY STUDENT MIGRATION AS IT RELATES TO THE STATE OF WASHINGTON ARE DISCUSSED. THE FIRST ASPECT INCLUDES ANALYSIS OF MIGRATION PATTERNS IN ACCORDANCE WITH ENROLLMENT CATEGORIES AND TYPES OF INSTITUTIONS, DIFFERENTIAL VOLUMES AND PATTERNS OF MIGRATION FOR SPECIFIC COLLEGES AND UNIVERSITIES IN THE STATE, AND…

Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico.

PubMed

Lu, Lu; Lycett, Samantha J; Leigh Brown, Andrew J

2014-01-01

Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the affected regions. In June/July 2012, new HP H7N3 outbreaks occurred at commercial farms in Jalisco, Mexico. Outbreaks continued to be identified in neighbouring states in Mexico till August 2013. To explore the origin of this outbreak, time resolved phylogenetic trees were generated from the eight segments of full-length AIV sequences in North America using BEAST. Location, subtype, avian host species and pathogenicity were modelled as discrete traits upon the trees using continuous time Markov chains. A further joint analysis among segments was performed using a hierarchical phylogenetic model (HPM) which allowed trait rates (location, subtype, host species) to be jointly inferred across different segments. The complete spatial diffusion process was visualised through virtual globe software. Our result indicated the Mexico HP H7N3 originated from the large North America low pathogenicity AIV pool through complicated reassortment events. Different segments were contributed by wild waterfowl from different N. American flyways. Five of the eight segments (HA, NA, NP, M, NS) were introduced from wild birds migrating along the central North American flyway, and PB2, PB1 and PA were introduced via the western North American flyway. These results highlight a potential role for Mexico as a hotspot of virus reassortment as it is where wild birds from different migration routes mix during the winter.

Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

PubMed Central

Lu, Lu; Lycett, Samantha J.; Leigh Brown, Andrew J.

2014-01-01

Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the affected regions. In June/July 2012, new HP H7N3 outbreaks occurred at commercial farms in Jalisco, Mexico. Outbreaks continued to be identified in neighbouring states in Mexico till August 2013. To explore the origin of this outbreak, time resolved phylogenetic trees were generated from the eight segments of full-length AIV sequences in North America using BEAST. Location, subtype, avian host species and pathogenicity were modelled as discrete traits upon the trees using continuous time Markov chains. A further joint analysis among segments was performed using a hierarchical phylogenetic model (HPM) which allowed trait rates (location, subtype, host species) to be jointly inferred across different segments. The complete spatial diffusion process was visualised through virtual globe software. Our result indicated the Mexico HP H7N3 originated from the large North America low pathogenicity AIV pool through complicated reassortment events. Different segments were contributed by wild waterfowl from different N. American flyways. Five of the eight segments (HA, NA, NP, M, NS) were introduced from wild birds migrating along the central North American flyway, and PB2, PB1 and PA were introduced via the western North American flyway. These results highlight a potential role for Mexico as a hotspot of virus reassortment as it is where wild birds from different migration routes mix during the winter. PMID:25226523

Tracing Jomon and Yayoi ancestries in Japan using ALDH2 and JC virus genotype distributions.

PubMed

Miyamori, Daisuke; Ishikawa, Noboru; Idota, Nozomi; Kakiuchi, Yasuhiro; McLean, Stuart; Kitamura, Tadaichi; Ikegaya, Hiroshi

2015-01-01

According to the dual structure model, the modern Japanese ethnic population consists of a mixture of the Jomon people, who have existed in Japan since at least the New Stone Age, and the Yayoi people, who migrated to western Japan from China around the year 300 bc Some reports show that the Yayoi are linked to a mutation of the aldehyde dehydrogenase 2 gene (ALDH2). Recent viral studies indicate two major groups found in the Japanese population: a group with the CY genotype JC virus (JCV) and a group with the MY genotype JCV. It is unclear whether either genotype of the JC virus is related to the Jomon or Yayoi. In this study, we attempted to detect JCV genotypes and ALDH2 mutations from the DNA of 247 Japanese urine samples to clarify the relationship between the dual structure model and the JCV genotype through ALDH2 mutation analysis and JCV genotyping. The ALDH2 polymorphism among 66 JC virus-positive samples was analyzed, and it was found that the ALDH2 variant is significantly higher in the population with CY genotype JCV (51.5 %) than in the population with the MY genotype (24.2 %) (p < 0.05). From these findings, it may be inferred that the ALDH2 mutation, which is related to the Yayoi, is related to CY genotype JCV. When the Yayoi migrated to the Japanese archipelago, they brought the ALDH2 mutation as well as the CY genotype JCV.

Kinematics and dynamics of the East Pacific Rise linked to a stable, deep-mantle upwelling

PubMed Central

Rowley, David B.; Forte, Alessandro M.; Rowan, Christopher J.; Glišović, Petar; Moucha, Robert; Grand, Stephen P.; Simmons, Nathan A.

2016-01-01

Earth’s tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth’s dominant MOR, has been characterized by limited ridge-perpendicular migration and persistent, asymmetric ridge accretion that are anomalous relative to other MORs. We reconstruct the subduction-related buoyancy fluxes of plates on either side of the EPR. The general expectation is that greater slab pull should correlate with faster plate motion and faster spreading at the EPR. Moreover, asymmetry in slab pull on either side of the EPR should correlate with either ridge migration or enhanced plate velocity in the direction of greater slab pull. Based on our analysis, none of the expected correlations are evident. This implies that other forces significantly contribute to EPR behavior. We explain these observations using mantle flow calculations based on globally integrated buoyancy distributions that require core-mantle boundary heat flux of up to 20 TW. The time-dependent mantle flow predictions yield a long-lived deep-seated upwelling that has its highest radial velocity under the EPR and is inferred to control its observed kinematics. The mantle-wide upwelling beneath the EPR drives horizontal components of asthenospheric flows beneath the plates that are similarly asymmetric but faster than the overlying surface plates, thereby contributing to plate motions through viscous tractions in the Pacific region. PMID:28028535

Kinematics and dynamics of the East Pacific Rise linked to a stable, deep-mantle upwelling.

PubMed

Rowley, David B; Forte, Alessandro M; Rowan, Christopher J; Glišović, Petar; Moucha, Robert; Grand, Stephen P; Simmons, Nathan A

2016-12-01

Earth's tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth's dominant MOR, has been characterized by limited ridge-perpendicular migration and persistent, asymmetric ridge accretion that are anomalous relative to other MORs. We reconstruct the subduction-related buoyancy fluxes of plates on either side of the EPR. The general expectation is that greater slab pull should correlate with faster plate motion and faster spreading at the EPR. Moreover, asymmetry in slab pull on either side of the EPR should correlate with either ridge migration or enhanced plate velocity in the direction of greater slab pull. Based on our analysis, none of the expected correlations are evident. This implies that other forces significantly contribute to EPR behavior. We explain these observations using mantle flow calculations based on globally integrated buoyancy distributions that require core-mantle boundary heat flux of up to 20 TW. The time-dependent mantle flow predictions yield a long-lived deep-seated upwelling that has its highest radial velocity under the EPR and is inferred to control its observed kinematics. The mantle-wide upwelling beneath the EPR drives horizontal components of asthenospheric flows beneath the plates that are similarly asymmetric but faster than the overlying surface plates, thereby contributing to plate motions through viscous tractions in the Pacific region.

Intertwined effects of gender and migration status on persistence in SET study programmes

NASA Astrophysics Data System (ADS)

Guenther, Elisabeth Anna; Koeszegi, Sabine Theresia

2017-11-01

This paper explores the intersectional interference of gender and migration status on students' persistence at an Austrian University of Technology. While controlling for the pre-university education and performance indicators, we estimate the odds for the persistence of male and female students, as well as of students with diverse migration statuses. We use the enrolment data of students from 1998 to 2010. The analysis reveals remarkable and significant effects of gender and migration status, as well as intersectional interference effects from both social categories on persistence. Female and students with immigration status are less likely to persist, even if performance and previous relevant experiences are controlled. A segregated analysis of the student population sheds further light on the interlocked and entangled effects of the social ascriptions underlying gender and migration status. The analysis supports the proposition of the accumulation of (dis-)advantages along students' careers. The profound quantification of gender and migration status effects can be utilised as basis for further research and purposeful policy measures to increase persistence in Science, Engineering and Technology for students with diverse backgrounds.

A Simple Force-Motion Relation for Migrating Cells Revealed by Multipole Analysis of Traction Stress

PubMed Central

Tanimoto, Hirokazu; Sano, Masaki

2014-01-01

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. PMID:24411233

Causal modeling in international migration research: a methodological prolegomenon.

PubMed

Papademetriou, D G; Hopple, G W

1982-10-01

The authors examine the value of using models to study the migration process. In particular, they demonstrate the potential utility of a partial least squares modeling approach to the causal analysis of international migration.

Differential gene expression in migratory streams of cortical interneurons

PubMed Central

Antypa, Mary; Faux, Clare; Eichele, Gregor; Parnavelas, John G; Andrews, William D

2011-01-01

Cortical interneurons originate in the ganglionic eminences of the subpallium and migrate into the cortex in well-defined tangential streams. At the start of corticogenesis, two streams of migrating neurons are evident: a superficial one at the level of the preplate (PPL), and a deeper one at the level of the intermediate zone (IZ). Currently, little is known about the signalling mechanisms that regulate interneuron migration, and almost nothing is known about the molecules that may be involved in their choice of migratory stream. Here, we performed a microarray analysis, comparing the changes in gene expression between cells migrating in the PPL and those migrating in the IZ at embryonic day 13.5. This analysis identified genes, many of them novel, that were upregulated in one of the two streams. Moreover, polymerase chain reaction, in situ hybridization experiments and immunohistochemistry showed the expression of these genes in interneurons migrating within the PPL or IZ, suggesting that they play a role in their migration and choice of stream. PMID:22103416

A Low-Level Carbon Dioxide Laser Promotes Fibroblast Proliferation and Migration through Activation of Akt, ERK, and JNK

PubMed Central

Shingyochi, Yoshiaki; Kanazawa, Shigeyuki; Tajima, Satoshi; Tanaka, Rica; Mizuno, Hiroshi; Tobita, Morikuni

2017-01-01

Background Low-level laser therapy (LLLT) with various types of lasers promotes fibroblast proliferation and migration during the process of wound healing. Although LLLT with a carbon dioxide (CO2) laser was also reported to promote wound healing, the underlying mechanisms at the cellular level have not been previously described. Herein, we investigated the effect of LLLT with a CO2 laser on fibroblast proliferation and migration. Materials and Methods Cultured human dermal fibroblasts were prepared. MTS and cell migration assays were performed with fibroblasts after LLLT with a CO2 laser at various doses (0.1, 0.5, 1.0, 2.0, or 5.0 J/cm2) to observe the effects of LLLT with a CO2 laser on the proliferation and migration of fibroblasts. The non-irradiated group served as the control. Moreover, western blot analysis was performed using fibroblasts after LLLT with a CO2 laser to analyze changes in the activities of Akt, extracellular signal-regulated kinase (ERK), and Jun N-terminal kinase (JNK), which are signaling molecules associated with cell proliferation and migration. Finally, the MTS assay, a cell migration assay, and western blot analysis were performed using fibroblasts treated with inhibitors of Akt, ERK, or JNK before LLLT with a CO2 laser. Results In MTS and cell migration assays, fibroblast proliferation and migration were promoted after LLLT with a CO2 laser at 1.0 J/cm2. Western blot analysis revealed that Akt, ERK, and JNK activities were promoted in fibroblasts after LLLT with a CO2 laser at 1.0 J/cm2. Moreover, inhibition of Akt, ERK, or JNK significantly blocked fibroblast proliferation and migration. Conclusions These findings suggested that LLLT with a CO2 laser would accelerate wound healing by promoting the proliferation and migration of fibroblasts. Activation of Akt, ERK, and JNK was essential for CO2 laser-induced proliferation and migration of fibroblasts. PMID:28045948

Insights into Gulf of Mexico Gas Hydrate Study Sites GC955 and WR313 from New Multicomponent and High-Resolution 2D Seismic Data

NASA Astrophysics Data System (ADS)

Haines, S. S.; Hart, P. E.; Collett, T. S.; Shedd, W. W.; Frye, M.

2014-12-01

In 2013, the U.S. Geological Survey led a seismic acquisition expedition in the Gulf of Mexico, acquiring multicomponent data and high-resolution 2D multichannel seismic (MCS) data at Green Canyon 955 (GC955) and Walker Ridge 313 (WR313). Based on previously collected logging-while-drilling (LWD) borehole data, these gas hydrate study sites are known to include high concentrations of gas hydrate within sand layers. At GC955 our new 2D data reveal at least three features that appear to be fluid-flow pathways (chimneys) responsible for gas migration and thus account for some aspects of the gas hydrate distribution observed in the LWD data. Our new data also show that the main gas hydrate target, a Pleistocene channel/levee complex, has an areal extent of approximately 5.5 square kilometers and that a volume of approximately 3 x 107 cubic meters of this body lies within the gas hydrate stability zone. Based on LWD-inferred values and reasonable assumptions for net sand, sand porosity, and gas hydrate saturation, we estimate a total equivalent gas-in-place volume of approximately 8 x 108 cubic meters for the inferred gas hydrate within the channel/levee deposits. At WR313 we are able to map the thin hydrate-bearing sand layers in considerably greater detail than that provided by previous data. We also can map the evolving and migrating channel feature that persists in this area. Together these data and the emerging results provide valuable new insights into the gas hydrate systems at these two sites.

Evidence of Ice Age humans in Beringia: new insights on the peopling of the Americas

NASA Astrophysics Data System (ADS)

Vachula, R. S.; Longo, W. M.; Daniels, W.; Dee, S.; Russell, J. M.; Huang, Y.

2017-12-01

The American continents were the final frontier of the global proliferation of Homo sapiens. The Bering Land Bridge that once connected Eurasia and North America, is widely accepted as the corridor for this human migration. However, the timeline, pathway, and environmental impact of human arrival to these previously unpeopled lands remain contentious in part due to a sparsity of physical archaeological or paleoenvironmental evidence. Recent conflicting genetic evidence suggests that humans lived in Beringia for an extended period of time (ca. 15,000 years) and did not diverge from Asian populations prior to 23,000 years before present (BP). The genetic evidence lacks supporting physical data, is prone to uncertainties inherent to molecular clocks, and thus further occludes our understanding of this segment of human history. Using a multi-disciplinary approach incorporating paleoecological and organic geochemical analyses of a lacustrine sediment record, and climate modelling methodologies, we present evidence of prolonged human-caused environmental disturbance in modern-day northern Alaska and show that humans were present in this area as early as 32,000 years ago. We measured fecal biomarkers preserved in the Lake E5 sediment archive to confirm prolonged human presence in the watershed, and find evidence of contemporaneous burning, as inferred from macroscopic charcoal and polycyclic aromatic hydrocarbons. Climate simulations show that natural lightning ignitions were suppressed during the period of greatest fire frequency, and so we infer that humans likely played an important role in fire ignitions. We thus present new physical evidence of sustained human presence in eastern Beringia throughout the last Glacial, which reorients our understanding of the human migration to the Americas. Furthermore, our research offers new insight into the ecology of the mammoth steppe and the role of humans in the extinction of the Pleistocene megafauna.

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

PubMed Central

Loh, Po-Ru; Lipson, Mark; Patterson, Nick; Moorjani, Priya; Pickrell, Joseph K.; Reich, David; Berger, Bonnie

2013-01-01

Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese. PMID:23410830

Health and demographic surveillance systems: contributing to an understanding of the dynamics in migration and health

PubMed Central

Gerritsen, Annette; Bocquier, Philippe; White, Michael; Mbacké, Cheikh; Alam, Nurul; Beguy, Donatien; Odhiambo, Frank; Sacoor, Charfudin; Phuc, Ho Dang; Punpuing, Sureeporn; Collinson, Mark A.

2013-01-01

Background Migration is difficult to measure because it is highly repeatable. Health and Demographic Surveillance Systems (HDSSs) provide a unique opportunity to study migration as multiple episodes of migration are captured over time. A conceptual framework is needed to show the public health implications of migration. Objective/design Research conducted in seven HDSS centres [International Network for the Demographic Evaluation of Populations and Their Health (INDEPTH) Network], published in a peer-reviewed volume in 2009, is summarised focussing on the age–sex profile of migrants, the relation between migration and livelihoods, and the impact of migration on health. This illustrates the conceptual structure of the implications of migration. The next phase is described, the Multi-centre Analysis of the Dynamics In Migration And Health (MADIMAH) project, consisting of workshops focussed on preparing data and conducting the analyses for comparative studies amongst HDSS centres in Africa and Asia. The focus here is on the (standardisation of) determinants of migration and the impact of migration on adult mortality. Results The findings in the volume showed a relatively regular age structure for migration among all HDSS centres. Furthermore, migration generally contributes to improved living conditions at the place of origin. However, there are potential negative consequences of migration on health. It was concluded that there is a need to compare results from multiple centres using uniform covariate definitions as well as longitudinal analysis techniques. This was the starting point for the on-going MADIMAH initiative, which has increased capacity at the participating HDSS centres to produce the required datasets and conduct the analyses. Conclusions HDSS centres brought together within INDEPTH Network have already provided strong evidence of the potential negative consequences of migration on health, which contrast with the beneficial impacts of migration on livelihoods. Future comparative evidence using standardised tools will help design policies for mitigating the negative effects, and enhancing the positive effects, of migration on health. PMID:23849188

Shallow plumbing systems inferred from spatial analysis of pockmark arrays

NASA Astrophysics Data System (ADS)

Maia, A.; Cartwright, J. A.; Andersen, E.

2016-12-01

This study describes and analyses an extraordinary array of pockmarks at the modern seabed of the Lower Congo Basin (offshore Angola), in order to understand the fluid migration routes and shallow plumbing system of the area. The 3D seismic visualization of feeding conduits (pipes) allowed the identification of the source interval for the fluids expelled during pockmark formation. Spatial statistics are used to show the relationship between the underlying (polarised) polygonal fault (PPFs) patterns and seabed pockmarks distributions. Our results show PPFs control the linear arrangement of pockmarks and feeder pipes along fault strike, but faults do not act as conduits. Spatial statistics also revealed pockmark occurrence is not considered to be random, especially at short distances to nearest neighbours (<200m) where anti-clustering distributions suggest the presence of an exclusion zone around each pockmark in which no other pockmark will form. The results of this study are relevant for the understanding of shallow fluid plumbing systems in offshore settings, with implications on our current knowledge of overall fluid flow systems in hydrocarbon-rich continental margins.

Assessing migration patterns in Passerina ciris using the world’s bird collections as an aggregated resource

PubMed Central

Bridge, Eli S.; Duckles, Jonah M.; Navarro-Sigüenza, Adolfo G.; Rohwer, Sievert

2016-01-01

Natural history museum collections (NHCs) represent a rich and largely untapped source of data on demography and population movements. NHC specimen records can be corrected to a crude measure of collecting effort and reflect relative population densities with a method known as abundance indices. We plotted abundance index values from georeferenced NHC data in a 12-month series for the new world migratory passerine Passerina ciris across its molting and wintering range in Mexico and Central America. We illustrated a statistically significant change in abundance index values across regions and months that suggests a quasi-circular movement around its non-breeding range, and used enhanced vegetation index (EVI) analysis of remote sensing plots to demonstrate non-random association of specimen record abundance with areas of high primary productivity. We demonstrated how abundance indices from NHC specimen records can be applied to infer previously unknown migratory behavior, and be integrated with remote sensing data to provide a deeper understanding of demography and behavioral ecology across time and space. PMID:27077001

On strain and stress in living cells

NASA Astrophysics Data System (ADS)

Cox, Brian N.; Smith, David W.

2014-11-01

Recent theoretical simulations of amelogenesis and network formation and new, simple analyses of the basic multicellular unit (BMU) allow estimation of the order of magnitude of the strain energy density in populations of living cells in their natural environment. A similar simple calculation translates recent measurements of the force-displacement relation for contacting cells (cell-cell adhesion energy) into equivalent volume energy densities, which are formed by averaging the changes in contact energy caused by a cell's migration over the cell's volume. The rates of change of these mechanical energy densities (energy density rates) are then compared to the order of magnitude of the metabolic activity of a cell, expressed as a rate of production of metabolic energy per unit volume. The mechanical energy density rates are 4-5 orders of magnitude smaller than the metabolic energy density rate in amelogenesis or bone remodeling in the BMU, which involve modest cell migration velocities, and 2-3 orders of magnitude smaller for innervation of the gut or angiogenesis, where migration rates are among the highest for all cell types. For representative cell-cell adhesion gradients, the mechanical energy density rate is 6 orders of magnitude smaller than the metabolic energy density rate. The results call into question the validity of using simple constitutive laws to represent living cells. They also imply that cells need not migrate as inanimate objects of gradients in an energy field, but are better regarded as self-powered automata that may elect to be guided by such gradients or move otherwise. Thus Ġel=d/dt 1/2 >[(C11+C12)ɛ02+2μγ02]=(C11+C12)ɛ0ɛ˙0+2μγ0γ˙0 or Ġel=ηEɛ0ɛ˙0+η‧Eγ0γ˙0 with 1.4≤η≤3.4 and 0.7≤η‧≤0.8 for Poisson's ratio in the range 0.2≤ν≤0.4 and η=1.95 and η‧=0.75 for ν=0.3. The spatial distribution of shear strains arising within an individual cell as cells slide past one another during amelogenesis is not known in detail. However, estimates can be inferred from the known relative velocities of the cells' centers of mass. When averaged over a volume comparable to the cell size, representative values of the strain are, to order of magnitude, ɛ0≈0.1 and γ0≈0.1. The shape distortions of cells seen, for example, in Fig. 1c, imply peak strains in minor segments of a cell of magnitude unity, ɛ0≈1 and γ0≈1; these values represent the upper bound of plausible values and are included for discussion of the extremes of attainable strain energy rates.Given the strain magnitudes, the strain rates follow from the fact that a cell switches from one contacting neighbor in the adjacent row to the next in approximately 0.25 d, during which motion the strains might vary from zero to their maximum values and back again. Thus the most probable shear strain rate is inferred to be γ˙0=10-6 s-1 and the most probable tensile strain rate is inferred to be ɛ˙0≈10-6 s-1, with high bounds γ˙0=10-5 s-1 and ɛ˙0=10-5 s-1.

Drug target inference through pathway analysis of genomics data

PubMed Central

Ma, Haisu; Zhao, Hongyu

2013-01-01

Statistical modeling coupled with bioinformatics is commonly used for drug discovery. Although there exist many approaches for single target based drug design and target inference, recent years have seen a paradigm shift to system-level pharmacological research. Pathway analysis of genomics data represents one promising direction for computational inference of drug targets. This article aims at providing a comprehensive review on the evolving issues is this field, covering methodological developments, their pros and cons, as well as future research directions. PMID:23369829

Inward migration of the TRAPPIST-1 planets as inferred from their water-rich compositions

NASA Astrophysics Data System (ADS)

Unterborn, Cayman T.; Desch, Steven J.; Hinkel, Natalie R.; Lorenzo, Alejandro

2018-04-01

Multiple planet systems provide an ideal laboratory for probing exoplanet composition, formation history and potential habitability. For the TRAPPIST-1 planets, the planetary radii are well established from transits1,2, with reasonable mass estimates coming from transit timing variations2,3 and dynamical modelling4. The low bulk densities of the TRAPPIST-1 planets demand substantial volatile content. Here we show, using mass-radius-composition models, that TRAPPIST-1f and g probably contain substantial (≥50 wt%) water/ice, with TRAPPIST-1 b and c being significantly drier (≤15 wt%). We propose that this gradient of water mass fractions implies that planets f and g formed outside the primordial snow line whereas b and c formed within it. We find that, compared with planets in our Solar System that also formed within the snow line, TRAPPIST-1b and c contain hundreds more oceans of water. We demonstrate that the extent and timescale of migration in the TRAPPIST-1 system depends on how rapidly the planets formed and the relative location of the primordial snow line. This work provides a framework for understanding the differences between the protoplanetary disks of our Solar System versus M dwarfs. Our results provide key insights into the volatile budgets, timescales of planet formation and migration history of M dwarf systems, probably the most common type of planetary host in the Galaxy.

Splay fault branching from the Hikurangi subduction shear zone: Implications for slow slip and fluid flow

NASA Astrophysics Data System (ADS)

Plaza-Faverola, A.; Henrys, S.; Pecher, I.; Wallace, L.; Klaeschen, D.

2016-12-01

Prestack depth migration data across the Hikurangi margin, East Coast of the North Island, New Zealand, are used to derive subducting slab geometry, upper crustal structure, and seismic velocities resolved to ˜14 km depth. We investigate the potential relationship between the crustal architecture, fluid migration, and short-term geodetically determined slow slip events. The subduction interface is a shallow dipping thrust at <7 km depth near the trench and steps down to 14 km depth along an ˜18 km long ramp, beneath Porangahau Ridge. This apparent step in the décollement is associated with splay fault branching and coincides with a zone of maximum slip (90 mm) inferred on the subduction interface during slow slip events in June and July 2011. A low-velocity zone beneath the plate interface, updip of the plate interface ramp, is interpreted as fluid-rich overpressured sediments capped with a low permeability condensed layer of chalk and interbedded mudstones. Fluid-rich sediments have been imbricated by splay faults in a region that coincides with the step down in the décollement from the top of subducting sediments to the oceanic crust and contribute to spatial variation in frictional properties of the plate interface that may promote slow slip behavior in the region. Further, transient fluid migration along splay faults at Porangahau Ridge may signify stress changes during slow slip.

Molecular Detection of Hematozoa Infections in Tundra Swans Relative to Migration Patterns and Ecological Conditions at Breeding Grounds

PubMed Central

Ramey, Andrew M.; Ely, Craig R.; Schmutz, Joel A.; Pearce, John M.; Heard, Darryl J.

2012-01-01

Tundra swans (Cygnus columbianus) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska. PMID:23049862

Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds

USGS Publications Warehouse

Ramey, Andrew M.; Ely, Craig R.; Schmutz, Joel A.; Pearce, John M.; Heard, Darryl J.

2012-01-01

Tundra swans (Cygnus columbianus) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska.

Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds.

PubMed

Ramey, Andrew M; Ely, Craig R; Schmutz, Joel A; Pearce, John M; Heard, Darryl J

2012-01-01

Tundra swans (Cygnus columbianus) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska.

Movement between Mexico and Canada: Analysis of a New Migration Stream

PubMed Central

Massey, Douglas; Brown, Amelia E.

2011-01-01

In this analysis we use data from the Mexican Migration Project to contrast processes of Mexican migration to Canada and the United States. All migrants to Canada entered through the Seasonal Agricultural Worker Program and consistent with program criteria, migration there is strongly predicted by marital status and number of dependents, yielding a migrant population that is made up of males of prime labor-force age who are married and have multiple children at home. In contrast, the vast majority of migrants to the United States are undocumented and thus self-selected without regard to marital status or parenthood. Migration to the United States is strongly predicted by age, and migration probabilities display the age curve classically associated with labor migration. Within countries of destination, migrants to Canada enjoy superior labor market outcomes compared with those to the United States, with higher wages and more compact work schedules that yield higher earnings and shorter periods away from families compared with undocumented migrants to the United States. Labor migration to Canada also tends to operate as a circular flow with considerable repeat migration whereas undocumented migrants to the United States do not come and go so regularly, as crossing the Mexico-U.S. border has become increasingly difficult and costly. PMID:24347678

Dancing Styles of Collective Cell Migration: Image-Based Computational Analysis of JRAB/MICAL-L2.

PubMed

Sakane, Ayuko; Yoshizawa, Shin; Yokota, Hideo; Sasaki, Takuya

2018-01-01

Collective cell migration is observed during morphogenesis, angiogenesis, and wound healing, and this type of cell migration also contributes to efficient metastasis in some kinds of cancers. Because collectively migrating cells are much better organized than a random assemblage of individual cells, there seems to be a kind of order in migrating clusters. Extensive research has identified a large number of molecules involved in collective cell migration, and these factors have been analyzed using dramatic advances in imaging technology. To date, however, it remains unclear how myriad cells are integrated as a single unit. Recently, we observed unbalanced collective cell migrations that can be likened to either precision dancing or awa-odori , Japanese traditional dancing similar to the style at Rio Carnival, caused by the impairment of the conformational change of JRAB/MICAL-L2. This review begins with a brief history of image-based computational analyses on cell migration, explains why quantitative analysis of the stylization of collective cell behavior is difficult, and finally introduces our recent work on JRAB/MICAL-L2 as a successful example of the multidisciplinary approach combining cell biology, live imaging, and computational biology. In combination, these methods have enabled quantitative evaluations of the "dancing style" of collective cell migration.

The mechanisms of substance P-mediated migration of bone marrow-derived mesenchymal stem cell-like ST2 cells.

PubMed

Dubon, Maria Jose; Park, Ki-Sook

2016-04-01

Substance P (SP) is known to induce the mobilization of bone marrow-derived mesenchymal stem cells (BM-MSCs) and thus participates in wound repair. However, the cellular and molecular mechanisms responsible for the SP-mediated migration of BM-MSCs were not fully understood. In the present study, we studied the molecular mechanisms that mediate the migration of the BM-derived MSC-like cell line ST2 in response to SP. Using a migration assay and western blot analysis, we noted that SP induced the chemotactic migration of ST2 cells through the intrinsic activation of extracellular signal-regulated kinases (ERKs) and protein kinase B (Akt), the phosphorylated expression levels of which were increased. We noted that Src is involved in the SP-mediated migration of ST2 cells and that focal adhesion kinase (FAK) was activated in the ST2 cells following SP treatment. Membrane ruffling increased in the ST2 cells after SP treatment, as was clearly demonstrated by immunocytochemical analysis. Importantly, using a blocking antibody against N-cadherin (GC-4), we studied cell migration and noted that SP mediated the migration of the ST2 cells through N-cadherin. The present study thus advanced our understanding of the mechanisms through which SP induces BM-MSC migration.

International migration patterns of physicians to the United States: a cross-national panel analysis.

PubMed

Hussey, Peter S

2007-12-01

To analyze the dynamics of physician international migration patterns and identify the countries deviating most from expected migration rates. A negative binomial log-linear model of physician migration to the United States from every other country was constructed using a panel of country-level data for years 1994-2000. The model was used to identify factors associated with physician migration and to identify countries with higher or lower rates of physician migration than expected. Physician migration varied with a country's GDP per capita in an inverse-U pattern, with highest migration rates from middle-income countries. The absence of medical schools, immigrant networks in the United States, medical instruction in English, proximity to the United States, and the lack of political and civil liberties were also associated with higher migration rates. Countries with higher-than-predicted migration rates included Iceland, Albania, Armenia, Dominica, Lebanon, Syria, the United Arab Emirates, and Bulgaria. Countries with lower-than-predicted migration rates included Mexico, Japan, Brazil, Zimbabwe, Mauritania, Portugal, Senegal, and France. This analysis shows that many of the most powerful factors associated with physician migration are difficult or impossible for countries to change through public policy. GDP per capita and proximity to the U.S. are two of the most powerful predictors of physician migration. Networks of immigrants in the U.S. and fewer political and civil liberties also put countries at higher risk for physician emigration. Several other factors that were associated with physician migration might be more easily amenable to policy intervention. These factors include the absence of a medical school and medical instruction in English. Policies addressing these factors would involve making several difficult tradeoffs, however. Other examples of policies that are effective in minimizing physician migration might be found by examining countries with lower-than-expected migration rates.

Contact Kinematics Correlates to Tibial Component Migration Following Single Radius Posterior Stabilized Knee Replacement.

PubMed

Teeter, Matthew G; Perry, Kevin I; Yuan, Xunhua; Howard, James L; Lanting, Brent A

2018-03-01

Contact kinematics between total knee arthroplasty components is thought to affect implant migration; however, the interaction between kinematics and tibial component migration has not been thoroughly examined in a modern implant system. A total of 24 knees from 23 patients undergoing total knee arthroplasty with a single radius, posterior stabilized implant were examined. Patients underwent radiostereometric analysis at 2 and 6 weeks, 3 and 6 months, and 1 and 2 years to measure migration of the tibial component in all planes. At 1 year, patients also had standing radiostereometric analysis examinations acquired in 0°, 20°, 40°, and 60° of flexion, and the location of contact and magnitude of any condylar liftoff was measured for each flexion angle. Regression analysis was performed between kinematic variables and migration at 1 year. The average magnitude of maximum total point motion across all patients was 0.671 ± 0.270 mm at 1 year and 0.608 ± 0.359 mm at 2 years (P = .327). Four implants demonstrated continuous migration of >0.2 mm between the first and second year of implantation. There were correlations between the location of contact and tibial component anterior-posterior tilt, varus-valgus tilt, and anterior-posterior translation. The patients with continuous migration demonstrated atypical kinematics and condylar liftoff in some instances. Kinematics can influence tibial component migration, likely through alterations of force transmission. Abnormal kinematics may play a role in long-term implant loosening. Copyright © 2017 Elsevier Inc. All rights reserved.

Migration velocity analysis using residual diffraction moveout: a real-data example

NASA Astrophysics Data System (ADS)

Gonzalez, Jaime A. C.; de Figueiredo, José J. S.; Coimbra, Tiago A.; Schleicher, Jörg; Novais, Amélia

2016-08-01

Unfocused seismic diffraction events carry direct information about errors in the migration-velocity model. The residual-diffraction-moveout (RDM) migration-velocity-analysis (MVA) method is a recent technique that extracts this information by means of adjusting ellipses or hyperbolas to uncollapsed migrated diffractions. In this paper, we apply this method, which has been tested so far only on synthetic data, to a real data set from the Viking Graben. After application of a plane-wave-destruction (PWD) filter to attenuate the reflected energy, the diffractions in the real data become interpretable and can be used for the RDM method. Our analysis demonstrates that the reflections need not be completely removed for this purpose. Beyond the need to identify and select diffraction events in post-stack migrated sections in the depth domain, the method has a very low computational cost and processing time. To reach an acceptable velocity model of comparable quality as one obtained with common-midpoint (CMP) processing, only two iterations were necessary.

Clathrin-independent carriers form a high capacity endocytic sorting system at the leading edge of migrating cells

PubMed Central

Howes, Mark T.; Kirkham, Matthew; Riches, James; Cortese, Katia; Walser, Piers J.; Simpson, Fiona; Hill, Michelle M.; Jones, Alun; Lundmark, Richard; Lindsay, Margaret R.; Hernandez-Deviez, Delia J.; Hadzic, Gordana; McCluskey, Adam; Bashir, Rumasia; Liu, Libin; Pilch, Paul; McMahon, Harvey; Robinson, Phillip J.; Hancock, John F.; Mayor, Satyajit

2010-01-01

Although the importance of clathrin- and caveolin-independent endocytic pathways has recently emerged, key aspects of these routes remain unknown. Using quantitative ultrastructural approaches, we show that clathrin-independent carriers (CLICs) account for approximately three times the volume internalized by the clathrin-mediated endocytic pathway, forming the major pathway involved in uptake of fluid and bulk membrane in fibroblasts. Electron tomographic analysis of the 3D morphology of the earliest carriers shows that they are multidomain organelles that form a complex sorting station as they mature. Proteomic analysis provides direct links between CLICs, cellular adhesion turnover, and migration. Consistent with this, CLIC-mediated endocytosis of key cargo proteins, CD44 and Thy-1, is polarized at the leading edge of migrating fibroblasts, while transient ablation of CLICs impairs their ability to migrate. These studies provide the first quantitative ultrastructural analysis and molecular characterization of the major endocytic pathway in fibroblasts, a pathway that provides rapid membrane turnover at the leading edge of migrating cells. PMID:20713605

Migration from printing inks in multilayer food packaging materials by GC-MS analysis and pattern recognition with chemometrics.

PubMed

Clemente, Isabel; Aznar, Margarita; Nerín, Cristina; Bosetti, Osvaldo

2016-01-01

Inks and varnishes used in food packaging multilayer materials can contain different substances that are potential migrants when packaging is in contact with food. Although printing inks are applied on the external layer, they can migrate due to set-off phenomena. In order to assess food safety, migration tests were performed from two materials sets: set A based on paper and set B based on PET; both contained inks. Migration was performed to four food simulants (EtOH 50%, isooctane, EtOH 95% and Tenax(®)) and the volatile compounds profile was analysed by GC-MS. The effect of presence/absence of inks and varnishes and also their position in the material was studied. A total of 149 volatile compounds were found in migration from set A and 156 from set B materials, some of them came from inks. Quantitative analysis and a principal component analysis were performed in order to identify patterns among sample groups.

Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

PubMed Central

Gerloff, U; Hartung, B; Fruth, B; Hohmann, G; Tautz, D

1999-01-01

Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community. PMID:10406131

Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

PubMed

Gerloff, U; Hartung, B; Fruth, B; Hohmann, G; Tautz, D

1999-06-07

Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community.

Cyclin-dependent Kinase 5: Novel role of gene variants identified in ADHD.

PubMed

Maitra, Subhamita; Chatterjee, Mahasweta; Sinha, Swagata; Mukhopadhyay, Kanchan

2017-07-28

Cortical neuronal migration and formation of filamentous actin cytoskeleton, needed for development, normal cell growth and differentiation, are regulated by the cyclin-dependent kinase 5 (Cdk5). Attention deficit hyperactivity disorder (ADHD) is associated with delayed maturation of the brain and hence we hypothesized that cdk5 may have a role in ADHD. Eight functional CDK5 gene variants were analyzed in 848 Indo-Caucasoid individuals including 217 families with ADHD probands and 250 healthy volunteers. Only three variants, rs2069454, rs2069456 and rs2069459, predicted to affect transcription, were found to be bimorphic. Significant difference in rs2069456 "AC" genotype frequency was noticed in the probands, more specifically in the males. Family based analysis revealed over transmission of rs2069454 "C" and rs2069456 "A" to the probands. Quantitative trait analysis exhibited association of haplotypes with inattention, domain specific impulsivity, and behavioral problem, though no significant contribution was noticed on the age of onset of ADHD. Gene variants also showed significant association with cognitive function and co-morbidity. Probands having rs2069459 "TT" showed betterment during follow up. It may be inferred from this pilot study that CDK5 may affect ADHD etiology, possibly by attenuating synaptic neurotransmission and could be a useful target for therapeutic intervention.

Inference of Ancestral Recombination Graphs through Topological Data Analysis

PubMed Central

Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

2016-01-01

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

The economics of amenities and migration in the Pacific Northwest: review of selected literature with implications for national forest management.

Treesearch

Brian E. Garber-Yonts

2004-01-01

This paper reviews literature on the influence of nonmarket amenity resources on population migration. Literature reviewed includes migration and demographic studies; urban and regional economics studies of amenities in labor markets, retirement migration, and firm location decisions; nonmarket valuation studies using hedonic price analysis of amenity resource values;...

Pressure as a limit to bloater (Coregonus hoyi) vertical migration

USGS Publications Warehouse

TeWinkel, Leslie M.; Fleischer, Guy W.

1998-01-01

Observations of bloater vertical migration showed a limit to the vertical depth changes that bloater experience. In this paper, we conducted an analysis of maximum differences in pressure encountered by bloater during vertical migration. Throughout the bottom depths studied, bloater experienced maximum reductions in swim bladder volume equal to approximately 50-60% of the volume in midwater. The analysis indicated that the limit in vertical depth change may be related to a maximum level of positive or negative buoyancy for which bloater can compensate using alternative mechanisms such as hydrodynamic lift. Bloater may be limited in the extent of migration by either their depth of neutral buoyancy or the distance above the depth of neutral buoyancy at which they can still maintain their position in the water column. Although a migration limit for the bloater population was evident, individual distances of migration varied at each site. These variations in migration distances may indicate differences in depths of neutral buoyancy within the population. However, in spite of these variations, the strong correlation between shallowest depths of migration and swim bladder volume reduction across depths provides evidence that hydrostatic pressure limits the extent of daily vertical movement in bloater.

Multigeneration data migration from legacy systems

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Liu, Brent J.; Kho, Hwa T.; Tao, Wenchao; Wang, Cun; McCoy, J. Michael

2003-05-01

The migration of image data from different generations of legacy archive systems represents a technical challenge and in incremental cost in transitions to newer generations of PACS. UCLA medical center has elected to completely replace the existing PACS infrastructure encompassing several generations of legacy systems by a new commercial system providing enterprise-wide image management and communication. One of the most challenging parts of the project was the migration of large volumes of legacy images into the new system. Planning of the migration required the development of specialized software and hardware, and included different phases of data mediation from existing databases to the new PACS database prior to the migration of the image data. The project plan included a detailed analysis of resources and cost of data migration to optimize the process and minimize the delay of a hybrid operation where the legacy systems need to remain operational. Our analysis and project planning showed that the data migration represents the most critical path in the process of PACS renewal. Careful planning and optimization of the project timeline and resources allocated is critical to minimize the financial impact and the time delays that such migrations can impose on the implementation plan.

Men’s Migration and Women’s Fertility in Rural Mozambique

PubMed Central

Yabiku, Scott T.; Cau, Boaventura

2012-01-01

Labor migration profoundly affects households throughout rural Africa. This study looks at how men’s labor migration influences marital fertility in a context where such migration has been massive while its economic returns are increasingly uncertain. Using data from a survey of married women in southern Mozambique, we start with an event-history analysis of birth rates among women married to migrants and those married to nonmigrants. The model detects a lower birth rate among migrants’ wives, which tends to be partially compensated for by an increased birth rate upon cessation of migration. An analysis of women’s lifetime fertility shows that it decreases as the time spent in migration by their husbands accrues. When we compare reproductive intentions stated by respondents with migrant and nonmigrant husbands, we find that migrants’ wives are more likely to want another child regardless of the number of living children, but the difference is significant only for women who see migration as economically benefiting their households. Yet, such women are also significantly more likely to use modern contraception than other women. We interpret these results in light of the debate on enhancing versus disrupting effects of labor migration on families and households in contemporary developing settings. PMID:21691931

The Role of Probability-Based Inference in an Intelligent Tutoring System.

ERIC Educational Resources Information Center

Mislevy, Robert J.; Gitomer, Drew H.

Probability-based inference in complex networks of interdependent variables is an active topic in statistical research, spurred by such diverse applications as forecasting, pedigree analysis, troubleshooting, and medical diagnosis. This paper concerns the role of Bayesian inference networks for updating student models in intelligent tutoring…

Application of Transformations in Parametric Inference

ERIC Educational Resources Information Center

Brownstein, Naomi; Pensky, Marianna

2008-01-01

The objective of the present paper is to provide a simple approach to statistical inference using the method of transformations of variables. We demonstrate performance of this powerful tool on examples of constructions of various estimation procedures, hypothesis testing, Bayes analysis and statistical inference for the stress-strength systems.…

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

PubMed Central

Shin, Junha; Lee, Insuk

2015-01-01

Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis within the domains of life will greatly potentiate the use of the expected onslaught of sequenced genomes in the study of molecular pathways in higher eukaryotes. PMID:26394049

Gap formation by inclined massive planets in locally isothermal three-dimensional discs

NASA Astrophysics Data System (ADS)

Chametla, Raúl O.; Sánchez-Salcedo, F. J.; Masset, F. S.; Hidalgo-Gámez, A. M.

2017-07-01

We study gap formation in gaseous protoplanetary discs by a Jupiter mass planet. The planet's orbit is circular and inclined relative to the mid-plane of the disc. We use the impulse approximation to estimate the gravitational tidal torque between the planet and the disc, and infer the gap profile. For low-mass discs, we provide a criterion for gap opening when the orbital inclination is ≤30°. Using the fargo3d code, we simulate the disc response to an inclined massive planet. The dependence of the depth and width of the gap obtained in the simulations on the inclination of the planet is broadly consistent with the scaling laws derived in the impulse approximation. Although we mainly focus on planets kept on fixed orbits, the formalism permits to infer the temporal evolution of the gap profile in the cases where the inclination of the planet changes with time. This study may be useful to understand the migration of massive planets on inclined orbit, because the strength of the interaction with the disc depends on whether a gap is opened or not.

The Maximum Mass of a Planet

NASA Astrophysics Data System (ADS)

Schlaufman, Kevin C.

2018-06-01

Giant planet occurrence is a steeply increasing function of FGK dwarf host star metallicity, and this is interpreted as support for the core-accretion model of giant planet formation. On the other hand, the occurrence of low-mass stellar companions to FGK dwarf stars does not appear to depend on stellar metallicity. The mass at which objects no longer prefer metal-rich FGK dwarf host stars can therefore be used to infer the maximum mass of objects that form like planets through core accretion. I'll show that objects more massive than about 10 M_Jup do not orbit metal-rich host stars and that this transition is coincident with a minimum in the occurrence rate of such objects. These facts suggest that the maximum mass of a celestial body formed through core accretion like a planet is less than 10 M_Jup. This observation can be used to infer the properties of protoplanetary disks and reveals that the Type I and Type II disk migration problems---two major issues for the modern model of planet formation---are not problems at all.

Constraining planetary migration and tidal dissipation with coeval hot Jupiters

NASA Astrophysics Data System (ADS)

O'Connor, Christopher E.; Hansen, Bradley M. S.

2018-06-01

We investigate the constraints on the formation of, and tidal dissipation processes in, hot Jupiters (HJs) that can be inferred based on reliable knowledge of the age of a system or population. Particular attention is paid to the role of young systems (such as those in open clusters or star-forming regions) in such studies. For an ensemble of coeval HJ (or proto-HJ) systems, we quantify the effect of age on the distribution of orbital eccentricities with respect to orbital periods as well as the location of the observed `pile-up' feature. We expect the effects of pre-main-sequence stellar evolution to be important only if a substantial fraction of HJs approach their current orbits early in protostellar contraction (ages ≲ 10 Myr). Application to the HJs presently known in the cluster M 67 yields constraints on the dissipation roughly consistent with those gleaned from planets in the field; for those in the Hyades and Praesepe, our results suggest a higher degree of dissipation at early times than that inferred from other populations.

High-dimensional inference with the generalized Hopfield model: principal component analysis and corrections.

PubMed

Cocco, S; Monasson, R; Sessak, V

2011-05-01

We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising model where the interaction matrix is defined through a set of patterns in the variable space, and is of rank much smaller than N. We show that maximum likelihood inference is deeply related to principal component analysis when the amplitude of the pattern components ξ is negligible compared to √N. Using techniques from statistical mechanics, we calculate the corrections to the patterns to the first order in ξ/√N. We stress the need to generalize the Hopfield model and include both attractive and repulsive patterns in order to correctly infer networks with sparse and strong interactions. We present a simple geometrical criterion to decide how many attractive and repulsive patterns should be considered as a function of the sampling noise. We moreover discuss how many sampled configurations are required for a good inference, as a function of the system size N and of the amplitude ξ. The inference approach is illustrated on synthetic and biological data.

A simple force-motion relation for migrating cells revealed by multipole analysis of traction stress.

PubMed

Tanimoto, Hirokazu; Sano, Masaki

2014-01-07

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Migration of lymphocytes on fibronectin-coated surfaces: temporal evolution of migratory parameters

NASA Technical Reports Server (NTRS)

Bergman, A. J.; Zygourakis, K.; McIntire, L. V. (Principal Investigator)

1999-01-01

Lymphocytes typically interact with implanted biomaterials through adsorbed exogenous proteins. To provide a more complete characterization of these interactions, analysis of lymphocyte migration on adsorbed extracellular matrix proteins must accompany the commonly performed adhesion studies. We report here a comparison of the migratory and adhesion behavior of Jurkat cells (a T lymphoblastoid cell line) on tissue culture treated and untreated polystyrene surfaces coated with various concentrations of fibronectin. The average speed of cell locomotion showed a biphasic response to substrate adhesiveness for cells migrating on untreated polystyrene and a monotonic decrease for cells migrating on tissue culture-treated polystyrene. A modified approach to the persistent random walk model was implemented to determine the time dependence of cell migration parameters. The random motility coefficient showed significant increases with time when cells migrated on tissue culture-treated polystyrene surfaces, while it remained relatively constant for experiments with untreated polystyrene plates. Finally, a cell migration computer model was developed to verify our modified persistent random walk analysis. Simulation results suggest that our experimental data were consistent with temporally increasing random motility coefficients.

Methods of quantitative and qualitative analysis of bird migration with a tracking radar

NASA Technical Reports Server (NTRS)

Bruderer, B.; Steidinger, P.

1972-01-01

Methods of analyzing bird migration by using tracking radar are discussed. The procedure for assessing the rate of bird passage is described. Three topics are presented concerning the grouping of nocturnal migrants, the velocity of migratory flight, and identification of species by radar echoes. The height and volume of migration under different weather conditions are examined. The methods for studying the directions of migration and the correlation between winds and the height and direction of migrating birds are presented.

Age constraints for the present fault configuration in the Imperial Valley, California: Evidence for northwestward propagation of the Gulf of California rift system

NASA Technical Reports Server (NTRS)

Larsen, Shawn; Reilinger, Robert

1990-01-01

Releveling and other geophysical data for the Imperial Valley of southern California suggest the northern section of the Imperial-Brawley fault system, which includes the Mesquite Basin and Brawley Seismic Zone, is much younger than the 4 to 5 million year age of the valley itself. A minimum age of 3000 years is calculated for the northern segment of the Imperial fault from correlations between surface topography and geodetically observed seismic/interseismic vertical movements. Calculations of a maximum age of 80,000 years is based upon displacements in the crystalline basement along the Imperial fault, inferred from seismic refraction surveys. This young age supports recent interpretations of heat flow measurements, which also suggest that the current patterns of seismicity and faults in the Imperial Valley are not long lived. The current fault geometry and basement morphology suggest northwestward growth of the Imperial fault and migration of the Brawley Seismic Zone. It is suggested that this migration is a manifestation of the propagation of the Gulf of California rift system into the North American continent.

The Probability Heuristics Model of Syllogistic Reasoning.

ERIC Educational Resources Information Center

Chater, Nick; Oaksford, Mike

1999-01-01

Proposes a probability heuristic model for syllogistic reasoning and confirms the rationality of this heuristic by an analysis of the probabilistic validity of syllogistic reasoning that treats logical inference as a limiting case of probabilistic inference. Meta-analysis and two experiments involving 40 adult participants and using generalized…

Massive optimal data compression and density estimation for scalable, likelihood-free inference in cosmology

NASA Astrophysics Data System (ADS)

Alsing, Justin; Wandelt, Benjamin; Feeney, Stephen

2018-07-01

Many statistical models in cosmology can be simulated forwards but have intractable likelihood functions. Likelihood-free inference methods allow us to perform Bayesian inference from these models using only forward simulations, free from any likelihood assumptions or approximations. Likelihood-free inference generically involves simulating mock data and comparing to the observed data; this comparison in data space suffers from the curse of dimensionality and requires compression of the data to a small number of summary statistics to be tractable. In this paper, we use massive asymptotically optimal data compression to reduce the dimensionality of the data space to just one number per parameter, providing a natural and optimal framework for summary statistic choice for likelihood-free inference. Secondly, we present the first cosmological application of Density Estimation Likelihood-Free Inference (DELFI), which learns a parametrized model for joint distribution of data and parameters, yielding both the parameter posterior and the model evidence. This approach is conceptually simple, requires less tuning than traditional Approximate Bayesian Computation approaches to likelihood-free inference and can give high-fidelity posteriors from orders of magnitude fewer forward simulations. As an additional bonus, it enables parameter inference and Bayesian model comparison simultaneously. We demonstrate DELFI with massive data compression on an analysis of the joint light-curve analysis supernova data, as a simple validation case study. We show that high-fidelity posterior inference is possible for full-scale cosmological data analyses with as few as ˜104 simulations, with substantial scope for further improvement, demonstrating the scalability of likelihood-free inference to large and complex cosmological data sets.

Mountain landscapes offer few opportunities for high-elevation tree species migration

USGS Publications Warehouse

Bell, David M.; Bradford, John B.; Lauenroth, William K.

2014-01-01

Climate change is anticipated to alter plant species distributions. Regional context, notably the spatial complexity of climatic gradients, may influence species migration potential. While high-elevation species may benefit from steep climate gradients in mountain regions, their persistence may be threatened by limited suitable habitat as land area decreases with elevation. To untangle these apparently contradictory predictions for mountainous regions, we evaluated the climatic suitability of four coniferous forest tree species of the western United States based on species distribution modeling (SDM) and examined changes in climatically suitable areas under predicted climate change. We used forest structural information relating to tree species dominance, productivity, and demography from an extensive forest inventory system to assess the strength of inferences made with a SDM approach. We found that tree species dominance, productivity, and recruitment were highest where climatic suitability (i.e., probability of species occurrence under certain climate conditions) was high, supporting the use of predicted climatic suitability in examining species risk to climate change. By predicting changes in climatic suitability over the next century, we found that climatic suitability will likely decline, both in areas currently occupied by each tree species and in nearby unoccupied areas to which species might migrate in the future. These trends were most dramatic for high elevation species. Climatic changes predicted over the next century will dramatically reduce climatically suitable areas for high-elevation tree species while a lower elevation species, Pinus ponderosa, will be well positioned to shift upslope across the region. Reductions in suitable area for high-elevation species imply that even unlimited migration would be insufficient to offset predicted habitat loss, underscoring the vulnerability of these high-elevation species to climatic changes.

Fluid-faulting evolution in high definition: Connecting fault structure and frequency-magnitude variations during the 2014 Long Valley Caldera, California earthquake swarm

USGS Publications Warehouse

Shelly, David R.; Ellsworth, William L.; Hill, David P.

2016-01-01

An extended earthquake swarm occurred beneath southeastern Long Valley Caldera between May and November 2014, culminating in three magnitude 3.5 earthquakes and 1145 cataloged events on 26 September alone. The swarm produced the most prolific seismicity in the caldera since a major unrest episode in 1997-1998. To gain insight into the physics controlling swarm evolution, we used large-scale cross-correlation between waveforms of cataloged earthquakes and continuous data, producing precise locations for 8494 events, more than 2.5 times the routine catalog. We also estimated magnitudes for 18,634 events (~5.5 times the routine catalog), using a principal component fit to measure waveform amplitudes relative to cataloged events. This expanded and relocated catalog reveals multiple episodes of pronounced hypocenter expansion and migration on a collection of neighboring faults. Given the rapid migration and alignment of hypocenters on narrow faults, we infer that activity was initiated and sustained by an evolving fluid pressure transient with a low-viscosity fluid, likely composed primarily of water and CO2 exsolved from underlying magma. Although both updip and downdip migration were observed within the swarm, downdip activity ceased shortly after activation, while updip activity persisted for weeks at moderate levels. Strongly migrating, single-fault episodes within the larger swarm exhibited a higher proportion of larger earthquakes (lower Gutenberg-Richter b value), which may have been facilitated by fluid pressure confined in two dimensions within the fault zone. In contrast, the later swarm activity occurred on an increasingly diffuse collection of smaller faults, with a much higher b value.

Inferring the distribution and demography of an invasive species from sighting data: the red fox incursion into Tasmania.

PubMed

Caley, Peter; Ramsey, David S L; Barry, Simon C

2015-01-01

A recent study has inferred that the red fox (Vulpes vulpes) is now widespread in Tasmania as of 2010, based on the extraction of fox DNA from predator scats. Heuristically, this inference appears at first glance to be at odds with the lack of recent confirmed discoveries of either road-killed foxes--the last of which occurred in 2006, or hunter killed foxes--the most recent in 2001. This paper demonstrates a method to codify this heuristic analysis and produce inferences consistent with assumptions and data. It does this by formalising the analysis in a transparent and repeatable manner to make inference on the past, present and future distribution of an invasive species. It utilizes Approximate Bayesian Computation to make inferences. Importantly, the method is able to inform management of invasive species within realistic time frames, and can be applied widely. We illustrate the technique using the Tasmanian fox data. Based on the pattern of carcass discoveries of foxes in Tasmania, we infer that the population of foxes in Tasmania is most likely extinct, or restricted in distribution and demographically weak as of 2013. It is possible, though unlikely, that that population is widespread and/or demographically robust. This inference is largely at odds with the inference from the predator scat survey data. Our results suggest the chances of successfully eradicating the introduced red fox population in Tasmania may be significantly higher than previously thought.

Inferring the Distribution and Demography of an Invasive Species from Sighting Data: The Red Fox Incursion into Tasmania

PubMed Central

Caley, Peter; Ramsey, David S. L.; Barry, Simon C.

2015-01-01

A recent study has inferred that the red fox (Vulpes vulpes) is now widespread in Tasmania as of 2010, based on the extraction of fox DNA from predator scats. Heuristically, this inference appears at first glance to be at odds with the lack of recent confirmed discoveries of either road-killed foxes—the last of which occurred in 2006, or hunter killed foxes—the most recent in 2001. This paper demonstrates a method to codify this heuristic analysis and produce inferences consistent with assumptions and data. It does this by formalising the analysis in a transparent and repeatable manner to make inference on the past, present and future distribution of an invasive species. It utilizes Approximate Bayesian Computation to make inferences. Importantly, the method is able to inform management of invasive species within realistic time frames, and can be applied widely. We illustrate the technique using the Tasmanian fox data. Based on the pattern of carcass discoveries of foxes in Tasmania, we infer that the population of foxes in Tasmania is most likely extinct, or restricted in distribution and demographically weak as of 2013. It is possible, though unlikely, that that population is widespread and/or demographically robust. This inference is largely at odds with the inference from the predator scat survey data. Our results suggest the chances of successfully eradicating the introduced red fox population in Tasmania may be significantly higher than previously thought. PMID:25602618

High Resolution Spatio Temporal Moments Analysis of Solute Migration Captured using Pre-clinical Medical Imaging Techniques

NASA Astrophysics Data System (ADS)

Dogan, M.; Moysey, S. M.; Powell, B. A.; DeVol, T. A.

2016-12-01

Advances in medical imaging technologies are continuously expanding the range of applications enabled within the earth sciences. While computed x-ray tomography (CT) scans have traditionally been used for investigating the structure of geologic materials, it is now possible to perform 3D time-lapse imaging of dynamic processes, such as monitoring the infiltration of water into a soil, with sub-millimeter resolution. Likewise, single photon emission computed tomography (SPECT) can provide information on the evolution of solute transport with spatial resolution on the order of a millimeter by tracking the migration of gamma-ray emitting isotopes like 99mTc and 111In. While these imaging techniques are revolutionizing our ability to look within porous media, techniques for the analysis of such rich and large data sets are limited. The spatial and temporal moments of a plume have long been used to provide quantitative measures to describe plume movement in a wide range of settings from the lab to field. Moment analysis can also be used to estimate the hydrologic properties of the porous media. In this research, we investigate the use of moments for analyzing a high resolution 4D SPECT data set collected during a 99mTc transport experiment performed in a heterogeneous column. The 4D nature of the data set makes it amenable to the use of data mining and pattern recognition methods, such as cluster analysis, to identify regions or zones within the data that exhibit abnormal or unexpected behaviors. We then compare anomalous features within the SPECT data to similar features identified within the CT image to relate the flow behavior to pore-scale structures, such as porosity differences and macropores. Such comparisons help to identify whether these features are good predictors of preferential transport. Likewise, we evaluate whether local analysis of moments can be used to infer apparent parameters governing non-conservative transport in a heterogeneous porous media, such as hydraulic conductivity, mass transfer coefficients, and geochemical reaction rates. Our work suggests that the combination of CT and SPECT imaging can provide useful insights into flow and transport processes that may contradict traditional assumptions regarding one-dimensional flow within a laboratory column.

A Time Series Analysis: Weather Factors, Human Migration and Malaria Cases in Endemic Area of Purworejo, Indonesia, 2005–2014

PubMed Central

REJEKI, Dwi Sarwani Sri; NURHAYATI, Nunung; AJI, Budi; MURHANDARWATI, E. Elsa Herdiana; KUSNANTO, Hari

2018-01-01

Background: Climatic and weather factors become important determinants of vector-borne diseases transmission like malaria. This study aimed to prove relationships between weather factors with considering human migration and previous case findings and malaria cases in endemic areas in Purworejo during 2005–2014. Methods: This study employed ecological time series analysis by using monthly data. The independent variables were the maximum temperature, minimum temperature, maximum humidity, minimum humidity, precipitation, human migration, and previous malaria cases, while the dependent variable was positive malaria cases. Three models of count data regression analysis i.e. Poisson model, quasi-Poisson model, and negative binomial model were applied to measure the relationship. The least Akaike Information Criteria (AIC) value was also performed to find the best model. Negative binomial regression analysis was considered as the best model. Results: The model showed that humidity (lag 2), precipitation (lag 3), precipitation (lag 12), migration (lag1) and previous malaria cases (lag 12) had a significant relationship with malaria cases. Conclusion: Weather, migration and previous malaria cases factors need to be considered as prominent indicators for the increase of malaria case projection. PMID:29900134

Research Techniques Made Simple: Analysis of Collective Cell Migration Using the Wound Healing Assay.

PubMed

Grada, Ayman; Otero-Vinas, Marta; Prieto-Castrillo, Francisco; Obagi, Zaidal; Falanga, Vincent

2017-02-01

Collective cell migration is a hallmark of wound repair, cancer invasion and metastasis, immune responses, angiogenesis, and embryonic morphogenesis. Wound healing is a complex cellular and biochemical process necessary to restore structurally damaged tissue. It involves dynamic interactions and crosstalk between various cell types, interaction with extracellular matrix molecules, and regulated production of soluble mediators and cytokines. In cutaneous wound healing, skin cells migrate from the wound edges into the wound to restore skin integrity. Analysis of cell migration in vitro is a useful assay to quantify alterations in cell migratory capacity in response to experimental manipulations. Although several methods exist to study cell migration (such as Boyden chamber assay, barrier assays, and microfluidics-based assays), in this short report we will explain the wound healing assay, also known as the "in vitro scratch assay" as a simple, versatile, and cost-effective method to study collective cell migration and wound healing. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Gas migration through Opouawe Bank at the Hikurangi margin offshore New Zealand

NASA Astrophysics Data System (ADS)

Koch, Stephanie; Schroeder, Henning; Haeckel, Matthias; Berndt, Christian; Bialas, Joerg; Papenberg, Cord; Klaeschen, Dirk; Plaza-Faverola, Andreia

2016-06-01

This study presents 2D seismic reflection data, seismic velocity analysis, as well as geochemical and isotopic porewater compositions from Opouawe Bank on New Zealand's Hikurangi subduction margin, providing evidence for essentially pure methane gas seepage. The combination of geochemical information and seismic reflection images is an effective way to investigate the nature of gas migration beneath the seafloor, and to distinguish between water advection and gas ascent. The maximum source depth of the methane that migrates to the seep sites on Opouawe Bank is 1,500-2,100 m below seafloor, generated by low-temperature degradation of organic matter via microbial CO2 reduction. Seismic velocity analysis enabled identifying a zone of gas accumulation underneath the base of gas hydrate stability (BGHS) below the bank. Besides structurally controlled gas migration along conduits, gas migration also takes place along dipping strata across the BGHS. Gas migration on Opouawe Bank is influenced by anticlinal focusing and by several focusing levels within the gas hydrate stability zone.

Automated analysis of cell migration and nuclear envelope rupture in confined environments.

PubMed

Elacqua, Joshua J; McGregor, Alexandra L; Lammerding, Jan

2018-01-01

Recent in vitro and in vivo studies have highlighted the importance of the cell nucleus in governing migration through confined environments. Microfluidic devices that mimic the narrow interstitial spaces of tissues have emerged as important tools to study cellular dynamics during confined migration, including the consequences of nuclear deformation and nuclear envelope rupture. However, while image acquisition can be automated on motorized microscopes, the analysis of the corresponding time-lapse sequences for nuclear transit through the pores and events such as nuclear envelope rupture currently requires manual analysis. In addition to being highly time-consuming, such manual analysis is susceptible to person-to-person variability. Studies that compare large numbers of cell types and conditions therefore require automated image analysis to achieve sufficiently high throughput. Here, we present an automated image analysis program to register microfluidic constrictions and perform image segmentation to detect individual cell nuclei. The MATLAB program tracks nuclear migration over time and records constriction-transit events, transit times, transit success rates, and nuclear envelope rupture. Such automation reduces the time required to analyze migration experiments from weeks to hours, and removes the variability that arises from different human analysts. Comparison with manual analysis confirmed that both constriction transit and nuclear envelope rupture were detected correctly and reliably, and the automated analysis results closely matched a manual analysis gold standard. Applying the program to specific biological examples, we demonstrate its ability to detect differences in nuclear transit time between cells with different levels of the nuclear envelope proteins lamin A/C, which govern nuclear deformability, and to detect an increase in nuclear envelope rupture duration in cells in which CHMP7, a protein involved in nuclear envelope repair, had been depleted. The program thus presents a versatile tool for the study of confined migration and its effect on the cell nucleus.

On the Ability To Infer Deficiency in Mathematics From Performance in Physics Using Hierarchies

ERIC Educational Resources Information Center

Riban, David M.

1971-01-01

Presents the procedures, results, and conclusions of a study designed to see if mathematical deficiencies can be inferred from PSSC students' performance by using a hierarchical model of requisite skills. Assuming inferences were possible, remediation was given. No effect due to remediation was observed but analysis indicated incidental learning…

Meta-learning framework applied in bioinformatics inference system design.

PubMed

Arredondo, Tomás; Ormazábal, Wladimir

2015-01-01

This paper describes a meta-learner inference system development framework which is applied and tested in the implementation of bioinformatic inference systems. These inference systems are used for the systematic classification of the best candidates for inclusion in bacterial metabolic pathway maps. This meta-learner-based approach utilises a workflow where the user provides feedback with final classification decisions which are stored in conjunction with analysed genetic sequences for periodic inference system training. The inference systems were trained and tested with three different data sets related to the bacterial degradation of aromatic compounds. The analysis of the meta-learner-based framework involved contrasting several different optimisation methods with various different parameters. The obtained inference systems were also contrasted with other standard classification methods with accurate prediction capabilities observed.

Middle School Learners' Use of Latin Roots to Infer the Meaning of Unfamiliar Words

ERIC Educational Resources Information Center

Crosson, Amy C.; McKeown, Margaret G.

2016-01-01

This study investigated how middle school students leverage information about bound Latin roots (e.g., "voc" in "advocate" and "vociferous") to infer meanings of unfamiliar words, and how instruction may facilitate morphological analysis using roots. A dynamic assessment of morphological analysis was administered to…

Pelagic Habitat Analysis Module (PHAM) for GIS Based Fisheries Decision Support

NASA Technical Reports Server (NTRS)

Kiefer, D. A.; Armstrong, Edward M.; Harrison, D. P.; Hinton, M. G.; Kohin, S.; Snyder, S.; O'Brien, F. J.

2011-01-01

We have assembled a system that integrates satellite and model output with fisheries data We have developed tools that allow analysis of the interaction between species and key environmental variables Demonstrated the capacity to accurately map habitat of Thresher Sharks Alopias vulpinus & pelagicus. Their seasonal migration along the California Current is at least partly driven by the seasonal migration of sardine, key prey of the sharks.We have assembled a system that integrates satellite and model output with fisheries data We have developed tools that allow analysis of the interaction between species and key environmental variables Demonstrated the capacity to accurately map habitat of Thresher Sharks Alopias vulpinus nd pelagicus. Their seasonal migration along the California Current is at least partly driven by the seasonal migration of sardine, key prey of the sharks.

Distribution of melt along the East Pacific Rise 9°50'N from amplitude variation with angle (AVA) of incidence technique

NASA Astrophysics Data System (ADS)

Marjanovic, M.; Carton, H. D.; Carbotte, S. M.; Mutter, J. C.; Nedimovic, M. R.; Canales, J.

2012-12-01

Multichannel seismic (MCS) data collected in 2008 along the crest of the East Pacific Rise (EPR) 8°20'-10°10'N offer an excellent opportunity for studying along-axis variations in seismic properties of the mid-crustal magma sill imaged at ˜1.6 km below seafloor and inferring along-axis variations in the physical properties of this melt body. Locally, pre-stack data show a clear decrease in the amplitude of the P-wave reflection off the top of the magma sill as a function of angle of incidence, an observation reminiscent of the amplitude response of some hydrocarbon-saturated reservoirs, which may imply that within these regions the sill contains fully molten material. In oil and gas exploration, a technique known as amplitude variation with angle of incidence (AVA) analysis has been developed to derive reservoir properties from amplitude behavior. One such method, developed recently, uses intercept (derived from near-angle of incidence information, A) vs. slope (derived from mid-angle of incidence information, B) as seismic attributes to infer reservoir properties. Here, for the first time, we apply this approach to the mid-ocean ridge environment to infer variations in melt content of the axial magma sill. Using the presence of a converted P- to S- phase at the AMC as the first-order proxy for melt, we limit the application of AVA analysis to the region between ~9°30' and 10°00'N along the EPR axis. Prior to conducting the AVA analysis properly, data preparation steps are required (Kirchhoff pre-stack time migration, Radon filtering, velocity analysis of the AMC event for its accurate normal move-out correction, conversion of CMP gathers from offset domain to angle of incidence domain, and near and mid angle stacking were carried out here) and an interpretation scheme adequate for the mid-ocean ridge environment is established. The individual regions for conducting the A vs. B AVA analysis were based on previously-defined small-scale segmentation of the axial magma sill. The AVA behavior suggests the presence of melt within the four segments (each 5 to 10 km in length) spanning between ~9°42.3'N and 9°56.2'N. Drainage related to the 2005-06 eruption appears to be limited to a narrow area (~500 m in length) centered at 9°50.6'N. Furthermore, data from the 9°53'N area shows increased scatter of the seismic attributes A and B that can be explained by the anomalous density/velocity relationship for iron-enriched rocks; within this same region, seafloor lavas show a relatively higher concentration of Fe. The intercept vs. slope AVA method tested here thus seems a very promising tool for the study of mid-ocean ridge magma systems.

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

PubMed Central

Hurley, Daniel; Araki, Hiromitsu; Tamada, Yoshinori; Dunmore, Ben; Sanders, Deborah; Humphreys, Sally; Affara, Muna; Imoto, Seiya; Yasuda, Kaori; Tomiyasu, Yuki; Tashiro, Kosuke; Savoie, Christopher; Cho, Vicky; Smith, Stephen; Kuhara, Satoru; Miyano, Satoru; Charnock-Jones, D. Stephen; Crampin, Edmund J.; Print, Cristin G.

2012-01-01

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions. PMID:22121215

Sexual Migration and HIV Risk in a Sample of Brazilian, Colombian and Dominican Immigrant MSM Living in New York City.

PubMed

Nieves-Lugo, Karen; Barnett, Andrew; Pinho, Veronica; Reisen, Carol; Poppen, Paul; Zea, Maria Cecilia

2018-03-01

We examined motivations for migration to the United States (US) among 482 Brazilian, Colombian, and Dominican men who have sex with men (MSM). Participants' most common reason for migration was to improve their financial situation (49%), followed by sexual migration in order to affirm their sexual orientation (40%). Fewer endorsed sexual migration motivated by avoiding persecution due to being gay (13%). We conducted further analyses among 276 participants who migrated after age 15 and were HIV-negative at the time of migration. We hypothesized that sexual migration would be associated with greater likelihood of HIV acquisition post-migration. Hierarchical logistic regression analysis indicated that sexual migration motivated by avoiding persecution due to being gay was associated with increased odds of contracting HIV after arrival in the US whereas sexual migration to lead a gay life was not. Our findings highlight the importance of addressing the negative impact of anti-gay discrimination in countries of origin.

Should total hip arthroplasty femoral components be designed to subside? A radiostereometric analysis study of the Charnley Elite and Exeter stems.

PubMed

Alfaro-Adrián, J; Gill, H S; Murray, D W

2001-08-01

The Charnley Elite and the Exeter stems have different design concepts: The former is designed not to subside, whereas the latter is expected to subside. This radiostereometric analysis study compares the early migration of the 2 stems. For both implants, the 1st year migration was about 4 times faster than the 2nd year. The Exeter migration was predominantly distal (1 mm/y in the 1st year). It also showed slight collapse into valgus, and the head migrated slowly posteriorly (0.3 mm/y in the 1st year). In contrast, the Elite had slow distal migration (0.2 mm/y in the 1st year) and rapid posterior head migration (0.8 mm/y in the 1st year). Four Elites and no Exeters had rapid posterior head migration rates (mean 2.8 mm/y in the 1st year and 0.8 mm/y in the 2nd year). The Elite and the Exeter stems have fundamentally different early patterns of migration, which affect their long-term function; 20% of the Elites and none of the Exeters had rapid posterior head migration in the 1st year and the 2nd year and are likely to fail early. Polished, collarless, tapered designs, such as the Exeter, may be more forgiving than conventional stems designed not to subside.

Repeat immigration: A previously unobserved source of heterogeneity?

PubMed

Aradhya, Siddartha; Scott, Kirk; Smith, Christopher D

2017-07-01

Register data allow for nuanced analyses of heterogeneities between sub-groups which are not observable in other data sources. One heterogeneity for which register data is particularly useful is in identifying unique migration histories of immigrant populations, a group of interest across disciplines. Years since migration is a commonly used measure of integration in studies seeking to understand the outcomes of immigrants. This study constructs detailed migration histories to test whether misclassified migrations may mask important heterogeneities. In doing so, we identify a previously understudied group of migrants called repeat immigrants, and show that they differ systematically from permanent immigrants. In addition, we quantify the degree to which migration information is misreported in the registers. The analysis is carried out in two steps. First, we estimate income trajectories for repeat immigrants and permanent immigrants to understand the degree to which they differ. Second, we test data validity by cross-referencing migration information with changes in income to determine whether there are inconsistencies indicating misreporting. From the first part of the analysis, the results indicate that repeat immigrants systematically differ from permanent immigrants in terms of income trajectories. Furthermore, income trajectories differ based on the way in which years since migration is calculated. The second part of the analysis suggests that misreported migration events, while present, are negligible. Repeat immigrants differ in terms of income trajectories, and may differ in terms of other outcomes as well. Furthermore, this study underlines that Swedish registers provide a reliable data source to analyze groups which are unidentifiable in other data sources.

Climate Induced Spillover and Implications for U.S. Security.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tidwell, Vincent C.; Naugle, Asmeret Bier; Backus, George A.

Developing nations incur a greater risk to climate change than the developed world due to poorly managed human/natural resources, unreliable infrastructure and brittle governing/economic institutions. These vulnerabilities often give rise to a climate induced “domino effect” of reduced natural resource production-leading to economic hardship, social unrest, and humanitarian crises. Integral to this cascading set of events is increased human migration, leading to the “spillover” of impacts to adjoining areas with even broader impact on global markets and security. Given the complexity of factors influencing human migration and the resultant spill-over effect, quantitative tools are needed to aid policy analysis. Towardmore » this need, a series of migration models were developed along with a system dynamics model of the spillover effect. The migration decision models were structured according to two interacting paths, one that captured long-term “chronic” impacts related to protracted deteriorating quality of life and a second focused on short-term “acute” impacts of disaster and/or conflict. Chronic migration dynamics were modeled for two different cases; one that looked only at emigration but at a national level for the entire world; and a second that looked at both emigration and immigration but focused on a single nation. Model parameterization for each of the migration models was accomplished through regression analysis using decadal data spanning the period 1960-2010. A similar approach was taken with acute migration dynamics except regression analysis utilized annual data sets limited to a shorter time horizon (2001-2013). The system dynamics spillover model was organized around two broad modules, one simulating the decision dynamics of migration and a second module that treats the changing environmental conditions that influence the migration decision. The environmental module informs the migration decision, endogenously simulating interactions/changes in the economy, labor, population, conflict, water, and food. A regional model focused on Mali in western Africa was used as a test case to demonstrate the efficacy of the model.« less

The Future of Digital Working: Knowledge Migration and Learning

ERIC Educational Resources Information Center

Malcolm, Irene

2014-01-01

Against the backdrop of intensified migration linked to globalisation, this article considers the implications of knowledge migration for future digital workers. It draws empirically on a socio-material analysis of the international software localisation industry. Localisers' work requires linguistic, cultural and software engineering skills to…

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

PubMed

Azarian, Taj; Grant, Lindsay R; Arnold, Brian J; Hammitt, Laura L; Reid, Raymond; Santosham, Mathuram; Weatherholtz, Robert; Goklish, Novalene; Thompson, Claudette M; Bentley, Stephen D; O'Brien, Katherine L; Hanage, William P; Lipsitch, Marc

2018-04-01

In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome

PubMed Central

Hammitt, Laura L.; Santosham, Mathuram; Goklish, Novalene; Thompson, Claudette M.; Bentley, Stephen D.; O’Brien, Katherine L.

2018-01-01

In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998–2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998–2000) than the preceding period (2006–2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines. PMID:29617440

Reviewing the history of HIV-1: spread of subtype B in the Americas.

PubMed

Junqueira, Dennis Maletich; de Medeiros, Rúbia Marília; Matte, Maria Cristina Cotta; Araújo, Leonardo Augusto Luvison; Chies, Jose Artur Bogo; Ashton-Prolla, Patricia; Almeida, Sabrina Esteves de Matos

2011-01-01

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950-1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.

Reviewing the History of HIV-1: Spread of Subtype B in the Americas

PubMed Central

Junqueira, Dennis Maletich; de Medeiros, Rúbia Marília; Matte, Maria Cristina Cotta; Araújo, Leonardo Augusto Luvison; Chies, Jose Artur Bogo; Ashton-Prolla, Patricia; Almeida, Sabrina Esteves de Matos

2011-01-01

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and Bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950–1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion. PMID:22132104

Controls on drainage divide migration in the northern Sierras Pampeanas assessed through morphometric indicators

NASA Astrophysics Data System (ADS)

Seagren, E. G.; Schoenbohm, L. M.

2017-12-01

Drainage reorganization, primarily through progressive divide migration leading to discrete stream captures, is increasingly recognized as a common phenomenon during mountain-building events. This drainage rearrangement reflects complex interactions between tectonics, climate, and lithology, and can fundamentally change erosion and sedimentation patterns; therefore, determining the spatial extent and potential controls of divide migration is vital to understanding the topographic evolution of orogenic landscapes. Both geomorphic and morphometric evidence can be used to identify such drainage reorganization. The northern Sierras Pampeanas is an ideal location in which to study divide migration as limited glaciation and low out-of-channel erosion rates preserve evidence of reorganization. Additionally, several ranges in the region, such as Sierra de las Planchadas, exhibit geomorphic evidence of drainage rearrangement, including wind gaps and hairpin turns. Using ArcGIS, LSDTopoTools, and TopoToolbox, we conducted a systematic analysis of the spatial distribution of three morphometric indicators of divide migration: χ, Mx, and local headwater relief. Local `hotspots' undergoing drainage divide migration were identified using spatial autocorrelation and clustering methods - Gi* and Moran's I. Using spatial regression analysis, we assessed the potential controls of lithology, modern TRMM precipitation rates, and tectonics over divide migration. Preliminary results suggest broad westward migration of main drainage divides, following both the orographic precipitation gradient and regional slope.

Migration of Undergraduate First-Time Transfers: Snapshot Analysis 2006-2008

ERIC Educational Resources Information Center

South Carolina Commission on Higher Education, 2010

2010-01-01

The Commission on Higher Education had a student intern from USC-Columbia initiate an analysis of data on the migration of undergraduate first-time transfers to compare trends, growth, and proportions of transfers to and from various sectors and institution types over a three-year period, from 2006-2008. Staff have refined the analysis and…

Inferring Functional Neural Connectivity with Phase Synchronization Analysis: A Review of Methodology

PubMed Central

Sun, Junfeng; Li, Zhijun; Tong, Shanbao

2012-01-01

Functional neural connectivity is drawing increasing attention in neuroscience research. To infer functional connectivity from observed neural signals, various methods have been proposed. Among them, phase synchronization analysis is an important and effective one which examines the relationship of instantaneous phase between neural signals but neglecting the influence of their amplitudes. In this paper, we review the advances in methodologies of phase synchronization analysis. In particular, we discuss the definitions of instantaneous phase, the indexes of phase synchronization and their significance test, the issues that may affect the detection of phase synchronization and the extensions of phase synchronization analysis. In practice, phase synchronization analysis may be affected by observational noise, insufficient samples of the signals, volume conduction, and reference in recording neural signals. We make comments and suggestions on these issues so as to better apply phase synchronization analysis to inferring functional connectivity from neural signals. PMID:22577470

Bird migration and avian influenza: a comparison of hydrogen stable isotopes and satellite tracking methods

USGS Publications Warehouse

Bridge, Eli S.; Kelly, Jeffrey F.; Xiao, Xiangming; Takekawa, John Y.; Hill, Nichola J.; Yamage, Mat; Haque, Enam Ul; Islam, Mohammad Anwarul; Mundkur, Taej; Yavuz, Kiraz Erciyas; Leader, Paul; Leung, Connie Y.H.; Smith, Bena; Spragens, Kyle A.; Vandegrift, Kurt J.; Hosseini, Parviez R.; Saif, Samia; Mohsanin, Samiul; Mikolon, Andrea; Islam, Ausrafal; George, Acty; Sivananinthaperumal, Balachandran; Daszak, Peter; Newman, Scott H.

2014-01-01

Satellite-based tracking of migratory waterfowl is an important tool for understanding the potential role of wild birds in the long-distance transmission of highly pathogenic avian influenza. However, employing this technique on a continental scale is prohibitively expensive. This study explores the utility of stable isotope ratios in feathers in examining both the distances traveled by migratory birds and variation in migration behavior. We compared the satellite-derived movement data of 22 ducks from 8 species captured at wintering areas in Bangladesh, Turkey, and Hong Kong with deuterium ratios (δD) in the feathers of these and other individuals captured at the same locations. We derived likely molting locations from the satellite tracking data and generated expected isotope ratios based on an interpolated map of δD in rainwater. Although δD was correlated with the distance between wintering and molting locations, surprisingly, measured δD values were not correlated with either expected values or latitudes of molting sites. However, population-level parameters derived from the satellite-tracking data, such as mean distance between wintering and molting locations and variation in migration distance, were reflected by means and variation of the stable isotope values. Our findings call into question the relevance of the rainfall isotope map for Asia for linking feather isotopes to molting locations, and underscore the need for extensive ground truthing in the form of feather-based isoscapes. Nevertheless, stable isotopes from feathers could inform disease models by characterizing the degree to which regional breeding populations interact at common wintering locations. Feather isotopes also could aid in surveying wintering locations to determine where high-resolution tracking techniques (e.g. satellite tracking) could most effectively be employed. Moreover, intrinsic markers such as stable isotopes offer the only means of inferring movement information from birds that have died as a result of infection. In the absence of feather based-isoscapes, we recommend a combination of isotope analysis and satellite-tracking as the best means of generating aggregate movement data for informing disease models.

Amphibious Magnetotelluric Investigation of the Aleutian Arc: Mantle Melt Generation and Migration beneath Okmok Caldera

NASA Astrophysics Data System (ADS)

Zelenak, G.; Key, K.; Bennington, N. L.; Bedrosian, P.

2015-12-01

Understanding the factors controlling the release of volatiles from the downgoing slab, the subsequent generation of melt in the overlying mantle wedge, the migration of melt to the crust, and its evolution and emplacement within the crust are important for advancing our understanding of arc magmatism and crustal genesis. Because melt and aqueous fluids are a few orders of magnitude more electrically conductive than unmelted peridotite, the conductivity-mapping magnetotelluric (MT) method is well-suited to imaging fluids and melt beneath arc volcanoes. Here we present conductivity results from an amphibious MT profile crossing Okmok volcano in the central Aleutian arc. The Aleutian arc is one of the most volcanically active regions in North America, making it an ideal location for studying arc magnetism. Okmok volcano, located on the northeastern portion of Umnak Island, is among the most active volcanoes in the Aleutian chain. In addition to two caldera-forming events in the Holocene, numerous eruptions in the past century indicate a robust magmatic supply. Previous coarse resolution seismic studies have inferred a crustal magma reservoir. In order to investigate the role fluids play in melting the mantle wedge, how melts ascend through the corner flow regime of the mantle wedge, how melt migrates and is stored within the upper mantle and crust, and how this impacts explosive caldera forming eruptions, we carried out an amphibious geophysical survey across the arc in June-July 2015. Twenty-nine onshore MT stations and 10 offshore stations were collected in a 3D array covering Okmok, and 43 additional offshore MT stations completed a 300 km amphibious profile starting at the trench, crossing the forearc, arc and backarc. Thirteen onshore passive seismic stations were also installed and will remain in place for one year to supplement the twelve permanent stations on the island. Data collected by this project will be used to map seismic velocity and electrical conductivity variations within the arc, providing unique constraints
on temperature, mineralogy and fluid content. This abstract covers preliminary MT constraints on the mantle and deep crust as inferred from the 300 km long amphibious profile. A companion abstract (Bennington et al.) considers the crustal magma chamber imaged by the 3D array.

Decoupling migration effects from income effects on reproduction in Central American migrant-sending households.

PubMed

Davis, Jason

2011-01-01

Contemporary data for three Central American countries (Costa Rica, Guatemala, and Nicaragua) surveyed by the Latin American Migration Project were analyzed to determine if migration length and remittance transfers had an influence on fertility. The analysis was structured to separate societal influences on fertility attributable to migration from the income effects associated with remittance transfers. At the couple level, the odds that a birth would occur were negatively associated with an increase in U.S. remittance receipts and an increase in a wife’s migration duration. However, no correlation was found between length of male migration and couple fertility.

Examining Pre-migration Health Among Filipino Nurses

PubMed Central

de Castro, A. B.; Gee, Gilbert; Fujishiro, Kaori; Rue, Tessa

2014-01-01

The healthy immigrant hypothesis asserts that immigrants arrive in the receiving country healthier than same race/ethnic counterparts born there. Contemporary research, however, has not evaluated pre-migration health among migrants, nor has explicitly considered comparisons with non-migrants in the country of origin. Pre-migration health was examined among 621 Filipino nurses, including self-reported physical health, mental health, health behaviors, and social stress. Measures were compared by intention to migrate and also tested as predictors of actual migration using time-to-event analysis. Nurses intending to migrate had higher proportion of depression and reported higher general perceived stress compared to those not. Predictors of actual migration included age, mentally unhealthy days, social strain, and social support. Physical health and health behavior measures had no association with migration intention or actual migration. Findings suggest that, relative to those not intending to migrate, nurses intending to migrate have worse mental health status and social stress; and, do not have a physical health advantage. Future research must span the pre- to post-migration continuum to better understand the impact of moving from one country to another on health and well-being. PMID:25385090

Examining Pre-migration Health Among Filipino Nurses.

PubMed

de Castro, A B; Gee, Gilbert; Fujishiro, Kaori; Rue, Tessa

2015-12-01

The healthy immigrant hypothesis asserts that immigrants arrive in the receiving country healthier than same race/ethnic counterparts born there. Contemporary research, however, has not evaluated pre-migration health among migrants, nor has explicitly considered comparisons with non-migrants in the country of origin. Pre-migration health was examined among 621 Filipino nurses, including self-reported physical health, mental health, health behaviors, and social stress. Measures were compared by intention to migrate and also tested as predictors of actual migration using time-to-event analysis. Nurses intending to migrate had higher proportion of depression and reported higher general perceived stress compared to those not. Predictors of actual migration included age, mentally unhealthy days, social strain, and social support. Physical health and health behavior measures had no association with migration intention or actual migration. Findings suggest that, relative to those not intending to migrate, nurses intending to migrate have worse mental health status and social stress; and, do not have a physical health advantage. Future research must span the pre- to post-migration continuum to better understand the impact of moving from one country to another on health and well-being.

Africa: Setting for Human Migration

ERIC Educational Resources Information Center

Buuba, Babacar Diop

2007-01-01

Analysis of African migrations can help to understand prehistoric, historical, ancient modern and contemporaneous migrations. Movements of populations were and continue to be so intense that, for some analysts, they constitute one of the dominant trends of the history and destiny of the very old continent. African and non-African states, whether…

Displacement correlations between a single mesenchymal-like cell and its nucleus effectively link subcellular activities and motility in cell migration analysis

NASA Astrophysics Data System (ADS)

Lan, Tian; Cheng, Kai; Ren, Tina; Arce, Stephen Hugo; Tseng, Yiider

2016-09-01

Cell migration is an essential process in organism development and physiological maintenance. Although current methods permit accurate comparisons of the effects of molecular manipulations and drug applications on cell motility, effects of alterations in subcellular activities on motility cannot be fully elucidated from those methods. Here, we develop a strategy termed cell-nuclear (CN) correlation to parameterize represented dynamic subcellular activities and to quantify their contributions in mesenchymal-like migration. Based on the biophysical meaning of the CN correlation, we propose a cell migration potential index (CMPI) to measure cell motility. When the effectiveness of CMPI was evaluated with respect to one of the most popular cell migration analysis methods, Persistent Random Walk, we found that the cell motility estimates among six cell lines used in this study were highly consistent between these two approaches. Further evaluations indicated that CMPI can be determined using a shorter time period and smaller cell sample size, and it possesses excellent reliability and applicability, even in the presence of a wide range of noise, as might be generated from individual imaging acquisition systems. The novel approach outlined here introduces a robust strategy through an analysis of subcellular locomotion activities for single cell migration assessment.

Introgression between cultivars and wild populations of Momordica charantia L. (Cucurbitaceae) in Taiwan.

PubMed

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae) in Taiwan

PubMed Central

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes. PMID:22754378

Magnetotelluric Investigation of Melt Storage Beneath Okmok Caldera, Alaska

NASA Astrophysics Data System (ADS)

Bennington, N. L.; Bedrosian, P.; Key, K.; Zelenak, G.

2015-12-01

Alaska accounts for nearly 99% of the seismic moment release within the US. Much of this is associated with the Aleutian volcanic arc, the most tectonically active region in North America, and an ideal location for studying arc magmatism. Okmok is an active volcano located in the central Aleutian arc, defined by a pair of nested, 10 km diameter calderas. The subdued topography of Okmok, relative to other Aleutian volcanoes, improves access and permits dense sampling within the caldera closer to the underlying magmatic system. Okmok volcano was selected as the site of study for this project due to frequent volcanic activity and the presence of a crustal magma reservoir as inferred from previous coarse resolution seismic studies. In June-July 2015, we carried out an amphibious geophysical field deployment at Okmok. Onshore work in and around the volcano included collection of an array of magnetotelluric (MT) stations and installation of a temporary, year-long seismic array. A ring of 3D offshore MT deployments made around the island augments the onshore array. An additional 2D tectonic-scale profile spans the trench, volcanic arc, and backarc. This new geophysical data will be used to gain a greater understanding of Aleutian arc melt generation, migration, and storage beneath an active caldera. We present results from the analysis of the newly collected amphibious 3D MT data. This data will be used to model the distribution and migration of melt within Okmok's crustal magma reservoir. Initial processing of the data shows strong MT signal levels, in particular from a geomagnetic storm that occurred from June 21-23, 2015. A companion abstract discussing the 2D tectonic scale MT profile, which constrains the mantle and deep crust beneath Okmok volcano, is discussed by Zelenak et al.

Kinematics and dynamics of the East Pacific Rise linked to a stable, deep-mantle upwelling [Kinematics and dynamics of the East Pacific Rise linked to whole mantel convective motions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rowley, David B.; Forte, Alessandro M.; Rowan, Christopher J.

Earth’s tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth’s dominant MOR, has been characterized by limited ridge-perpendicular migration and persistent, asymmetric ridge accretion that are anomalous relative to other MORs. We reconstruct the subduction-related buoyancy fluxes of plates on either side of the EPR. The general expectation is that greater slab pullmore » should correlate with faster plate motion and faster spreading at the EPR. Moreover, asymmetry in slab pull on either side of the EPR should correlate with either ridge migration or enhanced plate velocity in the direction of greater slab pull. Based on our analysis, none of the expected correlations are evident. This implies that other forces significantly contribute to EPR behavior. We explain these observations using mantle flow calculations based on globally integrated buoyancy distributions that require core-mantle boundary heat flux of up to 20 TW. The time-dependent mantle flow predictions yield a long-lived deep-seated upwelling that has its highest radial velocity under the EPR and is inferred to control its observed kinematics. Lastly, the mantle-wide upwelling beneath the EPR drives horizontal components of asthenospheric flows beneath the plates that are similarly asymmetric but faster than the overlying surface plates, thereby contributing to plate motions through viscous tractions in the Pacific region.« less

Identification and characterization of Taenia solium enolase as a plasminogen-binding protein.

PubMed

Ayón-Núñez, Dolores A; Fragoso, Gladis; Espitia, Clara; García-Varela, Martín; Soberón, Xavier; Rosas, Gabriela; Laclette, Juan P; Bobes, Raúl J

2018-06-01

The larval stage of Taenia solium (cysticerci) is the causal agent of human and swine cysticercosis. When ingested by the host, T. solium eggs are activated and hatch in the intestine, releasing oncospheres that migrate to various tissues and evolve into cysticerci. Plasminogen (Plg) receptor proteins have been reported to play a role in migration processes for several pathogens. This work is aimed to identify Plg-binding proteins in T. solium cysticerci and determine whether T. solium recombinant enolase (rTsEnoA) is capable of specifically binding and activating human Plg. To identify Plg-binding proteins, a 2D-SDS-PAGE ligand blotting was performed, and recognized spots were identified by MS/MS. Seven proteins from T. solium cysticerci were found capable of binding Plg: fascicilin-1, fasciclin-2, enolase, MAPK, annexin, actin, and cytosolic malate dehydrogenase. To determine whether rTsEnoA binds human Plg, a ligand blotting was performed and the results were confirmed by ELISA both in the presence and absence of εACA, a competitive Plg inhibitor. Finally, rTsEnoA-bound Plg was activated to plasmin in the presence of tPA. To better understand the evolution of enolase isoforms in T. solium, a phylogenetic inference analysis including 75 enolase amino acid sequences was conducted. The origin of flatworm enolase isoforms, except for Eno4, is independent of their vertebrate counterparts. Therefore, herein we propose to designate tapeworm protein isoforms as A, B, C, and 4. In conclusion, recombinant enolase showed a strong plasminogen binding and activating activity in vitro. T. solium enolase could play a role in parasite invasion along with other plasminogen-binding proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

Kinematics and dynamics of the East Pacific Rise linked to a stable, deep-mantle upwelling [Kinematics and dynamics of the East Pacific Rise linked to whole mantel convective motions

DOE PAGES

Rowley, David B.; Forte, Alessandro M.; Rowan, Christopher J.; ...

2016-12-23

Earth’s tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth’s dominant MOR, has been characterized by limited ridge-perpendicular migration and persistent, asymmetric ridge accretion that are anomalous relative to other MORs. We reconstruct the subduction-related buoyancy fluxes of plates on either side of the EPR. The general expectation is that greater slab pullmore » should correlate with faster plate motion and faster spreading at the EPR. Moreover, asymmetry in slab pull on either side of the EPR should correlate with either ridge migration or enhanced plate velocity in the direction of greater slab pull. Based on our analysis, none of the expected correlations are evident. This implies that other forces significantly contribute to EPR behavior. We explain these observations using mantle flow calculations based on globally integrated buoyancy distributions that require core-mantle boundary heat flux of up to 20 TW. The time-dependent mantle flow predictions yield a long-lived deep-seated upwelling that has its highest radial velocity under the EPR and is inferred to control its observed kinematics. Lastly, the mantle-wide upwelling beneath the EPR drives horizontal components of asthenospheric flows beneath the plates that are similarly asymmetric but faster than the overlying surface plates, thereby contributing to plate motions through viscous tractions in the Pacific region.« less

Geochemical investigation of UMTRAP designated site at Durango, Colorado

DOE Office of Scientific and Technical Information (OSTI.GOV)

Markos, G.; Bush, K.J.

1983-09-01

This report is the result of a geochemical investigation of the former uranium mill and tailings site at Durango, Colorado. This is one in a series of site specific geochemical investigations performed on the inactive uranium mill tailings included in the UMTRA Project. The objectives of the investigation are to characterize the geochemistry, to determine the contaminant distribution resulting from the former milling activities and tailings, and to infer chemical pathways and transport mechanisms from the contaminant distribution. The results will be used to model contaminant migration and to develop criteria for long-term containment media such as a cover systemmore » which is impermeable to contaminant migration. This report assumes a familiarity with the hydrologic conditions of the site and the geochemical concepts underlying the investigation. The results reported are based on a one-time sampling of waters and solid material from the background, the area adjacent to the site, and the site. The solid samples are water extracted remove easily soluble salts and acids extracted to remove cabonates and hydroxides. The water extracts and solid samples were analyzed for the major and trace elements. A limited number of samples were analyzed for radiological components. The report includes the methods of sampling, sample processing, analysis, and data interpretation. Three major conclusions are: (1) carbonate salts and low TDS characterize the tailings; (2) the adjacent area and raffinate ponds contain contaminants deposited by a single event of fluid permeation of the soils; and (3) the Animas River adjacent to the site has elevated gross alpha activity attributed to /sup 226/Ra in the sediments derived from the tailings or milling activities.« less

Early Back-to-Africa Migration into the Horn of Africa

PubMed Central

Hodgson, Jason A.; Mulligan, Connie J.; Al-Meeri, Ali; Raaum, Ryan L.

2014-01-01

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural. PMID:24921250

Divergent pattern of nuclear genetic diversity across the range of the Afromontane Prunus africana mirrors variable climate of African highlands

PubMed Central

Kadu, Caroline A. C.; Konrad, Heino; Schueler, Silvio; Muluvi, Geoffrey M.; Eyog-Matig, Oscar; Muchugi, Alice; Williams, Vivienne L.; Ramamonjisoa, Lolona; Kapinga, Consolatha; Foahom, Bernard; Katsvanga, Cuthbert; Hafashimana, David; Obama, Crisantos; Geburek, Thomas

2013-01-01

Background and Aims Afromontane forest ecosystems share a high similarity of plant and animal biodiversity, although they occur mainly on isolated mountain massifs throughout the continent. This resemblance has long provoked questions on former wider distribution of Afromontane forests. In this study Prunus africana (one of the character trees of Afromontane forests) is used as a model for understanding the biogeography of this vegetation zone. Methods Thirty natural populations from nine African countries covering a large part of Afromontane regions were analysed using six nuclear microsatellites. Standard population genetic analysis as well as Bayesian and maximum likelihood models were used to infer genetic diversity, population differentiation, barriers to gene flow, and recent and all migration among populations. Key Results Prunus africana exhibits strong divergence among five main Afromontane regions: West Africa, East Africa west of the Eastern Rift Valley (ERV), East Africa east of the ERV, southern Africa and Madagascar. The strongest divergence was evident between Madagascar and continental Africa. Populations from West Africa showed high similarity with East African populations west of the ERV, whereas populations east of the ERV are closely related to populations of southern Africa, respectively. Conclusions The observed patterns indicate divergent population history across the continent most likely associated to Pleistocene changes in climatic conditions. The high genetic similarity between populations of West Africa with population of East Africa west of the ERV is in agreement with faunistic and floristic patterns and provides further evidence for a historical migration route. Contrasting estimates of recent and historical gene flow indicate a shift of the main barrier to gene flow from the Lake Victoria basin to the ERV, highlighting the dynamic environmental and evolutionary history of the region. PMID:23250908

Deduced Inference in the Analysis of Experimental Data

ERIC Educational Resources Information Center

Bird, Kevin D.

2011-01-01

Any set of confidence interval inferences on J - 1 linearly independent contrasts on J means, such as the two comparisons [mu][subscript 1] - [mu][subscript 2] and [mu][subscript 2] - [mu][subscript 3] on 3 means, provides a basis for the deduction of interval inferences on all other contrasts, such as the redundant comparison [mu][subscript 1] -…

Social networks help to infer causality in the tumor microenvironment.

PubMed

Crespo, Isaac; Doucey, Marie-Agnès; Xenarios, Ioannis

2016-03-15

Networks have become a popular way to conceptualize a system of interacting elements, such as electronic circuits, social communication, metabolism or gene regulation. Network inference, analysis, and modeling techniques have been developed in different areas of science and technology, such as computer science, mathematics, physics, and biology, with an active interdisciplinary exchange of concepts and approaches. However, some concepts seem to belong to a specific field without a clear transferability to other domains. At the same time, it is increasingly recognized that within some biological systems--such as the tumor microenvironment--where different types of resident and infiltrating cells interact to carry out their functions, the complexity of the system demands a theoretical framework, such as statistical inference, graph analysis and dynamical models, in order to asses and study the information derived from high-throughput experimental technologies. In this article we propose to adopt and adapt the concepts of influence and investment from the world of social network analysis to biological problems, and in particular to apply this approach to infer causality in the tumor microenvironment. We showed that constructing a bidirectional network of influence between cell and cell communication molecules allowed us to determine the direction of inferred regulations at the expression level and correctly recapitulate cause-effect relationships described in literature. This work constitutes an example of a transfer of knowledge and concepts from the world of social network analysis to biomedical research, in particular to infer network causality in biological networks. This causality elucidation is essential to model the homeostatic response of biological systems to internal and external factors, such as environmental conditions, pathogens or treatments.

Data Analysis Techniques for Physical Scientists

NASA Astrophysics Data System (ADS)

Pruneau, Claude A.

2017-10-01

Preface; How to read this book; 1. The scientific method; Part I. Foundation in Probability and Statistics: 2. Probability; 3. Probability models; 4. Classical inference I: estimators; 5. Classical inference II: optimization; 6. Classical inference III: confidence intervals and statistical tests; 7. Bayesian inference; Part II. Measurement Techniques: 8. Basic measurements; 9. Event reconstruction; 10. Correlation functions; 11. The multiple facets of correlation functions; 12. Data correction methods; Part III. Simulation Techniques: 13. Monte Carlo methods; 14. Collision and detector modeling; List of references; Index.

Migration: a core public health ethics issue.

PubMed

Wild, V; Dawson, A

2018-05-01

In this article, we outline the link between migration, public health and ethics. Discussing relevant arguments about migration from the perspective of public health and public health ethics. Critical review of theories and frameworks, case-based analysis and systematic identification and discussion of challenges. Migration is a core issue of public health ethics and must take a case-based approach: seeking to identify the specific ethical dimensions and vulnerabilities in each particular context. Public health as a practice, built upon the core value of justice, requires the protection and promotion of migrants' well-being (even if this produces tension with immigration services). Ethical analysis should take all phases of migration into account: before, during and after transit. We argue that migration policies, at least as they relate to migrants' well-being, should be founded upon a shared humanity, respect for human rights and on the idea that effective public health cannot and should not be confined within the borders and to the citizens of any host country. We make the case for migration to be seen as a core issue of public health ethics. Copyright © 2018 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Obesity as a risk factor for developing functional limitation among older adults: A conditional inference tree analysis

USDA-ARS?s Scientific Manuscript database

Objective: To examine the risk factors of developing functional decline and make probabilistic predictions by using a tree-based method that allows higher order polynomials and interactions of the risk factors. Methods: The conditional inference tree analysis, a data mining approach, was used to con...

Structural Analysis of Treatment Cycles Representing Transitions between Nursing Organizational Units Inferred from Diabetes

PubMed Central

Dehmer, Matthias; Kurt, Zeyneb; Emmert-Streib, Frank; Them, Christa; Schulc, Eva; Hofer, Sabine

2015-01-01

In this paper, we investigate treatment cycles inferred from diabetes data by means of graph theory. We define the term treatment cycles graph-theoretically and perform a descriptive as well as quantitative analysis thereof. Also, we interpret our findings in terms of nursing and clinical management. PMID:26030296

Middle School Learners' Use of Latin Roots to Infer the Meaning of Unfamiliar Words

ERIC Educational Resources Information Center

Crosson, Amy C.; McKeown, Margaret G.

2016-01-01

This study investigated how middle school students leverage information about bound Latin roots (e.g., voc in "advocate" and "vociferous") to infer meanings of unfamiliar words, and how instruction may facilitate morphological analysis using roots. A dynamic assessment of morphological analysis was administered to 29 sixth…

A 15 year catalog of more than 1 million low-frequency earthquakes: Tracking tremor and slip along the deep San Andreas Fault

NASA Astrophysics Data System (ADS)

Shelly, David R.

2017-05-01

Low-frequency earthquakes (LFEs) are small, rapidly recurring slip events that occur on the deep extensions of some major faults. Their collective activation is often observed as a semicontinuous signal known as tectonic (or nonvolcanic) tremor. This manuscript presents a catalog of more than 1 million LFEs detected along the central San Andreas Fault from 2001 to 2016. These events have been detected via a multichannel matched-filter search, cross-correlating waveform templates representing 88 different LFE families with continuous seismic data. Together, these source locations span nearly 150 km along the central San Andreas Fault, ranging in depth from 16 to 30 km. This accumulating catalog has been the source for numerous studies examining the behavior of these LFE sources and the inferred slip behavior of the deep fault. The relatively high temporal and spatial resolutions of the catalog have provided new insights into properties such as tremor migration, recurrence, and triggering by static and dynamic stress perturbations. Collectively, these characteristics are inferred to reflect a very weak fault likely under near-lithostatic fluid pressure, yet the physical processes controlling the stuttering rupture observed as tremor and LFE signals remain poorly understood. This paper aims to document the LFE catalog assembly process and associated caveats, while also updating earlier observations and inferred physical constraints. The catalog itself accompanies this manuscript as part of the electronic supplement, with the goal of providing a useful resource for continued future investigations.

Determinants and Impact of Rural-Urban Migration: A Case Study of Selected Communities in Western Nigeria. African Rural Employment Paper No. 10.

ERIC Educational Resources Information Center

Essang, Sunday M.; Mabawonku, Adewale F.

This economic analysis of migration was designed to test the following six hypotheses on the causes of out-migration from agriculture and its effect on the rural economy of Western Nigeria: (1) age of the rural family, of which the migrant is a member, is positively related to rural-urban migration rate; (2) a positive relationship exists between…

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

PubMed

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

CADDIS Volume 4. Data Analysis: Biological and Environmental Data Requirements

EPA Pesticide Factsheets

Overview of PECBO Module, using scripts to infer environmental conditions from biological observations, statistically estimating species-environment relationships, methods for inferring environmental conditions, statistical scripts in module.

Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis.

PubMed

Anguiano, María; Castilla, Carlos; Maška, Martin; Ederra, Cristina; Peláez, Rafael; Morales, Xabier; Muñoz-Arrieta, Gorka; Mujika, Maite; Kozubek, Michal; Muñoz-Barrutia, Arrate; Rouzaut, Ana; Arana, Sergio; Garcia-Aznar, José Manuel; Ortiz-de-Solorzano, Carlos

2017-01-01

Microfluidic devices are becoming mainstream tools to recapitulate in vitro the behavior of cells and tissues. In this study, we use microfluidic devices filled with hydrogels of mixed collagen-Matrigel composition to study the migration of lung cancer cells under different cancer invasion microenvironments. We present the design of the microfluidic device, characterize the hydrogels morphologically and mechanically and use quantitative image analysis to measure the migration of H1299 lung adenocarcinoma cancer cells in different experimental conditions. Our results show the plasticity of lung cancer cell migration, which turns from mesenchymal in collagen only matrices, to lobopodial in collagen-Matrigel matrices that approximate the interface between a disrupted basement membrane and the underlying connective tissue. Our quantification of migration speed confirms a biphasic role of Matrigel. At low concentration, Matrigel facilitates migration, most probably by providing a supportive and growth factor retaining environment. At high concentration, Matrigel slows down migration, possibly due excessive attachment. Finally, we show that antibody-based integrin blockade promotes a change in migration phenotype from mesenchymal or lobopodial to amoeboid and analyze the effect of this change in migration dynamics, in regards to the structure of the matrix. In summary, we describe and characterize a robust microfluidic platform and a set of software tools that can be used to study lung cancer cell migration under different microenvironments and experimental conditions. This platform could be used in future studies, thus benefitting from the advantages introduced by microfluidic devices: precise control of the environment, excellent optical properties, parallelization for high throughput studies and efficient use of therapeutic drugs.

Prospects for the Comparative Study of International Migration using quasi-longitudinal micro-data

PubMed Central

Liu, Mao-Mei; Creighton, Mathew J.; Riosmena, Fernando; Baizán Mun͂oz, Pau

2017-01-01

BACKGROUND Longitudinal micro-level data about international migration behavior are notoriously difficult to collect, but data collection efforts have become more frequent in recent years. Comparative research of the patterns and processes of international migration, however, remains quite rare, especially that which compares across regions. OBJECTIVE We highlight the promises and difficulties of comparative international migration research, by offering a detailed comparison of two prominent data collection efforts. METHODS We systematically review existing sources of longitudinal and quasi-longitudinal individual-level and household-level data of international migration. We then compare two widely-used data sources: the Mexican Migration Project (MMP) and the Migration between Africa and Europe project (MAFE). RESULTS Data collection efforts are increasingly diverse, yet public accessibility of data remains limited. Also, comparability of data collected across settings can be complicated. In our MMP-MAFE analysis, we show some ways in which comparability can be achieved. CONCLUSIONS A primary roadblock to international comparative research is that, with some exceptions, the public accessibility of data remains low. Even when data is public and surveys are modeled after one another, comparability is not easy due to necessary trade-offs in adapting surveys to local settings and to developments in the field. CONTRIBUTION We demonstrate that, despite great strides in collecting quasi-longitudinal data of international migration, data accessibility still hinders the study of migration. With regards to comparability, our article provides important lessons for future data collection and analysis efforts that could improve comparability and thus advance understanding of the complex dynamics of international migration. PMID:29276429

Relative evolutionary rate inference in HyPhy with LEISR.

PubMed

Spielman, Stephanie J; Kosakovsky Pond, Sergei L

2018-01-01

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced "laser"), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for inferring relative site-wise evolutionary rates, primarily from protein data. We extend the original method for more general use in several key ways: (i) we increase the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu ("Relative evolutionary rate inference"), which calls the HyPhy batchfile LEISR.bf.

Bayesian inference of interaction properties of noisy dynamical systems with time-varying coupling: capabilities and limitations

NASA Astrophysics Data System (ADS)

Wilting, Jens; Lehnertz, Klaus

2015-08-01

We investigate a recently published analysis framework based on Bayesian inference for the time-resolved characterization of interaction properties of noisy, coupled dynamical systems. It promises wide applicability and a better time resolution than well-established methods. At the example of representative model systems, we show that the analysis framework has the same weaknesses as previous methods, particularly when investigating interacting, structurally different non-linear oscillators. We also inspect the tracking of time-varying interaction properties and propose a further modification of the algorithm, which improves the reliability of obtained results. We exemplarily investigate the suitability of this algorithm to infer strength and direction of interactions between various regions of the human brain during an epileptic seizure. Within the limitations of the applicability of this analysis tool, we show that the modified algorithm indeed allows a better time resolution through Bayesian inference when compared to previous methods based on least square fits.

Feasibility study on the use of probabilistic migration modeling in support of exposure assessment from food contact materials.

PubMed

Poças, Maria F; Oliveira, Jorge C; Brandsch, Rainer; Hogg, Timothy

2010-07-01

The use of probabilistic approaches in exposure assessments of contaminants migrating from food packages is of increasing interest but the lack of concentration or migration data is often referred as a limitation. Data accounting for the variability and uncertainty that can be expected in migration, for example, due to heterogeneity in the packaging system, variation of the temperature along the distribution chain, and different time of consumption of each individual package, are required for probabilistic analysis. The objective of this work was to characterize quantitatively the uncertainty and variability in estimates of migration. A Monte Carlo simulation was applied to a typical solution of the Fick's law with given variability in the input parameters. The analysis was performed based on experimental data of a model system (migration of Irgafos 168 from polyethylene into isooctane) and illustrates how important sources of variability and uncertainty can be identified in order to refine analyses. For long migration times and controlled conditions of temperature the affinity of the migrant to the food can be the major factor determining the variability in the migration values (more than 70% of variance). In situations where both the time of consumption and temperature can vary, these factors can be responsible, respectively, for more than 60% and 20% of the variance in the migration estimates. The approach presented can be used with databases from consumption surveys to yield a true probabilistic estimate of exposure.

Population, Migration, and Arctic Community Change

NASA Astrophysics Data System (ADS)

Hamilton, L.; Wirsing, J.

2017-12-01

North American Arctic communities commonly show decadal trends in population growth, driven by natural increase but variably offset by net migration with year-to-year volatility. Migration rates themselves can be a social indicator, integrating a range of push and pull factors. Population and population change of Arctic communities are basic scale properties affecting the resources needed to achieve sustainability, and the adaptations that may be required for climate change (such as relocation from flood-threatened locations). We examine interannual changes 1990-2016 in population and net migration of 43 Alaska Arctic communities, some facing serious threats of flooding. Our Alaska analysis updates previous work with additional years of data. We also extend this demographic analysis for the first time to 25 towns and villages of Nunavut, Canada.

Reconstructing the Indian Origin and Dispersal of the European Roma: A Maternal Genetic Perspective

PubMed Central

Mendizabal, Isabel; Valente, Cristina; Gusmão, Alfredo; Alves, Cíntia; Gomes, Verónica; Goios, Ana; Parson, Walther; Calafell, Francesc; Alvarez, Luis; Amorim, António; Gusmão, Leonor

2011-01-01

Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies. PMID:21264345

A test of the influence of continental axes of orientation on patterns of human gene flow

PubMed Central

Ramachandran, Sohini; Rosenberg, Noah A.

2012-01-01

The geographic distribution of genetic variation reflects trends in past population migrations, and can be used to make inferences about these migrations. It has been proposed that the east-west orientation of the Eurasian landmass facilitated the rapid spread of ancient technological innovations across Eurasia, while the north-south orientation of the Americas led to a slower diffusion of technology there. If the diffusion of technology was accompanied by gene flow, then this hypothesis predicts that genetic differentiation in the Americas along lines of longitude will be greater than that in Eurasia along lines of latitude. We use 678 microsatellite loci from 68 indigenous populations in Eurasia and the Americas to investigate the spatial axes that underlie population-genetic variation. We find that genetic differentiation increases more rapidly along lines of longitude in the Americas than along lines of latitude in Eurasia. Distance along lines of latitude explains a sizeable portion of genetic distance in Eurasia, whereas distance along lines of longitude does not explain a large proportion of Eurasian genetic variation. Genetic differentiation in the Americas occurs along both latitudinal and longitudinal axes and has a greater magnitude than corresponding differentiation in Eurasia, even when adjusting for the lower level of genetic variation in the American populations. These results support the view that continental orientation has influenced migration patterns and has played an important role in determining both the structure of human genetic variation and the distribution and spread of cultural traits. (240 words) PMID:21913175

Comparing internal migration across the countries of Latin America: A multidimensional approach

PubMed Central

Bernard, Aude; Rowe, Francisco; Bell, Martin; Ueffing, Philipp; Charles-Edwards, Elin

2017-01-01

While considerable progress has been made in understanding the way particular aspects of internal migration, such as its intensity, age profile and spatial impact, vary between countries around the world, little attention to date has been given to establishing how these dimensions of migration interact in different national settings. We use recently developed measures of internal migration that are scale-independent to compare the overall intensity, age composition, spatial impact, and distance profile of internal migration in 19 Latin American countries. Comparisons reveal substantial cross-national variation but cluster analysis suggests the different dimensions of migration evolve systematically to form a broad sequence characterised by low intensities, young ages at migration, unbalanced flows and high friction of distance at lower levels of development, trending to high intensities, an older age profile of migration, more closely balanced flows and lower friction of distance at later stages of development. However, the transition is not linear and local contingencies, such as international migration and political control, often distort the migration-development nexus, leading to unique migration patterns in individual national contexts. PMID:28328932

A refined method for multivariate meta-analysis and meta-regression.

PubMed

Jackson, Daniel; Riley, Richard D

2014-02-20

Making inferences about the average treatment effect using the random effects model for meta-analysis is problematic in the common situation where there is a small number of studies. This is because estimates of the between-study variance are not precise enough to accurately apply the conventional methods for testing and deriving a confidence interval for the average effect. We have found that a refined method for univariate meta-analysis, which applies a scaling factor to the estimated effects' standard error, provides more accurate inference. We explain how to extend this method to the multivariate scenario and show that our proposal for refined multivariate meta-analysis and meta-regression can provide more accurate inferences than the more conventional approach. We explain how our proposed approach can be implemented using standard output from multivariate meta-analysis software packages and apply our methodology to two real examples. Copyright © 2013 John Wiley & Sons, Ltd.

Early Migration Predicts Aseptic Loosening of Cementless Femoral Stems: A Long-term Study.

PubMed

Streit, Marcus R; Haeussler, Daniel; Bruckner, Thomas; Proctor, Tanja; Innmann, Moritz M; Merle, Christian; Gotterbarm, Tobias; Weiss, Stefan

2016-07-01

Excessive early migration of cemented stems and cups after THA has been associated with poor long-term survival and allows predictable evaluation of implant performance. However, there are few data regarding the relationship between early migration and aseptic loosening of cementless femoral components, and whether early migration might predict late failure has not been evaluated, to our knowledge. Einzel-Bild-Röntgen-Analyse-femoral component analysis (EBRA-FCA) is a validated technique to accurately measure axial femoral stem migration without the need for tantalum markers, can be performed retrospectively, and may be a suitable tool to identify poor performing implants before their widespread use. We asked: (1) Is axial migration within the first 24 months as assessed by EBRA-FCA greater among cementless stems that develop aseptic loosening than those that remain well fixed through the second decade; (2) what is the diagnostic performance of implant migration at 24 months postoperatively to predict later aseptic loosening of these components; and (3) how does long-term stem survivorship compare between groups with high and low early migration? We evaluated early axial stem migration in 158 cementless THAs using EBRA-FCA. The EBRA-FCA measurements were performed during the first week postoperatively (baseline measurement) and at regular followups of 3, 6, and 12 months postoperatively and annually thereafter. The mean duration of followup was 21 years (range, 18-24 years). The stems studied represented 45% (158 of 354) of the cementless THAs performed during that time, and cementless THAs represented 34% (354 of 1038) of the THA practice during that period. No patient enrolled in this study was lost to followup. Multivariate survivorship analysis using Cox's regression model was performed with an endpoint of aseptic loosening of the femoral component. Loosening was defined according to the criteria described by Engh et al. and assessed by two independent observers. Patients with a diagnosis of prosthetic joint infection were excluded. Receiver operating characteristic (ROC) curve analysis was used to evaluate diagnostic performance of axial stem migration 1, 2, 3, and 4 years postoperatively as a predictor of aseptic loosening. Survivorship of hips with high (≥ 2.7 mm) and low (< 2.7 mm) migration was compared using a competing-events analysis. Femoral components that had aseptic loosening develop showed greater mean distal migration at 24 months postoperatively than did components that remained well fixed throughout the surveillance period (4.2 mm ± 3.1 mm vs 0.8 mm ± 0.9 mm; mean difference, 3.4 mm, 95% CI, 2.5-4.4; p ≤ 0.001). Distal migration at 24 months postoperatively was a strong risk factor for aseptic loosening (hazard ratio, 1.98; 95% CI, 1.51-2.57; p < 0.001). The associated overall diagnostic performance of 2-year distal migration for predicting aseptic loosening was good (area under the ROC curve, 0.86; 95% CI, 0.72-1.00; p < 0.001). Sensitivity of early migration measurement was high for the prediction of aseptic loosening during the first decade after surgery but decreased markedly thereafter. Stems with large amounts of early migration (≥ 2.7 mm) had lower 18-year survivorship than did stems with little early migration (29% [95% CI, 0%-62%] versus 95% [95% CI, 90%-100%] p < 0.001). Early migration, as measured by EBRA-FCA at 2 years postoperatively, has good diagnostic capabilities for detection of uncemented femoral components at risk for aseptic loosening during the first and early second decades after surgery. However, there was no relationship between early migration patterns and aseptic loosening during the late second and third decades. EBRA-FCA can be used as a research tool to evaluate new cementless stems or in clinical practice to evaluate migration patterns in patients with painful femoral components. Level III, diagnostic study.

Transnationalism and Literacy: Investigating the Mobility of People, Languages, Texts, and Practices in Contexts of Migration

ERIC Educational Resources Information Center

Lam, Wan Shun Eva; Warriner, Doris S.

2012-01-01

This review of research offers a synthesis and analysis of research studies that address issues of language and literacy practices and learning in transnational contexts of migration. We consider how theoretical concepts from transnational migration studies, including particular Boudieusian-inspired concepts such as transnational social field,…

Migration in Deltas: An Integrated Analysis

NASA Astrophysics Data System (ADS)

Nicholls, Robert J.; Hutton, Craig W.; Lazar, Attila; Adger, W. Neil; Allan, Andrew; Arto, Inaki; Vincent, Katharine; Rahman, Munsur; Salehin, Mashfiqus; Sugata, Hazra; Ghosh, Tuhin; Codjoe, Sam; Appeaning-Addo, Kwasi

2017-04-01

Deltas and low-lying coastal regions have long been perceived as vulnerable to global sea-level rise, with the potential for mass displacement of exposed populations. The assumption of mass displacement of populations in deltas requires a comprehensive reassessment in the light of present and future migration in deltas, including the potential role of adaptation to influence these decisions. At present, deltas are subject to multiple drivers of environmental change and often have high population densities as they are accessible and productive ecosystems. Climate change, catchment management, subsidence and land cover change drive environmental change across all deltas. Populations in deltas are also highly mobile, with significant urbanization trends and the growth of large cities and mega-cities within or adjacent to deltas across Asia and Africa. Such migration is driven primarily by economic opportunity, yet environmental change in general, and climate change in particular, are likely to play an increasing direct and indirect role in future migration trends. The policy challenges centre on the role of migration within regional adaptation strategies to climate change; the protection of vulnerable populations; and the future of urban settlements within deltas. This paper reviews current knowledge on migration and adaptation to environmental change to discern specific issues pertinent to delta regions. It develops a new integrated methodology to assess present and future migration in deltas using the Volta delta in Ghana, Mahanadi delta in India and Ganges-Brahmaputra-Meghna delta across India and Bangladesh. The integrated method focuses on: biophysical changes and spatial distribution of vulnerability; demographic changes and migration decision-making using multiple methods and data; macro-economic trends and scenarios in the deltas; and the policies and governance structures that constrain and enable adaptation. The analysis is facilitated by a range of consistent scenarios from global to delta scales, developed in consultation with major stakeholders. Initial results suggest that migration decision-making strongly interacts with diverse measures for adaptation of land, water and agricultural management. A key normative challenge is to identify the parameters of successful migration and adaptation across delta regions, to inform policy analysis and formulation. Key words: Deltas, sea-level rise, migration and adaptation Acknowledgement: DECCMA (Deltas, Vulnerability & Climate Change: Migration & Adaptation) project is part of the Collaborative ADAPTATION Research Initiative in Africa and Asia (CARIAA), with financial support from the UK Government's Department for International Development (DFID) and the International Development Research Centre (IDRC), Canada.

Migration of the Duraloc cup after 5 years.

PubMed

Stihsen, Christoph; Pabinger, Christof; Radl, Roman; Rehak, Peter; Windhager, Reinhard

2008-12-01

The Duraloc cup is a frequently used metal-backed, porous-coated, hemispherical, press-fit acetabular component. Published data on loosening rates are contradictory. In this study we investigated migration patterns with computer-assisted Einzel-Bild-Roentgen-Analyse (EBRA) of 67 Duraloc 100 cups. Cup migration and clinical scores were analysed over a 5-year follow-up period. Median total migration of the Duraloc 100 cup was 1.21 mm at 5 years. Seventy-five percent of implants were radiologically stable at 2 years and 90% at 4 years. One cup loosened aseptically at 60 months, requiring revision. Cup diameters > or = 54 mm migrated significantly more than cups < 54 mm in diameter (p = 0.029 at 4 years). There was a significant correlation between high polyethylene wear and further migrating cups within the first post-operative year (p = 0.035 at 12 months). Our analysis revealed significantly higher wear in males (p = 0.029 at 4 years). Radiological loosening at two years could be calculated using receiver-operating characteristic curve analysis, and 1.2 mm as an adequate threshold value (sensitivity = 100%, specificity = 89%).

DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion.

PubMed

McLennan, Rebecca; Bailey, Caleb M; Schumacher, Linus J; Teddy, Jessica M; Morrison, Jason A; Kasemeier-Kulesa, Jennifer C; Wolfe, Lauren A; Gogol, Madeline M; Baker, Ruth E; Maini, Philip K; Kulesa, Paul M

2017-10-02

Neural crest cells are both highly migratory and significant to vertebrate organogenesis. However, the signals that regulate neural crest cell migration remain unclear. In this study, we test the function of differential screening-selected gene aberrant in neuroblastoma (DAN), a bone morphogenetic protein (BMP) antagonist we detected by analysis of the chick cranial mesoderm. Our analysis shows that, before neural crest cell exit from the hindbrain, DAN is expressed in the mesoderm, and then it becomes absent along cell migratory pathways. Cranial neural crest and metastatic melanoma cells avoid DAN protein stripes in vitro. Addition of DAN reduces the speed of migrating cells in vivo and in vitro, respectively. In vivo loss of function of DAN results in enhanced neural crest cell migration by increasing speed and directionality. Computer model simulations support the hypothesis that DAN restrains cell migration by regulating cell speed. Collectively, our results identify DAN as a novel factor that inhibits uncontrolled neural crest and metastatic melanoma invasion and promotes collective migration in a manner consistent with the inhibition of BMP signaling. © 2017 McLennan et al.

DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion

PubMed Central

McLennan, Rebecca; Bailey, Caleb M.; Schumacher, Linus J.; Teddy, Jessica M.; Morrison, Jason A.; Kasemeier-Kulesa, Jennifer C.; Wolfe, Lauren A.; Gogol, Madeline M.; Baker, Ruth E.; Maini, Philip K.

2017-01-01

Neural crest cells are both highly migratory and significant to vertebrate organogenesis. However, the signals that regulate neural crest cell migration remain unclear. In this study, we test the function of differential screening-selected gene aberrant in neuroblastoma (DAN), a bone morphogenetic protein (BMP) antagonist we detected by analysis of the chick cranial mesoderm. Our analysis shows that, before neural crest cell exit from the hindbrain, DAN is expressed in the mesoderm, and then it becomes absent along cell migratory pathways. Cranial neural crest and metastatic melanoma cells avoid DAN protein stripes in vitro. Addition of DAN reduces the speed of migrating cells in vivo and in vitro, respectively. In vivo loss of function of DAN results in enhanced neural crest cell migration by increasing speed and directionality. Computer model simulations support the hypothesis that DAN restrains cell migration by regulating cell speed. Collectively, our results identify DAN as a novel factor that inhibits uncontrolled neural crest and metastatic melanoma invasion and promotes collective migration in a manner consistent with the inhibition of BMP signaling. PMID:28811280

Causal inference in economics and marketing.

PubMed

Varian, Hal R

2016-07-05

This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference.

Aging and Predicting Inferences: A Diffusion Model Analysis

ERIC Educational Resources Information Center

McKoon, Gail; Ratcliff, Roger

2013-01-01

In the domain of discourse processing, it has been claimed that older adults (60-0-year-olds) are less likely to encode and remember some kinds of information from texts than young adults. The experiment described here shows that they do make a particular kind of inference to the same extent that college-age adults do. The inferences examined were…

Causal inference in economics and marketing

PubMed Central

Varian, Hal R.

2016-01-01

This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

"Magnitude-based inference": a statistical review.

PubMed

Welsh, Alan H; Knight, Emma J

2015-04-01

We consider "magnitude-based inference" and its interpretation by examining in detail its use in the problem of comparing two means. We extract from the spreadsheets, which are provided to users of the analysis (http://www.sportsci.org/), a precise description of how "magnitude-based inference" is implemented. We compare the implemented version of the method with general descriptions of it and interpret the method in familiar statistical terms. We show that "magnitude-based inference" is not a progressive improvement on modern statistics. The additional probabilities introduced are not directly related to the confidence interval but, rather, are interpretable either as P values for two different nonstandard tests (for different null hypotheses) or as approximate Bayesian calculations, which also lead to a type of test. We also discuss sample size calculations associated with "magnitude-based inference" and show that the substantial reduction in sample sizes claimed for the method (30% of the sample size obtained from standard frequentist calculations) is not justifiable so the sample size calculations should not be used. Rather than using "magnitude-based inference," a better solution is to be realistic about the limitations of the data and use either confidence intervals or a fully Bayesian analysis.

Comparison of Urban Human Movements Inferring from Multi-Source Spatial-Temporal Data

NASA Astrophysics Data System (ADS)

Cao, Rui; Tu, Wei; Cao, Jinzhou; Li, Qingquan

2016-06-01

The quantification of human movements is very hard because of the sparsity of traditional data and the labour intensive of the data collecting process. Recently, much spatial-temporal data give us an opportunity to observe human movement. This research investigates the relationship of city-wide human movements inferring from two types of spatial-temporal data at traffic analysis zone (TAZ) level. The first type of human movement is inferred from long-time smart card transaction data recording the boarding actions. The second type of human movement is extracted from citywide time sequenced mobile phone data with 30 minutes interval. Travel volume, travel distance and travel time are used to measure aggregated human movements in the city. To further examine the relationship between the two types of inferred movements, the linear correlation analysis is conducted on the hourly travel volume. The obtained results show that human movements inferred from smart card data and mobile phone data have a correlation of 0.635. However, there are still some non-ignorable differences in some special areas. This research not only reveals the citywide spatial-temporal human dynamic but also benefits the understanding of the reliability of the inference of human movements with big spatial-temporal data.

All Source Analysis System (ASAS): Migration from VAX to Alpha AXP computer systems

NASA Technical Reports Server (NTRS)

Sjoholm-Sierchio, Michael J.; Friedman, Steven Z. (Editor)

1994-01-01

The Jet Propulsion Laboratory's (JPL's) experience migrating existing VAX applications to Digital Equipment Corporation's new Alpha AXP processor is covered. The rapid development approach used during the 10-month period required to migrate the All Source Analysis System (ASAS), 1.5 million lines of FORTRAN, C, and Ada code, is also covered. ASAS, an automated tactical intelligence system, was developed by the Jet Propulsion Laboratory for the U. S. Army. Other benefits achieved as a result of the significant performance improvements provided by Alpha AXP platform are also described.

Recovery Migration After Hurricanes Katrina and Rita: Spatial Concentration and Intensification in the Migration System.

PubMed

Curtis, Katherine J; Fussell, Elizabeth; DeWaard, Jack

2015-08-01

Changes in the human migration systems of the Gulf of Mexico coastline counties affected by Hurricanes Katrina and Rita provide an example of how climate change may affect coastal populations. Crude climate change models predict a mass migration of "climate refugees," but an emerging literature on environmental migration suggests that most migration will be short-distance and short-duration within existing migration systems, with implications for the population recovery of disaster-stricken places. In this research, we derive a series of hypotheses on recovery migration predicting how the migration system of hurricane-affected coastline counties in the Gulf of Mexico was likely to have changed between the pre-disaster and the recovery periods. We test these hypotheses using data from the Internal Revenue Service on annual county-level migration flows, comparing the recovery period migration system (2007-2009) with the pre-disaster period (1999-2004). By observing county-to-county ties and flows, we find that recovery migration was strong: the migration system of the disaster-affected coastline counties became more spatially concentrated, while flows within it intensified and became more urbanized. Our analysis demonstrates how migration systems are likely to be affected by the more intense and frequent storms anticipated by climate change scenarios, with implications for the population recovery of disaster-affected places.

Inference of genetic network of Xenopus frog egg: improved genetic algorithm.

PubMed

Wu, Shinq-Jen; Chou, Chia-Hsien; Wu, Cheng-Tao; Lee, Tsu-Tian

2006-01-01

An improved genetic algorithm (IGA) is proposed to achieve S-system gene network modeling of Xenopus frog egg. Via the time-courses training datasets from Michaelis-Menten model, the optimal parameters are learned. The S-system can clearly describe activative and inhibitory interaction between genes as generating and consuming process. We concern the mitotic control in cell-cycle of Xenopus frog egg to realize cyclin-Cdc2 and Cdc25 for MPF activity. The proposed IGA can achieve global search with migration and keep the best chromosome with elitism operation. The generated gene regulatory networks can provide biological researchers for further experiments in Xenopus frog egg cell cycle control.

Geomorphic control of radionuclide diffusion in desert soils

USGS Publications Warehouse

Pelletier, J.D.; Harrington, C.D.; Whitney, J.W.; Cline, M.; DeLong, S.B.; Keating, G.; Ebert, T.K.

2005-01-01

Diffusion is a standard model for the vertical migration of radionuclides in soil profiles. Here we show that diffusivity values inferred from fallout 137CS profiles in soils on the Fortymile Wash alluvial fan, Nye County, Nevada, have a strong inverse correlation with the age of the geomorphic surface. This result suggests that radionuclide-bound particles are predominantly transported by infiltration rather than by bulk-mixing processes such as wetting/ drying, freeze/thaw, and bioturbation. Our results provide a preliminary basis for using soil-geomorphic mapping, point-based calibration data, and the diffusion model to predict radionuclide trans desert soils within a pedotransfer-function approach. Copyright 2005 by the American Geophysical Union.

IMa2p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model

PubMed Central

Sethuraman, Arun; Hey, Jody

2015-01-01

IMa2 and related programs are used to study the divergence of closely related species and of populations within species. These methods are based on the sampling of genealogies using MCMC, and they can proceed quite slowly for larger data sets. We describe a parallel implementation, called IMa2p, that provides a nearly linear increase in genealogy sampling rate with the number of processors in use. IMa2p is written in OpenMPI and C++, and scales well for demographic analyses of a large number of loci and populations, which are difficult to study using the serial version of the program. PMID:26059786

Separable Processes Before, During, and After the N400 Elicited by Previously Inferred and New Information: Evidence from Time-Frequency Decompositions

PubMed Central

Steele, Vaughn R.; Bernat, Edward M.; van den Broek, Paul; Collins, Paul F.; Patrick, Christopher J.; Marsolek, Chad J.

2012-01-01

Successful comprehension during reading often requires inferring information not explicitly presented. This information is readily accessible when subsequently encountered, and a neural correlate of this is an attenuation of the N400 event-related potential (ERP). We used ERPs and time-frequency (TF) analysis to investigate neural correlates of processing inferred information after a causal coherence inference had been generated during text comprehension. Participants read short texts, some of which promoted inference generation. After each text, they performed lexical decisions to target words that were unrelated or inference-related to the preceding text. Consistent with previous findings, inference-related words elicited an attenuated N400 relative to unrelated words. TF analyses revealed unique contributions to the N400 from activity occurring at 1–6 Hz (theta) and 0–2 Hz (delta), supporting the view that multiple, sequential processes underlie the N400. PMID:23165117

MicroRNA-21 promotes bone mesenchymal stem cells migration in vitro by activating PI3K/Akt/MMPs pathway.

PubMed

Lv, Chen; Yang, Shengwu; Chen, Xin; Zhu, Xiongbai; Lin, Wenjun; Wang, Lu; Huang, Zhengxiang; Wang, Mingyue; Tu, Guanjun

2017-12-01

MicroRNA-21 (miR-21) contributes to anti-apoptosis in bone marrow mesenchymal stem cells (BMSC), but its role in the migration of BMSCs remains vague. The aim of this study was to determine the possible effect of miR-21 on regulating BMSCs directional migration and the expression of MMP-2/MMP-9 in BMSCs in vitro. BMSCs were successfully infected with miR-21-up lentivirus. Cell migration using Transwell assay indicated that upregulated expression of miR-21 could significantly promote BMSCs migration. Western blot analysis indicated that miR-21 significantly upregulated the expression of MMP-2 and MMP-9, which were related to metastasis-associated genes. GM6001, the specific MMPs inhibitor, abrogated the upregulated expression of MMP-2/MMP-9 and abolished the positive effect of miR-21 on promoting BMSCs migration. Meanwhile, miR-21 significantly enhanced Akt phosphorylation, as measured by Western blot analysis. LY294002, an inhibitor of Akt activation, abrogated the phosphorylation of Akt and abolished the positive effect of miR-21 on promoting BMSCs migration and upregulating MMP-2/MMP-9 expression. These results suggest that miR-21 contributes to BMSCs migration by upregulating MMP-2/MMP-9, potentially via the PI3K/Akt pathway. Copyright © 2017 Elsevier Ltd. All rights reserved.

Statistics for nuclear engineers and scientists. Part 1. Basic statistical inference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beggs, W.J.

1981-02-01

This report is intended for the use of engineers and scientists working in the nuclear industry, especially at the Bettis Atomic Power Laboratory. It serves as the basis for several Bettis in-house statistics courses. The objectives of the report are to introduce the reader to the language and concepts of statistics and to provide a basic set of techniques to apply to problems of the collection and analysis of data. Part 1 covers subjects of basic inference. The subjects include: descriptive statistics; probability; simple inference for normally distributed populations, and for non-normal populations as well; comparison of two populations; themore » analysis of variance; quality control procedures; and linear regression analysis.« less

Patterns of Migration and Risks Associated with Leprosy among Migrants in Maranhão, Brazil

PubMed Central

Murto, Christine; Chammartin, Frédérique; Schwarz, Karolin; da Costa, Lea Marcia Melo; Kaplan, Charles; Heukelbach, Jorg

2013-01-01

Leprosy remains a public health problem in Brazil with new case incidence exceeding World Health Organization (WHO) goals in endemic clusters throughout the country. Migration can facilitate movement of disease between endemic and non-endemic areas, and has been considered a possible factor in continued leprosy incidence in Brazil. A study was conducted to investigate migration as a risk factor for leprosy. The study had three aims: (1) examine past five year migration as a risk factor for leprosy, (2) describe and compare geographic and temporal patterns of migration among past 5-year migrants with leprosy and a control group, and (3) examine social determinants of health associated with leprosy among past 5-year migrants. The study implemented a matched case-control design and analysis comparing individuals newly diagnosed with leprosy (n = 340) and a clinically unapparent control group (n = 340) without clinical signs of leprosy, matched for age, sex and location in four endemic municipalities in the state of Maranhão, northeastern Brazil. Fishers exact test was used to conduct bivariate analyses. A multivariate logistic regression analysis was employed to control for possible confounding variables. Eighty cases (23.5%) migrated 5-years prior to diagnosis, and 55 controls (16.2%) migrated 5-years prior to the corresponding case diagnosis. Past 5 year migration was found to be associated with leprosy (OR: 1.59; 95% CI 1.07–2.38; p = 0.02), and remained significantly associated with leprosy after controlling for leprosy contact in the family, household, and family/household contact. Poverty, as well as leprosy contact in the family, household and other leprosy contact, was associated with leprosy among past 5-year migrants in the bivariate analysis. Alcohol consumption was also associated with leprosy, a relevant risk factor in susceptibility to infection that should be explored in future research. Our findings provide insight into patterns of migration to localize focused control efforts in endemic areas with high population mobility. PMID:24040433

Levels and patterns of internal migration in Europe: A cohort perspective.

PubMed

Bernard, Aude

2017-11-01

Europe displays important variations in the level of internal migration, with a clear spatial gradient of high mobility in northern and western Europe but lower mobility in the south and east. However, cross-national variation in levels of internal migration remains poorly understood, because it is analysed almost exclusively using cross-sectional data and period measures. This paper seeks to advance understanding of cross-national variation in migration levels in 14 European countries by drawing on a recently proposed suite of migration cohort measures, coupled with internationally comparable retrospective residential histories. It shows that differences in migration levels are mainly attributable to variation in the extent of repeat movement, which is underpinned by the differences in mean ages at first and last move that together delineate the average length of migration careers. Cohort analysis provides a robust foundation for exploring the demographic mechanisms underpinning variation in migration levels across countries and over time.

[Improvement of reproducibility in capillary electrophoretic characterization of rhubarb by normalization of migration time].

PubMed

Zhang, Hongyi; Ge, Lijuan; Chen, Hui; Jing, Cong; Shi, Zhihong

2009-07-01

The principle of the normalization of migration time and its application on the traditional Chinese medicine (TCM) analysis by capillary electrophoresis (CE) are presented. It is the core of the normalization of migration time that the fluctuation of apparent migration velocity for each component at different runs is attributed to the difference of electroosmotic flow velocity. To transform migration time (t) to normalized migration time, one peak or two peaks in the original electropherogram are selected as internal peak. The normalization of migration time is therefore classified into two types based on the number of selected internal peaks, one-peak and two-peak approaches. The migration times processed by one-peak normalization and by two-peak normalization are conducted by the following equations, respectively: (t'(i))(j) = 1/ [1/(t(i))(j) - [1/(t(istd))(j) - 1/(t(istd))1

Health Costs of Wealth Gains: Labor Migration and Perceptions of HIV/AIDS Risks in Mozambique

PubMed Central

Agadjanian, Victor; Arnaldo, Carlos; Cau, Boaventura

2012-01-01

The study employs survey data from rural Mozambique to examine how men’s labor migration affects their non-migrating wives’ perceptions of HIV/AIDS risks. Using a conceptual framework centered on tradeoffs between economic security and health risks that men’s migration entails for their left-behind wives, it compares women married to migrants and those married to non-migrants while also distinguishing between economically successful and unsuccessful migration. The analysis finds that the economic success of men’s migration, rather than migration itself, significantly predicts women’s worries about getting infected by their husbands or their own extramarital partners, and their husbands’ stance on condom use. These findings are situated within a broader context of socio-economic, gender, and marital dynamics and vulnerabilities produced or amplified by male labor migration in sub-Saharan and similar developing settings. PMID:22500057

Characterizing the International Migration Barriers with a Probabilistic Multilateral Migration Model

PubMed Central

Li, Xiaomeng; Xu, Hongzhong; Chen, Jiawei; Chen, Qinghua; Zhang, Jiang; Di, Zengru

2016-01-01

Human migration is responsible for forming modern civilization and has had an important influence on the development of various countries. There are many issues worth researching, and “the reason to move” is the most basic one. The concept of migration cost in the classical self-selection theory, which was introduced by Roy and Borjas, is useful. However, migration cost cannot address global migration because of the limitations of deterministic and bilateral choice. Following the idea of migration cost, this paper developed a new probabilistic multilateral migration model by introducing the Boltzmann factor from statistical physics. After characterizing the underlying mechanism or driving force of human mobility, we reveal some interesting facts that have provided a deeper understanding of international migration, such as the negative correlation between migration costs for emigrants and immigrants and a global classification with clear regional and economic characteristics, based on clustering of migration cost vectors. In addition, we deconstruct the migration barriers using regression analysis and find that the influencing factors are complicated but can be partly (12.5%) described by several macro indexes, such as the GDP growth of the destination country, the GNI per capita and the HDI of both the source and destination countries. PMID:27597319

Characterizing the International Migration Barriers with a Probabilistic Multilateral Migration Model

NASA Astrophysics Data System (ADS)

Li, Xiaomeng; Xu, Hongzhong; Chen, Jiawei; Chen, Qinghua; Zhang, Jiang; di, Zengru

2016-09-01

Human migration is responsible for forming modern civilization and has had an important influence on the development of various countries. There are many issues worth researching, and “the reason to move” is the most basic one. The concept of migration cost in the classical self-selection theory, which was introduced by Roy and Borjas, is useful. However, migration cost cannot address global migration because of the limitations of deterministic and bilateral choice. Following the idea of migration cost, this paper developed a new probabilistic multilateral migration model by introducing the Boltzmann factor from statistical physics. After characterizing the underlying mechanism or driving force of human mobility, we reveal some interesting facts that have provided a deeper understanding of international migration, such as the negative correlation between migration costs for emigrants and immigrants and a global classification with clear regional and economic characteristics, based on clustering of migration cost vectors. In addition, we deconstruct the migration barriers using regression analysis and find that the influencing factors are complicated but can be partly (12.5%) described by several macro indexes, such as the GDP growth of the destination country, the GNI per capita and the HDI of both the source and destination countries.

Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China.

PubMed

Shi, Xiao-Jun; Zhang, Ming-Li

2015-03-01

Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.

CADDIS Volume 4. Data Analysis: Predicting Environmental Conditions from Biological Observations (PECBO Appendix)

EPA Pesticide Factsheets

Overview of PECBO Module, using scripts to infer environmental conditions from biological observations, statistically estimating species-environment relationships, methods for inferring environmental conditions, statistical scripts in module.

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

PubMed Central

Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea

2014-01-01

In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code. PMID:24663061

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

PubMed

Schaffter, Thomas; Marbach, Daniel; Floreano, Dario

2011-08-15

Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks. Here, we describe a novel and comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community as an open-source software called GeneNetWeaver (GNW). In addition to the generation of detailed dynamical models of gene regulatory networks to be used as benchmarks, GNW provides a network motif analysis that reveals systematic prediction errors, thereby indicating potential ways of improving inference methods. The accuracy of network inference methods is evaluated using standard metrics such as precision-recall and receiver operating characteristic curves. We show how GNW can be used to assess the performance and identify the strengths and weaknesses of six inference methods. Furthermore, we used GNW to provide the international Dialogue for Reverse Engineering Assessments and Methods (DREAM) competition with three network inference challenges (DREAM3, DREAM4 and DREAM5). GNW is available at http://gnw.sourceforge.net along with its Java source code, user manual and supporting data. Supplementary data are available at Bioinformatics online. dario.floreano@epfl.ch.

Algorithm Optimally Orders Forward-Chaining Inference Rules

NASA Technical Reports Server (NTRS)

James, Mark

2008-01-01

People typically develop knowledge bases in a somewhat ad hoc manner by incrementally adding rules with no specific organization. This often results in a very inefficient execution of those rules since they are so often order sensitive. This is relevant to tasks like Deep Space Network in that it allows the knowledge base to be incrementally developed and have it automatically ordered for efficiency. Although data flow analysis was first developed for use in compilers for producing optimal code sequences, its usefulness is now recognized in many software systems including knowledge-based systems. However, this approach for exhaustively computing data-flow information cannot directly be applied to inference systems because of the ubiquitous execution of the rules. An algorithm is presented that efficiently performs a complete producer/consumer analysis for each antecedent and consequence clause in a knowledge base to optimally order the rules to minimize inference cycles. An algorithm was developed that optimally orders a knowledge base composed of forwarding chaining inference rules such that independent inference cycle executions are minimized, thus, resulting in significantly faster execution. This algorithm was integrated into the JPL tool Spacecraft Health Inference Engine (SHINE) for verification and it resulted in a significant reduction in inference cycles for what was previously considered an ordered knowledge base. For a knowledge base that is completely unordered, then the improvement is much greater.

Drosophila hemocyte migration: an in vivo assay for directional cell migration.

PubMed

Moreira, Carolina G A; Regan, Jennifer C; Zaidman-Rémy, Anna; Jacinto, Antonio; Prag, Soren

2011-01-01

This protocol describes an in vivo assay for random and directed hemocyte migration in Drosophila. Drosophila is becoming an increasingly powerful model system for in vivo cell migration analysis, combining unique genetic tools with translucency of the embryo and pupa, which allows direct imaging and traceability of different cell types. In the assay we present here, we make use of the hemocyte response to epithelium wounding to experimentally induce a transition from random to directed migration. Time-lapse confocal microscopy of hemocyte migration in untreated conditions provides a random cell migration assay that allows identification of molecular mechanisms involved in this complex process. Upon laser-induced wounding of the thorax epithelium, a rapid chemotactic response changes hemocyte migratory behavior into a directed migration toward the wound site. This protocol provides a direct comparison of cells during both types of migration in vivo, and combined with recently developed resources such as transgenic RNAi, is ideal for forward genetic screens.

Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae).

PubMed

Gutiérrez-Rodríguez, Jorge; Barbosa, A Márcia; Martínez-Solano, Íñigo

2017-07-01

Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot. Copyright © 2017 Elsevier Inc. All rights reserved.

Tyrosine Kinase Inhibitor, Vatalanib, Inhibits Proliferation and Migration of Human Pterygial Fibroblasts.

PubMed

Kim, Hong Kyu; Choi, Ji-Young; Park, Sang Min; Rho, Chang Rae; Cho, Kyong Jin; Jo, Sangmee Ahn

2017-09-01

Vatalanib is a small-molecule tyrosine kinase inhibitor. We investigated the effects of vatalanib on the proliferation and migration of cultured human pterygial fibroblasts (HPFs). Pterygium tissues were obtained after pterygium excision surgery and subjected to primary culture. HPFs were treated with vatalanib at various concentrations. Mitomycin C (MMC) was used as a positive control. Cell proliferation and migration assays were used to investigate the effects of vatalanib. Cell death was measured using flow cytometry analysis. Western blot analysis was performed to identify signaling molecules associated with the response to vatalanib. Vatalanib inhibited both proliferation and migration of HPFs in a dose-dependent manner. Cell proliferation was significantly suppressed by vatalanib (10 and 100 μM) and MMC (0.004% and 0.04%) treatments. Migration assays revealed significant HPF delay when treated with vatalanib (1, 10, and 100 μM) and MMC (0.004% and 0.04%) compared with that in a negative control. Cell death analysis showed that high concentrations of vatalanib (100 μM) and MMC (0.004% and 0.04%) decreased cell numbers. Western blot analysis of vatalanib-treated cells showed vascular endothelial growth factor and transforming growth factor-β significantly reduced, but there was no alteration in p53 protein levels in HPFs. These results indicate that vatalanib significantly suppressed the proliferation and migration of HPFs by decreasing vascular endothelial growth factor and transforming growth factor-β. Vatalanib showed less toxicity than that of MMC. Based on these results, vatalanib may potentially serve as a new adjuvant treatment after pterygium excision surgery.

[Migration biography and culture as determinants of diagnostic and therapeutic processes in mentally ill immigrants. A systematic differentiation based on a qualitative content analysis of treatment courses].

PubMed

Behrens, Katharina; Calliess, Iris Tatjana

2008-01-01

A systematic differentiation of culture- in contrast to migration-related influence factors in diagnostic and therapeutic processes is introduced. "Culture-related" refers to characteristics caused by values, behavior norms and religious attitudes of the ethnic community a person belongs to. "Migration-specific" refers to consequences of moving one's residence from one country to another (e. g., absence of family, trouble with authorities concerning the legal status or ambivalence with respect to returning to the home country). Based on a theoretic background of these determinants, categories for a content analysis were defined and applied to the treatment records of n = 55 first generation immigrants treated in a psychiatric day clinic of an university hospital. The results suggest that migration biography should not only be considered as affecting vulnerability in the genesis of a mental illness, but rather be classified as a factor of at least as much relevance for therapeutic situations as the usually named cultural diversity: summarizing the results of the qualitative content analysis of the entire treatment courses more cases were influenced by migration specific aspects rather than culture specific aspects.

A novel method to measure femoral component migration by computed tomography: a cadaver study.

PubMed

Boettner, Friedrich; Sculco, Peter; Lipman, Joseph; Renner, Lisa; Faschingbauer, Martin

2016-06-01

Radiostereometric analysis (RSA) is the most accurate technique to measure implant migration. However, it requires special equipment, technical expertise and analysis software and has not gained wide acceptance. The current paper analyzes a novel method to measure implant migration utilizing widely available computer tomography (CT). Three uncemented total hip replacements were performed in three human cadavers and six tantalum beads were inserted into the femoral bone similar to RSA. Six different 28 mm heads (-3, 0, 2.5, 5.0, 7.5 and 10 mm) were added to simulate five reproducible translations (maximum total point migration) of the center of the head. Implant migration was measured in a 3-D analysis software (Geomagic Studio 7). Repeat manual reconstructions of the center of the head were performed by two investigators to determine repeatability and accuracy. The accuracy of measurements between the centers of two head sizes was 0.11 mm with a CI 95 % of 0.22 mm. The intra-observer repeatability was 0.13 mm (CI 95 % 0.25 mm). The interrater-reliability was 0.943. CT based measurement of head displacement in a cadaver model were highly accurate and reproducible.

Dual impacts of climate change: forest migration and turnover through life history

Treesearch

Kai Zhu; Christopher W. Woodall; Souparno Ghosh; Alan E. Gelfand; James S. Clark

2014-01-01

Tree species are predicted to track future climate by shifting their geographic distributions, but climate-mediated migrations are not apparent in a recent continental-scale analysis. To better understand the mechanisms of a possible migration lag, we analyzed relative recruitment patterns by comparing juvenile and adult tree abundances in climate space. One would...

Higher Education and Urban Migration for Community Resilience: Indigenous Amazonian Youth Promoting Place-Based Livelihoods and Identities in Peru

ERIC Educational Resources Information Center

Steele, Diana

2018-01-01

This paper offers an ethnographic analysis of indigenous Peruvian Amazonian youth pursuing higher education through urban migration to contribute to the resilience of their communities, place-based livelihoods, and indigenous Amazonian identities. Youth and their communities promoted education and migration as powerful tools in the context of…

International Migration and Human Development in Destination Countries: A Cross-National Analysis of Less-Developed Countries, 1970-2005

ERIC Educational Resources Information Center

Sanderson, Matthew

2010-01-01

Contemporary levels of international migration in less-developed countries are raising new and important questions regarding the consequences of immigration for human welfare and well-being. However, there is little systematic cross-national evidence of how international migration affects human development levels in migrant-receiving countries in…

Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis

PubMed Central

Maška, Martin; Ederra, Cristina; Peláez, Rafael; Morales, Xabier; Muñoz-Arrieta, Gorka; Mujika, Maite; Kozubek, Michal; Muñoz-Barrutia, Arrate; Rouzaut, Ana; Arana, Sergio; Garcia-Aznar, José Manuel; Ortiz-de-Solorzano, Carlos

2017-01-01

Microfluidic devices are becoming mainstream tools to recapitulate in vitro the behavior of cells and tissues. In this study, we use microfluidic devices filled with hydrogels of mixed collagen-Matrigel composition to study the migration of lung cancer cells under different cancer invasion microenvironments. We present the design of the microfluidic device, characterize the hydrogels morphologically and mechanically and use quantitative image analysis to measure the migration of H1299 lung adenocarcinoma cancer cells in different experimental conditions. Our results show the plasticity of lung cancer cell migration, which turns from mesenchymal in collagen only matrices, to lobopodial in collagen-Matrigel matrices that approximate the interface between a disrupted basement membrane and the underlying connective tissue. Our quantification of migration speed confirms a biphasic role of Matrigel. At low concentration, Matrigel facilitates migration, most probably by providing a supportive and growth factor retaining environment. At high concentration, Matrigel slows down migration, possibly due excessive attachment. Finally, we show that antibody-based integrin blockade promotes a change in migration phenotype from mesenchymal or lobopodial to amoeboid and analyze the effect of this change in migration dynamics, in regards to the structure of the matrix. In summary, we describe and characterize a robust microfluidic platform and a set of software tools that can be used to study lung cancer cell migration under different microenvironments and experimental conditions. This platform could be used in future studies, thus benefitting from the advantages introduced by microfluidic devices: precise control of the environment, excellent optical properties, parallelization for high throughput studies and efficient use of therapeutic drugs. PMID:28166248

Motivations of nurses who migrate to Canada as domestic workers.

PubMed

Salami, B; Nelson, S; Hawthorne, L; Muntaner, C; McGillis Hall, L

2014-12-01

While some trained nurses migrate to destination countries to work as domestic workers, little is known about their migration motivations. This study explores the motivations of Philippine educated nurses who migrated to Canada through the Live-in Caregiver Program from 2001 to 2011 (a Canadian domestic worker programme). A single case study qualitative methodology and the transnational feminist concept of global care chains were utilized for this study. Interviews of 15 Philippine educated nurses who migrated to Canada as domestic workers were conducted in the province of Ontario, Canada, between February to October 2012. All participants had a baccalaureate degree from the Philippines. Interviews were tape recorded, transcribed verbatim and analysed using critical discourse analysis, aided by NVIVO 10 data analysis software. Findings reveal a multi-step immigration process in which nurses migrate from the Philippines to the Middle East (especially Saudi Arabia) and finally to Canada. While emigration from the Philippines is mainly economically driven, migration from the Middle East to Canada is primarily motivated by the desire for Canadian citizenship for the family. Also, perceived social status and lifestyle in Canada as compared to the Middle East motivates this group of women to migrate to Canada. The major limitation of this study is the lack of input from nursing policy makers. Gender-based familial ideologies and perspective on social status influence the migration decision of this group of nurses. Implications for nursing and health policy makers include the provision of clear pre-migration information (including on the nursing registration process) to internationally educated nurses, advocacy for stronger immigration policies to ensure the integration of internationally educated nurses and a consideration of gender in all health human resource policies. © 2014 International Council of Nurses.

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

PubMed Central

Sun, Kuan; Ye, Yi; Luo, Tao; Hou, Yiping

2016-01-01

Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies. PMID:28004788

Causal inference in survival analysis using pseudo-observations.

PubMed

Andersen, Per K; Syriopoulou, Elisavet; Parner, Erik T

2017-07-30

Causal inference for non-censored response variables, such as binary or quantitative outcomes, is often based on either (1) direct standardization ('G-formula') or (2) inverse probability of treatment assignment weights ('propensity score'). To do causal inference in survival analysis, one needs to address right-censoring, and often, special techniques are required for that purpose. We will show how censoring can be dealt with 'once and for all' by means of so-called pseudo-observations when doing causal inference in survival analysis. The pseudo-observations can be used as a replacement of the outcomes without censoring when applying 'standard' causal inference methods, such as (1) or (2) earlier. We study this idea for estimating the average causal effect of a binary treatment on the survival probability, the restricted mean lifetime, and the cumulative incidence in a competing risks situation. The methods will be illustrated in a small simulation study and via a study of patients with acute myeloid leukemia who received either myeloablative or non-myeloablative conditioning before allogeneic hematopoetic cell transplantation. We will estimate the average causal effect of the conditioning regime on outcomes such as the 3-year overall survival probability and the 3-year risk of chronic graft-versus-host disease. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The Mechanics of Single Cell and Collective Migration of Tumor Cells

PubMed Central

Lintz, Marianne; Muñoz, Adam; Reinhart-King, Cynthia A.

2017-01-01

Metastasis is a dynamic process in which cancer cells navigate the tumor microenvironment, largely guided by external chemical and mechanical cues. Our current understanding of metastatic cell migration has relied primarily on studies of single cell migration, most of which have been performed using two-dimensional (2D) cell culture techniques and, more recently, using three-dimensional (3D) scaffolds. However, the current paradigm focused on single cell movements is shifting toward the idea that collective migration is likely one of the primary modes of migration during metastasis of many solid tumors. Not surprisingly, the mechanics of collective migration differ significantly from single cell movements. As such, techniques must be developed that enable in-depth analysis of collective migration, and those for examining single cell migration should be adopted and modified to study collective migration to allow for accurate comparison of the two. In this review, we will describe engineering approaches for studying metastatic migration, both single cell and collective, and how these approaches have yielded significant insight into the mechanics governing each process. PMID:27814431

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis

DOE PAGES

Sakhanenko, Nikita A.; Kunert-Graf, James; Galas, David J.

2017-10-13

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. Here, we present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discretemore » variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis—that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. Finally, we illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.« less

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakhanenko, Nikita A.; Kunert-Graf, James; Galas, David J.

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. Here, we present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discretemore » variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis—that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. Finally, we illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.« less

HLA-DQA1 and HLA-DQB1 genes in Tsachilas Indians from Ecuador: new insights in population analysis by Human Leukocyte Antigens.

PubMed

Iorio, A; De Angelis, F; Garzoli, A; Battistini, A; De Stefano, G F

2014-06-01

Human Leucocyte Antigen (HLA) loci are widely known for their role in the generation of immune responses and are often considered to be effective in reconstructing human relationships. This is due to the high degree of polymorphism and the rarity of recombination observed at HLA loci. In this study, we have made an attempt to support the potential of HLA class II loci by analysing DQA1 and DQB1 in 52 Ecuadorians with ties to the Tsachilas community. Little is known about this populations either ethnologically or historically: they are considered retaining much of the ancient Chibchan culture in spite of the lack of significant genetic characterization. A total of 21 alleles were observed, with very low heterozygosity. The obtained data were then assessed for relationship reconstruction. The compiled database of 63 populations was segregated and resolved in clusters corresponding to the ethnogeographic distribution of the populations. This analysis of Central and Southern Amerindians allowed us to support a historical hypothesis related to the origin and migration of Ecuadorian people. Indeed, the relationships with neighbour human groups, especially Cayapas and Colombians, could shed light on the genetic similarity within ancient Chibchan culture that was dispersed by tribes coming up the Barbacoas. This indicates that if an appropriate analysis was to be carried out on a set of populations representative of different geographic locations, and that analysis was properly interpreted, then there would be a high possibility that HLA class II loci could infer accurate assessments, as revealed by uniparental markers. © 2014 John Wiley & Sons Ltd.

The effect of sampling rate on observed statistics in a correlated random walk

PubMed Central

Rosser, G.; Fletcher, A. G.; Maini, P. K.; Baker, R. E.

2013-01-01

Tracking the movement of individual cells or animals can provide important information about their motile behaviour, with key examples including migrating birds, foraging mammals and bacterial chemotaxis. In many experimental protocols, observations are recorded with a fixed sampling interval and the continuous underlying motion is approximated as a series of discrete steps. The size of the sampling interval significantly affects the tracking measurements, the statistics computed from observed trajectories, and the inferences drawn. Despite the widespread use of tracking data to investigate motile behaviour, many open questions remain about these effects. We use a correlated random walk model to study the variation with sampling interval of two key quantities of interest: apparent speed and angle change. Two variants of the model are considered, in which reorientations occur instantaneously and with a stationary pause, respectively. We employ stochastic simulations to study the effect of sampling on the distributions of apparent speeds and angle changes, and present novel mathematical analysis in the case of rapid sampling. Our investigation elucidates the complex nature of sampling effects for sampling intervals ranging over many orders of magnitude. Results show that inclusion of a stationary phase significantly alters the observed distributions of both quantities. PMID:23740484

Population structure in Argentina.

PubMed

Muzzio, Marina; Motti, Josefina M B; Paz Sepulveda, Paula B; Yee, Muh-Ching; Cooke, Thomas; Santos, María R; Ramallo, Virginia; Alfaro, Emma L; Dipierri, Jose E; Bailliet, Graciela; Bravi, Claudio M; Bustamante, Carlos D; Kenny, Eimear E

2018-01-01

We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.

Stereotactic core needle breast biopsy marker migration: An analysis of factors contributing to immediate marker migration.

PubMed

Jain, Ashali; Khalid, Maria; Qureshi, Muhammad M; Georgian-Smith, Dianne; Kaplan, Jonah A; Buch, Karen; Grinstaff, Mark W; Hirsch, Ariel E; Hines, Neely L; Anderson, Stephan W; Gallagher, Katherine M; Bates, David D B; Bloch, B Nicolas

2017-11-01

To evaluate breast biopsy marker migration in stereotactic core needle biopsy procedures and identify contributing factors. This retrospective study analyzed 268 stereotactic biopsy markers placed in 263 consecutive patients undergoing stereotactic biopsies using 9G vacuum-assisted devices from August 2010-July 2013. Mammograms were reviewed and factors contributing to marker migration were evaluated. Basic descriptive statistics were calculated and comparisons were performed based on radiographically-confirmed marker migration. Of the 268 placed stereotactic biopsy markers, 35 (13.1%) migrated ≥1 cm from their biopsy cavity. Range: 1-6 cm; mean (± SD): 2.35 ± 1.22 cm. Of the 35 migrated biopsy markers, 9 (25.7%) migrated ≥3.5 cm. Patient age, biopsy pathology, number of cores, and left versus right breast were not associated with migration status (P> 0.10). Global fatty breast density (P= 0.025) and biopsy in the inner region of breast (P = 0.031) were associated with marker migration. Superior biopsy approach (P= 0.025), locally heterogeneous breast density, and t-shaped biopsy markers (P= 0.035) were significant for no marker migration. Multiple factors were found to influence marker migration. An overall migration rate of 13% supports endeavors of research groups actively developing new biopsy marker designs for improved resistance to migration. • Breast biopsy marker migration is documented in 13% of 268 procedures. • Marker migration is affected by physical, biological, and pathological factors. • Breast density, marker shape, needle approach etc. affect migration. • Study demonstrates marker migration prevalence; marker design improvements are needed.

Constraints on planetesimal disk mass from the cratering record and equatorial ridge on Iapetus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivera-Valentin, E. G.; Barr, A. C.; Lopez Garcia, E. J.

2014-09-10

Iapetus, the outermost regular satellite of Saturn, has a drastic albedo dichotomy and an equatorial circumferential ridge that reaches heights of 20 km and widths of 70 km. This moon is thought to have formed concurrently with Saturn, and so would have experienced an intense bombardment after its formation. The ridge, which has been inferred to be one of the most ancient features on Iapetus' surface, could reasonably be expected to have been eroded by impacts; however, it has retained long continuous sections and a nearly pristine triangular shape with ridge slopes reaching ∼40°. We use these observations, along withmore » crater counts on Iapetus' surface, to constrain the total bombardment mass experienced by the satellite since its formation. The ridge morphology and the global crater population recorded on Iapetus both suggest similar bombardment masses, indicating the ridge is indeed ancient. We find that the inferred total bombardment mass incident on Iapetus is less than 20% of the bombardment predicted by the classic Nice model for early solar system evolution. Our results, though, support the recently proposed scenarios of planetesimal-driven migration of the young outer planets including more realistic disk conditions.« less

Inferring Core Tungsten Behavior Using SPRED During the DIII-D Metal Rings Campaign

NASA Astrophysics Data System (ADS)

Thomas, D. M.; Kaplan, D.; Groebner, R.; Grierson, B.; Unterberg, Z.; Victor, B.

2016-10-01

The GA SPRED EUV spectrometer was used to study core emission of highly charged tungsten ions (W40+-W45+) in the 120-135Å region during the recent Metal Rings Campaign. These experiments used two 5-cm wide toroidal rings of W-coated metal inserts exposed to a variety of DIII-D discharges to study effects of high-Z divertor erosion, migration, core uptake, and effects on advanced tokamak performance. For the proper core temperature range (2-4 keV), the measured multistate W emission forms a well defined spectral pattern that can be used to study the relative importance of strike point location, flux expansion, injected power, ELM characteristics and magnetic drift direction for high-Z core contamination in DIII-D. The spectra are fit using simple Gaussians to estimate concentrations using the historical SPRED intensity calibration. Calibration shots using known core dosages of pellet injected W are used to help infer the relative response of the instrument. Supported by US DOE under DE-FC02-04ER54698, DE-AC02-09CH11466, DE-AC05-00OR22725, DE-AC52-07NA27344.

Genetic connectivity and self-replenishment of inshore and offshore populations of the endemic anemonefish, Amphiprion latezonatus

NASA Astrophysics Data System (ADS)

Steinberg, Rosemary; van der Meer, Martin; Walker, Emily; Berumen, Michael L.; Hobbs, Jean-Paul A.; van Herwerden, Lynne

2016-09-01

Globally, marine species are under increasing pressure from human activities, including ocean warming, acidification, pollution, and overfishing. Species most vulnerable to these pressures tend to be ecological specialists that have low abundance and small distribution ranges (endemics). Marine endemics often exist as meta-populations distributed among few isolated locations. Determining genetic connectivity among these locations is essential to understanding the recovery potential of endemics after local extinction events. This study examined connectivity in the endemic anemonefish, Amphiprion latezonatus, a habitat specialist with low abundance at most locations. Evolutionary and contemporary migration, genetic diversity, and self-replenishment among the four main locations (Sunshine Coast, North Solitary Island, Lord Howe Island, and Norfolk Island) that comprise the entire A. latezonatus geographic range were assessed using mtDNA and microsatellite markers. Though historical gene flow inferred from mtDNA appeared high, population genetic differentiation was evident and contemporary gene flow inferred from microsatellites was limited, alongside very high (≥89 %) self-replenishment at all locations. Together, these data suggest prolonged recovery times following severe population decline (or extirpation) and indicate a need to protect this species at all locations, particularly Norfolk Island and Sunshine Coast where marine protected areas are lacking.

Inferring the demographic history of European Ficedula flycatcher populations

PubMed Central

2013-01-01

Background Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account. PMID:23282063

Aspects of First Year Statistics Students' Reasoning When Performing Intuitive Analysis of Variance: Effects of Within- and Between-Group Variability

ERIC Educational Resources Information Center

Trumpower, David L.

2015-01-01

Making inferences about population differences based on samples of data, that is, performing intuitive analysis of variance (IANOVA), is common in everyday life. However, the intuitive reasoning of individuals when making such inferences (even following statistics instruction), often differs from the normative logic of formal statistics. The…

A Meta-Analysis of Multiple Matched Copy Number and Transcriptomics Data Sets for Inferring Gene Regulatory Relationships

PubMed Central

Newton, Richard; Wernisch, Lorenz

2014-01-01

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments. PMID:25148247

Environmental change and seasonal behavior of mastodons in the Great Lakes region inferred from stable isotope analysis

NASA Astrophysics Data System (ADS)

Metcalfe, Jessica Z.; Longstaffe, Fred J.

2014-09-01

We investigate seasonal variations in the diet and drinking water of four Great Lakes mastodon (Mammut americanum) specimens using stable isotope analysis of serially sampled inner-enamel bioapatite structural carbonate (δ13Csc, δ18Osc), and previously published bulk analyses. Isotopic analyses and thin section measurements showed that mastodon tooth enamel extension rates (~ 12-4 mm/yr, decreasing toward the cervix) were lower than those of mammoths or modern elephants. Mastodons had distinct and highly regular seasonal variations in δ13Csc and δ18Osc, which we interpret in the context of local glacial history and vegetation changes. Seasonal variations in δ18O were large but variations in δ13C were small, and may have been obscured if coarser sampling methods than our inner-enamel sampling approach were used. Thus, our approach may be particularly useful for understanding relatively small seasonal changes in δ13C within C3 environments. The seasonal patterns, though not entirely conclusive, suggest that the Ontario mastodons did not migrate over very long distances. Rather, the climate and seasonal dietary patterns of mastodons within the region changed over time, from ~ 12,400 to 10,400 14C yr BP (~ 15,000 - 12,000 cal yr BP). Insights gained using these methods can contribute to a better understanding of megafaunal extinctions and Paleoamerican lifeways.

Collaborative analysis of Planetary Waves in the Mesospheric Neutral Winds with SuperDARN and TIMED Observations

NASA Astrophysics Data System (ADS)

Ruohoniemi, J. M.

2004-12-01

The SuperDARN HF radars are best known for observing the ExB drift of ionospheric plasma in the high-latitude F region. At mesospheric altitudes the trails of ionization produced by meteors provide another kind of target for radar backscatter, and the motions imparted to these trails by winds in the neutral atmosphere can be measured. In the northern hemisphere the coverage of mesospheric winds currently extends over a 180 deg longitude sector but is confined by propagation conditions to latitudes near 55 deg geographic. We have analyzed several extended periods of simultaneous observations of the neutral wind involving SuperDARN and the TIMED suite of instruments. Often, the winds show clear evidence of large-scale wave events. The quasi 2-day planetary waves are prominent and their occurrence is seen to depend on season. By comparing the wave characteristics between the satellite and ground observations we obtain a complete breakdown of the wave activity in terms of wave periods and zonal wavenumbers. In addition, the semidiurnal tide is a ubiquitous feature of the mid-latitude mesosphere. A single radar station cannot resolve the sun-synchronous component from other contributions at the semidiurnal frequency. We show that with a chain of radars along a latitude band, the true sun-synchronous, or migrating, component can be inferred. Joint analysis can be performed chiefly with data from the SABRE and TIDI instruments.

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci.

PubMed Central

Roberts, Mark A; Schwartz, Tonia S; Karl, Stephen A

2004-01-01

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model. PMID:15126404

Automated Tracking of Cell Migration with Rapid Data Analysis.

PubMed

DuChez, Brian J

2017-09-01

Cell migration is essential for many biological processes including development, wound healing, and metastasis. However, studying cell migration often requires the time-consuming and labor-intensive task of manually tracking cells. To accelerate the task of obtaining coordinate positions of migrating cells, we have developed a graphical user interface (GUI) capable of automating the tracking of fluorescently labeled nuclei. This GUI provides an intuitive user interface that makes automated tracking accessible to researchers with no image-processing experience or familiarity with particle-tracking approaches. Using this GUI, users can interactively determine a minimum of four parameters to identify fluorescently labeled cells and automate acquisition of cell trajectories. Additional features allow for batch processing of numerous time-lapse images, curation of unwanted tracks, and subsequent statistical analysis of tracked cells. Statistical outputs allow users to evaluate migratory phenotypes, including cell speed, distance, displacement, and persistence, as well as measures of directional movement, such as forward migration index (FMI) and angular displacement. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Recovery Migration after Hurricanes Katrina and Rita: Spatial Concentration and Intensification in the Migration System

PubMed Central

Fussell, Elizabeth; DeWaard, Jack

2015-01-01

Changes in the human migration systems of Hurricane Katrina- and Rita-affected Gulf of Mexico coastline counties provide an example of how climate change may affect coastal populations. Crude climate change models predict a mass migration of “climate refugees,” but an emerging literature on environmental migration suggests most migration will be short-distance and short-duration within existing migration systems, with implications for the population recovery of disaster-struck places. In this research, we derive a series of hypotheses on recovery migration predicting how the migration system of hurricane-affected coastline counties in the Gulf of Mexico was likely to have changed between the pre-disaster and the recovery periods. We test these hypotheses using data from the Internal Revenue Service on annual county-level migration flows, comparing the recovery period migration system (2007–2009) to the pre-disaster period (1999–2004). By observing county-to-county ties and flows we find that recovery migration was strong, as the migration system of the disaster-affected coastline counties became more spatially concentrated while flows within it intensified and became more urbanized. Our analysis demonstrates how migration systems are likely to be affected by the more intense and frequent storms anticipated by climate change scenarios with implications for the population recovery of disaster-affected places. PMID:26084982

Cadherin-2 Is Required Cell Autonomously for Collective Migration of Facial Branchiomotor Neurons.

PubMed

Rebman, Jane K; Kirchoff, Kathryn E; Walsh, Gregory S

2016-01-01

Collective migration depends on cell-cell interactions between neighbors that contribute to their overall directionality, yet the mechanisms that control the coordinated migration of neurons remains to be elucidated. During hindbrain development, facial branchiomotor neurons (FBMNs) undergo a stereotypic tangential caudal migration from their place of birth in rhombomere (r)4 to their final location in r6/7. FBMNs engage in collective cell migration that depends on neuron-to-neuron interactions to facilitate caudal directionality. Here, we demonstrate that Cadherin-2-mediated neuron-to-neuron adhesion is necessary for directional and collective migration of FBMNs. We generated stable transgenic zebrafish expressing dominant-negative Cadherin-2 (Cdh2ΔEC) driven by the islet1 promoter. Cell-autonomous inactivation of Cadherin-2 function led to non-directional migration of FBMNs and a defect in caudal tangential migration. Additionally, mosaic analysis revealed that Cdh2ΔEC-expressing FBMNs are not influenced to migrate caudally by neighboring wild-type FBMNs due to a defect in collective cell migration. Taken together, our data suggest that Cadherin-2 plays an essential cell-autonomous role in mediating the collective migration of FBMNs.

Fast-crawling cell types migrate to avoid the direction of periodic substratum stretching

PubMed Central

Okimura, Chika; Ueda, Kazuki; Sakumura, Yuichi; Iwadate, Yoshiaki

2016-01-01

ABSTRACT To investigate the relationship between mechanical stimuli from substrata and related cell functions, one of the most useful techniques is the application of mechanical stimuli via periodic stretching of elastic substrata. In response to this stimulus, Dictyostelium discoideum cells migrate in a direction perpendicular to the stretching direction. The origins of directional migration, higher migration velocity in the direction perpendicular to the stretching direction or the higher probability of a switch of migration direction to perpendicular to the stretching direction, however, remain unknown. In this study, we applied periodic stretching stimuli to neutrophil-like differentiated HL-60 cells, which migrate perpendicular to the direction of stretch. Detailed analysis of the trajectories of HL-60 cells and Dictyostelium cells obtained in a previous study revealed that the higher probability of a switch of migration direction to that perpendicular to the direction of stretching was the main cause of such directional migration. This directional migration appears to be a strategy adopted by fast-crawling cells in which they do not migrate faster in the direction they want to go, but migrate to avoid a direction they do not want to go. PMID:26980079

Children’s welfare and short term migration from rural India

PubMed Central

Coffey, Diane

2013-01-01

Few papers in the literature provide quantitative analysis of the difficult circumstances faced by children of short-term labour migrants. This paper uses new survey data from rural northwest India to study both children who migrate and those left behind. It finds that, unlike in other contexts, children who migrate rarely work when they accompany adult migrants. Additionally, this paper reports a robust, previously unquantified negative relationship between children’s migration and educational outcomes and investments. It calls for further research about externalities of migration for children and suggests that expansion of a large public employment program might help these children. PMID:24049212

``Carbon Credits'' for Resource-Bounded Computations Using Amortised Analysis

NASA Astrophysics Data System (ADS)

Jost, Steffen; Loidl, Hans-Wolfgang; Hammond, Kevin; Scaife, Norman; Hofmann, Martin

Bounding resource usage is important for a number of areas, notably real-time embedded systems and safety-critical systems. In this paper, we present a fully automatic static type-based analysis for inferring upper bounds on resource usage for programs involving general algebraic datatypes and full recursion. Our method can easily be used to bound any countable resource, without needing to revisit proofs. We apply the analysis to the important metrics of worst-case execution time, stack- and heap-space usage. Our results from several realistic embedded control applications demonstrate good matches between our inferred bounds and measured worst-case costs for heap and stack usage. For time usage we infer good bounds for one application. Where we obtain less tight bounds, this is due to the use of software floating-point libraries.

Velocity of climate change algorithms for guiding conservation and management.

PubMed

Hamann, Andreas; Roberts, David R; Barber, Quinn E; Carroll, Carlos; Nielsen, Scott E

2015-02-01

The velocity of climate change is an elegant analytical concept that can be used to evaluate the exposure of organisms to climate change. In essence, one divides the rate of climate change by the rate of spatial climate variability to obtain a speed at which species must migrate over the surface of the earth to maintain constant climate conditions. However, to apply the algorithm for conservation and management purposes, additional information is needed to improve realism at local scales. For example, destination information is needed to ensure that vectors describing speed and direction of required migration do not point toward a climatic cul-de-sac by pointing beyond mountain tops. Here, we present an analytical approach that conforms to standard velocity algorithms if climate equivalents are nearby. Otherwise, the algorithm extends the search for climate refugia, which can be expanded to search for multivariate climate matches. With source and destination information available, forward and backward velocities can be calculated allowing useful inferences about conservation of species (present-to-future velocities) and management of species populations (future-to-present velocities). © 2014 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

SCALEUS: Semantic Web Services Integration for Biomedical Applications.

PubMed

Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

2017-04-01

In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

Reconstructing Roma History from Genome-Wide Data

PubMed Central

Moorjani, Priya; Patterson, Nick; Loh, Po-Ru; Lipson, Mark; Kisfali, Péter; Melegh, Bela I.; Bonin, Michael; Kádaši, Ľudevít; Rieß, Olaf; Berger, Bonnie; Reich, David; Melegh, Béla

2013-01-01

The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000–1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry–derived from a combination of European and South Asian sources–and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe. PMID:23516520

Identifying Seizure Onset Zone From the Causal Connectivity Inferred Using Directed Information

NASA Astrophysics Data System (ADS)

Malladi, Rakesh; Kalamangalam, Giridhar; Tandon, Nitin; Aazhang, Behnaam

2016-10-01

In this paper, we developed a model-based and a data-driven estimator for directed information (DI) to infer the causal connectivity graph between electrocorticographic (ECoG) signals recorded from brain and to identify the seizure onset zone (SOZ) in epileptic patients. Directed information, an information theoretic quantity, is a general metric to infer causal connectivity between time-series and is not restricted to a particular class of models unlike the popular metrics based on Granger causality or transfer entropy. The proposed estimators are shown to be almost surely convergent. Causal connectivity between ECoG electrodes in five epileptic patients is inferred using the proposed DI estimators, after validating their performance on simulated data. We then proposed a model-based and a data-driven SOZ identification algorithm to identify SOZ from the causal connectivity inferred using model-based and data-driven DI estimators respectively. The data-driven SOZ identification outperforms the model-based SOZ identification algorithm when benchmarked against visual analysis by neurologist, the current clinical gold standard. The causal connectivity analysis presented here is the first step towards developing novel non-surgical treatments for epilepsy.

The mechanisms of temporal inference

NASA Technical Reports Server (NTRS)

Fox, B. R.; Green, S. R.

1987-01-01

The properties of a temporal language are determined by its constituent elements: the temporal objects which it can represent, the attributes of those objects, the relationships between them, the axioms which define the default relationships, and the rules which define the statements that can be formulated. The methods of inference which can be applied to a temporal language are derived in part from a small number of axioms which define the meaning of equality and order and how those relationships can be propagated. More complex inferences involve detailed analysis of the stated relationships. Perhaps the most challenging area of temporal inference is reasoning over disjunctive temporal constraints. Simple forms of disjunction do not sufficiently increase the expressive power of a language while unrestricted use of disjunction makes the analysis NP-hard. In many cases a set of disjunctive constraints can be converted to disjunctive normal form and familiar methods of inference can be applied to the conjunctive sub-expressions. This process itself is NP-hard but it is made more tractable by careful expansion of a tree-structured search space.

In defence of model-based inference in phylogeography

PubMed Central

Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisson, Scott A.; Fagundes, Nelson; Chikhi, Lounès; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Francois; Balding, David; Excoffier, Laurent

2017-01-01

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics. PMID:29284924

The dynamics of sediment size and transient erosional signals in heterogeneous lithologies

NASA Astrophysics Data System (ADS)

Lyons, N. J.; Gasparini, N. M.; Crosby, B. T.; Wehrs, K.; Willenbring, J. K.

2017-12-01

Sediment supply and transport dynamics convey, transform, and destroy climatic and tectonic signals in channels and depositional landforms. The South Fork Eel River (SFER) in the northern California Coast Ranges, USA exhibits characteristics suggestive of transient landscape adjustment: strath terraces, knickpoints, and headwater terrain eroding more slowly than downstream areas. A tectonically-induced uplift wave is commonly invoked as the driver of transience in this region. The wave is attributed to the northward migration of the Mendocino Triple Junction (MTJ). Nested basin-mean erosion rates calculated from 10Be detrital quartz sand increase down the mainstem of the SFER, roughly coinciding with the direction of MTJ migration. This erosion trend is attributed to the proportion of adjusted and unadjusted landscape portions upstream of the locations where the nested 10Be samples were collected. Adjusted and unadjusted landscape portions are separated by a broad knickzone that contains 28% of relief along the mainstem. Knickzone propagation and considerable stream incision is suggested by projection of the upper SFER above the knickzone through the highest flight of strath terraces. Field observations and outcomes of numerical simulations using the Landlab modeling framework are incompatible with uplift modeled as a wave. Alternative uplift and variable sediment flux scenarios more reliably predict the pattern of terraces, knickpoints, and accelerated erosion. In the natural landscape, landforms and erosion rates follow the patterns expected for transient erosion along the mainstem, although a local base level lowering signal is not resolvable in many tributaries. Topographic relief, presence of knickpoints, and rock properties differ in the SFER tributaries. The tributaries draining mélange are over-steepened by boulders detached from hillslopes by earthflows. Here, we propose a framework in which rock properties and sediment size are a key control upon preservation of a base level change signal in low order streams. This result implies that transient erosion signals inferred using topography can be transformed or destroyed in certain lithologies, complicating efforts to infer climatic and tectonic history from topography.

Characterization of intrabasin faulting and deformation for earthquake hazards in southern Utah Valley, Utah, from high-resolution seismic imaging

USGS Publications Warehouse

Stephenson, William J.; Odum, Jack K.; Williams, Robert A.; McBride, John H.; Tomlinson, Iris

2012-01-01

We conducted active and passive seismic imaging investigations along a 5.6-km-long, east–west transect ending at the mapped trace of the Wasatch fault in southern Utah Valley. Using two-dimensional (2D) P-wave seismic reflection data, we imaged basin deformation and faulting to a depth of 1.4 km and developed a detailed interval velocity model for prestack depth migration and 2D ground-motion simulations. Passive-source microtremor data acquired at two sites along the seismic reflection transect resolve S-wave velocities of approximately 200 m/s at the surface to about 900 m/s at 160 m depth and confirm a substantial thickening of low-velocity material westward into the valley. From the P-wave reflection profile, we interpret shallow (100–600 m) bedrock deformation extending from the surface trace of the Wasatch fault to roughly 1.5 km west into the valley. The bedrock deformation is caused by multiple interpreted fault splays displacing fault blocks downward to the west of the range front. Further west in the valley, the P-wave data reveal subhorizontal horizons from approximately 90 to 900 m depth that vary in thickness and whose dip increases with depth eastward toward the Wasatch fault. Another inferred fault about 4 km west of the mapped Wasatch fault displaces horizons within the valley to as shallow as 100 m depth. The overall deformational pattern imaged in our data is consistent with the Wasatch fault migrating eastward through time and with the abandonment of earlier synextensional faults, as part of the evolution of an inferred 20-km-wide half-graben structure within Utah Valley. Finite-difference 2D modeling suggests the imaged subsurface basin geometry can cause fourfold variation in peak ground velocity over distances of 300 m.

Implications of mitochondrial DNA polyphyly in two ecologically undifferentiated but morphologically distinct migratory birds, the masked and white-browed woodswallows Artamus spp. of inland Australia

USGS Publications Warehouse

Joseph, Leo; Wilke, Thomas; Ten Have, Jose; Chesser, R. Terry

2006-01-01

The white-browed woodswallow Artamus superciliosus and masked woodswallow A. personatus(Passeriformes: Artamidae) are members of Australia's diverse arid- and semi-arid zone avifauna. Widely sympatric and among Australia's relatively few obligate long-distance temperate-tropical migrants, the two are well differentiated morphologically but not ecologically and vocally. They are pair breeders unlike other Artamus species, which are at least facultative cooperative breeders. For these reasons they are an excellent case in which to use molecular data in integrative study of their evolution from ecological and biogeographical perspectives. We used mitochondrial DNA (mtDNA) to test whether they are each other's closest relatives, whether they evolved migration independently, whether they have molecular signatures of population expansions like some other Australian arid zone birds, and to estimate the timing of any inferred population expansions. Their mtDNAs are monophyletic with respect to other species of Artamusbut polyphyletic with respect to each other. The two species appear not to have evolved migration independently of each other but their morphological and mtDNA evolution have been strongly decoupled. Some level of hybridization and introgression cannot be dismissed outright as being involved in their mtDNA polyphyly but incomplete sorting of their most recent common ancestor's mtDNA is a simpler explanation consistent with their ecology. Bayesian phylogenetic inference and analyses of diversity within the two species (n=77) with conventional diversity statistics, statistical parsimony, and tests for population expansion vs stability (Tajima's D, Fu's Fsand Ramos-Onsin and Rozas's R2) all favour recent population increases. However, a non-starlike network suggests expansion(s) relatively early in the Pleistocene. Repeated population bottlenecks corresponding with multiple peaks of Pleistocene aridity could explain our findings, which add a new dimension to accruing data on the effects of Pleistocene aridity on the Australian biota.

Sensitivity to imputation models and assumptions in receiver operating characteristic analysis with incomplete data

PubMed Central

Karakaya, Jale; Karabulut, Erdem; Yucel, Recai M.

2015-01-01

Modern statistical methods using incomplete data have been increasingly applied in a wide variety of substantive problems. Similarly, receiver operating characteristic (ROC) analysis, a method used in evaluating diagnostic tests or biomarkers in medical research, has also been increasingly popular problem in both its development and application. While missing-data methods have been applied in ROC analysis, the impact of model mis-specification and/or assumptions (e.g. missing at random) underlying the missing data has not been thoroughly studied. In this work, we study the performance of multiple imputation (MI) inference in ROC analysis. Particularly, we investigate parametric and non-parametric techniques for MI inference under common missingness mechanisms. Depending on the coherency of the imputation model with the underlying data generation mechanism, our results show that MI generally leads to well-calibrated inferences under ignorable missingness mechanisms. PMID:26379316

Preconditioning of bone marrow-derived mesenchymal stromal cells by tetramethylpyrazine enhances cell migration and improves functional recovery after focal cerebral ischemia in rats.

PubMed

Li, Lin; Chu, Lisheng; Fang, Yan; Yang, Yan; Qu, Tiebing; Zhang, Jianping; Yin, Yuanjun; Gu, Jingjing

2017-05-12

Transplantation of bone marrow-derived mesenchymal stem cells (BMSCs) is one of the new therapeutic strategies for treating ischemic stroke. However, the relatively poor migratory capacity of BMSCs toward infarcted regions limited the therapeutic potential of this approach. Pharmacological preconditioning can increase the expression of CXC chemokine receptor 4 (CXCR4) in BMSCs and enhance cell migration toward the injury site. In the present study, we investigated whether tetramethylpyrazine (TMP) preconditioning could enhance BMSCs migration to the ischemic brain and improve functional recovery through upregulating CXCR4 expression. BMSCs were identified by flow cytometry analysis. BMSCs migration was evaluated in vitro by transwell migration assay, and CXCR4 expression was measured by quantitative reverse transcription-polymerase chain reaction and western blot analysis. In rats with focal cerebral ischemia, the neurological function was evaluated by the modified neurological severity score, the adhesive removal test and the corner test. The homing BMSCs and angiogenesis were detected by immunofluorescence, and expression of stromal cell-derived factor-1 (SDF-1) and CXCR4 was measured by western blot analysis. Flow cytometry analysis demonstrated that BMSCs expressed CD29 and CD90, but not CD34 and CD45. TMP pretreatment dose-dependently induced BMSCs migration and CXCR4 expression in vitro, which was significantly inhibited by AMD3100, a CXCR4 antagonist. In rat stroke models, we found more TMP-preconditioned BMSCs homing toward the infarcted regions than nonpreconditioned cells, leading to improved neurological performance and enhanced angiogenesis. Moreover, TMP-preconditioned BMSCs significantly upregulated the protein expression of SDF-1 and CXCR4 in the ischemic boundary regions. These beneficial effects of TMP preconditioning were blocked by AMD3100. TMP preconditioning enhances the migration and homing ability of BMSCs, increases CXCR4 expression, promotes angiogenesis, and improves neurological performance. Therefore, TMP preconditioning may be an effective strategy to improve the therapeutic potency of BMSCs for ischemic stroke due to enhanced BMSCs migration to ischemic regions.

Controlled levels of canonical Wnt signaling are required for neural crest migration.

PubMed

Maj, Ewa; Künneke, Lutz; Loresch, Elisabeth; Grund, Anita; Melchert, Juliane; Pieler, Tomas; Aspelmeier, Timo; Borchers, Annette

2016-09-01

Canonical Wnt signaling plays a dominant role in the development of the neural crest (NC), a highly migratory cell population that generates a vast array of cell types. Canonical Wnt signaling is required for NC induction as well as differentiation, however its role in NC migration remains largely unknown. Analyzing nuclear localization of β-catenin as readout for canonical Wnt activity, we detect nuclear β-catenin in premigratory but not migratory Xenopus NC cells suggesting that canonical Wnt activity has to decrease to basal levels to enable NC migration. To define a possible function of canonical Wnt signaling in Xenopus NC migration, canonical Wnt signaling was modulated at different time points after NC induction. This was accomplished using either chemical modulators affecting β-catenin stability or inducible glucocorticoid fusion constructs of Lef/Tcf transcription factors. In vivo analysis of NC migration by whole mount in situ hybridization demonstrates that ectopic activation of canonical Wnt signaling inhibits cranial NC migration. Further, NC transplantation experiments confirm that this effect is tissue-autonomous. In addition, live-cell imaging in combination with biophysical data analysis of explanted NC cells confirms the in vivo findings and demonstrates that modulation of canonical Wnt signaling affects the ability of NC cells to perform single cell migration. Thus, our data support the hypothesis that canonical Wnt signaling needs to be tightly controlled to enable migration of NC cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Determinants of labour migration of elite sport coaches.

PubMed

Orlowski, Johannes; Wicker, Pamela; Breuer, Christoph

2016-09-01

Previous research examining labour migration in sport focused on athletes in professional team sports. The purpose of this study is to analyse the factors influencing the migration probability of elite sport coaches in Germany (i.e. national coaches, state coaches, and coaches at Olympic training bases). From a theoretical perspective, labour migration of athletes is affected by economic, social, political, competitive, geographic and cultural factors. This study examines whether these factors can be applied to coaches. Primary data were collected using an online survey of elite sport coaches in Germany. Applying a conjoint design, respondents were presented with 10 migration scenarios leading to a sample size of n = 1860 for the empirical analysis. In the scenarios, the coaching position openings abroad differed in terms of income level, contract length, weekly workload, responsibility for personnel, reputation of coaching job, career perspectives, sporting performance of athletes, distance from Germany, and predominant job language. Coaches were asked for their migration probability contingent on the specific scenario. On average, migration probability was 24.2%. The results of regression analysis showed that higher income, contracts of longer duration, responsibility for personnel and speaking the respective language significantly increased the migration probability, while distances of nine flight hours and more, lower reputation and career perspectives reduced it. The findings have implications for policy-makers: they indicate in what areas the situation of coaches needs improvement to increase the likelihood of retaining elite sport coaches in the German sport system.

Semi-blind Bayesian inference of CMB map and power spectrum

NASA Astrophysics Data System (ADS)

Vansyngel, Flavien; Wandelt, Benjamin D.; Cardoso, Jean-François; Benabed, Karim

2016-04-01

We present a new blind formulation of the cosmic microwave background (CMB) inference problem. The approach relies on a phenomenological model of the multifrequency microwave sky without the need for physical models of the individual components. For all-sky and high resolution data, it unifies parts of the analysis that had previously been treated separately such as component separation and power spectrum inference. We describe an efficient sampling scheme that fully explores the component separation uncertainties on the inferred CMB products such as maps and/or power spectra. External information about individual components can be incorporated as a prior giving a flexible way to progressively and continuously introduce physical component separation from a maximally blind approach. We connect our Bayesian formalism to existing approaches such as Commander, spectral mismatch independent component analysis (SMICA), and internal linear combination (ILC), and discuss possible future extensions.

Evaluation of Second-Level Inference in fMRI Analysis

PubMed Central

Roels, Sanne P.; Loeys, Tom; Moerkerke, Beatrijs

2016-01-01

We investigate the impact of decisions in the second-level (i.e., over subjects) inferential process in functional magnetic resonance imaging on (1) the balance between false positives and false negatives and on (2) the data-analytical stability, both proxies for the reproducibility of results. Second-level analysis based on a mass univariate approach typically consists of 3 phases. First, one proceeds via a general linear model for a test image that consists of pooled information from different subjects. We evaluate models that take into account first-level (within-subjects) variability and models that do not take into account this variability. Second, one proceeds via inference based on parametrical assumptions or via permutation-based inference. Third, we evaluate 3 commonly used procedures to address the multiple testing problem: familywise error rate correction, False Discovery Rate (FDR) correction, and a two-step procedure with minimal cluster size. Based on a simulation study and real data we find that the two-step procedure with minimal cluster size results in most stable results, followed by the familywise error rate correction. The FDR results in most variable results, for both permutation-based inference and parametrical inference. Modeling the subject-specific variability yields a better balance between false positives and false negatives when using parametric inference. PMID:26819578

Effects of Migration on Sending Countries: What Do We Know? OECD Development Centre Working Paper No. 250

ERIC Educational Resources Information Center

Katseli, Louka T.; Lucas, Robert E. B.; Xenogiani, Theodora

2006-01-01

This report evaluates the evidence on how migration may promote or hinder development in countries of origin, and explores possible win-win solutions for both sending and receiving countries. The analysis of recent OECD data of foreign-born nationals into Europe documents the presence of multiple migration patterns and reveals that the EU lags…

A Comparison of Freshmen Who Attend College in Their Home Community and Freshmen Who Migrate to College.

ERIC Educational Resources Information Center

Fenske, Robert H.; Scott, Craig S.

This study of student migration patterns is based on the assumption that an important determinant of change in student migration patterns in recent years has been the increase in the number of two-year colleges. The present study utilizes data which makes possible an analysis of the relationship between student characteristics and their migration…

Migration of the Duraloc cup after 5 years

PubMed Central

Stihsen, Christoph; Pabinger, Christof; Radl, Roman; Rehak, Peter

2007-01-01

The Duraloc cup is a frequently used metal-backed, porous-coated, hemispherical, press-fit acetabular component. Published data on loosening rates are contradictory. In this study we investigated migration patterns with computer-assisted Einzel-Bild-Roentgen-Analyse (EBRA) of 67 Duraloc 100 cups. Cup migration and clinical scores were analysed over a 5-year follow-up period. Median total migration of the Duraloc 100 cup was 1.21 mm at 5 years. Seventy-five percent of implants were radiologically stable at 2 years and 90% at 4 years. One cup loosened aseptically at 60 months, requiring revision. Cup diameters ≥54 mm migrated significantly more than cups <54 mm in diameter (p = 0.029 at 4 years). There was a significant correlation between high polyethylene wear and further migrating cups within the first post-operative year (p = 0.035 at 12 months). Our analysis revealed significantly higher wear in males (p = 0.029 at 4 years). Radiological loosening at two years could be calculated using receiver-operating characteristic curve analysis, and 1.2 mm as an adequate threshold value (sensitivity = 100%, specificity = 89%). PMID:17609953

An analysis of file migration in a UNIX supercomputing environment

NASA Technical Reports Server (NTRS)

Miller, Ethan L.; Katz, Randy H.

1992-01-01

The super computer center at the National Center for Atmospheric Research (NCAR) migrates large numbers of files to and from its mass storage system (MSS) because there is insufficient space to store them on the Cray supercomputer's local disks. This paper presents an analysis of file migration data collected over two years. The analysis shows that requests to the MSS are periodic, with one day and one week periods. Read requests to the MSS account for the majority of the periodicity; as write requests are relatively constant over the course of a week. Additionally, reads show a far greater fluctuation than writes over a day and week since reads are driven by human users while writes are machine-driven.

The relationship between annual survival rate and migration distance in mallards: an examination of the time-allocation hypothesis for the evolution of migration

USGS Publications Warehouse

Hestbeck, J.B.; Nichols, J.D.; Hines, J.E.

1992-01-01

Predictions of the time-allocation hypothesis were tested with several a posteriori analyses of banding data for the mallard (Anas platyrhynchos). The time-allocation hypothesis states that the critical difference between resident and migrant birds is their allocation of time to reproduction on the breeding grounds and survival on the nonbreeding grounds. Residents have higher reproduction and migrants have higher survival. Survival and recovery rates were estimated by standard band-recovery methods for banding reference areas in the central United States and central Canada. A production-rate index was computed for each reference area with data from the U.S. Fish and Wildlife Service May Breeding Population Survey and July Production Survey. An analysis of covariance was used to test for the effects of migration distance and time period (decade) on survival, recovery, and production rates. Differences in migration chronology were tested by comparing direct-recovery distributions for different populations during the fall migration. Differences in winter locations were tested by comparing distributions of direct recoveries reported during December and January. A strong positive relationship was found between survival rate, and migration distance for 3 of the 4 age and sex classes. A weak negative relationship was found between recovery rate and migration distance. No relationship was found between production rate and migration distance. During the fall migration, birds from the northern breeding populations were located north of birds from the southern breeding populations. No pattern could be found in the relative locations of breeding and wintering areas. Although our finding that survival rate increased with migration distance was consistent with the time-allocation hypothesis, our results on migration chronology and location of wintering areas were not consistent with the mechanism underlying the time-allocation hypothesis. Neither this analysis nor other recent studies of life-history characteristics of migratory and resident birds supported the timeallocation hypothesis.

Common reflection point migration and velocity analysis for anisotropic media

NASA Astrophysics Data System (ADS)

Oropeza, Ernesto V.

An efficient Kirchhoff-style prestack depth migration, called 'parsimonious' migration was developed a decade ago for isotropic 2D and 3D media. The common-reflection point (CRP) migration velocity analysis (MVA) was developed later for isotropic media. The isotropic parsimonious migration produces incorrect images when the media is actually anisotropic. Similarly, isotropic CRP MVA produces incorrect inversions when the medium is anisotropic. In this study both parsimonious depth migration and common-reflection point migration velocity analysis are extended for application to 2D tilted transversely isotropic (TTI) media and illustrated with synthetic P-wave data. While the framework of isotropic parsimonious migration may be retained, the extension to TTI media requires redevelopment of each of the numerical components, including calculation of the phase and group velocity for TTI media, development of a new two-point anisotropic ray tracer, and substitution of an initial-angle and anisotropic shooting ray-trace algorithm to replace the isotropic one. The 2D model parameterization consists of Thomsen's parameters (Vpo, epsilon, delta) and the tilt angle of the symmetry axis of the TI medium. The parsimonious anisotropic migration algorithm is successfully applied to synthetic data from a TTI version of the Marmousi-2 model. The quality of the image improves by weighting the impulse response by the calculation of the anisotropic Fresnel radius. The accuracy and speed of this migration makes it useful for anisotropic velocity model building. The common-reflection point migration velocity analysis for TTI media for P-waves includes (and inverts for) Vpo, epsilon, and delta. The orientation of the anisotropic symmetry axis have to be constrained. If it constrained orthogonal to the layer bottom (as it conventionally is), it is estimated at each CRP and updated at each iteration without intermediate picking. The extension to TTI media requires development of a new inversion procedure to include Vpo, epsilon, and delta in the perturbations. The TTI CRP MVA is applied to a single layer to demonstrate its feasibility. Errors in the estimation of the orientation of the symmetry axis larger that 5 degrees affect the inversion of epsilon and delta while Vpo is less sensitive to this parameter. The TTI CRP MVA is also applied to a version of the TTI BP model by layer stripping so one group of CRPs are used do to inversion top to bottom, constraining the model parameter after each previous group of CRPs converges. Vpo, delta and the orientation of the anisotropic symmetry axis (constrained orthogonal to the local reflector orientation) are successfully inverted. epsilon is less well constrained by the small acquisition aperture in the data .

A prior-based integrative framework for functional transcriptional regulatory network inference

PubMed Central

Siahpirani, Alireza F.

2017-01-01

Abstract Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to infer regulatory networks, however, networks inferred from such methods have low overlap with experimentally derived (e.g. ChIP-chip and transcription factor (TF) knockouts) networks. Currently we have a limited understanding of this discrepancy. To address this gap, we first develop a regulatory network inference algorithm, based on probabilistic graphical models, to integrate expression with auxiliary datasets supporting a regulatory edge. Second, we comprehensively analyze our and other state-of-the-art methods on different expression perturbation datasets. Networks inferred by integrating sequence-specific motifs with expression have substantially greater agreement with experimentally derived networks, while remaining more predictive of expression than motif-based networks. Our analysis suggests natural genetic variation as the most informative perturbation for network inference, and, identifies core TFs whose targets are predictable from expression. Multiple reasons make the identification of targets of other TFs difficult, including network architecture and insufficient variation of TF mRNA level. Finally, we demonstrate the utility of our inference algorithm to infer stress-specific regulatory networks and for regulator prioritization. PMID:27794550

Intra-seasonal Oscillations Inferred from SABER (TIMED) and MLS (UARS) Temperature Measurements

NASA Technical Reports Server (NTRS)

Huang, F. T.; Mayr, H. G.; Russell, J.; Mlynczak, M.; Reber, C. A.; Mengel, J. G.

2006-01-01

In the zonal mean meridional winds of the upper mesosphere, intra-seasonal oscillations with periods between 1 and 4 months have been inferred from UARS measurements and independently predicted with the Numerical Spectral Model WSM). The wind oscillations tend to be confined to low latitudes and appear to be driven, at least in part, by small-scale gravity waves propagating in the meridional direction. Winds across the equator should generate, due to dynamical heating and cooling, temperature oscillations with opposite phase in the two hemispheres. Investigating this phenomenon, we have analyzed SABER temperatures from TIMED in the altitude range between 55 and 95 km to delineate with an empirical model, the year-long variability of the migrating tides and zonal mean components. The inferred seasonal variations of the diurnal tide, characterized by amplitude maxima near equinox, are in substantial agreement with UARS observations and results from the NSM. For the zonal mean, the dominant seasonal variations in the SABER temperatures, with annual (12 months) and semiannual (6 months) periodicities, agree well with those derived from UARS measurements. The intra-seasonal variations with periods between 2 and 4 months have amplitudes close to 2 K, almost half as large as those for the dominant seasonal variations. Their amplitudes are in qualitative agreement with the corresponding values inferred from UARS during different years. The SABER and UARS temperature variations reveal pronounced hemispherical asymmetries, consistent with meridional wind oscillations across the equator. The phase of the semi-annual temperature oscillations from the NSM agrees with the observations from UARS and SABER. But the amplitudes are systematically smaller, which may indicate that planetary waves are more important than is allowed for in the model. For the shorter-period intra-seasonal variations, which can be generated by gravity wave drag, the model results are generally in better agreement with the observations.

Post-Boreotropical dispersals explain the pantropical disjunction in Paederia (Rubiaceae)

PubMed Central

Nie, Ze-Long; Deng, Tao; Meng, Ying; Sun, Hang; Wen, Jun

2013-01-01

Background and Aims Pantropical intercontinental disjunction is a common biogeographical pattern in flowering plants exhibiting a discontinuous distribution primarily in tropical Asia, Africa and the Americas. Only a few plant groups with this pattern have been investigated at the generic level with molecular phylogenetic and biogeographical methods. Paederia (Rubiaceae) is a pantropical genus of 31 species of woody lianas, with the greatest species diversity in continental Asia and Madagascar and only two species from tropical America. The aim of this study was to reconstruct the biogeographical history of Paederia based on phylogenetic analyses to explore how the genus attained its pantropical distribution. Methods Maximum parsimony and Bayesian inference were used for phylogenetic analyses using sequences of five plastid markers (the rbcL gene, rps16 intron, trnT-F region, atpB-rbcL spacer and psbA-trnH spacer). Biogeographical inferences were based on a Bayesian uncorrelated lognormal relaxed molecular clock together with both Bayesian and likelihood ancestral area reconstructions. Key Results The data suggest an early diverged Asian lineage sister to the clade of the remaining species consisting of a predominantly Asian sub-clade and a primarily Malagasy sub-clade. Paederia is inferred to have originated in the Oligocene in tropical continental Asia. It then reached Africa in the early to middle Miocene, most probably via long-distance dispersal across the Indian Ocean. The two Neotropical species are inferred to have derived independently in the late Miocene from ancestors of Asia and East Africa, respectively. Conclusions The results demonstrate the importance of post-Boreotropical long-distance dispersals (across three major oceans) in shaping the global pantropical disjunction in some plants, such as Paederia, with small, winged diaspores adapted to long-distance dispersal by various agents including wind, ocean currents or birds. Overland migration is less likely to explain its palaeotropical disjunction between Asia and Africa. PMID:23478944

Political motivations for intra-European migration

PubMed Central

Flipo, Aurore

2016-01-01

Motivations for migrating within the European Union have mainly been attributed to economic, career and lifestyle choices. This article suggests that political dissatisfaction is also an important motivator of recent intra-European migration. In our analysis of in-depth interviews with Romanian migrants in Spain and with Spanish migrants in Norway, we found a common emphasis on the political dimensions of their decision to migrate. In the interviews, the economic component of migration was often related to bad governance and negative perceptions of the state. The similarities of Spanish and Romanian migration narratives are especially striking because Spain and Romania represent substantially different migratory, political and economic contexts. However, migration is more obviously intertwined with conventional acts of political protest in the Spanish case. We suggest that differences in democratic contexts are pivotal in people’s reactions to and framing of their deep dissatisfaction with domestic politics, as found in many European countries today. PMID:28751786

Political motivations for intra-European migration.

PubMed

Bygnes, Susanne; Flipo, Aurore

2017-08-01

Motivations for migrating within the European Union have mainly been attributed to economic, career and lifestyle choices. This article suggests that political dissatisfaction is also an important motivator of recent intra-European migration. In our analysis of in-depth interviews with Romanian migrants in Spain and with Spanish migrants in Norway, we found a common emphasis on the political dimensions of their decision to migrate. In the interviews, the economic component of migration was often related to bad governance and negative perceptions of the state. The similarities of Spanish and Romanian migration narratives are especially striking because Spain and Romania represent substantially different migratory, political and economic contexts. However, migration is more obviously intertwined with conventional acts of political protest in the Spanish case. We suggest that differences in democratic contexts are pivotal in people's reactions to and framing of their deep dissatisfaction with domestic politics, as found in many European countries today.

Measuring the Environmental Dimensions of Human Migration: The Demographer's Toolkit.

PubMed

Fussell, Elizabeth; Hunter, Lori M; Gray, Clark L

2014-09-01

In recent years, the empirical literature linking environmental factors and human migration has grown rapidly and gained increasing visibility among scholars and the policy community. Still, this body of research uses a wide range of methodological approaches for assessing environment-migration relationships. Without comparable data and measures across a range of contexts, it is impossible to make generalizations that would facilitate the development of future migration scenarios. Demographic researchers have a large methodological toolkit for measuring migration as well as modeling its drivers. This toolkit includes population censuses, household surveys, survival analysis and multi-level modeling. This paper's purpose is to introduce climate change researchers to demographic data and methods and to review exemplary studies of the environmental dimensions of human migration. Our intention is to foster interdisciplinary understanding and scholarship, and to promote high quality research on environment and migration that will lead toward broader knowledge of this association.

Pioneers and Followers: Migrant Selectivity and the Development of U.S. Migration Streams in Latin America

PubMed Central

Lindstrom, David P.; Ramírez, Adriana López

2013-01-01

We present a method for dividing the historical development of community migration streams into an initial period and a subsequent takeoff stage with the purpose of systemically differentiating pioneer migrants from follower migrants. The analysis is organized around five basic research questions. First, can we empirically identify a juncture in the historical development of community-based migration that marks the transition from an initial stage of low levels of migration and gradual growth into a takeoff stage in which the prevalence of migration grows at a more accelerated rate? Second, does this juncture point exist at roughly similar migration prevalence levels across communities? Third, are first-time migrants in the initial stage (pioneers) different from first-time migrants in the takeoff stage (followers)? Fourth, what is the nature of this migrant selectivity? Finally, does the nature and degree of pioneer selectivity vary across country migration streams? PMID:24489382

Measuring the Environmental Dimensions of Human Migration: The Demographer’s Toolkit

PubMed Central

Hunter, Lori M.; Gray, Clark L.

2014-01-01

In recent years, the empirical literature linking environmental factors and human migration has grown rapidly and gained increasing visibility among scholars and the policy community. Still, this body of research uses a wide range of methodological approaches for assessing environment-migration relationships. Without comparable data and measures across a range of contexts, it is impossible to make generalizations that would facilitate the development of future migration scenarios. Demographic researchers have a large methodological toolkit for measuring migration as well as modeling its drivers. This toolkit includes population censuses, household surveys, survival analysis and multi-level modeling. This paper’s purpose is to introduce climate change researchers to demographic data and methods and to review exemplary studies of the environmental dimensions of human migration. Our intention is to foster interdisciplinary understanding and scholarship, and to promote high quality research on environment and migration that will lead toward broader knowledge of this association. PMID:25177108

Effects of human and mosquito migrations on the dynamical behavior of the spread of malaria

NASA Astrophysics Data System (ADS)

Beay, Lazarus Kalvein; Kasbawati, Toaha, Syamsuddin

2017-03-01

Malaria is one of infectious diseases which become the main public health problem especially in Indonesia. Mathematically, the spread of malaria can be modeled to predict the outbreak of the disease. This research studies about mathematical model of the spread of malaria which takes into consideration the migration of human and mosquito populations. By determining basic reproduction number of the model, we analyze effects of migration parameter with respect to the reduction of malaria outbreak. Sensitivity analysis of basic reproduction number shows that mosquito migration has greater effect in reducing the outbreak of malaria compared with human migration. Basic reproduction number of the model is monotonically decreasing as mosquito migration increasing. We then confirm the analytic result by doing numerical simulation. The results show that migrations in human and mosquito populations have big influences in eliminating and eradicating the disease from the system.

Separable processes before, during, and after the N400 elicited by previously inferred and new information: evidence from time-frequency decompositions.

PubMed

Steele, Vaughn R; Bernat, Edward M; van den Broek, Paul; Collins, Paul F; Patrick, Christopher J; Marsolek, Chad J

2013-01-25

Successful comprehension during reading often requires inferring information not explicitly presented. This information is readily accessible when subsequently encountered, and a neural correlate of this is an attenuation of the N400 event-related potential (ERP). We used ERPs and time-frequency (TF) analysis to investigate neural correlates of processing inferred information after a causal coherence inference had been generated during text comprehension. Participants read short texts, some of which promoted inference generation. After each text, they performed lexical decisions to target words that were unrelated or inference-related to the preceding text. Consistent with previous findings, inference-related words elicited an attenuated N400 relative to unrelated words. TF analyses revealed unique contributions to the N400 from activity occurring at 1-6 Hz (theta) and 0-2 Hz (delta), supporting the view that multiple, sequential processes underlie the N400. Copyright © 2012 Elsevier B.V. All rights reserved.

Do Daphnia use metalimnetic organic matter in a north temperate lake? An analysis of vertical migration

USGS Publications Warehouse

Brosseau, Chase Julian; Cline, Timothy J.; Cole, Jonathan J.; Hodgson, James R.; Pace, Michael L.; Weidel, Brian C.

2012-01-01

Diel vertical migration of zooplankton is influenced by a variety of factors including predation, food, and temperature. Research has recently shifted from a focus on factors influencing migration to how migration affects nutrient cycling and habitat coupling. Here we evaluate the potential for Daphnia migrations to incorporate metalimnetic productivity in a well-studied northern Wisconsin lake. We use prior studies conducted between 1985 and 1990 and current diel migration data (2008) to compare day and night Daphnia vertical distributions with the depth of the metalimnion (between the thermocline and 1% light depth). Daphnia migrate from a daytime mean residence depth of between about 1.7 and 2.5 m to a nighttime mean residence depth of between 0 and 2.0 m. These migrations are consistent between the prior period and current measurements. Daytime residence depths of Daphnia are rarely deep enough to reach the metalimnion; hence, metalimnetic primary production is unlikely to be an important resource for Daphnia in this system.

Assays for in vitro monitoring of human airway smooth muscle (ASM) and human pulmonary arterial vascular smooth muscle (VSM) cell migration.

PubMed

Goncharova, Elena A; Goncharov, Dmitry A; Krymskaya, Vera P

2006-01-01

Migration of human pulmonary vascular smooth muscle (VSM) cells contributes to vascular remodeling in pulmonary arterial hypertension and atherosclerosis. Evidence also indicates that, in part, migration of airway smooth muscle (ASM) cells may contribute to airway remodeling associated with asthma. Here we describe migration of VSM and ASM cells in vitro using Transwell or Boyden chamber assays. Because dissecting signaling mechanisms regulating cell migration requires molecular approaches, our protocol also describes how to assess migration of transfected VSM and ASM cells. Transwell or Boyden chamber assays can be completed in approximately 8 h and include plating of serum-deprived VSM or ASM cell suspension on membrane precoated with collagen, migration of cells toward chemotactic gradient and visual (Transwell) or digital (Boyden chamber) analysis of membrane. Although the Transwell assay is easy, the Boyden chamber assay requires hands-on experience; however, both assays are reliable cell-based approaches providing valuable information on how chemotactic and inflammatory factors modulate VSM and ASM migration.

Can lagrangian models reproduce the migration time of European eel obtained from otolith analysis?

NASA Astrophysics Data System (ADS)

Rodríguez-Díaz, L.; Gómez-Gesteira, M.

2017-12-01

European eel can be found at the Bay of Biscay after a long migration across the Atlantic. The duration of migration, which takes place at larval stage, is of primary importance to understand eel ecology and, hence, its survival. This duration is still a controversial matter since it can range from 7 months to > 4 years depending on the method to estimate duration. The minimum migration duration estimated from our lagrangian model is similar to the duration obtained from the microstructure of eel otoliths, which is typically on the order of 7-9 months. The lagrangian model showed to be sensitive to different conditions like spatial and time resolution, release depth, release area and initial distribution. In general, migration showed to be faster when decreasing the depth and increasing the resolution of the model. In average, the fastest migration was obtained when only advective horizontal movement was considered. However, faster migration was even obtained in some cases when locally oriented random migration was taken into account.

Statistical Signal Models and Algorithms for Image Analysis

DTIC Science & Technology

1984-10-25

In this report, two-dimensional stochastic linear models are used in developing algorithms for image analysis such as classification, segmentation, and object detection in images characterized by textured backgrounds. These models generate two-dimensional random processes as outputs to which statistical inference procedures can naturally be applied. A common thread throughout our algorithms is the interpretation of the inference procedures in terms of linear prediction

A refined method for multivariate meta-analysis and meta-regression

PubMed Central

Jackson, Daniel; Riley, Richard D

2014-01-01

Making inferences about the average treatment effect using the random effects model for meta-analysis is problematic in the common situation where there is a small number of studies. This is because estimates of the between-study variance are not precise enough to accurately apply the conventional methods for testing and deriving a confidence interval for the average effect. We have found that a refined method for univariate meta-analysis, which applies a scaling factor to the estimated effects’ standard error, provides more accurate inference. We explain how to extend this method to the multivariate scenario and show that our proposal for refined multivariate meta-analysis and meta-regression can provide more accurate inferences than the more conventional approach. We explain how our proposed approach can be implemented using standard output from multivariate meta-analysis software packages and apply our methodology to two real examples. © 2013 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd. PMID:23996351

Bayesian data analysis in population ecology: motivations, methods, and benefits

USGS Publications Warehouse

Dorazio, Robert

2016-01-01

During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.

Population genomics reveals seahorses (Hippocampus erectus) of the western mid-Atlantic coast to be residents rather than vagrants.

PubMed

Boehm, J T; Waldman, John; Robinson, John D; Hickerson, Michael J

2015-01-01

Understanding population structure and areas of demographic persistence and transients is critical for effective species management. However, direct observational evidence to address the geographic scale and delineation of ephemeral or persistent populations for many marine fishes is limited. The Lined seahorse (Hippocampus erectus) can be commonly found in three western Atlantic zoogeographic provinces, though inhabitants of the temperate northern Virginia Province are often considered tropical vagrants that only arrive during warm seasons from the southern provinces and perish as temperatures decline. Although genetics can locate regions of historical population persistence and isolation, previous evidence of Virginia Province persistence is only provisional due to limited genetic sampling (i.e., mitochondrial DNA and five nuclear loci). To test alternative hypotheses of historical persistence versus the ephemerality of a northern Virginia Province population we used a RADseq generated dataset consisting of 11,708 single nucleotide polymorphisms (SNP) sampled from individuals collected from the eastern Gulf of Mexico to Long Island, NY. Concordant results from genomic analyses all infer three genetically divergent subpopulations, and strongly support Virginia Province inhabitants as a genetically diverged and a historically persistent ancestral gene pool. These results suggest that individuals that emerge in coastal areas during the warm season can be considered "local" and supports offshore migration during the colder months. This research demonstrates how a large number of genes sampled across a geographical range can capture the diversity of coalescent histories (across loci) while inferring population history. Moreover, these results clearly demonstrate the utility of population genomic data to infer peripheral subpopulation persistence in difficult-to-observe species.

Pliocene Warm Period Upwelling in the Southern Benguela Region

NASA Astrophysics Data System (ADS)

Petrick, B. F.; McClymont, E.; Felder, S.; Leng, M. J.; Rosell Mele, A.; Rueda, G.

2014-12-01

The mid-Pliocene has been proposed as a possible analogue for understanding future climate change and testing climate models. Previous work has shown that during the Pliocene the major upwelling systems were relatively warm, and thus either inactive, contracted, or upwelling warmer waters than present. Here we examine evidence from a core site located on the margins of the modern Benguela upwelling system, to test whether the upwelling cells had migrated or contracted relative to present during the Pliocene. We applied several organic geochemistry proxies and foraminiferal analyses to reconstruct the Pliocene history of ODP site 1087 (31º28'S, 15º19'E, 1374m water depth), including the UK37' index and TEX86 index (for reconstructing sea surface temperatures), chlorins (for estimating primary productivity) and planktonic foraminifera assemblages (for inferring water mass changes). These proxies show that between 3.5 and 3.0 Ma the southern Benguela region was significantly cooler than the northern Benguela region, the latter where the main upwelling cells are found today. Coupled with higher primary production, a shift in planktonic foraminifera assemblage, and an offset between the UK37' index and TEX86 index, we infer that more extensive upwelling was present in the southern Benguela region during the Pliocene. We infer that the main Benguela upwelling cells had shifted southward relative to today, as a result of changes in the local wind field. We find evidence for pronounced cooling and a shift in the planktonic foraminifera assemblage during the M2 and KM2 glacial stages, showing a sensitivity of Benguela upwelling to these short-lived climate events.

Restructuring of the labour market and the role of third world migrations in Europe.

PubMed

Pugliese, E

1993-10-01

"This paper is an analysis of the way in which the changes in the labour market and in the occupational structure in Europe affect the situation and the role of Third World migrants." Changes in European labor migration patterns since the 1960s are first analyzed. The author notes that "intra-European migrations were industrial migrations because manufacturing and building industries were the most important and growing economic activities....Present-day migrations are postindustrial migrations. Immigrants work mostly in service activities and not infrequently in the informal economy. In any case migrant workers are located in the secondary labour market. The picture is made more complex by the fact than many immigrants are alegal or illegal because of the restrictive immigration policies in European countries." excerpt

Socioeconomic context and the association between marriage and Mexico-U.S. migration.

PubMed

Riosmena, Fernando

2009-06-01

In this paper, I analyze how the association between Mexico-U.S. migration and marriage varies across socioeconomic settings in origins. Using Mexican Migration Project data and employing bilevel survival analysis with controls for socioeconomic, migrant network, and marriage market characteristics and family size, I find that single people are most likely to migrate relative to those married in areas of recent industrialization, where the Mexican patriarchal system is weaker and economic opportunities for both men and women make post-marital migration less attractive. Marital status is not significant in agriculture-dependent areas, where the bargaining power of husbands might be higher relative to other settings; their age-profiles of earnings flatter; and remunerated female work scarcer, making migration attractive later in the life course.

Socioeconomic context and the association between marriage and Mexico–U.S. migration

PubMed Central

Riosmena, Fernando

2009-01-01

In this paper, I analyze how the association between Mexico–U.S. migration and marriage varies across socioeconomic settings in origins. Using Mexican Migration Project data and employing bilevel survival analysis with controls for socioeconomic, migrant network, and marriage market characteristics and family size, I find that single people are most likely to migrate relative to those married in areas of recent industrialization, where the Mexican patriarchal system is weaker and economic opportunities for both men and women make post-marital migration less attractive. Marital status is not significant in agriculture-dependent areas, where the bargaining power of husbands might be higher relative to other settings; their age-profiles of earnings flatter; and remunerated female work scarcer, making migration attractive later in the life course. PMID:19756216

Quantitative Analysis of Cancer Cell Migration in Gradients Of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device

DTIC Science & Technology

2005-01-01

Quantitative Analysis of Cancer Cell Migration in Gradients of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device The University of California...allowing for parallel analysis . Additionally, simple methods of localizing gels into microdevices are demonstrated. The device was characterized by...To overcome some of these drawbacks, several approaches have utilized free diffusion to produce gradients in static environ - ments.5-9 However

Development and validation of an automated and marker-free CT-based spatial analysis method (CTSA) for assessment of femoral hip implant migration: In vitro accuracy and precision comparable to that of radiostereometric analysis (RSA).

PubMed

Scheerlinck, Thierry; Polfliet, Mathias; Deklerck, Rudi; Van Gompel, Gert; Buls, Nico; Vandemeulebroucke, Jef

2016-01-01

We developed a marker-free automated CT-based spatial analysis (CTSA) method to detect stem-bone migration in consecutive CT datasets and assessed the accuracy and precision in vitro. Our aim was to demonstrate that in vitro accuracy and precision of CTSA is comparable to that of radiostereometric analysis (RSA). Stem and bone were segmented in 2 CT datasets and both were registered pairwise. The resulting rigid transformations were compared and transferred to an anatomically sound coordinate system, taking the stem as reference. This resulted in 3 translation parameters and 3 rotation parameters describing the relative amount of stem-bone displacement, and it allowed calculation of the point of maximal stem migration. Accuracy was evaluated in 39 comparisons by imposing known stem migration on a stem-bone model. Precision was estimated in 20 comparisons based on a zero-migration model, and in 5 patients without stem loosening. Limits of the 95% tolerance intervals (TIs) for accuracy did not exceed 0.28 mm for translations and 0.20° for rotations (largest standard deviation of the signed error (SD(SE)): 0.081 mm and 0.057°). In vitro, limits of the 95% TI for precision in a clinically relevant setting (8 comparisons) were below 0.09 mm and 0.14° (largest SD(SE): 0.012 mm and 0.020°). In patients, the precision was lower, but acceptable, and dependent on CT scan resolution. CTSA allows detection of stem-bone migration with an accuracy and precision comparable to that of RSA. It could be valuable for evaluation of subtle stem loosening in clinical practice.

Challenging a 15-year-old claim: The North Atlantic Oscillation index as a predictor of spring migration phenology of birds.

PubMed

Haest, Birgen; Hüppop, Ommo; Bairlein, Franz

2018-04-01

Many migrant bird species that breed in the Northern Hemisphere show advancement in spring arrival dates. The North Atlantic Oscillation (NAO) index is one of the climatic variables that have been most often investigated and shown to be correlated with these changes in spring arrival. Although the NAO is often claimed to be a good predictor or even to have a marked effect on interannual changes in spring migration phenology of Northern Hemisphere breeding birds, the results on relations between spring migration phenology and NAO show a large variety, ranging from no, over weak, to a strong association. Several factors, such as geographic location, migration phase, and the NAO index time window, have been suggested to partly explain these observed differences in association. A combination of a literature meta-analysis, and a meta-analysis and sliding time window analysis of a dataset of 23 short- and long-distance migrants from the constant-effort trapping garden at Helgoland, Germany, however, paints a completely different picture. We found a statistically significant overall effect size of the NAO on spring migration phenology (coefficient = -0.14, SE = 0.054), but this on average only explains 0%-6% of the variance in spring migration phenology across all species. As such, the value and biological meaning of the NAO as a general predictor or explanatory variable for climate change effects on migration phenology of birds, seems highly questionable. We found little to no definite support for previously suggested factors, such as geographic location, migration phenology phase, or the NAO time window, to explain the heterogeneity in correlation differences. We, however, did find compelling evidence that the lack of accounting for trends in both time series has led to strongly inflated (spurious) correlations in many studies (coefficient = -0.13, SE = 0.019). © 2017 John Wiley & Sons Ltd.

Magma migration at the onset of the 2012-13 Tolbachik eruption revealed by Seismic Amplitude Ratio Analysis

NASA Astrophysics Data System (ADS)

Caudron, Corentin; Taisne, Benoit; Kugaenko, Yulia; Saltykov, Vadim

2015-12-01

In contrast of the 1975-76 Tolbachik eruption, the 2012-13 Tolbachik eruption was not preceded by any striking change in seismic activity. By processing the Klyuchevskoy volcano group seismic data with the Seismic Amplitude Ratio Analysis (SARA) method, we gain insights into the dynamics of magma movement prior to this important eruption. A clear seismic migration within the seismic swarm, started 20 hours before the reported eruption onset (05:15 UTC, 26 November 2012). This migration proceeded in different phases and ended when eruptive tremor, corresponding to lava flows, was recorded (at 11:00 UTC, 27 November 2012). In order to get a first order approximation of the magma location, we compare the calculated seismic intensity ratios with the theoretical ones. As expected, the observations suggest that the seismicity migrated toward the eruption location. However, we explain the pre-eruptive observed ratios by a vertical migration under the northern slope of Plosky Tolbachik volcano followed by a lateral migration toward the eruptive vents. Another migration is also captured by this technique and coincides with a seismic swarm that started 16-20 km to the south of Plosky Tolbachik at 20:31 UTC on November 28 and lasted for more than 2 days. This seismic swarm is very similar to the seismicity preceding the 1975-76 Tolbachik eruption and can be considered as a possible aborted eruption.

Transcription factor FOXO1 promotes cell migration toward exogenous ATP via controlling P2Y1 receptor expression in lymphatic endothelial cells.

PubMed

Niimi, Kenta; Ueda, Mizuha; Fukumoto, Moe; Kohara, Misaki; Sawano, Toshinori; Tsuchihashi, Ryo; Shibata, Satoshi; Inagaki, Shinobu; Furuyama, Tatsuo

2017-08-05

Sprouting migration of lymphatic endothelial cell (LEC) is a pivotal step in lymphangiogenic process. However, its molecular mechanism remains unclear including effective migratory attractants. Meanwhile, forkhead transcription factor FOXO1 highly expresses in LEC nuclei, but its significance in LEC migratory activity has not been researched. In this study, we investigated function of FOXO1 transcription factor associated with LEC migration toward exogenous ATP which has recently gathered attentions as a cell migratory attractant. The transwell membrane assay indicated that LECs migrated toward exogenous ATP, which was impaired by FOXO1 knockdown. RT-PCR analysis showed that P2Y1, a purinergic receptor, expression was markedly reduced by FOXO1 knockdown in LECs. Moreover, P2Y1 blockage impaired LEC migration toward exogenous ATP. Western blot analysis revealed that Akt phosphorylation contributed to FOXO1-dependent LEC migration toward exogenous ATP and its blockage affected LEC migratory activity. Furthermore, luciferase reporter assay and ChIP assay suggested that FOXO1 directly bound to a conserved binding site in P2RY1 promoter and regulated its activity. These results indicated that FOXO1 serves a pivotal role in LEC migration toward exogenous ATP via direct transcriptional regulation of P2Y1 receptor. Copyright © 2017 Elsevier Inc. All rights reserved.

Progesterone stimulates the long-distance migration of capacitated ram spermatozoa through viscous media under geotactic condition.

PubMed

Martínez-Rodríguez, Carmen; Anel-López, Luis; Alvarez, Mercedes; Ortega-Ferrusola, Cristina; Boixo, Juan Carlos; Peña, Fernando J; Anel, Luis; de Paz, Paulino

2018-05-15

Forward progressive motility of spermatozoa is an essential prerequisite for reproductive success, and sperm navigation is assisted by guidance mechanisms that may depend on micro-environmental factors. In the present study, we performed an integrated analysis of long-distance ram sperm migration in vitro that combined two environmental factors (10 μM progesterone and a geotactic effect) and the physiological status of the cells (capacitation treatment). A penetration assay was used in which spermatozoa had to travel 20 mm in a viscous medium (two media of differing viscosity: acrylamide and hyaluronic acid) through a tube device. The number of migrating spermatozoa, the physiology of the cells (motility analyzed using a CASA system; acrosomal status, viability and active mitochondria evaluated by flow cytometry; DNA fragmentation index calculated by quantitative PCR) and the morphometry of sperm heads (performed using an image analysis system) were evaluated after long-distance sperm migration. Ram sperm capacitation significantly stimulates cell migration through viscous media under geotactic conditions, and this effect is enhanced by progesterone induction. The rheological characteristics of viscous media have a marked impact on ram sperm migration, and acrylamide more favorably facilitates navigation over a large distance. The migrating spermatozoa are morphologically better adapted (high ellipticity) for displacement in viscous media and exhibit remarkably depleted mitochondrial membrane potential. Copyright © 2018 Elsevier Inc. All rights reserved.

Human Inferences about Sequences: A Minimal Transition Probability Model

PubMed Central

2016-01-01

The brain constantly infers the causes of the inputs it receives and uses these inferences to generate statistical expectations about future observations. Experimental evidence for these expectations and their violations include explicit reports, sequential effects on reaction times, and mismatch or surprise signals recorded in electrophysiology and functional MRI. Here, we explore the hypothesis that the brain acts as a near-optimal inference device that constantly attempts to infer the time-varying matrix of transition probabilities between the stimuli it receives, even when those stimuli are in fact fully unpredictable. This parsimonious Bayesian model, with a single free parameter, accounts for a broad range of findings on surprise signals, sequential effects and the perception of randomness. Notably, it explains the pervasive asymmetry between repetitions and alternations encountered in those studies. Our analysis suggests that a neural machinery for inferring transition probabilities lies at the core of human sequence knowledge. PMID:28030543

Quantifying uncertainty in soot volume fraction estimates using Bayesian inference of auto-correlated laser-induced incandescence measurements

NASA Astrophysics Data System (ADS)

Hadwin, Paul J.; Sipkens, T. A.; Thomson, K. A.; Liu, F.; Daun, K. J.

2016-01-01

Auto-correlated laser-induced incandescence (AC-LII) infers the soot volume fraction (SVF) of soot particles by comparing the spectral incandescence from laser-energized particles to the pyrometrically inferred peak soot temperature. This calculation requires detailed knowledge of model parameters such as the absorption function of soot, which may vary with combustion chemistry, soot age, and the internal structure of the soot. This work presents a Bayesian methodology to quantify such uncertainties. This technique treats the additional "nuisance" model parameters, including the soot absorption function, as stochastic variables and incorporates the current state of knowledge of these parameters into the inference process through maximum entropy priors. While standard AC-LII analysis provides a point estimate of the SVF, Bayesian techniques infer the posterior probability density, which will allow scientists and engineers to better assess the reliability of AC-LII inferred SVFs in the context of environmental regulations and competing diagnostics.

Stent migration following endoscopic suture fixation of esophageal self-expandable metal stents: a systematic review and meta-analysis.

PubMed

Law, Ryan; Prabhu, Anoop; Fujii-Lau, Larissa; Shannon, Carol; Singh, Siddharth

2018-02-01

Covered self-expandable metal stents (SEMS) are utilized for the management of benign and malignant esophageal conditions; however, covered SEMS are prone to migration. Endoscopic suture fixation may mitigate the migration risk of covered esophageal SEMS. Hence, we conducted a systematic review and meta-analysis to evaluate the effectiveness and safety of endoscopic suture fixation for covered esophageal SEMS. Following PRISMA guidelines, we performed a systematic review from 2011 to 2016 to identify studies (case control/case series) reporting the technical success and migration rate of covered esophageal SEMS following endoscopic suture fixation. We searched multiple electronic databases and conference proceedings. We calculated pooled rates (and 95% confidence intervals [CI]) of technical success and stent migration using a random effects model. We identified 14 studies (212 patients) describing covered esophageal SEMS placement with endoscopic suture fixation. When reported, SEMS indications included leak/fistula (n = 75), stricture (n = 65), perforation (n = 10), and achalasia (n = 4). The pooled technical success rate was 96.7% (95% CI 92.3-98.6), without heterogeneity (I 2  = 0%). We identified 29 SEMS migrations at rate of 15.9% (95% CI 11.4-21.6), without heterogeneity (I 2  = 0%). Publication bias was observed, and using the trim-and-fill method, a more conservative estimate for stent migration was 17.0%. Suture-related adverse events were estimated to occur in 3.7% (95% CI 1.6-8.2) of cases. Endoscopic suture fixation of covered esophageal SEMS appears to reduce stent migration when compared to published rates of non-anchored SEMS. However, SEMS migration still occurs in approximately 1 out of 6 cases despite excellent immediate technical success and low risk of suture-related adverse events.

The Utility of the Extended Images in Ambient Seismic Wavefield Migration

NASA Astrophysics Data System (ADS)

Girard, A. J.; Shragge, J. C.

2015-12-01

Active-source 3D seismic migration and migration velocity analysis (MVA) are robust and highly used methods for imaging Earth structure. One class of migration methods uses extended images constructed by incorporating spatial and/or temporal wavefield correlation lags to the imaging conditions. These extended images allow users to directly assess whether images focus better with different parameters, which leads to MVA techniques that are based on the tenets of adjoint-state theory. Under certain conditions (e.g., geographical, cultural or financial), however, active-source methods can prove impractical. Utilizing ambient seismic energy that naturally propagates through the Earth is an alternate method currently used in the scientific community. Thus, an open question is whether extended images are similarly useful for ambient seismic migration processing and verifying subsurface velocity models, and whether one can similarly apply adjoint-state methods to perform ambient migration velocity analysis (AMVA). Herein, we conduct a number of numerical experiments that construct extended images from ambient seismic recordings. We demonstrate that, similar to active-source methods, there is a sensitivity to velocity in ambient seismic recordings in the migrated extended image domain. In synthetic ambient imaging tests with varying degrees of error introduced to the velocity model, the extended images are sensitive to velocity model errors. To determine the extent of this sensitivity, we utilize acoustic wave-equation propagation and cross-correlation-based migration methods to image weak body-wave signals present in the recordings. Importantly, we have also observed scenarios where non-zero correlation lags show signal while zero-lags show none. This may be a valuable missing piece for ambient migration techniques that have yielded largely inconclusive results, and might be an important piece of information for performing AMVA from ambient seismic recordings.

Hedgehog signaling contributes to basic fibroblast growth factor-regulated fibroblast migration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Zhong Xin; Sun, Cong Cong; Wenzhou People's Hospital, Wenzhou, Zhejiang

Fibroblast migration is a central process in skin wound healing, which requires the coordination of several types of growth factors. bFGF, a well-known fibroblast growth factor (FGF), is able to accelerate fibroblast migration; however, the underlying mechanism of bFGF regulation fibroblast migration remains unclear. Through the RNA-seq analysis, we had identified that the hedgehog (Hh) canonical pathway genes including Smoothened (Smo) and Gli1, were regulated by bFGF. Further analysis revealed that activation of the Hh pathway via up-regulation of Smo promoted fibroblast migration, invasion, and skin wound healing, but which significantly reduced by GANT61, a selective antagonist of Gli1/Gli2. Westernmore » blot analyses and siRNA transfection assays demonstrated that Smo acted upstream of phosphoinositide 3-kinase (PI3K)-c-Jun N-terminal kinase (JNK)-β-catenin to promote cell migration. Moreover, RNA-seq and qRT-PCR analyses revealed that Hh pathway genes including Smo and Gli1 were under control of β-catenin, suggesting that β-catenin turn feedback activates Hh signaling. Taken together, our analyses identified a new bFGF-regulating mechanism by which Hh signaling regulates human fibroblast migration, and the data presented here opens a new avenue for the wound healing therapy. - Highlights: • bFGF regulates Hedgehog (Hh) signaling in fibroblasts. • The Smo and Gli two master regulators of Hh signaling positively regulate fibroblast migration. • Smo facilitates β-catenin nuclear translocation via activation PI3K/JNK/GSK3β. • β-catenin positively regulates fibroblast cell migration and the expression of Hh signaling genes including Smo and Gli.« less

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.

PubMed

Shimizu, Tokurou; Kitajima, Akira; Nonaka, Keisuke; Yoshioka, Terutaka; Ohta, Satoshi; Goto, Shingo; Toyoda, Atsushi; Fujiyama, Asao; Mochizuki, Takako; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2016-01-01

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

PubMed Central

Kitajima, Akira; Nonaka, Keisuke; Yoshioka, Terutaka; Ohta, Satoshi; Goto, Shingo; Toyoda, Atsushi; Fujiyama, Asao; Mochizuki, Takako; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2016-01-01

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies. PMID:27902727

Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors.

PubMed

Cau, Andrea

2017-01-01

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus , Equinoxiodus, Lavocatodus and Neoceratodus , but reject those to Ceratodus and Ferganoceratodus . The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Higher failure rate and stem migration of an uncemented femoral component in patients with femoral head osteonecrosis than in patients with osteoarthrosis.

PubMed

Radl, Roman; Hungerford, Marc; Materna, Wilfried; Rehak, Peter; Windhager, Reinhard

2005-02-01

Several authors have found poorer outcome after hip replacement for osteonecrosis than after hip replacement for arthrosis. In a retrospective study we evaluated the performance of an uncemented femoral component in patients with osteonecrosis and arthrosis of the hip. 31 patients operated for osteonecrosis, and 49 patients operated for osteoarthrosis were included. The median follow-up time was 6.1 (2-11) years for the patients with osteonecrosis, and 5.9 (4-8) for the arthrosis patients. Migration analysis performed by the Einzel-Bild-Roentgen Analysis (EBRA) technique revealed a median stem migration of 1.5 (-8.8-0) mm in the patients with osteonecrosis, but only 0.6 (-2.8-0.7) mm in the patients with arthrosis (p < 0.001). Survivorship analysis with stem revision as endpoint for failure was 74% (95% CI: 55-94) in the osteonecrosis, and 98% (95% CI: 94-100) in the arthrosis group (p = 0.01). We suggest that the higher failure rate and stem migration of uncemented total hip replacement in the patients with osteonecrosis is a consequence of the disease. On the basis of these findings, we recommend close monitoring of the patients with osteonecrosis, which should include migration measurements.

Evolutionary history of continental southeast Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data.

PubMed

Jinam, Timothy A; Hong, Lih-Chun; Phipps, Maude E; Stoneking, Mark; Ameen, Mahmood; Edo, Juli; Saitou, Naruya

2012-11-01

The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two major migrations: the ancient "Out of Africa" migration ∼50,000 years before present (YBP) and the relatively recent "Out of Taiwan" expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated from the ancient migration, whereas the majority of island Southeast Asians are associated with the Austronesian expansion. We determined 86 mitochondrial DNA (mtDNA) complete genome sequences in four indigenous Malaysian populations, together with a reanalysis of published autosomal single-nucleotide polymorphism (SNP) data of Southeast Asians to test the plausibility and impact of those migration models. The three Austronesian groups (Bidayuh, Selatar, and Temuan) showed high frequencies of mtDNA haplogroups, which originated from the Asian mainland ∼30,000-10,000 YBP, but low frequencies of "Out of Taiwan" markers. Principal component analysis and phylogenetic analysis using autosomal SNP data indicate a dichotomy between continental and island Austronesian groups. We argue that both the mtDNA and autosomal data suggest an "Early Train" migration originating from Indochina or South China around the late-Pleistocene to early-Holocene period, which predates, but may not necessarily exclude, the Austronesian expansion.

A New Modified Histogram Matching Normalization for Time Series Microarray Analysis.

PubMed

Astola, Laura; Molenaar, Jaap

2014-07-01

Microarray data is often utilized in inferring regulatory networks. Quantile normalization (QN) is a popular method to reduce array-to-array variation. We show that in the context of time series measurements QN may not be the best choice for this task, especially not if the inference is based on continuous time ODE model. We propose an alternative normalization method that is better suited for network inference from time series data.

Gender and climate change-induced migration: proposing a framework for analysis

NASA Astrophysics Data System (ADS)

Chindarkar, Namrata

2012-06-01

This paper proposes frameworks to analyze the gender dimensions of climate change-induced migration. The experiences, needs and priorities of climate migrants will vary by gender and these differences need to be accounted for if policies are to be inclusive. Among the vulnerable groups, women are likely to be disproportionately affected due to climate change because on average women tend to be poorer, less educated, have a lower health status and have limited direct access to or ownership of natural resources. Both the process (actual movement) and the outcomes (rural-rural or rural-urban migration, out-migration mainly of men) of climate change-induced migration are also likely to be highly gendered.

Disruption, not displacement: Environmental variability and temporary migration in Bangladesh

PubMed Central

Gray, Clark; Yunus, Mohammad; Emch, Michael

2018-01-01

Mass migration is one of the most concerning potential outcomes of global climate change. Recent research into environmentally induced migration suggests that relationship is much more complicated than originally posited by the ‘environmental refugee’ hypothesis. Climate change is likely to increase migration in some cases and reduce it in others, and these movements will more often be temporary and short term than permanent and long term. However, few large-sample studies have examined the evolution of temporary migration under changing environmental conditions. To address this gap, we measure the extent to which temperature, precipitation, and flooding can predict temporary migration in Matlab, Bangladesh. Our analysis incorporates high-frequency demographic surveillance data, a discrete time event history approach, and a range of sociodemographic and contextual controls. This approach reveals that migration declines immediately after flooding but quickly returns to normal. In contrast, optimal precipitation and high temperatures have sustained positive effects on temporary migration that persist over one to two year periods. Building on previous studies of long-term migration, these results challenge the common assumption that flooding, precipitation extremes and high temperatures will consistently increase temporary migration. Instead, our results are consistent with a livelihoods interpretation of environmental migration in which households draw on a range of strategies to cope with environmental variability. PMID:29375196

Disruption, not displacement: Environmental variability and temporary migration in Bangladesh.

PubMed

Call, Maia A; Gray, Clark; Yunus, Mohammad; Emch, Michael

2017-09-01

Mass migration is one of the most concerning potential outcomes of global climate change. Recent research into environmentally induced migration suggests that relationship is much more complicated than originally posited by the 'environmental refugee' hypothesis. Climate change is likely to increase migration in some cases and reduce it in others, and these movements will more often be temporary and short term than permanent and long term. However, few large-sample studies have examined the evolution of temporary migration under changing environmental conditions. To address this gap, we measure the extent to which temperature, precipitation, and flooding can predict temporary migration in Matlab, Bangladesh. Our analysis incorporates high-frequency demographic surveillance data, a discrete time event history approach, and a range of sociodemographic and contextual controls. This approach reveals that migration declines immediately after flooding but quickly returns to normal. In contrast, optimal precipitation and high temperatures have sustained positive effects on temporary migration that persist over one to two year periods. Building on previous studies of long-term migration, these results challenge the common assumption that flooding, precipitation extremes and high temperatures will consistently increase temporary migration. Instead, our results are consistent with a livelihoods interpretation of environmental migration in which households draw on a range of strategies to cope with environmental variability.

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

PubMed

Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

2017-10-01

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Phytogeographical implication of Bridelia Will. (Phyllanthaceae) fossil leaf from the late Oligocene of India.

PubMed

Srivastava, Gaurav; Mehrotra, R C

2014-01-01

The family Phyllanthaceae has a predominantly pantropical distribution. Of its several genera, Bridelia Willd. is of a special interest because it has disjunct equally distributed species in Africa and tropical Asia i.e. 18-20 species in Africa-Madagascar (all endemic) and 18 species in tropical Asia (some shared with Australia). On the basis of molecular phylogenetic study on Bridelia, it has been suggested that the genus evolved in Southeast Asia around 33±5 Ma, while speciation and migration to other parts of the world occurred at 10±2 Ma. Fossil records of Bridelia are equally important to support the molecular phylogenetic studies and plate tectonic models. We describe a new fossil leaf of Bridelia from the late Oligocene (Chattian, 28.4-23 Ma) sediments of Assam, India. The detailed venation pattern of the fossil suggests its affinities with the extant B. ovata, B. retusa and B. stipularis. Based on the present fossil evidence and the known fossil records of Bridelia from the Tertiary sediments of Nepal and India, we infer that the genus evolved in India during the late Oligocene (Chattian, 28.4-23 Ma) and speciation occurred during the Miocene. The stem lineage of the genus migrated to Africa via "Iranian route" and again speciosed in Africa-Madagascar during the late Neogene resulting in the emergence of African endemic clades. Similarly, the genus also migrated to Southeast Asia via Myanmar after the complete suturing of Indian and Eurasian plates. The emergence and speciation of the genus in Asia and Africa is the result of climate change during the Cenozoic. On the basis of present and known fossil records of Bridelia, we have concluded that the genus evolved during the late Oligocene in northeast India. During the Neogene, the genus diversified and migrated to Southeast Asia via Myanmar and Africa via "Iranian Route".

Migration of Lebanese nurses: a questionnaire survey and secondary data analysis.

PubMed

El-Jardali, Fadi; Dumit, Nuhad; Jamal, Diana; Mouro, Gladys

2008-10-01

Nursing is becoming a mobile profession. Nurse migration is multifactorial and not limited to financial incentives. Non-economic factors that might lead to migration include poor recruitment and retention strategies, poor job satisfaction and working conditions, socio-political and economic stability, and the poor social image of the nursing profession. Lebanon is facing a problem of excessive nurse migration to countries of the Gulf, North America and Europe. No study has been conducted to understand the determinants and magnitude of the problem. The objective of this study is to provide an evidence base for understanding the incidence of nurse migration out of Lebanon, its magnitude and reasons. A cross-sectional research design comprising both quantitative and qualitative methods was employed to achieve the stated objectives. This includes a survey of nursing schools in Lebanon, survey of nurse recruitment agencies, secondary data analysis and survey of migrant nurses. An estimated one in five nurses that receive a bachelors of science in nursing migrates out of Lebanon within 1 or 2 years of graduation. The majority of nurses migrate to countries of the Gulf. The main reasons for migration included: shift work, high patient/nurse ratios, lack of autonomy in decision-making, lack of a supportive environment, and poor commitment to excellent nursing care. Further, nurses reported that combinations of financial and non-financial incentives can encourage them to return to practice in Lebanon. The most recurring incentives (pull factors) to encourage nurses to return to practice in Lebanon included educational support, managerial support, better working conditions, utilization of best nursing practices and autonomy. Nurse migration and retention have become major health workforce issues confronting many health systems in the East Mediterranean Region. Our study demonstrated that nurse migration is a product of poor management and lack of effective retention strategies and sufficient knowledge about the context, needs and challenges facing nurses. Nurse migration in Lebanon underscores the importance of developing a monitoring system that would identify implications and help implement innovative retention strategies. Nurse migration out of Lebanon is likely to persist and even increase if underlying factors are not properly resolved.

A molecular phylogeny of Dichocarpum (Ranunculaceae): Implications for eastern Asian biogeography.

PubMed

Xiang, Kun-Li; Zhao, Liang; Erst, Andrey S; Yu, Sheng-Xiang; Jabbour, Florian; Wang, Wei

2017-02-01

East Asia is characterized by high levels of species diversity and endemism. However, the biogeographical patterns and processes underlying the distribution of biodiversity within the area are still poorly known. In this study, we used plastid (matK, trnL-F, and trnH-psbA) and nuclear (ITS) DNA sequences to investigate the historical biogeography of Dichocarpum (Ranunculaceae), an eastern Asian endemic genus throughout warm-temperate and subtropical forests of the area. Phylogenetic analyses strongly support Dichocarpum as monophyletic, which contains two major clades. Clade I corresponds to section Hutchinsonia, and clade II includes sections Dichocarpum and Fargesia. Section Dichocarpum and its subsections Dalzielia and Dichocarpum are not recognized as monophyletic. Our results suggest that the most recent common ancestor of Dichocarpum occurred in central China and Japan in the earliest Early Miocene, and thus support an ancient vicariance event between Japan and China. Within mainland China, three migrations at the species level were hypothesized to explain the expansion of Dichocarpum from central China to southeastern Yunnan, Hengduan mountains, and eastern Himalaya. These migration events occurred in the Late Miocene to Early Pliocene, which may be associated with the uplift of the southeastern Qinghai-Tibetan Plateau and accordingly the expansion of subtropical forests in China around that period. A migration or dispersal from central China to Taiwan was inferred in the Early Pleistocene, which supports the close floristic affinity between Taiwan and mainland China. This study contributes to our knowledge on the historical biogeography of plants in eastern Asia. Copyright © 2016 Elsevier Inc. All rights reserved.

Migratory bats respond to artificial green light with positive phototaxis.

PubMed

Voigt, Christian C; Roeleke, Manuel; Marggraf, Lara; Pētersons, Gunārs; Voigt-Heucke, Silke L

2017-01-01

Artificial light at night is spreading worldwide at unprecedented rates, exposing strictly nocturnal animals such as bats to a novel anthropogenic stressor. Previous studies about the effect of artificial light on bats focused almost exclusively on non-migratory species, yet migratory animals such as birds are known to be largely affected by light pollution. Thus, we conducted a field experiment to evaluate if bat migration is affected by artificial light at night. In late summer, we presented artificial green light of 520 nm wavelength to bats that were migrating south along the shoreline of the Baltic Sea. Using a light on-off treatment, we observed that the activity of Pipistrellus nathusii and P. pygmaeus, the two most abundant migratory species at our site, increased by more than 50% in the light-on compared to the light-off treatment. We observed an increased number of feeding buzzes during the light-on compared to the light-off treatment for P. nathusii. However, feeding activity was low in general and did not increase disproportionately during the light-on treatment in relation to the overall echolocation call activity of bats. Further, P. nathusii were attracted towards the green light at a distance of about 23 m, which is way beyond the echolocation detection range for insects of Nathusius' bats. We therefore infer that migratory bats were not attracted to artificial green light because of high insect densities, but instead by positive phototaxis. We conclude that artificial light at night may potentially impact bat migration in a yet unrecognized way.

A Modular Artificial Intelligence Inference Engine System (MAIS) for support of on orbit experiments

NASA Technical Reports Server (NTRS)

Hancock, Thomas M., III

1994-01-01

This paper describes a Modular Artificial Intelligence Inference Engine System (MAIS) support tool that would provide health and status monitoring, cognitive replanning, analysis and support of on-orbit Space Station, Spacelab experiments and systems.

Investigating Electrostatic Precipitator Design Parameters for Efficient Control of Particulate Matter in Thermal Power Plant: A Case Study

NASA Astrophysics Data System (ADS)

Rai, P.; Gautam, N.; Chandra, H.

2018-06-01

This work deals with the analysis and modification of operational parameters for meeting the emission standards, set by Central Pollution Control Board (CPCB)/State Pollution Control Board (SPCB) from time to time of electrostatic precipitator (ESP). The analysis is carried out by using standard chemical analysis supplemented by the relevant data collected from Korba East Phase (Ph)-III thermal power plant, under Chhattisgarh State Electricity Board (CSEB) operating at Korba, Chhattisgarh. Chemical analysis is used to predict the emission level for different parameters of ESP. The results reveal that for a constant outlet PM concentration and fly ash percentage, the total collection area decreases with the increase in migration velocity. For constant migration velocity and outlet PM concentration, the total collection area increases with the increase in the fly ash percent. For constant migration velocity and outlet e PM concentration, the total collection area increases with the ash content in the coal. i.e. from minimum ash to maximum ash. As far as the efficiency is concerned, it increases with the fly ash percent, ash content and the inlet dust concentration but decreases with the outlet PM concentration at constant migration velocity, fly ash and ash content.

Investigating Electrostatic Precipitator Design Parameters for Efficient Control of Particulate Matter in Thermal Power Plant: A Case Study

NASA Astrophysics Data System (ADS)

Rai, P.; Gautam, N.; Chandra, H.

2018-02-01

This work deals with the analysis and modification of operational parameters for meeting the emission standards, set by Central Pollution Control Board (CPCB)/State Pollution Control Board (SPCB) from time to time of electrostatic precipitator (ESP). The analysis is carried out by using standard chemical analysis supplemented by the relevant data collected from Korba East Phase (Ph)-III thermal power plant, under Chhattisgarh State Electricity Board (CSEB) operating at Korba, Chhattisgarh. Chemical analysis is used to predict the emission level for different parameters of ESP. The results reveal that for a constant outlet PM concentration and fly ash percentage, the total collection area decreases with the increase in migration velocity. For constant migration velocity and outlet PM concentration, the total collection area increases with the increase in the fly ash percent. For constant migration velocity and outlet e PM concentration, the total collection area increases with the ash content in the coal. i.e. from minimum ash to maximum ash. As far as the efficiency is concerned, it increases with the fly ash percent, ash content and the inlet dust concentration but decreases with the outlet PM concentration at constant migration velocity, fly ash and ash content.

Java Source Code Analysis for API Migration to Embedded Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winter, Victor; McCoy, James A.; Guerrero, Jonathan

Embedded systems form an integral part of our technological infrastructure and oftentimes play a complex and critical role within larger systems. From the perspective of reliability, security, and safety, strong arguments can be made favoring the use of Java over C in such systems. In part, this argument is based on the assumption that suitable subsets of Java’s APIs and extension libraries are available to embedded software developers. In practice, a number of Java-based embedded processors do not support the full features of the JVM. For such processors, source code migration is a mechanism by which key abstractions offered bymore » APIs and extension libraries can made available to embedded software developers. The analysis required for Java source code-level library migration is based on the ability to correctly resolve element references to their corresponding element declarations. A key challenge in this setting is how to perform analysis for incomplete source-code bases (e.g., subsets of libraries) from which types and packages have been omitted. This article formalizes an approach that can be used to extend code bases targeted for migration in such a manner that the threats associated the analysis of incomplete code bases are eliminated.« less

Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays.

PubMed

Kim, Sung-Cheol; Wunsch, Benjamin H; Hu, Huan; Smith, Joshua T; Austin, Robert H; Stolovitzky, Gustavo

2017-06-27

Deterministic lateral displacement (DLD) is a technique for size fractionation of particles in continuous flow that has shown great potential for biological applications. Several theoretical models have been proposed, but experimental evidence has demonstrated that a rich class of intermediate migration behavior exists, which is not predicted. We present a unified theoretical framework to infer the path of particles in the whole array on the basis of trajectories in a unit cell. This framework explains many of the unexpected particle trajectories reported and can be used to design arrays for even nanoscale particle fractionation. We performed experiments that verify these predictions and used our model to develop a condenser array that achieves full particle separation with a single fluidic input.