Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

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

Lorenzi, Tommaso; Chisholm, Rebecca H.; Lorz, Alexander

We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

Genetic population structure in the yellow mongoose, Cynictis penicillata.

PubMed

Van Vuuren, B J; Robinson, T J

1997-12-01

Phylogeographic structure was determined for the yellow mongoose, Cynictis penicillata, using mtDNA RFLPs and control region sequences. The RFLP analysis revealed 13 haplotypes which showed weak geographical patterning consistent with a recent range expansion from a refugial population(s). An analysis of molecular variance (AMOVA) revealed no correspondence between mtDNA phylogeography and subspecies delimitation, nor between matrilines and areas characterized by a high incidence of the viverrid-type rabies, of which the yellow mongoose is the principal vector. The lack of structure was also shown by control region sequences although four of the maternal lineages shared a near-perfect 81 bp repeat. We speculate that regional hot spots of the viverrid rabies biotype reflect population density differences in the yellow mongoose that are not underscored by genetic partitioning, at least at the level of resolution provided by our analyses.

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

USGS Publications Warehouse

Kanno, Yoichiro; Vokoun, Jason C.; Letcher, Benjamin H.

2011-01-01

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5–2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by ‘riverscape’ variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-01-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-06-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

PubMed Central

Cherifi, Youcef Amine; Gaouar, Suheil Bechir Semir; Guastamacchia, Rosangela; El-Bahrawy, Khalid Ahmed; Abushady, Asmaa Mohammed Aly; Sharaf, Abdoallah Aboelnasr; Harek, Derradji; Lacalandra, Giovanni Michele; Saïdi-Mehtar, Nadhira

2017-01-01

Knowledge on genetic diversity and structure of camel populations is fundamental for sustainable herd management and breeding program implementation in this species. Here we characterized a total of 331 camels from Northern Africa, representative of six populations and thirteen Algerian and Egyptian geographic regions, using 20 STR markers. The nineteen polymorphic loci displayed an average of 9.79 ± 5.31 alleles, ranging from 2 (CVRL8) to 24 (CVRL1D). Average He was 0.647 ± 0.173. Eleven loci deviated significantly from Hardy-Weinberg proportions (P<0.05), due to excess of homozygous genotypes in all cases except one (CMS18). Distribution of genetic diversity along a weak geographic gradient as suggested by network analysis was not supported by either unsupervised and supervised Bayesian clustering. Traditional extensive/nomadic herding practices, together with the historical use as a long-range beast of burden and its peculiar evolutionary history, with domestication likely occurring from a bottlenecked and geographically confined wild progenitor, may explain the observed genetic patterns. PMID:28103238

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

USGS Publications Warehouse

Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

2007-01-01

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

How Often Do They Have Sex? A Comparative Analysis of the Population Structure of Seven Eukaryotic Microbial Pathogens

PubMed Central

Tomasini, Nicolás; Lauthier, Juan José; Ayala, Francisco José; Tibayrenc, Michel; Diosque, Patricio

2014-01-01

The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered. PMID:25054834

The structured ancestral selection graph and the many-demes limit.

PubMed

Slade, Paul F; Wakeley, John

2005-02-01

We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

Weak ergodicity of population evolution processes.

PubMed

Inaba, H

1989-10-01

The weak ergodic theorems of mathematical demography state that the age distribution of a closed population is asymptotically independent of the initial distribution. In this paper, we provide a new proof of the weak ergodic theorem of the multistate population model with continuous time. The main tool to attain this purpose is a theory of multiplicative processes, which was mainly developed by Garrett Birkhoff, who showed that ergodic properties generally hold for an appropriate class of multiplicative processes. First, we construct a general theory of multiplicative processes on a Banach lattice. Next, we formulate a dynamical model of a multistate population and show that its evolution operator forms a multiplicative process on the state space of the population. Subsequently, we investigate a sufficient condition that guarantees the weak ergodicity of the multiplicative process. Finally, we prove the weak and strong ergodic theorems for the multistate population and resolve the consistency problem.

Weak-interaction rates in stellar conditions

NASA Astrophysics Data System (ADS)

Sarriguren, Pedro

2018-05-01

Weak-interaction rates, including β-decay and electron captures, are studied in several mass regions at various densities and temperatures of astrophysical interest. In particular, we study odd-A nuclei in the pf-shell region, which are involved in presupernova formations. Weak rates are relevant to understand the late stages of the stellar evolution, as well as the nucleosynthesis of heavy nuclei. The nuclear structure involved in the weak processes is studied within a quasiparticle proton-neutron random-phase approximation with residual interactions in both particle-hole and particle-particle channels on top of a deformed Skyrme Hartree-Fock mean field with pairing correlations. First, the energy distributions of the Gamow-Teller strength are discussed and compared with the available experimental information, measured under terrestrial conditions from charge-exchange reactions. Then, the sensitivity of the weak-interaction rates to both astrophysical densities and temperatures is studied. Special attention is paid to the relative contribution to these rates of thermally populated excited states in the decaying nucleus and to the electron captures from the degenerate electron plasma.

Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities.

PubMed

Zhang, Lai; Andersen, Ken H; Dieckmann, Ulf; Brännström, Åke

2015-09-07

We investigate how four types of interference competition - which alternatively affect foraging, metabolism, survival, and reproduction - impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population׳s reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogeographic pattern suggests a general northeastward dispersal in the distribution of Machilus pauhoi in South China

PubMed Central

Zhu, Qin; Liao, Bo-Yong; Li, Pei; Li, Jun-Cheng; Deng, Xiao-Mei; Chen, Xiao-Yang

2017-01-01

Machilus pauhoi Kanehira is an important timber species in China. A provenance trial was recently set up to evaluate the growth performance of trees from different localities, with the aim of designing seed transfer guidelines. Here, we tested twelve nuclear microsatellite markers derived from other species of the Lauraceae family and investigated population genetic structure in M. pauhoi. Both the number of observed alleles per locus (Na) and the polymorphic information content (PIC) significantly decreased against the latitude, but showed an insignificant decrease against the longitude. Heterozygosity (Ho) and gene diversity (h) exhibited a weak correlation with geographic location. Private alleles were present in multiple populations, and a moderate level of population genetic differentiation was detected (Gst = 0.1691). The joint pattern of genetic diversity (Na, PIC, Ho, and h) suggests that general northeastward dispersal led to the current distribution of M. pauhoi. Significant but weak effects of isolation-by-distance (IBD) occurred, implicating the mountain ranges as the major barrier to gene flow. Both STRUCTURE and hierarchical clustering analyses showed three distinct groups of populations related to the physical connectivity among mountain ranges. A priority in designing genetic conservation should be given to the populations at the southwest side of the species’ distribution. This conservation strategy can also be combined with the pattern of adaptive genetic variation from the provenance trial for comprehensive genetic resource management of native M. pauhoi. PMID:28886133

Weak genetic divergence suggests extensive gene flow at the northeastern range limit of a dioecious Ficus species

NASA Astrophysics Data System (ADS)

Wang, Rong; Yang, Chang-Hong; Ding, Yuan-Yuan; Tong, Xin; Chen, Xiao-Yong

2018-07-01

Genus Ficus (Moraceae) plays a critical role in the sustainability and biodiversity in tropical and subtropical ecosystems. Ficus species and their host specific pollinating fig wasps (Agaonidae) represent a classic example of obligate mutualism. The genetic consequence of range expansion and range shift is still under investigation, but extensive gene flow and subsequently low level of genetic divergence may be expected to occur among the populations at the poleward range limit of some Ficus species due to long distance gene flow in the genus. In the present study, we focused on populations of F. sarmentosa var. henryi at its northeastern range limit in southeast China to test whether edge populations were genetically fragile. Consistent with our hypothesis, high level of genetic diversity and weak genetic structure were revealed in Ficus sarmentosa var. henryi populations, suggesting extensive gene flow at the plant's range limit. Long-distance movements of both pollinators and frugivorous birds were likely to be frequent and thereby predominantly contributed to the extensive gene flow at large scale despite of some magnificent landscape elements like huge mountains.

Games of multicellularity.

PubMed

Kaveh, Kamran; Veller, Carl; Nowak, Martin A

2016-08-21

Evolutionary game dynamics are often studied in the context of different population structures. Here we propose a new population structure that is inspired by simple multicellular life forms. In our model, cells reproduce but can stay together after reproduction. They reach complexes of a certain size, n, before producing single cells again. The cells within a complex derive payoff from an evolutionary game by interacting with each other. The reproductive rate of cells is proportional to their payoff. We consider all two-strategy games. We study deterministic evolutionary dynamics with mutations, and derive exact conditions for selection to favor one strategy over another. Our main result has the same symmetry as the well-known sigma condition, which has been proven for stochastic game dynamics and weak selection. For a maximum complex size of n=2 our result holds for any intensity of selection. For n≥3 it holds for weak selection. As specific examples we study the prisoner's dilemma and hawk-dove games. Our model advances theoretical work on multicellularity by allowing for frequency-dependent interactions within groups. Copyright © 2016 Elsevier Ltd. All rights reserved.

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

2008-01-01

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin

PubMed Central

Williams, Samuel M.; Otway, Nicholas M.; Nielsen, Einar E.; Maher, Safia L.; Bennett, Mike B.; Ovenden, Jennifer R.

2017-01-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier. PMID:28791159

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin.

PubMed

Holmes, Bonnie J; Williams, Samuel M; Otway, Nicholas M; Nielsen, Einar E; Maher, Safia L; Bennett, Mike B; Ovenden, Jennifer R

2017-07-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST  > 0.14, p  < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

PubMed

Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

2016-12-14

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean F ST  = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

PubMed Central

Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M.; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

2016-01-01

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds. PMID:27966592

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency

PubMed Central

Perrier, Charles; Guyomard, René; Bagliniere, Jean-Luc; Nikolic, Natacha; Evanno, Guillaume

2013-01-01

While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals. PMID:23919174

Microsatellites indicate minimal barriers to mule deer Odocoileus hemionus dispersal across Montana, USA

USGS Publications Warehouse

Powell, John H.; Kalinowski, Steven T.; Higgs, Megan D.; Ebinger, Michael R.; Vu, Ninh V.; Cross, Paul C.

2013-01-01

To better understand the future spread of chronic wasting disease, we conducted a genetic assessment of mule deer Odocoileus hemionus population structure across the state of Montana, USA. Individual based analyses were used to test for population structure in the absence of a priori designations of population membership across the sampling area. Samples from the states of Wyoming, Colorado and Utah were also included in the analysis to provide a geographic context to the levels of population structure observed within Montana. Results showed that mule deer across our entire study region were characterized by weak isolation by distance and a lack of spatial autocorrelation at distances > 10 km. We found evidence for contemporary male bias in dispersal, with female mule deer exhibiting higher mean individual pairwise genetic distance than males. We tested for potential homogenizing effects of past translocations within Montana, but were unable to detect a genetic signature of these events. Our results indicate high levels of connectivity among mule deer populations in Montana and suggest few, if any, detectable barriers to mule deer gene flow or chronic wasting disease transmission.

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications

PubMed Central

2014-01-01

Background Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Results Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). Conclusions According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area. PMID:24929425

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications.

PubMed

Aketarawong, Nidchaya; Isasawin, Siriwan; Thanaphum, Sujinda

2014-06-14

Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area.

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

PubMed

Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

2014-01-01

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan.

PubMed

Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

2015-01-01

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

AzTEC Millimetre Survey of the COSMOS field - II. Source count overdensity and correlations with large-scale structure

NASA Astrophysics Data System (ADS)

Austermann, J. E.; Aretxaga, I.; Hughes, D. H.; Kang, Y.; Kim, S.; Lowenthal, J. D.; Perera, T. A.; Sanders, D. B.; Scott, K. S.; Scoville, N.; Wilson, G. W.; Yun, M. S.

2009-03-01

We report an overdensity of bright submillimetre galaxies (SMGs) in the 0.15 deg2 AzTEC/COSMOS survey and a spatial correlation between the SMGs and the optical-IR galaxy density at z <~ 1.1. This portion of the COSMOS field shows a ~3σ overdensity of robust SMG detections when compared to a background, or `blank-field', population model that is consistent with SMG surveys of fields with no extragalactic bias. The SMG overdensity is most significant in the number of very bright detections (14 sources with measured fluxes S1.1mm > 6 mJy), which is entirely incompatible with sample variance within our adopted blank-field number densities and infers an overdensity significance of >> 4σ. We find that the overdensity and spatial correlation to optical-IR galaxy density are most consistent with lensing of a background SMG population by foreground mass structures along the line of sight, rather than physical association of the SMGs with the z <~ 1.1 galaxies/clusters. The SMG positions are only weakly correlated with weak-lensing maps, suggesting that the dominant sources of correlation are individual galaxies and the more tenuous structures in the survey region, and not the massive and compact clusters. These results highlight the important roles cosmic variance and large-scale structure can play in the study of SMGs.

The scaling of weak field phase-only control in Markovian dynamics

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

Am-Shallem, Morag; Kosloff, Ronnie

We consider population transfer in open quantum systems, which are described by quantum dynamical semigroups (QDS). Using second order perturbation theory of the Lindblad equation, we show that it depends on a weak external field only through the field's autocorrelation function, which is phase independent. Therefore, for leading order in perturbation, QDS cannot support dependence of the population transfer on the phase properties of weak fields. We examine an example of weak-field phase-dependent population transfer, and show that the phase-dependence comes from the next order in the perturbation.

Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers

PubMed Central

Qin, Yu-Jia; Buahom, Nopparat; Krosch, Matthew N.; Du, Yu; Wu, Yi; Malacrida, Anna R.; Deng, Yu-Liang; Liu, Jia-Qi; Jiang, Xiao-Long; Li, Zhi-Hong

2016-01-01

Bactrocera correcta is one of the most destructive pests of horticultural crops in tropical and subtropical regions. Despite the economic risk, the population genetics of this pest have remained relatively unexplored. This study explores population genetic structure and contemporary gene flow in B. correcta in Chinese Yunnan Province and attempts to place observed patterns within the broader geographical context of the species’ total range. Based on combined data from mtDNA cox1 sequences and 12 microsatellite loci obtained from 793 individuals located in 7 countries, overall genetic structuring was low. The expansion history of this species, including likely human-mediated dispersal, may have played a role in shaping the observed weak structure. The study suggested a close relationship between Yunnan Province and adjacent countries, with evidence for Western and/or Southern Yunnan as the invasive origin of B. correcta within Yunnan Province. The information gleaned from this analysis of gene flow and population structure has broad implications for quarantine, trade and management of this pest, especially in China where it is expanding northward. Future studies should concentrate effort on sampling South Asian populations, which would enable better inferences of the ancestral location of B. correcta and its invasion history into and throughout Asia. PMID:27929126

Fine-scale spatial genetic structure of common and declining bumble bees across an agricultural landscape.

PubMed

Dreier, Stephanie; Redhead, John W; Warren, Ian A; Bourke, Andrew F G; Heard, Matthew S; Jordan, William C; Sumner, Seirian; Wang, Jinliang; Carvell, Claire

2014-07-01

Land-use changes have threatened populations of many insect pollinators, including bumble bees. Patterns of dispersal and gene flow are key determinants of species' ability to respond to land-use change, but have been little investigated at a fine scale (<10 km) in bumble bees. Using microsatellite markers, we determined the fine-scale spatial genetic structure of populations of four common Bombus species (B. terrestris, B. lapidarius, B. pascuorum and B. hortorum) and one declining species (B. ruderatus) in an agricultural landscape in Southern England, UK. The study landscape contained sown flower patches representing agri-environment options for pollinators. We found that, as expected, the B. ruderatus population was characterized by relatively low heterozygosity, number of alleles and colony density. Across all species, inbreeding was absent or present but weak (FIS  = 0.01-0.02). Using queen genotypes reconstructed from worker sibships and colony locations estimated from the positions of workers within these sibships, we found that significant isolation by distance was absent in B. lapidarius, B. hortorum and B. ruderatus. In B. terrestris and B. pascuorum, it was present but weak; for example, in these two species, expected relatedness of queens founding colonies 1 m apart was 0.02. These results show that bumble bee populations exhibit low levels of spatial genetic structure at fine spatial scales, most likely because of ongoing gene flow via widespread queen dispersal. In addition, the results demonstrate the potential for agri-environment scheme conservation measures to facilitate fine-scale gene flow by creating a more even distribution of suitable habitats across landscapes. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Seven challenges for metapopulation models of epidemics, including households models.

PubMed

Ball, Frank; Britton, Tom; House, Thomas; Isham, Valerie; Mollison, Denis; Pellis, Lorenzo; Scalia Tomba, Gianpaolo

2015-03-01

This paper considers metapopulation models in the general sense, i.e. where the population is partitioned into sub-populations (groups, patches,...), irrespective of the biological interpretation they have, e.g. spatially segregated large sub-populations, small households or hosts themselves modelled as populations of pathogens. This framework has traditionally provided an attractive approach to incorporating more realistic contact structure into epidemic models, since it often preserves analytic tractability (in stochastic as well as deterministic models) but also captures the most salient structural inhomogeneity in contact patterns in many applied contexts. Despite the progress that has been made in both the theory and application of such metapopulation models, we present here several major challenges that remain for future work, focusing on models that, in contrast to agent-based ones, are amenable to mathematical analysis. The challenges range from clarifying the usefulness of systems of weakly-coupled large sub-populations in modelling the spread of specific diseases to developing a theory for endemic models with household structure. They include also developing inferential methods for data on the emerging phase of epidemics, extending metapopulation models to more complex forms of human social structure, developing metapopulation models to reflect spatial population structure, developing computationally efficient methods for calculating key epidemiological model quantities, and integrating within- and between-host dynamics in models. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

PubMed

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

Hierarchical Genetic Analysis of German Cockroach (Blattella germanica) Populations from within Buildings to across Continents

PubMed Central

Vargo, Edward L.; Crissman, Jonathan R.; Booth, Warren; Santangelo, Richard G.; Mukha, Dmitry V.; Schal, Coby

2014-01-01

Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

PubMed

Yoon, M; Park, W; Nam, Y K; Kim, D S

2012-02-01

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters

PubMed Central

Yoon, M.; Park, W.; Nam, Y. K.; Kim, D. S.

2012-01-01

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05), and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species. PMID:25049547

Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae).

PubMed

Hou, Yan; Lou, Anru

2011-01-01

Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.

Population Genetic Diversity and Structure of a Naturally Isolated Plant Species, Rhodiola dumulosa (Crassulaceae)

PubMed Central

Hou, Yan; Lou, Anru

2011-01-01

Aims Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Methods Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. Important Findings The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations. PMID:21909437

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

NASA Astrophysics Data System (ADS)

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-01

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Counterfactual statements and weak measurements: an experimental proposal

NASA Astrophysics Data System (ADS)

Mølmer, Klaus

2001-12-01

A recent analysis suggests that weak measurements can be used to give observational meaning to counterfactual reasoning in quantum physics. A weak measurement is predicted to assign a negative unit population to a specific state in an interferometric Gedankenexperiment proposed by Hardy. We propose an experimental implementation with trapped ions of the Gedankenexperiment and of the weak measurement. In our standard quantum mechanical analysis of the proposal no states have negative population, but we identify the registration of a negative population by particles being displaced on average in the direction opposite to a force acting upon them.

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.

PubMed

Hoffman, J I; Kowalski, G J; Klimova, A; Eberhart-Phillips, L J; Staniland, I J; Baylis, A M M

2016-07-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

PubMed Central

Hoffman, J. I.; Kowalski, G. J.; Klimova, A.; Staniland, I. J.; Baylis, A. M. M.

2016-01-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations. PMID:27493782

Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality

PubMed Central

Poortvliet, Marloes; Longo, Gary C; Selkoe, Kimberly; Barber, Paul H; White, Crow; Caselle, Jennifer E; Perez-Matus, Alejandro; Gaines, Steven D; Bernardi, Giacomo

2013-01-01

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation. PMID:24340195

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Self-Fertilization and Genetic Population Structure in a Colonizing Land Snail

PubMed Central

Selander, Robert K.; Kaufman, Donald W.

1973-01-01

The pulmonate land snail Rumina decollata in its native Mediterranean range is a complex of monogenic or weakly polygenic strains generated by a breeding system of facultative self-fertilization. One strain colonized North America and now occupies much of the southern United States and northern Mexico. No genetic variation within or among populations in the United States was detected in an electrophoretic analysis of proteins encoded by 25 loci. These findings emphasize the potential for adaptive convergence in the genetic systems of hermaphroditic animals and plants. PMID:16592078

Self-Organized Lattices of Nonlinear Optochemical Waves in Photopolymerizable Fluids: The Spontaneous Emergence of 3-D Order in a Weakly Correlated System.

PubMed

Ponte, Matthew R; Hudson, Alexander D; Saravanamuttu, Kalaichelvi

2018-03-01

Many of the extraordinary three-dimensional architectures that pattern our physical world emerge from complex nonlinear systems or dynamic populations whose individual constituents are only weakly correlated to each other. Shoals of fish, murmuration behaviors in birds, congestion patterns in traffic, and even networks of social conventions are examples of spontaneous pattern formation, which cannot be predicted from the properties of individual elements alone. Pattern formation at a different scale has been observed or predicted in weakly correlated systems including superconductors, atomic gases near Bose Einstein condensation, and incoherent optical fields. Understanding pattern formation in nonlinear weakly correlated systems, which are often unified through mathematical expression, could pave intelligent self-organizing pathways to functional materials, architectures, and computing technologies. However, it is experimentally difficult to directly visualize the nonlinear dynamics of pattern formation in most populations-especially in three dimensions. Here, we describe the collective behavior of large populations of nonlinear optochemical waves, which are poorly correlated in both space and time. The optochemical waves-microscopic filaments of white light entrapped within polymer channels-originate from the modulation instability of incandescent light traveling in photopolymerizable fluids. By tracing the three-dimensional distribution of optical intensity in the nascent polymerizing system, we find that populations of randomly distributed, optochemical waves synergistically and collectively shift in space to form highly ordered lattices of specific symmetries. These, to our knowledge, are the first three-dimensionally periodic structures to emerge from a system of weakly correlated waves. Their spontaneous formation in an incoherent and effectively chaotic field is counterintuitive, but the apparent contradiction of known behaviors of light including the laws of optical interference can be explained through the soliton-like interactions of optochemical waves with nearest neighbors. Critically, this work casts fundamentally new insight into the collective behaviors of poorly correlated nonlinear waves in higher dimensions and provides a rare, accessible platform for further experimental studies of these previously unexplored behaviors. Furthermore, it defines a self-organization paradigm that, unlike conventional counterparts, could generate polymer microstructures with symmetries spanning all the Bravais lattices.

Aspiration dynamics in structured population acts as if in a well-mixed one.

PubMed

Du, Jinming; Wu, Bin; Wang, Long

2015-01-26

Understanding the evolution of human interactive behaviors is important. Recent experimental results suggest that human cooperation in spatial structured population is not enhanced as predicted in previous works, when payoff-dependent imitation updating rules are used. This constraint opens up an avenue to shed light on how humans update their strategies in real life. Studies via simulations show that, instead of comparison rules, self-evaluation driven updating rules may explain why spatial structure does not alter the evolutionary outcome. Though inspiring, there is a lack of theoretical result to show the existence of such evolutionary updating rule. Here we study the aspiration dynamics, and show that it does not alter the evolutionary outcome in various population structures. Under weak selection, by analytical approximation, we find that the favored strategy in regular graphs is invariant. Further, we show that this is because the criterion under which a strategy is favored is the same as that of a well-mixed population. By simulation, we show that this holds for random networks. Although how humans update their strategies is an open question to be studied, our results provide a theoretical foundation of the updating rules that may capture the real human updating rules.

Genetic structure and demographic history of the endangered and endemic schizothoracine fish Gymnodiptychus pachycheilus in Qinghai-Tibetan Plateau.

PubMed

Su, Junhu; Ji, Weihong; Wei, Yanming; Zhang, Yanping; Gleeson, Dianne M; Lou, Zhongyu; Ren, Jing

2014-08-01

The endangered schizothoracine fish Gymnodiptychus pachycheilus is endemic to the Qinghai-Tibetan Plateau (QTP), but very little genetic information is available for this species. Here, we accessed the current genetic divergence of G. pachycheilus population to evaluate their distributions modulated by contemporary and historical processes. Population structure and demographic history were assessed by analyzing 1811-base pairs of mitochondrial DNA from 61 individuals across a large proportion of its geographic range. Our results revealed low nucleotide diversity, suggesting severe historical bottleneck events. Analyses of molecular variance and the conventional population statistic FST (0.0435, P = 0.0215) confirmed weak genetic structure. The monophyly of G. pachycheilus was statistically well-supported, while two divergent evolutionary clusters were identified by phylogenetic analyses, suggesting a microgeographic population structure. The consistent scenario of recent population expansion of two clusters was identified based on several complementary analyses of demographic history (0.096 Ma and 0.15 Ma). This genetic divergence and evolutionary process are likely to have resulted from a series of drainage arrangements triggered by the historical tectonic events of the region. The results obtained here provide the first insights into the evolutionary history and genetic status of this little-known fish.

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

USGS Publications Warehouse

Patirana, A.; Hatcher, S.A.; Friesen, Vicki L.

2002-01-01

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

Optional games on cycles and complete graphs.

PubMed

Jeong, Hyeong-Chai; Oh, Seung-Yoon; Allen, Benjamin; Nowak, Martin A

2014-09-07

We study stochastic evolution of optional games on simple graphs. There are two strategies, A and B, whose interaction is described by a general payoff matrix. In addition, there are one or several possibilities to opt out from the game by adopting loner strategies. Optional games lead to relaxed social dilemmas. Here we explore the interaction between spatial structure and optional games. We find that increasing the number of loner strategies (or equivalently increasing mutational bias toward loner strategies) facilitates evolution of cooperation both in well-mixed and in structured populations. We derive various limits for weak selection and large population size. For some cases we derive analytic results for strong selection. We also analyze strategy selection numerically for finite selection intensity and discuss combined effects of optionality and spatial structure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Plague circulation and population genetics of the reservoir Rattus rattus: the influence of topographic relief on the distribution of the disease within the Madagascan focus.

PubMed

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.

Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus).

PubMed

Limborg, M T; Hanel, R; Debes, P V; Ring, A K; André, C; Tsigenopoulos, C S; Bekkevold, D

2012-08-01

Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.

The Oriental Fruit Fly, Bactrocera dorsalis, in China: Origin and Gradual Inland Range Expansion Associated with Population Growth

PubMed Central

Wan, Xuanwu; Nardi, Francesco; Zhang, Bin; Liu, Yinghong

2011-01-01

The oriental fruit fly, Bactrocera dorsalis, expanded throughout mainland China in the last century to become one of the most serious pests in the area, yet information on this process are fragmentary. Three mitochondrial genes (nad1, cytb and nad5) were used to infer the genetic diversity, population structure and demographic history of the oriental fruit fly from its entire distribution range in China. High levels of genetic diversity, as well as a significant correspondence between genetic and geographic distances, suggest that the invasion process might have been gradual, with no associated genetic bottlenecks. Three population groups could be identified, nevertheless the overall genetic structure was weak. The effective number of migrants between populations, estimated using the coalescent method, suggested asymmetric gene flow from the costal region of Guangdong to most inland regions. The demographic analysis indicates the oriental fruit fly underwent a recent population expansion in the Central China. We suggest the species originated in the costal region facing the South China Sea and gradually expanded to colonize mainland China, expanding here to high population numbers. PMID:21984907

The oriental fruit fly, Bactrocera dorsalis, in China: origin and gradual inland range expansion associated with population growth.

PubMed

Wan, Xuanwu; Nardi, Francesco; Zhang, Bin; Liu, Yinghong

2011-01-01

The oriental fruit fly, Bactrocera dorsalis, expanded throughout mainland China in the last century to become one of the most serious pests in the area, yet information on this process are fragmentary. Three mitochondrial genes (nad1, cytb and nad5) were used to infer the genetic diversity, population structure and demographic history of the oriental fruit fly from its entire distribution range in China. High levels of genetic diversity, as well as a significant correspondence between genetic and geographic distances, suggest that the invasion process might have been gradual, with no associated genetic bottlenecks. Three population groups could be identified, nevertheless the overall genetic structure was weak. The effective number of migrants between populations, estimated using the coalescent method, suggested asymmetric gene flow from the costal region of Guangdong to most inland regions. The demographic analysis indicates the oriental fruit fly underwent a recent population expansion in the Central China. We suggest the species originated in the costal region facing the South China Sea and gradually expanded to colonize mainland China, expanding here to high population numbers.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Childhood obesity in transition zones: an analysis using structuration theory.

PubMed

Chan, Christine; Deave, Toity; Greenhalgh, Trisha

2010-07-01

Childhood obesity is particularly prevalent in areas that have seen rapid economic growth, urbanisation, cultural transition, and commodification of food systems. Structuration theory may illuminate the interaction between population and individual-level causes of obesity. We conducted in-depth ethnographies of six overweight/obese and four non-overweight preschool children in Hong Kong, each followed for 12-18 months. Analysis was informed by Stones' strong structuration theory. Risk factors played out differently for different children as social structures were enacted at the level of family and preschool. The network of caregiving roles and relationships around the overweight/obese child was typically weak and disjointed, and the primary caregiver appeared confused by mixed messages about what is normal, expected and legitimate behaviour. In particular, external social structures created pressure to shift childcare routines from the logic of nurturing to the logic of consumption. Our findings suggest that threats to what Giddens called ontological security in the primary caregiver may underpin the poor parenting, family stress and weak mealtime routines that mediate the relationship between an obesogenic environment and the development of obesity in a particular child. This preliminary study offers a potentially transferable approach for studying emerging epidemics of diseases of modernity in transition societies.

Long-distance dispersal and recolonization of a fire-destroyed niche by a mite-associated fungus.

PubMed

Aylward, Janneke; Dreyer, Léanne L; Steenkamp, Emma T; Wingfield, Michael J; Roets, Francois

2015-04-01

The Fynbos Biome in the Core Cape Subregion of South Africa is prone to recurrent fires that can clear vast areas of vegetation. Between periods of fire, ophiostomatoid fungi colonize the fruiting structures of serotinous Protea species through arthropod-mediated dispersal. Using microsatellite markers, this study considered the process whereby a Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, recolonizes a burnt area. The genetic diversity, composition and structure of fungal populations from young P. repens plants in a recently burnt area were compared to populations from the adjacent, unburnt Protea population. The only difference between K. proteae populations from the two areas was found in the number of private alleles, which was significantly higher in the unburnt population. The population structure, although weak, indicated that most K. proteae individuals from recently burnt areas originated from the unburnt population. However, individuals from unsampled source populations were also detected. This, together with the lack of isolation-by-distance across the landscape, suggested that long-distance dispersal is important for K. proteae to recolonize burnt areas. Similarly, the high level of gene flow and low differentiation observed between two distantly separated K. proteae populations also supported the existence of long-distance dispersal. The genetic cohesiveness of populations over long distances and the genetic diversity within populations could be attributed to frequent multiple fungal migration events mediated primarily by arthropods but, potentially, also by birds. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types

PubMed Central

2013-01-01

Background Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Results Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Conclusions Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits. PMID:23647851

Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types.

PubMed

Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie

2013-05-06

Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Weak Lensing Peaks in Simulated Light-Cones: Investigating the Coupling between Dark Matter and Dark Energy

NASA Astrophysics Data System (ADS)

Giocoli, Carlo; Moscardini, Lauro; Baldi, Marco; Meneghetti, Massimo; Metcalf, Robert B.

2018-05-01

In this paper, we study the statistical properties of weak lensing peaks in light-cones generated from cosmological simulations. In order to assess the prospects of such observable as a cosmological probe, we consider simulations that include interacting Dark Energy (hereafter DE) models with coupling term between DE and Dark Matter. Cosmological models that produce a larger population of massive clusters have more numerous high signal-to-noise peaks; among models with comparable numbers of clusters those with more concentrated haloes produce more peaks. The most extreme model under investigation shows a difference in peak counts of about 20% with respect to the reference ΛCDM model. We find that peak statistics can be used to distinguish a coupling DE model from a reference one with the same power spectrum normalisation. The differences in the expansion history and the growth rate of structure formation are reflected in their halo counts, non-linear scale features and, through them, in the properties of the lensing peaks. For a source redshift distribution consistent with the expectations of future space-based wide field surveys, we find that typically seventy percent of the cluster population contributes to weak-lensing peaks with signal-to-noise ratios larger than two, and that the fraction of clusters in peaks approaches one-hundred percent for haloes with redshift z ≤ 0.5. Our analysis demonstrates that peak statistics are an important tool for disentangling DE models by accurately tracing the structure formation processes as a function of the cosmic time.

RAD SNP markers as a tool for conservation of dolphinfish Coryphaena hippurus in the Mediterranean Sea: Identification of subtle genetic structure and assessment of populations sex-ratios.

PubMed

Maroso, Francesco; Franch, Rafaella; Dalla Rovere, Giulia; Arculeo, Marco; Bargelloni, Luca

2016-08-01

Dolphinfish is an important fish species for both commercial and sport fishing, but so far limited information is available on genetic variability and pattern of differentiation of dolphinfish populations in the Mediterranean basin. Recently developed techniques allow genome-wide identification of genetic markers for better understanding of population structure in species with limited genome information. Using restriction-site associated DNA analysis we successfully genotyped 140 individuals of dolphinfish from eight locations in the Mediterranean Sea at 3324 SNP loci. We identified 311 sex-related loci that were used to assess sex-ratio in dolphinfish populations. In addition, we identified a weak signature of genetic differentiation of the population closer to Gibraltar Strait in comparison to other Mediterranean populations, which might be related to introgression of individuals from Atlantic. No further genetic differentiation could be detected in the other populations sampled, as expected considering the known highly mobility of the species. The results obtained improve our knowledge of the species and can help managing dolphinfish stock in the future. Copyright © 2016 Elsevier B.V. All rights reserved.

Theoretical Study of near Neutrality. II. Effect of Subdivided Population Structure with Local Extinction and Recolonization

PubMed Central

Ohta, T.

1992-01-01

There are several unsolved problems concerning the model of nearly neutral mutations. One is the interaction of subdivided population structure and weak selection that spatially fluctuates. The model of nearly neutral mutations whose selection coefficient spatially fluctuates has been studied by adopting the island model with periodic extinction-recolonization. Both the number of colonies and the migration rate play significant roles in determining mutants' behavior, and selection is ineffective when the extinction-recolonization is frequent with low migration rate. In summary, the number of mutant substitutions decreases and the polymorphism increases by increasing the total population size, and/or decreasing the extinction-recolonization rate. However, by increasing the total size of the population, the mutant substitution rate does not become as low when compared with that in panmictic populations, because of the extinction-recolonization, especially when the migration rate is limited. It is also found that the model satisfactorily explains the contrasting patterns of molecular polymorphisms observed in sibling species of Drosophila, including heterozygosity, proportion of polymorphism and fixation index. PMID:1582566

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

PubMed

Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

PubMed

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-07

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Emergence of parochial altruism in well-mixed populations of multiple groups

NASA Astrophysics Data System (ADS)

Gao, Shiping; Wu, Te; Nie, Suli; Wang, Long

2015-10-01

Understanding the evolution of parochial altruism is of great importance. We here institute an analytical model to study the emergence of parochial altruism in group-structured populations. Individuals' strategy is contingent on interacting partners' group property. Only when sharing common tag(s), they play the prisoner's dilemma game; otherwise they play the punishment game. The conditions for the emergence of parochial altruism are specified for weak selection. Emergence of parochial altruism is promoted by assortment as well as by intergroup punishment. Furthermore, the affiliation plays a negative (positive) role in the emergence of parochial altruism for low (high) mutation.

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

PubMed Central

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Background Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. Methodology/Principal Findings We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150–200 km2 within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Conclusions/Significance Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations. PMID:23755317

Continuous and Discrete Structured Population Models with Applications to Epidemiology and Marine Mammals

NASA Astrophysics Data System (ADS)

Tang, Tingting

In this dissertation, we develop structured population models to examine how changes in the environmental affect population processes. In Chapter 2, we develop a general continuous time size structured model describing a susceptible-infected (SI) population coupled with the environment. This model applies to problems arising in ecology, epidemiology, and cell biology. The model consists of a system of quasilinear hyperbolic partial differential equations coupled with a system of nonlinear ordinary differential equations that represent the environment. We develop a second-order high resolution finite difference scheme to numerically solve the model. Convergence of this scheme to a weak solution with bounded total variation is proved. We numerically compare the second order high resolution scheme with a first order finite difference scheme. Higher order of convergence and high resolution property are observed in the second order finite difference scheme. In addition, we apply our model to a multi-host wildlife disease problem, questions regarding the impact of the initial population structure and transition rate within each host are numerically explored. In Chapter 3, we use a stage structured matrix model for wildlife population to study the recovery process of the population given an environmental disturbance. We focus on the time it takes for the population to recover to its pre-event level and develop general formulas to calculate the sensitivity or elasticity of the recovery time to changes in the initial population distribution, vital rates and event severity. Our results suggest that the recovery time is independent of the initial population size, but is sensitive to the initial population structure. Moreover, it is more sensitive to the reduction proportion to the vital rates of the population caused by the catastrophe event relative to the duration of impact of the event. We present the potential application of our model to the amphibian population dynamic and the recovery of a certain plant population. In addition, we explore, in details, the application of the model to the sperm whale population in Gulf of Mexico after the Deepwater Horizon oil spill. In Chapter 4, we summarize the results from Chapter 2 and Chapter 3 and explore some further avenues of our research.

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

PubMed

Zavodna, Monika; Grueber, Catherine E; Gemmell, Neil J

2013-01-01

Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.

Contrasting Patterns of Genetic Differentiation among Blackcaps (Sylvia atricapilla) with Divergent Migratory Orientations in Europe

PubMed Central

Mettler, Raeann; Schaefer, H. Martin; Chernetsov, Nikita; Fiedler, Wolfgang; Hobson, Keith A.; Ilieva, Mihaela; Imhof, Elisabeth; Johnsen, Arild; Renner, Swen C.; Rolshausen, Gregor; Serrano, David; Wesołowski, Tomasz; Segelbacher, Gernot

2013-01-01

Migratory divides are thought to facilitate behavioral, ecological, and genetic divergence among populations with different migratory routes. However, it is currently contentious how much genetic divergence is needed to maintain distinct migratory behavior across migratory divides. Here we investigate patterns of neutral genetic differentiation among Blackcap (Sylvia atricapilla) populations with different migratory strategies across Europe. We compare the level of genetic divergence of populations migrating to southwestern (SW) or southeastern (SE) wintering areas with birds wintering in the British Isles following a recently established northwesterly (NW) migration route. The migratory divide between SW and SE wintering areas can be interpreted as a result of a re-colonization process after the last glaciation. Thus we predicted greater levels of genetic differentiation among the SW/SE populations. However, a lack of genetic differentiation was found between SW and SE populations, suggesting that interbreeding likely occurs among Blackcaps with different migratory orientations across a large area; therefore the SW/SE migratory divide can be seen as diffuse, broad band and is, at best, a weak isolating barrier. Conversely, weak, albeit significant genetic differentiation was evident between NW and SW migrants breeding sympatrically in southern Germany, suggesting a stronger isolating mechanism may be acting in this population. Populations located within/near the SW/SE contact zone were the least genetically divergent from NW migrants, confirming NW migrants likely originated from within the contact zone. Significant isolation-by-distance was found among eastern Blackcap populations (i.e. SE migrants), but not among western populations (i.e. NW and SW migrants), revealing different patterns of genetic divergence among Blackcap populations in Europe. We discuss possible explanations for the genetic structure of European Blackcaps and how gene flow influences the persistence of divergent migratory behaviors. PMID:24278428

Genetic variation among interconnected populations of Catostomus occidentalis: Implications for distinguishing impacts of contaminants from biogeographical structuring

USGS Publications Warehouse

Whitehead, A.; Anderson, S.L.; Kuivila, K.M.; Roach, J.L.; May, B.

2003-01-01

Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is discussed.

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity

PubMed Central

Athanasiadis, Georgios; Cheng, Jade Y.; Vilhjálmsson, Bjarni J.; Jørgensen, Frank G.; Als, Thomas D.; Le Hellard, Stephanie; Espeseth, Thomas; Sullivan, Patrick F.; Hultman, Christina M.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas

2016-01-01

Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country. PMID:27535931

Aspiration dynamics of multi-player games in finite populations

PubMed Central

Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

2014-01-01

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

Aspiration dynamics of multi-player games in finite populations.

PubMed

Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast.

PubMed

Britto, Fábio B; Schmidt, Anders J; Carvalho, Adriana M F; Vasconcelos, Carolina C M P; Farias, Antonia M; Bentzen, Paul; Diniz, Fábio M

2018-01-01

The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of F ST (= 0.019; P < 0.001). F ST and Jost's D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs ( P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition ( P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation ( F CT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus . Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PubMed Central

Schmidt, Anders J.; Carvalho, Adriana M.F.; Vasconcelos, Carolina C.M.P.; Farias, Antonia M.; Bentzen, Paul

2018-01-01

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs. PMID:29736340

Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

PubMed Central

Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

2015-01-01

Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

Genetic Structure and the North American Postglacial Expansion of the Barnacle, Semibalanus balanoides

PubMed Central

O’Brien, Megan A.; Schmidt, Paul S.; Rand, David M.

2012-01-01

Population genetic characteristics are shaped by the life-history traits of organisms and the geologic history of their habitat. This study provides a neutral framework for understanding the population dynamics and opportunities for selection in Semibalanus balanoides, a species that figures prominently in ecological and evolutionary studies in the Atlantic intertidal. We used mitochondrial DNA (mtDNA) control region (N = 131) and microsatellite markers (∼40 individuals/site/locus) to survey populations of the broadly dispersing acorn barnacle from 8 sites spanning 800 km of North American coast and 1 site in Europe. Patterns of mtDNA sequence evolution were consistent with larger population sizes in Europe and population expansion at the conclusion of the last ice age, approximately 20 000 years ago, in North America. A significant portion of mitochondrial diversity was partitioned between the continents (φST = 0.281), but there was only weak structure observed from mtDNA within North America. Microsatellites showed significant structuring between the continents (FST = 0.021) as well as within North America (FST = 0.013). Isolation by distance in North America was largely driven by a split between populations south of Cape Cod and all others (P < 10−4). The glacial events responsible for generating allelic diversity at mtDNA and microsatellites may also be responsible for generating selectable variation at metabolic enzymes in S. balanoides. PMID:21885571

Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

PubMed

Oyen, David; Fenwick, R Bryn; Aoto, Phillip C; Stanfield, Robyn L; Wilson, Ian A; Dyson, H Jane; Wright, Peter E

2017-08-16

The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

PubMed Central

Kijas, James W.; Townley, David; Dalrymple, Brian P.; Heaton, Michael P.; Maddox, Jillian F.; McGrath, Annette; Wilson, Peter; Ingersoll, Roxann G.; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John; Cockett, Noelle; Oddy, V. Hutton; Nicholas, Frank W.; Raadsma, Herman

2009-01-01

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability. PMID:19270757

Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations.

PubMed

Hirata, Daisuke; Mano, Tsutomu; Abramov, Alexei V; Baryshnikov, Gennady F; Kosintsev, Pavel A; Murata, Koichi; Masuda, Ryuichi

2017-01-01

Sex-biased dispersal is widespread among mammals, including the brown bear ( Ursus arctos ). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow. We analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins. Brown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.

Population genetics of seaside Sparrow (Ammodramus maritimus) subspecies along the gulf of Mexico.

PubMed

Woltmann, Stefan; Stouffer, Philip C; Bergeon Burns, Christine M; Woodrey, Mark S; Cashner, Mollie F; Taylor, Sabrina S

2014-01-01

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this "Gulf Coast" clade using microsatellite and mtDNA data. Results of Bayesian analyses (Structure, GeneLand) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. fisheri near Corpus Christi. The two subspecies along the northern Gulf Coast of Florida are significantly differentiated from both A. m. sennetti and A. m. fisheri, but are not distinct from each other. We found a weak signal of isolation by distance within A. m. fisheri, indicating this population is not entirely panmictic throughout its range. Although continued conservation concern is warranted for all populations along the Gulf Coast, A. m. fisheri appears to be more secure than the far smaller populations in south Texas and the northern Florida Gulf Coast. In particular, the most genetically distinct populations, those in Texas south of Corpus Christi, occupy unique habitats within a very small geographic range.

Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes

PubMed Central

Arkin, Adam P.

2015-01-01

ABSTRACT Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level of homologous recombination (r/m = 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is <107. An argument for high Ne values for bacteria has been the high genetic diversity within many bacterial “species,” but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate of Ne, standard population genetics models imply that selection should be sufficient to drive evolution if Ne × s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10−7 or so. PMID:26670382

Structural Stability of Mathematical Models of National Economy

NASA Astrophysics Data System (ADS)

Ashimov, Abdykappar A.; Sultanov, Bahyt T.; Borovskiy, Yuriy V.; Adilov, Zheksenbek M.; Ashimov, Askar A.

2011-12-01

In the paper we test robustness of particular dynamic systems in a compact regions of a plane and a weak structural stability of one dynamic system of high order in a compact region of its phase space. The test was carried out based on the fundamental theory of dynamical systems on a plane and based on the conditions for weak structural stability of high order dynamic systems. A numerical algorithm for testing the weak structural stability of high order dynamic systems has been proposed. Based on this algorithm we assess the weak structural stability of one computable general equilibrium model.

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Stead, M G; Harris, J B C; Lowe, A J

2015-01-01

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha−1; isolated pasture=1.7 trees ha−1; population area=10 km2). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow. PMID:23188172

Different Context but Similar Cognitive Structures: Older Adults in Rural Bangladesh.

PubMed

Sternäng, Ola; Lövdén, Martin; Kabir, Zarina N; Hamadani, Jena D; Wahlin, Åke

2016-06-01

Most research in cognitive aging is based on literate participants from high-income and Western populations. The extent to which findings generalize to low-income and illiterate populations is unknown. The main aim was to examine the structure of between-person differences in cognitive functions among elderly from rural Bangladesh. We used data from the Poverty and Health in Aging (PHA) project in Bangladesh. The participants (n = 452) were in the age range 60-92 years. Structural equation modeling was used to estimate the fit of a five-factor model (episodic recall, episodic recognition, verbal fluency, semantic knowledge, processing speed) and to examine whether the model generalized across age, sex, and literacy. This study demonstrates that an established model of cognition is valid also among older persons from rural Bangladesh. The model demonstrated strong (or scalar) invariance for age, and partial strong invariance for sex and literacy. Semantic knowledge and processing speed showed weak (or metric) sex invariance, and semantic knowledge demonstrated also sensitivity to illiteracy. In general, women performed poorer on all abilities. The structure of individual cognitive differences established in Western populations also fits a population in rural Bangladesh well. This is an important prerequisite for comparisons of cognitive functioning (e.g., declarative memory) across cultures. It is also worth noting that absolute sex differences in cognitive performance among rural elderly in Bangladesh differ from those usually found in Western samples.

Early-onset facioscapulohumeral muscular dystrophy type 1 with some atypical features.

PubMed

Dorobek, Małgorzata; van der Maarel, Silvère M; Lemmers, Richard J L F; Ryniewicz, Barbara; Kabzińska, Dagmara; Frants, Rune R; Gawel, Malgorzata; Walecki, Jerzy; Hausmanowa-Petrusewicz, Irena

2015-04-01

Facioscapulohumeral muscular dystrophy cases with facial weakness before the age of 5 and signs of shoulder weakness by the age of 10 are defined as early onset. Contraction of the D4Z4 repeat on chromosome 4q35 is causally related to facioscapulohumeral muscular dystrophy type 1, and the residual size of the D4Z4 repeat shows a roughly inverse correlation with the severity of the disease. Contraction of the D4Z4 repeat on chromosome 4q35 is believed to induce a local change in chromatin structure and consequent transcriptional deregulation of 4qter genes. We present early-onset cases in the Polish population that amounted to 21% of our total population with facioscapulohumeral muscular dystrophy. More than 27% of them presented with severe phenotypes (wheelchair dependency). The residual D4Z4 repeat sizes ranged from 1 to 4 units. In addition, even within early-onset facioscapulohumeral muscular dystrophy type 1 phenotypes, some cases had uncommon features (head drop, early disabling contractures, progressive ptosis, and respiratory insufficiency and cardiomyopathy). © The Author(s) 2014.

DIFFUSIVE SHOCK ACCELERATION SIMULATIONS OF RADIO RELICS

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

Kang, Hyesung; Ryu, Dongsu; Jones, T. W., E-mail: kang@uju.es.pusan.ac.kr, E-mail: ryu@canopus.cnu.ac.kr, E-mail: twj@msi.umn.edu

2012-09-01

Recent radio observations have identified a class of structures, so-called radio relics, in clusters of galaxies. The radio emission from these sources is interpreted as synchrotron radiation from GeV electrons gyrating in {mu}G-level magnetic fields. Radio relics, located mostly in the outskirts of clusters, seem to associate with shock waves, especially those developed during mergers. In fact, they seem to be good structures to identify and probe such shocks in intracluster media (ICMs), provided we understand the electron acceleration and re-acceleration at those shocks. In this paper, we describe time-dependent simulations for diffusive shock acceleration at weak shocks that aremore » expected to be found in ICMs. Freshly injected as well as pre-existing populations of cosmic-ray (CR) electrons are considered, and energy losses via synchrotron and inverse Compton are included. We then compare the synchrotron flux and spectral distributions estimated from the simulations with those in two well-observed radio relics in CIZA J2242.8+5301 and ZwCl0008.8+5215. Considering that CR electron injection is expected to be rather inefficient at weak shocks with Mach number M {approx}< a few, the existence of radio relics could indicate the pre-existing population of low-energy CR electrons in ICMs. The implication of our results on the merger shock scenario of radio relics is discussed.« less

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

PubMed

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

Patterns of range-wide genetic variation in six North American bumble bee (Apidae: Bombus) species.

PubMed

Lozier, Jeffrey D; Strange, James P; Stewart, Isaac J; Cameron, Sydney A

2011-12-01

The increasing evidence for population declines in bumble bee (Bombus) species worldwide has accelerated research efforts to explain losses in these important pollinators. In North America, a number of once widespread Bombus species have suffered serious reductions in range and abundance, although other species remain healthy. To examine whether declining and stable species exhibit different levels of genetic diversity or population fragmentation, we used microsatellite markers to genotype populations sampled across the geographic distributions of two declining (Bombus occidentalis and Bombus pensylvanicus) and four stable (Bombus bifarius; Bombus vosnesenskii; Bombus impatiens and Bombus bimaculatus) Bombus species. Populations of declining species generally have reduced levels of genetic diversity throughout their range compared to codistributed stable species. Genetic diversity can be affected by overall range size and degree of isolation of local populations, potentially confounding comparisons among species in some cases. We find no evidence for consistent differences in gene flow among stable and declining species, with all species exhibiting weak genetic differentiation over large distances (e.g. >1000 km). Populations on islands and at high elevations experience relatively strong genetic drift, suggesting that some conditions lead to genetic isolation in otherwise weakly differentiated species. B. occidentalis and B. bifarius exhibit stronger genetic differentiation than the other species, indicating greater phylogeographic structure consistent with their broader geographic distributions across topographically complex regions of western North America. Screening genetic diversity in North American Bombus should prove useful for identifying species that warrant monitoring, and developing management strategies that promote high levels of gene flow will be a key component in efforts to maintain healthy populations. © 2011 Blackwell Publishing Ltd.

Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management.

PubMed

Walker, Anne-Sophie; Gladieux, Pierre; Decognet, Véronique; Fermaud, Marc; Confais, Johann; Roudet, Jean; Bardin, Marc; Bout, Alexandre; Nicot, Philippe C; Poncet, Christine; Fournier, Elisabeth

2015-04-01

Understanding the causes of population subdivision is of fundamental importance, as studying barriers to gene flow between populations may reveal key aspects of the process of adaptive divergence and, for pathogens, may help forecasting disease emergence and implementing sound management strategies. Here, we investigated population subdivision in the multihost fungus Botrytis cinerea based on comprehensive multiyear sampling on different hosts in three French regions. Analyses revealed a weak association between population structure and geography, but a clear differentiation according to the host plant of origin. This was consistent with adaptation to hosts, but the distribution of inferred genetic clusters and the frequency of admixed individuals indicated a lack of strict host specificity. Differentiation between individuals collected in the greenhouse (on Solanum) and outdoor (on Vitis and Rubus) was stronger than that observed between individuals from the two outdoor hosts, probably reflecting an additional isolating effect associated with the cropping system. Three genetic clusters coexisted on Vitis but did not persist over time. Linkage disequilibrium analysis indicated that outdoor populations were regularly recombining, whereas clonality was predominant in the greenhouse. Our findings open up new perspectives for disease control by managing plant debris in outdoor conditions and reinforcing prophylactic measures indoor. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

PubMed Central

Jia, Huixia; Yang, Haifeng; Sun, Pei; Li, Jianbo; Zhang, Jin; Guo, Yinghua; Han, Xiaojiao; Zhang, Guosheng; Lu, Mengzhu; Hu, Jianjun

2016-01-01

Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006–0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045–0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila. PMID:27995985

Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged and commercial orchard interface.

PubMed

Fuentes-Contreras, Eduardo; Basoalto, Esteban; Franck, Pierre; Lavandero, Blas; Knight, Alan L; Ramírez, Claudio C

2014-04-01

The genetic structure of adult codling moth, Cydia pomonella (L.), populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and nonhost trees in central Chile during 2006-2007. Adult males were collected using an array of sex pheromone-baited traps. Five microsatellite genetic markers were used to study the population genetic structure across both spatial (1-100 ha) and temporal (generations within a season) gradients. Analysis of molecular variance (AMOVA) found a significant, but weak, association in both the spatial and temporal genetic structures. Discriminant analysis also found significant differentiation between the first and second generation for traps located either inside or outside the managed orchard. The Bayesian assignment test detected three genetic clusters during each of the two generations, which corresponded to different areas within the unmanaged and managed apple orchard interface. The lack of a strong spatial structure at a local scale was hypothesized to be because of active adult movement between the managed and unmanaged hosts and the asymmetry in the insecticide selection pressure inside and outside the managed habitats. These data highlight the importance of developing area-wide management programs that incorporate management tactics effective at the landscape level for successful codling moth control.

Larval dispersal underlies demographically important inter-system connectivity in a Great Lakes yellow perch (Perca flavescens) population

USGS Publications Warehouse

Brodnik, Reed M.; Fraker, Michael E.; Anderson, Eric J.; Carreon-Martinez, Lucia; DeVanna, Kristen M.; Heath, Dan D.; Reichert, Julie M.; Roseman, Edward F.; Ludsin, Stuart A.

2016-01-01

Ability to quantify connectivity among spawning subpopulations and their relative contribution of recruits to the broader population is a critical fisheries management need. By combining microsatellite and age information from larval yellow perch (Perca flavescens) collected in the Lake St. Clair – Detroit River system (SC-DRS) and western Lake Erie with a hydrodynamic backtracking approach, we quantified subpopulation structure, connectivity, and contributions of recruits to the juvenile stage in western Lake Erie during 2006-2007. After finding weak (yet stable) genetic structure between the SC-DRS and two western Lake Erie subpopulations, microsatellites also revealed measurable recruitment of SC-DRS larvae to the juvenile stage in western Lake Erie (17-21% during 2006-2007). Consideration of pre-collection larval dispersal trajectories, using hydrodynamic backtracking, increased estimated contributions to 65% in 2006 and 57% in 2007. Our findings highlight the value of complementing subpopulation discrimination methods with hydrodynamic predictions of larval dispersal by revealing the SC-DRS as a source of recruits to western Lake Erie and also showing that connectivity through larval dispersal can affect the structure and dynamics of large-lake fish populations.

Nuclear and Chloroplast Microsatellites Show Multiple Introductions in the Worldwide Invasion History of Common Ragweed, Ambrosia artemisiifolia

PubMed Central

Gaudeul, Myriam; Giraud, Tatiana; Kiss, Levente; Shykoff, Jacqui A.

2011-01-01

Background Ambrosia artemisiifolia is a North American native that has become one of the most problematic invasive plants in Europe and Asia. We studied its worldwide population genetic structure, using both nuclear and chloroplast microsatellite markers and an unprecedented large population sampling. Our goals were (i) to identify the sources of the invasive populations; (ii) to assess whether all invasive populations were founded by multiple introductions, as previously found in France; (iii) to examine how the introductions have affected the amount and structure of genetic variation in Europe; (iv) to document how the colonization of Europe proceeded; (v) to check whether populations exhibit significant heterozygote deficiencies, as previously observed. Principal Findings We found evidence for multiple introductions of A. artemisiifolia, within regions but also within populations in most parts of its invasive range, leading to high levels of diversity. In Europe, introductions probably stem from two different regions of the native area: populations established in Central Europe appear to have originated from eastern North America, and Eastern European populations from more western North America. This may result from differential commercial exchanges between these geographic regions. Our results indicate that the expansion in Europe mostly occurred through long-distance dispersal, explaining the absence of isolation by distance and the weak influence of geography on the genetic structure in this area in contrast to the native range. Last, we detected significant heterozygote deficiencies in most populations. This may be explained by partial selfing, biparental inbreeding and/or a Wahlund effect and further investigation is warranted. Conclusions This insight into the sources and pathways of common ragweed expansion may help to better understand its invasion success and provides baseline data for future studies on the evolutionary processes involved during range expansion in novel environments. PMID:21423697

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

PubMed Central

2011-01-01

Background Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Results Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. Conclusions In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run. PMID:21859457

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe.

PubMed

Vanden-Broeck, An; Gruwez, Robert; Cox, Karen; Adriaenssens, Sandy; Michalczyk, Inga M; Verheyen, Kris

2011-08-22

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.

Floral variation and environmental heterogeneity in a tristylous clonal aquatic of the Pantanal wetlands of Brazil

PubMed Central

Leme da Cunha, Nicolay; Fischer, Erich; Lorenz-Lemke, Aline P.; Barrett, Spencer C. H.

2014-01-01

Background and Aims The balance between stochastic forces and frequency-dependent mating largely governs style morph frequencies in heterostylous populations. In clonal species, deviations from equal morph ratios often result from founder events and unfavourable conditions for sexual reproduction. The aim of this study was to investigate whether different flooding regimes, because of their influence on sexual vs. clonal reproduction, are associated with regional variation in morph frequencies and floral trait differentiation in populations of the clonal, tristylous, aquatic Eichhornia azurea (Pontederiaceae) in the Pantanal wetlands of Brazil. Methods Style morph frequencies were sampled from 73 populations distributed across four flooding regimes differing in depth and duration. Measurements of flower size, sex-organ dimension, pollen size and pollen production were made in selected populations, and pollinator assemblages and their functional traits were recorded. Key Results Most populations of E. azurea were tristylous (78 %), but the majority exhibited uneven morph ratios. The frequency of the mid-styled morph was significantly lower than that of the long- and short-styled morphs. Morph evenness was positively associated with population size but not with flooding regime. There were significant phenotypic differences among flooding regimes for all floral traits, including populations with reduced flower size, sex-organ length and smaller pollen. Pollinator assemblages varied with flood duration. Conclusions The similar morph structure and evenness of populations, regardless of flooding regime, suggest that sexual reproduction and clonal dispersal are sufficiently common to prevent the signature of founder events from dominating in a region. However, the pervasive occurrence of biased morph ratios in most populations suggests that many are in a non-equilibrium state. The reduced frequency of the mid-styled morph in trimorphic and dimorphic populations may be associated with the weak self-incompatibility of this morph resulting in selfing and inbreeding depression. Clonality in E. azurea and the weak self-incompatibility of the mid-styled morph may make it more vulnerable to geitonogamous selfing. PMID:25180289

Home educating in an extended family culture and aging society may fare best during a pandemic.

PubMed

Dawson, Wayne; Yamamoto, Kenji

2009-09-28

Large cities can contain populations that move rapidly from one section to another in an efficient transportation network. An emerging air-borne or contact based pathogen could use these transportation routes to rapidly spread an infection throughout an entire population in a short time. Further, in many developed countries, the aging population is increasing. The family structure in these societies may also affect the course of a disease. To help understand the impact of an epidemic on family structure in a networked population, an individual based computer model that randomly generates networked cities with a specified range of population and disease characteristics and individual schedules, infectivity, transmission and hygiene factors was developed. Several salient issues emerged. First, a city of highly active individuals may in fact diminish the number of fatalities because the average duration of the interactions between agents is reduced. Second, home schooling can significantly improve survival because the institutional clustering of weak individuals is minimized. Third, the worst scenario for an aging population is the nuclear family where the aged population is confined to large housing facilities. Naturally, hygiene is the first barrier to infection. The results suggest that societies where extended families and small groups manage most of their own affairs may also be the most suitable for defense against a pandemic. This may prove applicable in city planning and policy making.

Linking Theory of Mind and Central Coherence Bias in Autism and in the General Population.

ERIC Educational Resources Information Center

Jarrold, Christopher; Butler, David W.; Cottington, Emily M.; Jimenez, Flora

2000-01-01

Three experiments investigated whether theory-of-mind deficits and weak central coherence might be functionally related. Found that theory-of-mind performance was inversely related to a measure of central coherence bias in the general population. Poor theory-of-mind performance was linked to weak central coherence among children with typical…

Barriers to and acceptability of provider-initiated HIV testing and counselling and adopting HIV-prevention behaviours in rural Uganda: a qualitative study.

PubMed

Kiene, Susan M; Sileo, Katelyn; Wanyenze, Rhoda K; Lule, Haruna; Bateganya, Moses H; Jasperse, Joseph; Nantaba, Harriet; Jayaratne, Kia

2015-02-01

In Uganda, a nationwide scale-up of provider-initiated HIV testing and counselling presents an opportunity to deliver HIV-prevention services to large numbers of people. In a rural Ugandan hospital, focus group discussions and key informant interviews were conducted with outpatients receiving provider-initiated HIV testing and counselling and staff to explore the HIV-prevention information, motivation and behavioural skills strengths and weaknesses, and community-level and structural barriers to provider-initiated HIV testing and counselling acceptability and HIV prevention among this population. Strengths and weakness occurred at all levels, and results suggest brief client-centred interventions during provider-initiated HIV testing and counselling may be an effective approach to increase prevention behaviours in outpatient settings. © The Author(s) 2013.

A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

PubMed

Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

2016-01-01

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

New insights into the correlation structure of DSM-IV depression symptoms in the general population v. subsamples of depressed individuals.

PubMed

Foster, S; Mohler-Kuo, M

2018-06-01

Previous research failed to uncover a replicable dimensional structure underlying the symptoms of depression. We aimed to examine two neglected methodological issues in this research: (a) adjusting symptom correlations for overall depression severity; and (b) analysing general population samples v. subsamples of currently depressed individuals. Using population-based cross-sectional and longitudinal data from two nations (Switzerland, 5883 young men; USA, 2174 young men and 2244 young women) we assessed the dimensions of the nine DSM-IV depression symptoms in young adults. In each general-population sample and each subsample of currently depressed participants, we conducted a standardised process of three analytical steps, based on exploratory and confirmatory factor and bifactor analysis, to reveal any replicable dimensional structure underlying symptom correlations while controlling for overall depression severity. We found no evidence of a replicable dimensional structure across samples when adjusting symptom correlations for overall depression severity. In the general-population samples, symptoms correlated strongly and a single dimension of depression severity was revealed. Among depressed participants, symptom correlations were surprisingly weak and no replicable dimensions were identified, regardless of severity-adjustment. First, caution is warranted when considering studies assessing dimensions of depression because general population-based studies and studies of depressed individuals generate different data that can lead to different conclusions. This problem likely generalises to other models based on the symptoms' inter-relationships such as network models. Second, whereas the overall severity aligns individuals on a continuum of disorder intensity that allows non-affected individuals to be distinguished from affected individuals, the clinical evaluation and treatment of depressed individuals should focus directly on each individual's symptom profile.

Shock Structure Analysis and Aerodynamics in a Weakly Ionized Gas Flow

NASA Technical Reports Server (NTRS)

Saeks, R.; Popovic, S.; Chow, A. S.

2006-01-01

The structure of a shock wave propagating through a weakly ionized gas is analyzed using an electrofluid dynamics model composed of classical conservation laws and Gauss Law. A viscosity model is included to correctly model the spatial scale of the shock structure, and quasi-neutrality is not assumed. A detailed analysis of the structure of a shock wave propagating in a weakly ionized gas is presented, together with a discussion of the physics underlying the key features of the shock structure. A model for the flow behind a shock wave propagating through a weakly ionized gas is developed and used to analyze the effect of the ionization on the aerodynamics and performance of a two-dimensional hypersonic lifting body.

THE VELOCITY DISTRIBUTION OF NEARBY STARS FROM HIPPARCOS DATA. II. THE NATURE OF THE LOW-VELOCITY MOVING GROUPS

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

Bovy, Jo; Hogg, David W., E-mail: jo.bovy@nyu.ed

2010-07-10

The velocity distribution of nearby stars ({approx}<100 pc) contains many overdensities or 'moving groups', clumps of comoving stars, that are inconsistent with the standard assumption of an axisymmetric, time-independent, and steady-state Galaxy. We study the age and metallicity properties of the low-velocity moving groups based on the reconstruction of the local velocity distribution in Paper I of this series. We perform stringent, conservative hypothesis testing to establish for each of these moving groups whether it could conceivably consist of a coeval population of stars. We conclude that they do not: the moving groups are neither trivially associated with their eponymousmore » open clusters nor with any other inhomogeneous star formation event. Concerning a possible dynamical origin of the moving groups, we test whether any of the moving groups has a higher or lower metallicity than the background population of thin disk stars, as would generically be the case if the moving groups are associated with resonances of the bar or spiral structure. We find clear evidence that the Hyades moving group has higher than average metallicity and weak evidence that the Sirius moving group has lower than average metallicity, which could indicate that these two groups are related to the inner Lindblad resonance of the spiral structure. Further, we find weak evidence that the Hercules moving group has higher than average metallicity, as would be the case if it is associated with the bar's outer Lindblad resonance. The Pleiades moving group shows no clear metallicity anomaly, arguing against a common dynamical origin for the Hyades and Pleiades groups. Overall, however, the moving groups are barely distinguishable from the background population of stars, raising the likelihood that the moving groups are associated with transient perturbations.« less

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl.

PubMed

Cloutier, D; Kanashiro, M; Ciampi, A Y; Schoen, D J

2007-02-01

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.

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

Walker, Heidi, E-mail: heidi.mwalker@yahoo.ca; Sinclair, A. John, E-mail: john.sinclair@ad.umanitoba.ca; Spaling, Harry, E-mail: harry.spaling@kingsu.ca

Meaningful public engagement is a challenging, but promising, feature of strategic environmental assessment (SEA) due to its potential for integrating sustainability principles into policies, plans and programs in developing countries such as Kenya. This research examined two selected SEA case studies to identify the extent of participation, learning outcomes attributable to participation, and if any learning outcomes led to social action for sustainability at the community level. Strengths across the two cases were the inclusion of marginalized populations and consideration of socio-economic concerns. Consistent weaknesses included inadequate notice, document inaccessibility, lack of feedback and communication, and late analysis of alternatives.more » Despite some learning conditions being unfulfilled, examples of instrumental, communicative, and transformative learning were identified through a focus group and semi-structured interviews with community participants and public officials. Some of these learning outcomes led to individual and social actions that contribute to sustainability. -- Highlights: • The strengths and weaknesses of Kenyan SEA public participation processes were identified. • Multiple deficiencies in the SEA process likely frustrate meaningful public engagement. • Participant learning was observed despite process weaknesses. • Participant learning can lead to action for sustainability at the community level.« less

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat.

PubMed

Wingen, Luzie U; Orford, Simon; Goram, Richard; Leverington-Waite, Michelle; Bilham, Lorelei; Patsiou, Theofania S; Ambrose, Mike; Dicks, Jo; Griffiths, Simon

2014-08-01

A high level of genetic diversity was found in the A. E. Watkins bread wheat landrace collection. Genotypic information was used to determine the population structure and to develop germplasm resources. In the 1930s A. E. Watkins acquired landrace cultivars of bread wheat (Triticum aestivum L.) from official channels of the board of Trade in London, many of which originated from local markets in 32 countries. The geographic distribution of the 826 landrace cultivars of the current collection, here called the Watkins collection, covers many Asian and European countries and some from Africa. The cultivars were genotyped with 41 microsatellite markers in order to investigate the genetic diversity and population structure of the collection. A high level of genetic diversity was found, higher than in a collection of modern European winter bread wheat varieties from 1945 to 2000. Furthermore, although weak, the population structure of the Watkins collection reveals nine ancestral geographical groupings. An exchange of genetic material between ancestral groups before commercial wheat-breeding started would be a possible explanation for this. The increased knowledge regarding the diversity of the Watkins collection was used to develop resources for wheat research and breeding, one of them a core set, which captures the majority of the genetic diversity detected. The understanding of genetic diversity and population structure together with the availability of breeding resources should help to accelerate the detection of new alleles in the Watkins collection.

[Genetic variation of some varieties of common juniper Juniperus communis L. inferred from analysis of allozyme loci].

PubMed

Khantemirova, E V; Semerikov, V L

2010-05-01

Using the method of allozyme analysis, genetic variation, diversity, and population structure of Juniperus communis L. var. communis and J. communis L. var. saxatilis Pall. (= J. sibirica Burgsd. = J. nana Wild), growing on the territory of Russia, J. c. var. communis from Sweden, and J. c. var. depressa Pursh from Northern America (Alaska), was investigated. The total level of genetic variation of these varieties was found to be higher than the values obtained for the other conifers. The population samples of J. c. var. depressa from Alaska and J. c. var. saxatilis from Sakhalin were noticeably different from all other populations examined. Between the other samples, no substantial genetic differences were observed. These populations were characterized by weak interpopulation differentiation along with the absence of expressed geographical pattern of the allele frequency spatial distribution. The only exception was the procumbent form of common juniper from the high mountain populations of South and North Ural, which was somewhat different from the others.

Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid-diploid life history and intertidal rocky shore landscape on fine-scale genetic structure.

PubMed

Engel, C R; Destombe, C; Valero, M

2004-04-01

The impact of haploid-diploidy and the intertidal landscape on a fine-scale genetic structure was explored in a red seaweed Gracilaria gracilis. The pattern of genetic structure was compared in haploid and diploid stages at a microgeographic scale (< 5 km): a total of 280 haploid and 296 diploid individuals located in six discrete, scattered rock pools were genotyped using seven microsatellite loci. Contrary to the theoretical expectation of predominantly endogamous mating systems in haploid-diploid organisms, G. gracilis showed a clearly allogamous mating system. Although within-population allele frequencies were similar between haploids and diploids, genetic differentiation among haploids was more than twice that of diploids, suggesting that there may be a lag between migration and (local) breeding due to the long generation times in G. gracilis. Weak, but significant, population differentiation was detected in both haploids and diploids and varied with landscape features, and not with geographic distance. Using an assignment test, we establish that effective migration rates varied according to height on the shore. In this intertidal species, biased spore dispersal may occur during the transport of spores and gametes at low tide when small streams flow from high- to lower-shore pools. The longevity of both haploid and diploid free-living stages and the long generation times typical of G. gracilis populations may promote the observed pattern of high genetic diversity within populations relative to that among populations.

Geographical genetic structuring and phenotypic variation in the Vellozia hirsuta (Velloziaceae) ochlospecies complex.

PubMed

Barbosa, Ariane R; Fiorini, Cecília F; Silva-Pereira, Viviane; Mello-Silva, Renato; Borba, Eduardo L

2012-09-01

Vellozia hirsuta forms a complex presenting wide morphological and anatomical variation, resulting in five specific names and 14 morpho-anatomical patterns occurring in disjunct populations. We carried out a phylogeographical study to investigate the existence of correlation among the genetic and morphological patterns within this complex, and to determine whether it is composed of various species or should be treated as an ochlospecies, a species having widely polymorphic and weakly polytypic complex variation, with morphological characteristics varying independently. We carried out phylogeographical analyses using cpDNA rpl32F-trnL intergenic region. We found 20 haplotypes in 23 populations sampled. The populations are genetically structured (Φ(ST) = 0.818) into four phylogeographical groups demonstrating geographical structuring but with no correlation with morpho-anatomical patterns. Our analyses do not support recognizing any of the species now synonymized under Vellozia hirsuta. The northern populations were the most genetically differentiated and could be considered a distinct taxon, as they are also morphologically different. It is recommended that Vellozia hirsuta be considered a single enormously variable species. The patterns of variation within V. hirsuta probably are related to climatic changes that occurred during the Pleistocene Epoch in tropical Brazil when reductions in forest cover favored the expansion of V. hirsuta populations into extensive lowland areas. The expansion of forest cover at the end of the glaciations would have again restricted the occurrence of campos rupestres vegetation to high elevations, which constitute the current centers of diversity of this species.

Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas.

PubMed

Boissin, E; Micu, D; Janczyszyn-Le Goff, M; Neglia, V; Bat, L; Todorova, V; Panayotova, M; Kruschel, C; Macic, V; Milchakova, N; Keskin, Ç; Anastasopoulou, A; Nasto, I; Zane, L; Planes, S

2016-05-01

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level. © 2016 John Wiley & Sons Ltd.

[Special mechanisms for reducing life span of cells and organisms, initiated by some weak external signals].

PubMed

Bychkovskaia, I B; Fedortseva, R F

2014-01-01

The study presents the results of many-years research conducted using biological objects of different organization level. It demonstrates special species-nonspecific form of weak external signals negative effect to cells life expectancy reduction caused by program damage of cells populations. This effect is detected after weak radiation, radio-chemical and thermal influences. It leads to faster extinction of postmitotic populations which can be a reason for life expectancy reduction of multicellular organisms. A possibility of such effect inheritance in the asexual and sexual reproduction is shown. Epigenetic mechanisms of this phenomenon are assumed.

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia.

PubMed

Ansmann, Ina C; Parra, Guido J; Lanyon, Janet M; Seddon, Jennifer M

2012-09-01

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F(ST) = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ(ST) = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure among bottlenose dolphins in Moreton Bay. © 2012 Blackwell Publishing Ltd.

Recovery of Weak Factor Loadings When Adding the Mean Structure in Confirmatory Factor Analysis: A Simulation Study

PubMed Central

Ximénez, Carmen

2016-01-01

This article extends previous research on the recovery of weak factor loadings in confirmatory factor analysis (CFA) by exploring the effects of adding the mean structure. This issue has not been examined in previous research. This study is based on the framework of Yung and Bentler (1999) and aims to examine the conditions that affect the recovery of weak factor loadings when the model includes the mean structure, compared to analyzing the covariance structure alone. A simulation study was conducted in which several constraints were defined for one-, two-, and three-factor models. Results show that adding the mean structure improves the recovery of weak factor loadings and reduces the asymptotic variances for the factor loadings, particularly for the models with a smaller number of factors and a small sample size. Therefore, under certain circumstances, modeling the means should be seriously considered for covariance models containing weak factor loadings. PMID:26779071

Method and apparatus for evaluating structural weakness in polymer matrix composites

DOEpatents

Wachter, E.A.; Fisher, W.G.

1996-01-09

A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image. 6 figs.

Method and apparatus for evaluating structural weakness in polymer matrix composites

DOEpatents

Wachter, Eric A.; Fisher, Walter G.

1996-01-01

A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image.

Structural Changes in Isometrically Contracting Insect Flight Muscle Trapped following a Mechanical Perturbation

PubMed Central

Wu, Shenping; Liu, Jun; Perz-Edwards, Robert J.; Tregear, Richard T.; Winkler, Hanspeter; Franzini-Armstrong, Clara; Sasaki, Hiroyuki; Goldman, Yale E.; Reedy, Michael K.; Taylor, Kenneth A.

2012-01-01

The application of rapidly applied length steps to actively contracting muscle is a classic method for synchronizing the response of myosin cross-bridges so that the average response of the ensemble can be measured. Alternatively, electron tomography (ET) is a technique that can report the structure of the individual members of the ensemble. We probed the structure of active myosin motors (cross-bridges) by applying 0.5% changes in length (either a stretch or a release) within 2 ms to isometrically contracting insect flight muscle (IFM) fibers followed after 5–6 ms by rapid freezing against a liquid helium cooled copper mirror. ET of freeze-substituted fibers, embedded and thin-sectioned, provides 3-D cross-bridge images, sorted by multivariate data analysis into ∼40 classes, distinct in average structure, population size and lattice distribution. Individual actin subunits are resolved facilitating quasi-atomic modeling of each class average to determine its binding strength (weak or strong) to actin. ∼98% of strong-binding acto-myosin attachments present after a length perturbation are confined to “target zones” of only two actin subunits located exactly midway between successive troponin complexes along each long-pitch helical repeat of actin. Significant changes in the types, distribution and structure of actin-myosin attachments occurred in a manner consistent with the mechanical transients. Most dramatic is near disappearance, after either length perturbation, of a class of weak-binding cross-bridges, attached within the target zone, that are highly likely to be precursors of strong-binding cross-bridges. These weak-binding cross-bridges were originally observed in isometrically contracting IFM. Their disappearance following a quick stretch or release can be explained by a recent kinetic model for muscle contraction, as behaviour consistent with their identification as precursors of strong-binding cross-bridges. The results provide a detailed model for contraction in IFM that may be applicable to contraction in other types of muscle. PMID:22761792

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PubMed Central

Suárez-Montes, Pilar; Chávez-Pesqueira, Mariana

2016-01-01

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Discussion Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. PMID:28028460

The Weak Shall Inherit: Bacteriocin-Mediated Interactions in Bacterial Populations

PubMed Central

Majeed, Hadeel; Lampert, Adam; Ghazaryan, Lusine; Gillor, Osnat

2013-01-01

Background Evolutionary arms race plays a major role in shaping biological diversity. In microbial systems, competition often involves chemical warfare and the production of bacteriocins, narrow-spectrum toxins aimed at killing closely related strains by forming pores in their target’s membrane or by degrading the target’s RNA or DNA. Although many empirical and theoretical studies describe competitive exclusion of bacteriocin-sensitive strains by producers of bacteriocins, the dynamics among producers are largely unknown. Methodology/Principal findings We used a reporter-gene assay to show that the bacterial response to bacteriocins’ treatment mirrors the inflicted damage Potent bacteriocins are lethal to competing strains, but at sublethal doses can serve as strong inducing agents, enhancing their antagonists’ bacteriocin production. In contrast, weaker bacteriocins are less toxic to their competitors and trigger mild bacteriocin expression. We used empirical and numerical models to explore the role of cross-induction in the arms race between bacteriocin-producing strains. We found that in well-mixed, unstructured environments where interactions are global, producers of weak bacteriocins are selectively advantageous and outcompete producers of potent bacteriocins. However, in spatially structured environments, where interactions are local, each producer occupies its own territory, and competition takes place only in “no man’s lands” between territories, resulting in much slower dynamics. Conclusion/Significance The models we present imply that producers of potent bacteriocins that trigger a strong response in neighboring bacteriocinogenic strains are doomed, while producers of weak bacteriocins that trigger a mild response in bacteriocinogenic strains flourish. This counter-intuitive outcome might explain the preponderance of weak bacteriocin producers in nature. However, the described scenario is prolonged in spatially structured environments thus promoting coexistence, allowing migration and evolution, and maintaining bacterial diversity. PMID:23704942

The impact of baryons on massive galaxy clusters: halo structure and cluster mass estimates

NASA Astrophysics Data System (ADS)

Henson, Monique A.; Barnes, David J.; Kay, Scott T.; McCarthy, Ian G.; Schaye, Joop

2017-03-01

We use the BAHAMAS (BAryons and HAloes of MAssive Systems) and MACSIS (MAssive ClusterS and Intercluster Structures) hydrodynamic simulations to quantify the impact of baryons on the mass distribution and dynamics of massive galaxy clusters, as well as the bias in X-ray and weak lensing mass estimates. These simulations use the subgrid physics models calibrated in the BAHAMAS project, which include feedback from both supernovae and active galactic nuclei. They form a cluster population covering almost two orders of magnitude in mass, with more than 3500 clusters with masses greater than 1014 M⊙ at z = 0. We start by characterizing the clusters in terms of their spin, shape and density profile, before considering the bias in both weak lensing and hydrostatic mass estimates. Whilst including baryonic effects leads to more spherical, centrally concentrated clusters, the median weak lensing mass bias is unaffected by the presence of baryons. In both the dark matter only and hydrodynamic simulations, the weak lensing measurements underestimate cluster masses by ≈10 per cent for clusters with M200 ≤ 1015 M⊙ and this bias tends to zero at higher masses. We also consider the hydrostatic bias when using both the true density and temperature profiles, and those derived from X-ray spectroscopy. When using spectroscopic temperatures and densities, the hydrostatic bias decreases as a function of mass, leading to a bias of ≈40 per cent for clusters with M500 ≥ 1015 M⊙. This is due to the presence of cooler gas in the cluster outskirts. Using mass weighted temperatures and the true density profile reduces this bias to 5-15 per cent.

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

PubMed Central

2013-01-01

Background Elucidating the native structure of a protein molecule from its sequence of amino acids, a problem known as de novo structure prediction, is a long standing challenge in computational structural biology. Difficulties in silico arise due to the high dimensionality of the protein conformational space and the ruggedness of the associated energy surface. The issue of multiple minima is a particularly troublesome hallmark of energy surfaces probed with current energy functions. In contrast to the true energy surface, these surfaces are weakly-funneled and rich in comparably deep minima populated by non-native structures. For this reason, many algorithms seek to be inclusive and obtain a broad view of the low-energy regions through an ensemble of low-energy (decoy) conformations. Conformational diversity in this ensemble is key to increasing the likelihood that the native structure has been captured. Methods We propose an evolutionary search approach to address the multiple-minima problem in decoy sampling for de novo structure prediction. Two population-based evolutionary search algorithms are presented that follow the basic approach of treating conformations as individuals in an evolving population. Coarse graining and molecular fragment replacement are used to efficiently obtain protein-like child conformations from parents. Potential energy is used both to bias parent selection and determine which subset of parents and children will be retained in the evolving population. The effect on the decoy ensemble of sampling minima directly is measured by additionally mapping a conformation to its nearest local minimum before considering it for retainment. The resulting memetic algorithm thus evolves not just a population of conformations but a population of local minima. Results and conclusions Results show that both algorithms are effective in terms of sampling conformations in proximity of the known native structure. The additional minimization is shown to be key to enhancing sampling capability and obtaining a diverse ensemble of decoy conformations, circumventing premature convergence to sub-optimal regions in the conformational space, and approaching the native structure with proximity that is comparable to state-of-the-art decoy sampling methods. The results are shown to be robust and valid when using two representative state-of-the-art coarse-grained energy functions. PMID:24565020

Population genetic structure of eelgrass (Zostera marina) on the Korean coast: Current status and conservation implications for future management

PubMed Central

Kim, Jae Hwan; Kang, Ji Hyoun; Jang, Ji Eun; Choi, Sun Kyeong; Kim, Min Ji; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name “eelgrass”) is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers. The level of genetic diversity was found to be significantly lower for populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal diversity (R) = 0.51], which is located approximately 155 km off the southernmost region of the Korean Peninsula, than for those in the South Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the mainland. South Korean eelgrass populations were substantially genetically divergent from one another (FST = 0.061–0.573), suggesting that limited contemporary gene flow has been taking place among populations. We also found weak but detectable temporal variation in genetic structure within a site over 10 years. In additional depth comparisons, statistically significant genetic differentiation was observed between shallow (or middle) and deep zones in two of three sites tested. Depleted genetic diversity, small effective population sizes (Ne) and limited connectivity for populations on Jeju Island indicate that these populations may be vulnerable to local extinction under changing environmental conditions, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of the Korean Peninsula, for this ecologically important species. PMID:28323864

Population genetic structure of eelgrass (Zostera marina) on the Korean coast: Current status and conservation implications for future management.

PubMed

Kim, Jae Hwan; Kang, Ji Hyoun; Jang, Ji Eun; Choi, Sun Kyeong; Kim, Min Ji; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name "eelgrass") is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers. The level of genetic diversity was found to be significantly lower for populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal diversity (R) = 0.51], which is located approximately 155 km off the southernmost region of the Korean Peninsula, than for those in the South Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the mainland. South Korean eelgrass populations were substantially genetically divergent from one another (FST = 0.061-0.573), suggesting that limited contemporary gene flow has been taking place among populations. We also found weak but detectable temporal variation in genetic structure within a site over 10 years. In additional depth comparisons, statistically significant genetic differentiation was observed between shallow (or middle) and deep zones in two of three sites tested. Depleted genetic diversity, small effective population sizes (Ne) and limited connectivity for populations on Jeju Island indicate that these populations may be vulnerable to local extinction under changing environmental conditions, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of the Korean Peninsula, for this ecologically important species.

Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

USGS Publications Warehouse

Hotaling, Scott; Muhlfeld, Clint C.; Giersch, J. Joseph; Ali, Omar; Jordan, Steve; Miller, Michael R.; Luikart, Gordon; Weisrock, David W.

2018-01-01

AimClimate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results.LocationAlpine streams in the Rocky Mountains of Glacier National Park, Montana, USA.TaxonLednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae.MethodsWe generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results.ResultsContemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation.Main conclusionsWe identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.

Stability in Real Food Webs: Weak Links in Long Loops

NASA Astrophysics Data System (ADS)

Neutel, Anje-Margriet; Heesterbeek, Johan A. P.; de Ruiter, Peter C.

2002-05-01

Increasing evidence that the strengths of interactions among populations in biological communities form patterns that are crucial for system stability requires clarification of the precise form of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links. We show and explain mathematically that this patterning enhances stability, because it reduces maximum ``loop weight'' and thus reduces the amount of intraspecific interaction needed for matrix stability. The patterns are brought about by biomass pyramids, a feature common to most ecosystems. Incorporation of biomass pyramids in 104 food-web descriptions reveals that the low weight of the long loops stabilizes complex food webs. Loop-weight analysis could be a useful tool for exploring the structure and organization of complex communities.

Genetic Structure and Potential Environmental Determinants of Local Genetic Diversity in Japanese Honeybees (Apis cerana japonica)

PubMed Central

Nagamitsu, Teruyoshi; Yasuda, Mika; Saito-Morooka, Fuki; Inoue, Maki N.; Nishiyama, Mio; Goka, Koichi; Sugiura, Shinji; Maeto, Kaoru; Okabe, Kimiko; Taki, Hisatomo

2016-01-01

Declines in honeybee populations have been a recent concern. Although causes of the declines remain unclear, environmental factors may be responsible. We focused on the potential environmental determinants of local populations of wild honeybees, Apis cerana japonica, in Japan. This subspecies has little genetic variation in terms of its mitochondrial DNA sequences, and genetic variations at nuclear loci are as yet unknown. We estimated the genetic structure and environmental determinants of local genetic diversity in nuclear microsatellite genotypes of fathers and mothers, inferred from workers collected at 139 sites. The genotypes of fathers and mothers showed weak isolation by distance and negligible genetic structure. The local genetic diversity was high in central Japan, decreasing toward the peripheries, and depended on the climate and land use characteristics of the sites. The local genetic diversity decreased as the annual precipitation increased, and increased as the proportion of urban and paddy field areas increased. Positive effects of natural forest area, which have also been observed in terms of forager abundance in farms, were not detected with respect to the local genetic diversity. The findings suggest that A. cerana japonica forms a single population connected by gene flow in its main distributional range, and that climate and landscape properties potentially affect its local genetic diversity. PMID:27898704

Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: The role of male-biased dispersal in a Holarctic sea duck

USGS Publications Warehouse

Peters, Jeffrey L.; Bolender, Kimberly A.; Pearce, John M.

2012-01-01

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from apparent panmixia to deep, reciprocally monophyletic lineages. Yet, these studies often found weak or no nuclear (nu) DNA structure, which was often attributed to male-biased gene flow, a common behaviour within this family. An alternative explanation for this ‘conflict’ is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA lead to different signals of population structure. We tested these alternatives by sequencing 12 nuDNA introns for a Holarctic pair of waterfowl subspecies, the European goosander (Mergus merganser merganser) and the North American common merganser (M. m. americanus), which exhibit strong population structure in mtDNA. We inferred effective population sizes, gene flow and divergence times from published mtDNA sequences and simulated expected differentiation for nuDNA based on those histories. Between Europe and North America, nuDNA ФST was 3.4-fold lower than mtDNA ФST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA ФST values were generally zero and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by nonmolecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.

Bivariate spline solution of time dependent nonlinear PDE for a population density over irregular domains.

PubMed

Gutierrez, Juan B; Lai, Ming-Jun; Slavov, George

2015-12-01

We study a time dependent partial differential equation (PDE) which arises from classic models in ecology involving logistic growth with Allee effect by introducing a discrete weak solution. Existence, uniqueness and stability of the discrete weak solutions are discussed. We use bivariate splines to approximate the discrete weak solution of the nonlinear PDE. A computational algorithm is designed to solve this PDE. A convergence analysis of the algorithm is presented. We present some simulations of population development over some irregular domains. Finally, we discuss applications in epidemiology and other ecological problems. Copyright © 2015 Elsevier Inc. All rights reserved.

Genetic Population Structure of Dastarcus helophoroides (Coleoptera: Bothrideridae) From Different Long-Horned Beetle Hosts Based on Complete Sequences of Mitochondrial COI.

PubMed

Zhang, Zhengqing; Chang, Yong; Li, Menglou

2017-06-01

Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) is an important natural enemy of long-horned beetles in China, Japan, and Korea. In this study, the genetic sequence of cytochrome oxidase subunit Ι was used to investigate the genetics and relationships within and among D. helophoroides populations collected from five different geographic locations. We used principal component analysis, heatmap, and Venn diagram results to determine the relationship between haplotypes and populations. In total, 26 haplotypes with 51 nucleotide polymorphic sites were defined, and low genetic diversity was found among the different populations. Significant genetic variations were observed mainly within populations, and no correlation was found between genetic distribution and geographical distance. Low pairwise fixation index values (-0.01424 to 0.04896) and high gene flows show that there was high gene exchange between populations. The codistributed haplotype DH01 was suggested to be the most ancestral haplotype, and other haplotypes were thought to have evolved from it through several mutations. In four of the populations, both common haplotypes (DH01, DH03, and DH22) and unique haplotypes were found. Low genetic diversity among different populations is related to a relatively high flight capacity, host movement, and human-aided dispersal of D. helophoroides. The high gene exchange and typically weak population genetic structure among five populations, especially among populations of Anoplophora glabripennis (Motschulsky), Monochamus alternatus (Hope), and Massicus raddei (Blessig), may suggest that these populations cross naturally in the field. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Population biology of the Florida manatee: An overview

USGS Publications Warehouse

O'Shea, Thomas J.; Ackerman, B.B.; O'Shea, Thomas J.; Ackerman, B.B.; Percival, H. Franklin

1995-01-01

In the following overview we discuss progress toward meeting the three objectives of the 1992 workshop: to provide a synthesis of existing information about manatee population biology; to evaluate the strengths and weaknesses of current data sets and approaches to research on manatee population biology; and to provide recommendations for research. We discuss progress in six topics that were assigned to working groups at the workshop: aerial survey and estimation of population size, reproduction, age structure, mortality, photoidentification and estimation of survival, and integration and modeling of population data. The overview includes recommendations by working group participants (*2 0'Shea et al. 1992). This workshop on manatee population biology was the most recent conference on the topic since 1978 (*BrowneIl and Rails 1981). Partly as a result of recommendations made at the 1978 workshop, several long-term population-related research projects were established. Therefore, we also measure progress in relation to knowledge available at the time of the earlier workshop. Finally, we provide a brief synopsis of pertinent new information on manatee population biology that became available between the 1992 workshop and publication of the proceedings and our conclusions about the status of the Florida manatee.

Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: panmixia or complex stock structure?

PubMed

Leone, Agostino; Urso, Ilenia; Damalas, Dimitrios; Martinsohn, Jann; Zanzi, Antonella; Mariani, Stefano; Sperone, Emilio; Micarelli, Primo; Garibaldi, Fulvio; Megalofonou, Persefoni; Bargelloni, Luca; Franch, Rafaella; Macias, David; Prodöhl, Paulo; Fitzpatrick, Séan; Stagioni, Marco; Tinti, Fausto; Cariani, Alessia

2017-01-01

The blue shark ( Prionace glauca , Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as "Critically Endangered", unlike its open-ocean counterpart. Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4-0.1 million of years. The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour.

An Aryl Hydrocarbon Receptor from the Salamander Ambystoma mexicanum Exhibits Low Sensitivity to 2,3,7,8-Tetrachlorodibenzo-p-dioxin.

PubMed

Shoots, Jenny; Fraccalvieri, Domenico; Franks, Diana G; Denison, Michael S; Hahn, Mark E; Bonati, Laura; Powell, Wade H

2015-06-02

Structural features of the aryl hydrocarbon receptor (AHR) can underlie species- and population-specific differences in its affinity for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These differences often explain variations in TCDD toxicity. Frogs are relatively insensitive to dioxin, and Xenopus AHRs bind TCDD with low affinity. Weak TCDD binding results from the combination of three residues in the ligand-binding domain: A354 and A370, and N325. Here we sought to determine whether this mechanism of weak TCDD binding is shared by other amphibian AHRs. We isolated an AHR cDNA from the Mexican axolotl (Ambystoma mexicanum). The encoded polypeptide contains identical residues at positions that confer low TCDD affinity to X. laevis AHRs (A364, A380, and N335), and homology modeling predicts they protrude into the binding cavity. Axolotl AHR bound one-tenth the TCDD of mouse AHR in velocity sedimentation analysis, and in transactivation assays, the EC50 for TCDD was 23 nM, similar to X. laevis AHR1β (27 nM) and greater than AHR containing the mouse ligand-binding domain (0.08 nM). Sequence, modeled structure, and function indicate that axolotl AHR binds TCDD weakly, predicting that A. mexicanum lacks sensitivity toTCDD toxicity. We hypothesize that this characteristic of axolotl and Xenopus AHRs arose in a common ancestor of the Caudata and Anura.

Crystallographic Phasing from Weak Anomalous Signals

PubMed Central

Liu, Qun; Hendrickson, Wayne A.

2015-01-01

The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin ≥ 3.5 Å) or where only lighter atoms (Z ≤ 20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization. PMID:26432413

Crystallographic phasing from weak anomalous signals.

PubMed

Liu, Qun; Hendrickson, Wayne A

2015-10-01

The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin≥3.5Å) or where only lighter atoms (Z≤20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

PubMed Central

Teacher, Amber GF; André, Carl; Jonsson, Per R; Merilä, Juha

2013-01-01

Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≍ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision. PMID:23745145

Evolution of cooperation in multilevel public goods games with community structures

NASA Astrophysics Data System (ADS)

Wang, Jing; Wu, Bin; Ho, Daniel W. C.; Wang, Long

2011-03-01

In a community-structured population, public goods games (PGG) occur both within and between communities. Such type of PGG is referred as multilevel public goods games (MPGG). We propose a minimalist evolutionary model of the MPGG and analytically study the evolution of cooperation. We demonstrate that in the case of sufficiently large community size and community number, if the imitation strength within community is weak, i.e., an individual imitates another one in the same community almost randomly, cooperation as well as punishment are more abundant than defection in the long run; if the imitation strength between communities is strong, i.e., the more successful strategy in two individuals from distinct communities is always imitated, cooperation and punishment are also more abundant. However, when both of the two imitation intensities are strong, defection becomes the most abundant strategy in the population. Our model provides insight into the investigation of the large-scale cooperation in public social dilemma among contemporary communities.

Environmental factors influence both abundance and genetic diversity in a widespread bird species

PubMed Central

Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

2013-01-01

Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites

PubMed Central

Song, Zhijiao; Zhang, Miaomiao; Li, Fagen; Weng, Qijie; Zhou, Chanpin; Li, Mei; Li, Jie; Huang, Huanhua; Mo, Xiaoyong; Gan, Siming

2016-01-01

Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations. PMID:27748400

Genetic seascape of the threatened Caribbean elkhorn coral, Acropora palmata, on the Puerto Rico Shelf.

PubMed

Mège, Pascal; Schizas, Nikolaos V; Reyes, Joselyd García; Hrbek, Tomas

2015-06-01

It has been proposed that the elkhorn coral, Acropora palmata , is genetically separated into two distinct provinces in the Caribbean, an Eastern and a Western population admixing in western Puerto Rico and around the Mona Passage. In this study, the genetic structure of A. palmata sampled at 11 Puerto Rican localities and localities from Curaçao, the Bahamas and Guadeloupe were examined. Analyses using five microsatellite markers showed that 75% of sampled colonies had unique genotypes, the rest being clone mates. Genetic diversity among genets was high (H E = 0.761) and consistent across localities (0.685 to 0.844). F ST ranged from -0.011 to 0.047 supporting low but significant genetic differentiation between localities within the previously reported Eastern and Western genetic provinces. Plots of genetic per geographic distances and significant Mantel tests supported isolation-by-distance (IBD) within Puerto Rico. Analysis with the software Structure favored a scenario with weak differentiation between two populations, assigning eastern Puerto Rican locations (Fajardo and Culebra), Guadeloupe and Curaçao to the Caribbean Eastern population and western Puerto Rican locations (west of Vega Baja and Ponce), Mona and the Bahamas to the Caribbean Western population. Vieques and San Juan area harbored admixed profiles. Standardized F ST s per 1,000 km unit further supported higher differentiation between localities belonging to different Structure populations, with IBD being stronger within Puerto Rico than on larger regional scales. This stronger genetic transition seems to separate localities between putative Eastern and Western provinces in the eastern Puerto Rican region, not around the Mona Passage.

Genetic seascape of the threatened Caribbean elkhorn coral, Acropora palmata, on the Puerto Rico Shelf

PubMed Central

Mège, Pascal; Schizas, Nikolaos V.; Reyes, Joselyd García; Hrbek, Tomas

2014-01-01

It has been proposed that the elkhorn coral, Acropora palmata, is genetically separated into two distinct provinces in the Caribbean, an Eastern and a Western population admixing in western Puerto Rico and around the Mona Passage. In this study, the genetic structure of A. palmata sampled at 11 Puerto Rican localities and localities from Curaçao, the Bahamas and Guadeloupe were examined. Analyses using five microsatellite markers showed that 75% of sampled colonies had unique genotypes, the rest being clone mates. Genetic diversity among genets was high (HE = 0.761) and consistent across localities (0.685 to 0.844). FST ranged from −0.011 to 0.047 supporting low but significant genetic differentiation between localities within the previously reported Eastern and Western genetic provinces. Plots of genetic per geographic distances and significant Mantel tests supported isolation-by-distance (IBD) within Puerto Rico. Analysis with the software Structure favored a scenario with weak differentiation between two populations, assigning eastern Puerto Rican locations (Fajardo and Culebra), Guadeloupe and Curaçao to the Caribbean Eastern population and western Puerto Rican locations (west of Vega Baja and Ponce), Mona and the Bahamas to the Caribbean Western population. Vieques and San Juan area harbored admixed profiles. Standardized FSTs per 1,000 km unit further supported higher differentiation between localities belonging to different Structure populations, with IBD being stronger within Puerto Rico than on larger regional scales. This stronger genetic transition seems to separate localities between putative Eastern and Western provinces in the eastern Puerto Rican region, not around the Mona Passage. PMID:26085704

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush)

PubMed Central

Coon, Andrew; Carson, Robert; Debes, Paul V.

2016-01-01

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists. PMID:27680019

Kinetic theory for the ion humps at the foot of the Earth's bow shock

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

Jovanovic, D.; Krasnoselskikh, V. V.

2009-10-15

The nonlinear kinetic theory is presented for the ion acoustic perturbations at the foot of the Earth's quasiperpendicular bow shock, that is characterized by weakly magnetized electrons and unmagnetized ions. The streaming ions, due to the reflection of the solar wind ions from the shock, provide the free energy source for the linear instability of the acoustic wave. In the fully nonlinear regime, a coherent localized solution is found in the form of a stationary ion hump, which is traveling with the velocity close to the phase velocity of the linear mode. The structure is supported by the nonlinearities comingmore » from the increased population of the resonant beam ions, trapped in the self-consistent potential. As their size in the direction perpendicular to the local magnetic field is somewhat smaller that the electron Larmor radius and much larger that the Debye length, their spatial properties are determined by the effects of the magnetic field on weakly magnetized electrons. These coherent structures provide a theoretical explanation for the bipolar electric pulses, observed upstream of the shock by Polar and Cluster satellite missions.« less

Psychometric evaluation of the Swedish adaptation of the Inventory for Assessing the Process of Cultural Competence Among Healthcare Professionals--Revised (IAPCC-R).

PubMed

Olt, Helen; Jirwe, Maria; Gustavsson, Petter; Emami, Azita

2010-01-01

The purpose of this study was to describe the translation, adaption, and psychometric evaluation process in relation to validity and reliability of the Swedish version of the instrument, Inventory for Assessing The Process of Cultural Competence Among Healthcare Professionals-Revised (IAPCC-R) following the translation, adaptation, and psychometric evaluation process. Validity tests were conducted on the response processes (N = 15), the content (N = 7), and the internal structure of the instrument (N = 334). Reliability (alpha = .65 for the total scale varying between -.01 and .65 for the different subscales) was evaluated in terms of internal consistency. Results indicated weak validity and reliability though it is difficult to conclude whether this is related to adaptation issues or the original construction.The testing of the response process identified problems in relation to respondents' conceptualization of cultural competence. The test of the content identified a weak correspondence between the items and the underlying model. In addition, a confirmatory factor analysis did not confirm the proposed structure of the instrument. This study concludes that this instrument is not valid and reliable for use with a Swedish population of practicing nurses or nursing students.

Dynamics of weakly inhomogeneous oscillator populations: perturbation theory on top of Watanabe-Strogatz integrability

NASA Astrophysics Data System (ADS)

Vlasov, Vladimir; Rosenblum, Michael; Pikovsky, Arkady

2016-08-01

As has been shown by Watanabe and Strogatz (WS) (1993 Phys. Rev. Lett. 70 2391), a population of identical phase oscillators, sine-coupled to a common field, is a partially integrable system: for any ensemble size its dynamics reduce to equations for three collective variables. Here we develop a perturbation approach for weakly nonidentical ensembles. We calculate corrections to the WS dynamics for two types of perturbations: those due to a distribution of natural frequencies and of forcing terms, and those due to small white noise. We demonstrate that in both cases, the complex mean field for which the dynamical equations are written is close to the Kuramoto order parameter, up to the leading order in the perturbation. This supports the validity of the dynamical reduction suggested by Ott and Antonsen (2008 Chaos 18 037113) for weakly inhomogeneous populations.

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

PubMed

Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

2016-05-10

Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Cryosolution infrared study of hydrogen bonded halothane acetylene complex

NASA Astrophysics Data System (ADS)

Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

2018-05-01

The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

Electron acoustic-Langmuir solitons in a two-component electron plasma

NASA Astrophysics Data System (ADS)

McKenzie, J. F.

2003-04-01

We investigate the conditions under which ‘high-frequency’ electron acoustic Langmuir solitons can be constructed in a plasma consisting of protons and two electron populations: one ‘cold’ and the other ‘hot’. Conservation of total momentum can be cast as a structure equation either for the ‘cold’ or ‘hot’ electron flow speed in a stationary wave using the Bernoulli energy equations for each species. The linearized version of the governing equations gives the dispersion equation for the stationary waves of the system, from which follows the necessary but not sufficient conditions for the existence of soliton structures; namely that the wave speed must be less than the acoustic speed of the ‘hot’ electron component and greater than the low-frequency compound acoustic speed of the two electron populations. In this wave speed regime linear waves are ‘evanescent’, giving rise to the exponential growth or decay, which readily can give rise to non-linear effects that may balance dispersion and allow soliton formation. In general the ‘hot’ component must be more abundant than the ‘cold’ one and the wave is characterized by a compression of the ‘cold’ component and an expansion in the ‘hot’ component necessitating a potential dip. Both components are driven towards their sonic points; the ‘cold’ from above and the ‘hot’ from below. It is this transonic feature which limits the amplitude of the soliton. If the ‘hot’ component is not sufficiently abundant the window for soliton formation shrinks to a narrow speed regime which is quasi-transonic relative to the ‘hot’ electron acoustic speed, and it is shown that smooth solitons cannot be constructed. In the special case of a very cold electron population (i.e. ‘highly supersonic’) and the other population being very hot (i.e. ‘highly subsonic’) with adiabatic index 2, the structure equation simplifies and can be integrated in terms of elementary transcendental functions that provide the fully non-linear counterpart to the weakly non-linear sech(2) -type solitons. In this case the limiting soliton is comprised of an infinite compression in the cold component, a weak rarefaction in the ‘hot’ electrons and a modest potential dip.

Part I. Student success in intensive versus traditional introductory chemistry courses. Part II. Synthesis of salts of the weakly coordinating trisphat anion

NASA Astrophysics Data System (ADS)

Hall, Mildred V.

Part I. Intensive courses have been shown to be associated with equal or greater student success than traditional-length courses in a wide variety of disciplines and education levels. Student records from intensive and traditional-length introductory general chemistry courses were analyzed to determine the effects, of the course format, the level of academic experience, life experience (age), GPA, academic major and gender on student success in the course. Pretest scores, GPA and ACT composite scores were used as measures of academic ability and prior knowledge; t-tests comparing the means of these variables were used to establish that the populations were comparable prior to the course. Final exam scores, total course points and pretest-posttest differences were used as measures of student success; t-tests were used to determine if differences existed between the populations. ANCOVA analyses revealed that student GPA, pretest scores and course format were the only variables tested that were significant in accounting for the variance of the academic success measures. In general, the results indicate that students achieved greater academic success in the intensive-format course, regardless of the level of academic experience, life experience, academic major or gender. Part II. Weakly coordinating anions have many important applications, one of which is to function as co-catalysts in the polymerization of olefins by zirconocene. The structure of tris(tetrachlorobenzenedialato) phosphate(V) or "trisphat" anion suggests that it might be an outstanding example of a weakly coordinating anion. Trisphat acid was synthesized and immediately used to prepare the stable tributylammonium trisphat, which was further reacted to produce trisphat salts of Group I metal cations in high yields. Results of the 35Cl NQR analysis of these trisphat salts indicate only very weak coordination between the metal cations and the chlorine atoms of the trisphat anion.

Frequency dependence 3.0: an attempt at codifying the evolutionary ecology perspective.

PubMed

Metz, Johan A J; Geritz, Stefan A H

2016-03-01

The fitness concept and perforce the definition of frequency independent fitnesses from population genetics is closely tied to discrete time population models with non-overlapping generations. Evolutionary ecologists generally focus on trait evolution through repeated mutant substitutions in populations with complicated life histories. This goes with using the per capita invasion speed of mutants as their fitness. In this paper we develop a concept of frequency independence that attempts to capture the practical use of the term by ecologists, which although inspired by population genetics rarely fits its strict definition. We propose to call the invasion fitnesses of an eco-evolutionary model frequency independent when the phenotypes can be ranked by competitive strength, measured by who can invade whom. This is equivalent to the absence of weak priority effects, protected dimorphisms and rock-scissor-paper configurations. Our concept differs from that of Heino et al. (TREE 13:367-370, 1998) in that it is based only on the signs of the invasion fitnesses, whereas Heino et al. based their definitions on the structure of the feedback environment, summarising the effect of all direct and indirect interactions between individuals on fitness. As it turns out, according to our new definition an eco-evolutionary model has frequency independent fitnesses if and only if the effect of the feedback environment on the fitness signs can be summarised by a single scalar with monotonic effect. This may be compared with Heino et al.'s concept of trivial frequency dependence defined by the environmental feedback influencing fitness, and not just its sign, in a scalar manner, without any monotonicity restriction. As it turns out, absence of the latter restriction leaves room for rock-scissor-paper configurations. Since in 'realistic' (as opposed to toy) models frequency independence is exceedingly rare, we also define a concept of weak frequency dependence, which can be interpreted intuitively as almost frequency independence, and analyse in which sense and to what extent the restrictions on the potential model outcomes of the frequency independent case stay intact for models with weak frequency dependence.

Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

PubMed Central

Voith von Voithenberg, Lena; Sánchez-Rico, Carolina; Kang, Hyun-Seo; Madl, Tobias; Zanier, Katia; Barth, Anders; Warner, Lisa R.; Sattler, Michael; Lamb, Don C.

2016-01-01

An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein–RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants. PMID:27799531

Environmental versus geographical determinants of genetic structure in two subalpine conifers.

PubMed

Mosca, Elena; González-Martínez, Santiago C; Neale, David B

2014-01-01

Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Targeted population screening of late onset Pompe disease in unspecified myopathy patients for Korean population.

PubMed

Lee, Jung Hwan; Shin, Jin-Hong; Park, Hyung Jun; Kim, Sook Za; Jeon, Young Mi; Kim, Hye Kyoung; Kim, Dae-Seong; Choi, Young-Chul

2017-06-01

We performed targeted population screening of late onset Pompe disease (LOPD) in unspecified myopathy patients, because early diagnosis is difficult due to its heterogeneous clinical features. We prospectively enrolled 90 unrelated myopathic patients who had one or more signs out of five LOPD-like clinical findings (proximal weakness, axial weakness, lingual weakness, respiratory difficulty, idiopathic hyperCKemia). Acid alpha glucosidase activity was evaluated with dried blood spot and mixed leukocyte simultaneously. For a final diagnosis of LOPD, 16 patients with decreased enzyme activity were genotyped by GAA molecular analysis. We found two patients with LOPD (2.2%), and the remaining 14 patients had at least one G576S or E689K mutation, known as the pseudodeficiency allele. Acid alpha glucosidase activity of LOPD patients was significantly lower than that of patients with at least one pseudodeficiency allele (p = 0.017). This study is the first LOPD screening study for targeted Korean population, and more generally, an Asian population. Our findings suggest that for diagnosis of LOPD in Asian population, modified cutoff value of acid alpha glucosidase activity with dry blood spot considering that of patients having heterozygote pathogenic variants or pseudodeficiency alleles may reduce time and cost requirements and increase the comfort of patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

PubMed

Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

2012-08-01

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Structure coefficients and strategy selection in multiplayer games.

PubMed

McAvoy, Alex; Hauert, Christoph

2016-01-01

Evolutionary processes based on two-player games such as the Prisoner's Dilemma or Snowdrift Game are abundant in evolutionary game theory. These processes, including those based on games with more than two strategies, have been studied extensively under the assumption that selection is weak. However, games involving more than two players have not received the same level of attention. To address this issue, and to relate two-player games to multiplayer games, we introduce a notion of reducibility for multiplayer games that captures what it means to break down a multiplayer game into a sequence of interactions with fewer players. We discuss the role of reducibility in structured populations, and we give examples of games that are irreducible in any population structure. Since the known conditions for strategy selection, otherwise known as [Formula: see text]-rules, have been established only for two-player games with multiple strategies and for multiplayer games with two strategies, we extend these rules to multiplayer games with many strategies to account for irreducible games that cannot be reduced to those simpler types of games. In particular, we show that the number of structure coefficients required for a symmetric game with [Formula: see text]-player interactions and [Formula: see text] strategies grows in [Formula: see text] like [Formula: see text]. Our results also cover a type of ecologically asymmetric game based on payoff values that are derived not only from the strategies of the players, but also from their spatial positions within the population.

The limits of weak selection and large population size in evolutionary game theory.

PubMed

Sample, Christine; Allen, Benjamin

2017-11-01

Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed. Formal mathematical definitions of the [Formula: see text] and [Formula: see text] limits are provided. Applying these definitions to the Moran process of evolutionary game theory, we obtain asymptotic expressions for fixation probability and conditions for success in these limits. We find that the asymptotic expressions for fixation probability, and the conditions for a strategy to be favored over a neutral mutation, are different in the [Formula: see text] and [Formula: see text] limits. However, the ordering of limits does not affect the conditions for one strategy to be favored over another.

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals

PubMed Central

Baker, Christa A.; Ma, Lisa; Casareale, Chelsea R.

2016-01-01

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8–12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. SIGNIFICANCE STATEMENT The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. PMID:27559179

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals.

PubMed

Baker, Christa A; Ma, Lisa; Casareale, Chelsea R; Carlson, Bruce A

2016-08-24

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8-12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. Copyright © 2016 the authors 0270-6474/16/368985-16$15.00/0.

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

PubMed Central

Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

2012-01-01

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations.

PubMed

Szövényi, P; Terracciano, S; Ricca, M; Giordano, S; Shaw, A J

2008-12-01

Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (IM and MIGRATE) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F(ST) = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289,000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.

Behavioral variability of choices versus structural inconsistency of preferences.

PubMed

Regenwetter, Michel; Davis-Stober, Clintin P

2012-04-01

Theories of rational choice often make the structural consistency assumption that every decision maker's binary strict preference among choice alternatives forms a strict weak order. Likewise, the very concept of a utility function over lotteries in normative, prescriptive, and descriptive theory is mathematically equivalent to strict weak order preferences over those lotteries, while intransitive heuristic models violate such weak orders. Using new quantitative interdisciplinary methodologies, we dissociate the variability of choices from the structural inconsistency of preferences. We show that laboratory choice behavior among stimuli of a classical "intransitivity" paradigm is, in fact, consistent with variable strict weak order preferences. We find that decision makers act in accordance with a restrictive mathematical model that, for the behavioral sciences, is extraordinarily parsimonious. Our findings suggest that the best place to invest future behavioral decision research is not in the development of new intransitive decision models but rather in the specification of parsimonious models consistent with strict weak order(s), as well as heuristics and other process models that explain why preferences appear to be weakly ordered.

Using genetic profiles of African forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in Gabon.

PubMed

Eggert, L S; Buij, R; Lee, M E; Campbell, P; Dallmeier, F; Fleischer, R C; Alonso, A; Maldonado, J E

2014-02-01

Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA containing energy and forestry concessions, we studied forest elephants to evaluate the importance of the MUA to wide-ranging species. We extracted DNA from elephant dung samples and used genetic information to identify over 500 individuals in the MUA and the parks. We then examined patterns of nuclear microsatellites and mitochondrial control-region sequences to infer population structure, movement patterns, and habitat use by age and sex. Population structure was weak but significant, and differentiation was more pronounced during the wet season. Within the MUA, males were more strongly associated with open habitats, such as wetlands and savannas, than females during the dry season. Many of the movements detected within and between seasons involved the wetlands and bordering lagoons. Our results suggest that the MUA provides year-round habitat for some elephants and additional habitat for others whose primary range is in the parks. With the continuing loss of roadless wilderness areas in Central Africa, well-managed MUAs will likely be important to the conservation of wide-ranging species. © 2013 Society for Conservation Biology.

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST).

PubMed

Dan, Tong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

2015-05-20

Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (I A (S)) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products.

The influence of habitat fragmentation on multiple plant-animal interactions and plant reproduction.

PubMed

Brudvig, Lars A; Damschen, Ellen I; Haddad, Nick M; Levey, Douglas J; Tewksbury, Joshua J

2015-10-01

Despite broad recognition that habitat loss represents the greatest threat to the world's biodiyersity, a mechanistic understanding of how habitat loss and associated fragmentation affect ecological systems has proven remarkably challenging. The challenge stems from the multiple interdependent ways that landscapes change following fragmentation and the ensuing complex impacts on populations and communities of interacting species. We confronted these challenges by evaluating how fragmentation affects individual plants through interactions with animals, across five herbaceous species native to longleaf pine savannas. We created a replicated landscape experiment that provides controlled tests of three major fragmentation effects (patch isolation, patch shape [i.e., edge-to-area ratio], and distance to edge), established experimental founder populations of the five species to control for spatial distributions and densities of individual plants, and employed structural equation modeling to evaluate the effects of fragmentation on plant reproductive output and the degree to which these impacts are mediated through altered herbivory, pollination, or pre-dispersal seed predation. Across species, the most consistent response to fragmentation was a reduction in herbivory. Herbivory, however, had little impact.on plant reproductive output, and thus we found little evidence for any resulting benefit to plants in fragments. In contrast, fragmentation rarely impacted pollination or pre-dispersal seed predation, but both of these interactions had strong and consistent impacts on plant reproductive output. As a result, our models robustly predicted plant reproductive output (r2 = 0.52-0.70), yet due to the weak effects of fragmentation on pollination and pre-dispersal seed predation, coupled with the weak effect of herbivory on plant reproduction, the effects of fragmentation on reproductive output were generally small in magnitude and inconsistent. This work provides mechanistic insight into landscape-scale variation in plant reproductive success, the relative importance of plant-animal interactions for structuring these dynamics, and the nuanced nature of how habitat fragmentation can affect populations and communities of interacting species.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae).

PubMed

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M; Marcet, Paula L

2013-12-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. Copyright © 2013. Published by Elsevier B.V.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae)

PubMed Central

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M.; Marcet, Paula L.

2016-01-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. PMID:24035810

Population size vs. social connectedness - A gene-culture coevolutionary approach to cumulative cultural evolution.

PubMed

Kobayashi, Yutaka; Ohtsuki, Hisashi; Wakano, Joe Y

2016-10-01

It has long been debated if population size is a crucial determinant of the level of culture. While empirical results are mixed, recent theoretical studies suggest that social connectedness between people may be a more important factor than the size of the entire population. These models, however, do not take into account evolutionary responses of learning strategies determining the mode of transmission and innovation and are hence not suitable for predicting the long-term implications of parameters of interest. In the present paper, to address this issue, we provide a gene-culture coevolution model, in which the microscopic learning process of each individual is explicitly described as a continuous-time stochastic process and time allocation to social and individual learning is allowed to evolve. We have found that social connectedness has a larger impact on the equilibrium level of culture than population size especially when connectedness is weak and population size is large. This result, combined with those of previous culture-only models, points to the importance of studying separate effects of population size and internal social structure to better understand spatiotemporal variation in the level of culture. Copyright © 2016 Elsevier Inc. All rights reserved.

Exposing the structure of an Arctic food web.

PubMed

Wirta, Helena K; Vesterinen, Eero J; Hambäck, Peter A; Weingartner, Elisabeth; Rasmussen, Claus; Reneerkens, Jeroen; Schmidt, Niels M; Gilg, Olivier; Roslin, Tomas

2015-09-01

How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) and their two dominant prey orders (Diptera and Lepidoptera). The resultant web shows a dense link structure and no compartmentalization or modularity across the three predator guilds. Thus, both individual predators and predator guilds tap heavily into the prey community of each other, offering versatile scope for indirect interactions across different parts of the web. The current description of a first but single arctic web may serve as a benchmark toward which to gauge future webs resolved by similar techniques. Targeting an unusual breadth of predator guilds, and relying on techniques with a high resolution, it suggests that species in this web are closely connected. Thus, our findings call for similar explorations of link structure across multiple guilds in both arctic and other webs. From an applied perspective, our description of an arctic web suggests new avenues for understanding how arctic food webs are built and function and of how they respond to current climate change. It suggests that to comprehend the community-level consequences of rapid arctic warming, we should turn from analyses of populations, population pairs, and isolated predator-prey interactions to considering the full set of interacting species.

The genetical theory of social behaviour

PubMed Central

Lehmann, Laurent; Rousset, François

2014-01-01

We survey the population genetic basis of social evolution, using a logically consistent set of arguments to cover a wide range of biological scenarios. We start by reconsidering Hamilton's (Hamilton 1964 J. Theoret. Biol. 7, 1–16 (doi:10.1016/0022-5193(64)90038-4)) results for selection on a social trait under the assumptions of additive gene action, weak selection and constant environment and demography. This yields a prediction for the direction of allele frequency change in terms of phenotypic costs and benefits and genealogical concepts of relatedness, which holds for any frequency of the trait in the population, and provides the foundation for further developments and extensions. We then allow for any type of gene interaction within and between individuals, strong selection and fluctuating environments and demography, which may depend on the evolving trait itself. We reach three conclusions pertaining to selection on social behaviours under broad conditions. (i) Selection can be understood by focusing on a one-generation change in mean allele frequency, a computation which underpins the utility of reproductive value weights; (ii) in large populations under the assumptions of additive gene action and weak selection, this change is of constant sign for any allele frequency and is predicted by a phenotypic selection gradient; (iii) under the assumptions of trait substitution sequences, such phenotypic selection gradients suffice to characterize long-term multi-dimensional stochastic evolution, with almost no knowledge about the genetic details underlying the coevolving traits. Having such simple results about the effect of selection regardless of population structure and type of social interactions can help to delineate the common features of distinct biological processes. Finally, we clarify some persistent divergences within social evolution theory, with respect to exactness, synergies, maximization, dynamic sufficiency and the role of genetic arguments. PMID:24686929

The genetical theory of social behaviour.

PubMed

Lehmann, Laurent; Rousset, François

2014-05-19

We survey the population genetic basis of social evolution, using a logically consistent set of arguments to cover a wide range of biological scenarios. We start by reconsidering Hamilton's (Hamilton 1964 J. Theoret. Biol. 7, 1-16 (doi:10.1016/0022-5193(64)90038-4)) results for selection on a social trait under the assumptions of additive gene action, weak selection and constant environment and demography. This yields a prediction for the direction of allele frequency change in terms of phenotypic costs and benefits and genealogical concepts of relatedness, which holds for any frequency of the trait in the population, and provides the foundation for further developments and extensions. We then allow for any type of gene interaction within and between individuals, strong selection and fluctuating environments and demography, which may depend on the evolving trait itself. We reach three conclusions pertaining to selection on social behaviours under broad conditions. (i) Selection can be understood by focusing on a one-generation change in mean allele frequency, a computation which underpins the utility of reproductive value weights; (ii) in large populations under the assumptions of additive gene action and weak selection, this change is of constant sign for any allele frequency and is predicted by a phenotypic selection gradient; (iii) under the assumptions of trait substitution sequences, such phenotypic selection gradients suffice to characterize long-term multi-dimensional stochastic evolution, with almost no knowledge about the genetic details underlying the coevolving traits. Having such simple results about the effect of selection regardless of population structure and type of social interactions can help to delineate the common features of distinct biological processes. Finally, we clarify some persistent divergences within social evolution theory, with respect to exactness, synergies, maximization, dynamic sufficiency and the role of genetic arguments.

Elderly persons with ICU-acquired weakness: the potential role for β-hydroxy-β-methylbutyrate (HMB) supplementation?

PubMed

Rahman, Adam; Wilund, Kenneth; Fitschen, Peter J; Jeejeebhoy, Khursheed; Agarwala, Ravi; Drover, John W; Mourtzakis, Marina

2014-07-01

Intensive care unit (ICU)-acquired weakness is common and characterized by muscle loss, weakness, and paralysis. It is associated with poor short-term outcomes, including increased mortality, but the consequences of reduced long-term outcomes, including decreased physical function and quality of life, can be just as devastating. ICU-acquired weakness is particularly relevant to elderly patients who are increasingly consuming ICU resources and are at increased risk for ICU-acquired weakness and complications, including mortality. Elderly patients often enter critical illness with reduced muscle mass and function and are also at increased risk for accelerated disuse atrophy with acute illness. Increasingly, intensivists and researchers are focusing on strategies and therapies aimed at improving long-term neuromuscular function. β-Hydroxy-β-methylbutyrate (HMB), an ergogenic supplement, has shown efficacy in elderly patients and certain clinical populations in counteracting muscle loss. The present review discusses ICU-acquired weakness, as well as the unique physiology of muscle loss and skeletal muscle function in elderly patients, and then summarizes the evidence for HMB in elderly patients and in clinical populations. We subsequently postulate on the potential role and strategies in studying HMB in elderly ICU patients to improve muscle mass and function. © 2013 American Society for Parenteral and Enteral Nutrition.

Reflective Amplification without Population Inversion from a Strongly Driven Superconducting Qubit

NASA Astrophysics Data System (ADS)

Wen, P. Y.; Kockum, A. F.; Ian, H.; Chen, J. C.; Nori, F.; Hoi, I.-C.

2018-02-01

Amplification of optical or microwave fields is often achieved by strongly driving a medium to induce population inversion such that a weak probe can be amplified through stimulated emission. Here we strongly couple a superconducting qubit, an artificial atom, to the field in a semi-infinite waveguide. When driving the qubit strongly on resonance such that a Mollow triplet appears, we observe a 7% amplitude gain for a weak probe at frequencies in between the triplet. This amplification is not due to population inversion, neither in the bare qubit basis nor in the dressed-state basis, but instead results from a four-photon process that converts energy from the strong drive to the weak probe. We find excellent agreement between the experimental results and numerical simulations without any free fitting parameters. Since our device consists of a single two-level artificial atom, the simplest possible quantum system, it can be viewed as the most fundamental version of a four-wave-mixing parametric amplifier.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats.

PubMed

Wereszczuk, Anna; Leblois, Raphaël; Zalewski, Andrzej

2017-12-22

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species' ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris

PubMed Central

Piotti, A.; Satovic, Z.; de la Rosa, R.; Belaj, A.

2017-01-01

Abstract Background and Aims Wild olive (Olea europaea subsp. europaea var. sylvestris) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. Methods The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. Key Results The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Conclusions Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources. PMID:28028015

Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris.

PubMed

Beghè, D; Piotti, A; Satovic, Z; de la Rosa, R; Belaj, A

2017-03-01

Wild olive ( Olea europaea subsp. europaea var. sylvestris ) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Disentangling association patterns in fission-fusion societies using African buffalo as an example

USGS Publications Warehouse

Cross, P.C.; Lloyd-Smith, James O.; Getz, W.M.

2005-01-01

A description of the social network of a population aids us in understanding dispersal, the spread of disease, and genetic structure in that population. Many animal populations can be classified as fission–fusion societies, whereby groups form and separate over time. Examples discussed in the literature include ungulates, primates and cetaceans (Lott and Minta, 1983, Whitehead et al., 1991, Henzi et al., 1997, Christal et al., 1998 and Chilvers and Corkeron, 2002). In this study, we use a heuristic simulation model to illustrate potential problems in applying traditional techniques of association analysis to fission–fusion societies and propose a new index of association: the fission decision index (FDI). We compare the conclusions resulting from traditional methods with those of the FDI using data from African buffalo, Syncerus caffer, in the Kruger National Park. The traditional approach suggested that the buffalo population was spatially and temporally structured into four different ‘herds’ with adult males only peripherally associated with mixed herds. Our FDI method indicated that association decisions of adult males appeared random, but those of other sex and age categories were nonrandom, particularly when we included the fission events associated with adult males. Furthermore, the amount of time that individuals spent together was only weakly correlated with their propensity to remain together during fission events. We conclude with a discussion of the applicability of the FDI to other studies.

Development of urbanization in arid and semi arid regions based on the water resource carrying capacity -- a case study of Changji, Xinjiang

NASA Astrophysics Data System (ADS)

Xiao, H.; Zhang, L.; Chai, Z.

2017-07-01

The arid and semiarid region in China where have a relatively weak economic foundation, independent development capacity, and the low-level of urbanization. The new urbanization within these regions is facing severe challenges brought by the constraints of resources. In this paper, we selected the Changji Hui Autonomous Prefecture, Xinjiang Uyghur Autonomous Region as study area. We found that agricultural planting structure is the key water consumption index based on the research about the main water demands of domestic, agriculture and industry. Finally, we suggest that more attentions should be paid to the rational utilization of water resources, population carrying capacity, and adjust and upgrade the industrial structure, with the purpose of coordination with the Silk Road Economic Belt.

Genetic diversity and structure of Megabalanus azoricus in the Azores: Implications for aquaculture management

NASA Astrophysics Data System (ADS)

De Girolamo, Mirko; Torboli, Valentina; Pallavicini, Alberto; Isidro, Eduardo

2017-11-01

Megabalanus azoricus giant barnacles are the most traditional seafood of the Azores archipelago (NE Atlantic). This valuable commercial species has been highly exploited in the past and it is considered one of the key species for the development of aquaculture in the region. Despite the importance for conservation and aquaculture there is still a lack of basic information about M. azoricus genetic diversity and population structure. Here we used seven microsatellites markers to analyse 300 samples collected at six out of nine islands of the Azores archipelago, including also different locations from a single island, to provide information on the scale of genetic diversity and population structure of this species. Parameters like heterozygosity, allelic richness and effective number of alleles indicated a high genetic diversity and variability among islands. Pairwise comparisons and PCoA analysis on FST and Jost's DEST showed significant and evident differentiation among sampling locations. Additionally, AMOVA allocates a small (6.02%) but statistically significant portion of the variance to the among Island level revealing also a weak resolution (1.87%) at finer scale. Additionally Monte Carlo resampling methods indicated the most likely sources of the recruits were the local or adjacent populations. Genetic risks associated with the giant barnacle potential production scheme should be taken into account in a future management plan delimiting, as precautionary measure, this culture at a single island or at groups of islands here identified. Moreover a monitoring strategy should be implemented with the aim to evaluate possible changes in genetic parameters of native populations.

Detection of selective sweeps in structured populations: a comparison of recent methods.

PubMed

Vatsiou, Alexandra I; Bazin, Eric; Gaggiotti, Oscar E

2016-01-01

Identifying genomic regions targeted by positive selection has been a long-standing interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of next-generation sequencing, which is fostering the development of large-scale catalogues of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyse these rich data sets, but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome-scan methods that consider explicitly the physical linkage among SNPs surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps (iHS, nSL, EHHST, xp-EHH, XP-EHHST, XPCLR and hapFLK). We use an individual-based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hapFLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate-to-high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods (XPCLR or hapFLK with iHS or nSL) can greatly increase the power to pinpoint the selected region. © 2015 John Wiley & Sons Ltd.

Ethical Considerations in HIV/AIDS Biobehavioral Surveys That Use Respondent-Driven Sampling: Illustrations From Lebanon

PubMed Central

DeJong, Jocelyn; Mahfoud, Ziyad; Khoury, Danielle; Barbir, Farah

2009-01-01

Respondent-driven sampling is especially useful for reaching hidden populations and is increasingly used internationally in public health research, particularly on HIV. Respondent-driven sampling involves peer recruitment and has a dual-incentive structure: both recruiters and their peer recruits are paid. Recent literature focusing on the ethical dimensions of this method in the US context has identified integral safeguards that protect against ethical violations. We analyzed a study of 3 groups in Lebanon who are at risk for HIV (injection drug users, men who have sex with men, female sex workers) and the ethical issues that arose. More explicit attention should be given to ethical issues involved in research implementing respondent-driven sampling of at-risk populations in developing countries, where ethical review mechanisms may be weak. PMID:19608961

Approximate probabilistic cellular automata for the dynamics of single-species populations under discrete logisticlike growth with and without weak Allee effects.

PubMed

Mendonça, J Ricardo G; Gevorgyan, Yeva

2017-05-01

We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor. We also investigate the conditions under which a one-parameter PCA derived from the more general six-parameter model can generate valid population growth dynamics. Numerical simulations illustrate the behavior of some of the PCA found.

Study on the Weak Stress in Flexural MEMS Cantilever

NASA Astrophysics Data System (ADS)

Ge, Yuetao; Ren, Yan

2018-03-01

In order to design a better piezoresistive MEMS cantilever beam, especially for cantilever beams that will detect weak forces or will be subjected to weak forces, this paper uses study on the weak stress in flexural MEMS cantilever. The sensor design structure, divided into protective layer, piezoresistive layer, support layer. The protective layer is responsible for protecting the piezoresistive layer so that the varistor is insulated from the outside; the piezoresistive layer is used to make the varistor; the support layer forms the main part of the cantilever beam, the majority of the cantilever beam. This paper has some value for cantilever multilayer structure design and cantilever beam size design.

Prediction of weak topological insulators in layered semiconductors.

PubMed

Yan, Binghai; Müchler, Lukas; Felser, Claudia

2012-09-14

We report the discovery of weak topological insulators by ab initio calculations in a honeycomb lattice. We propose a structure with an odd number of layers in the primitive unit cell as a prerequisite for forming weak topological insulators. Here, the single-layered KHgSb is the most suitable candidate for its large bulk energy gap of 0.24 eV. Its side surface hosts metallic surface states, forming two anisotropic Dirac cones. Although the stacking of even-layered structures leads to trivial insulators, the structures can host a quantum spin Hall layer with a large bulk gap, if an additional single layer exists as a stacking fault in the crystal. The reported honeycomb compounds can serve as prototypes to aid in the finding of new weak topological insulators in layered small-gap semiconductors.

Von Bertalanffy's dynamics under a polynomial correction: Allee effect and big bang bifurcation

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, A. K.; Fournier-Prunaret, D.

2016-02-01

In this work we consider new one-dimensional populational discrete dynamical systems in which the growth of the population is described by a family of von Bertalanffy's functions, as a dynamical approach to von Bertalanffy's growth equation. The purpose of introducing Allee effect in those models is satisfied under a correction factor of polynomial type. We study classes of von Bertalanffy's functions with different types of Allee effect: strong and weak Allee's functions. Dependent on the variation of four parameters, von Bertalanffy's functions also includes another class of important functions: functions with no Allee effect. The complex bifurcation structures of these von Bertalanffy's functions is investigated in detail. We verified that this family of functions has particular bifurcation structures: the big bang bifurcation of the so-called “box-within-a-box” type. The big bang bifurcation is associated to the asymptotic weight or carrying capacity. This work is a contribution to the study of the big bang bifurcation analysis for continuous maps and their relationship with explosion birth and extinction phenomena.

Designing future dark energy space missions. II. Photometric redshift of space weak lensing optimized surveys

NASA Astrophysics Data System (ADS)

Jouvel, S.; Kneib, J.-P.; Bernstein, G.; Ilbert, O.; Jelinsky, P.; Milliard, B.; Ealet, A.; Schimd, C.; Dahlen, T.; Arnouts, S.

2011-08-01

Context. With the discovery of the accelerated expansion of the universe, different observational probes have been proposed to investigate the presence of dark energy, including possible modifications to the gravitation laws by accurately measuring the expansion of the Universe and the growth of structures. We need to optimize the return from future dark energy surveys to obtain the best results from these probes. Aims: A high precision weak-lensing analysis requires not an only accurate measurement of galaxy shapes but also a precise and unbiased measurement of galaxy redshifts. The survey strategy has to be defined following both the photometric redshift and shape measurement accuracy. Methods: We define the key properties of the weak-lensing instrument and compute the effective PSF and the overall throughput and sensitivities. We then investigate the impact of the pixel scale on the sampling of the effective PSF, and place upper limits on the pixel scale. We then define the survey strategy computing the survey area including in particular both the Galactic absorption and Zodiacal light variation accross the sky. Using the Le Phare photometric redshift code and realistic galaxy mock catalog, we investigate the properties of different filter-sets and the importance of the u-band photometry quality to optimize the photometric redshift and the dark energy figure of merit (FoM). Results: Using the predicted photometric redshift quality, simple shape measurement requirements, and a proper sky model, we explore what could be an optimal weak-lensing dark energy mission based on FoM calculation. We find that we can derive the most accurate the photometric redshifts for the bulk of the faint galaxy population when filters have a resolution ℛ ~ 3.2. We show that an optimal mission would survey the sky through eight filters using two cameras (visible and near infrared). Assuming a five-year mission duration, a mirror size of 1.5 m and a 0.5 deg2 FOV with a visible pixel scale of 0.15'', we found that a homogeneous survey reaching a survey population of IAB = 25.6 (10σ) with a sky coverage of ~11 000 deg2 maximizes the weak lensing FoM. The effective number density of galaxies used for WL is then ~45 gal/arcmin2, which is at least a factor of two higher than ground-based surveys. Conclusions: This study demonstrates that a full account of the observational strategy is required to properly optimize the instrument parameters and maximize the FoM of the future weak-lensing space dark energy mission.

Long-slit optical spectroscopy of powerful far-infrared galaxies - The nature of the nuclear energy source

NASA Technical Reports Server (NTRS)

Armus, Lee; Heckman, Timothy M.; Miley, George K.

1989-01-01

Optical spectroscopic data are presented for a sample of 47 powerful far-IR galaxies chosen for IR spectral shape, and for six other IR-bright galaxies. The stellar absorption lines expected from a population of old stars are generally very weak in the nuclei of the galaxies. Very weak Mg I absorption is found in regions well off the nucleus, implying that the visible spectrum is dominated by young stars and not by an AGN. At least one, and probably five, of the galaxies have detectable WR emission features, providing additional evidence for a young stellar population. About 20 percent of the galaxies have strong Balmer absorption lines, indicating the presence of a substantial intermediate-age stellar population. The equivalent width of the H-alpha emission line can be modeled as arising from a mixture of a large young population and an intermediate-age population of stars.

Effects of seed bank disturbance on the fine-scale genetic structure of populations of the rare shrub Grevillea macleayana.

PubMed

England, P R; Whelan, R J; Ayre, D J

2003-11-01

Dispersal in most plants is mediated by the movement of seeds and pollen, which move genes across the landscape differently. Grevillea macleayana is a rare, fire-dependent Australian shrub with large seeds lacking adaptations for dispersal; yet it produces inflorescences adapted to pollination by highly mobile vertebrates (eg birds). Interpreting fine-scale genetic structure in the light of these two processes is confounded by the recent imposition of anthropogenic disturbances with potentially contrasting genetic consequences: (1) the unusual foraging behaviour of exotic honeybees and 2. widespread disturbance of the soil-stored seedbank by road building and quarrying. To test for evidence of fine-scale genetic structure within G. macleayana populations and to test the prediction that such structure might be masked by disturbance of the seed bank, we sampled two sites in undisturbed habitat and compared their genetic structure with two sites that had been strongly affected by road building using a test for spatial autocorrelation of genotypes. High selfing levels inferred from genotypes at all four sites implies that pollen dispersal is limited. Consistent with this, we observed substantial spatial clustering of genes at 10 m or less in the two undisturbed populations and argue that this reflects the predicted effects of both high selfing levels and limited seed dispersal. In contrast, at the two sites disturbed by road building, spatial autocorrelation was weak. This suggests there has been mixing of the seed bank, counteracting the naturally low dispersal and elevated selfing due to honeybees. Pollination between near neighbours with reduced relatedness potentially has fitness consequences for G. macleayana in disturbed sites.

No evidence for host specialization or host-race formation in the European bitterling (Rhodeus amarus), a fish that parasitizes freshwater mussels.

PubMed

Reichard, M; Bryja, J; Polačik, M; Smith, C

2011-09-01

Coevolutionary relationships between parasites and hosts can elevate the rate of evolutionary changes owing to reciprocal adaptations between coevolving partners. Such relationships can result in the evolution of host specificity. Recent methodological advances have permitted the recognition of cryptic lineages, with important consequences for our understanding of biological diversity. We used the European bitterling (Rhodeus amarus), a freshwater fish that parasitizes unionid mussels, to investigate host specialization across regions of recent and ancient sympatry between coevolving partners. We combined genetic data (12 microsatellite and 2 mitochondrial markers) from five populations with experimental data for possible mechanisms of host species recognition (imprinting and conditioning). We found no strong evidence for the existence of cryptic lineages in R. amarus, though a small proportion of variation among individuals in an area of recent bitterling-mussel association was statistically significant in explaining host specificity. No other measures supported the existence of host-specific lineages. Behavioural data revealed a weak effect of conditioning that biased behavioural preferences towards specific host species. Host imprinting had no effect on oviposition behaviour. Overall, we established that populations of R. amarus show limited potential for specialization, manifested as weak effects of host conditioning and genetic within-population structure. Rhodeus amarus is the only species of mussel-parasitizing fish in Europe, which contrasts with the species-rich communities of bitterling in eastern Asia where several host-specific bitterling occur. We discuss costs and constraints on the evolution of host-specific lineages in our study system and more generally. © 2011 Blackwell Publishing Ltd.

Phase behaviour and structure of stable complexes of oppositely charged polyelectrolytes

NASA Astrophysics Data System (ADS)

Mengarelli, V.; Auvray, L.; Zeghal, M.

2009-03-01

We study the formation and structure of stable electrostatic complexes between oppositely charged polyelectrolytes, a long polymethacrylic acid and a shorter polyethylenimine, at low pH, where the polyacid is weakly charged. We explore the phase diagram as a function of the charge and concentration ratio of the constituents. In agreement with theory, turbidity and ζ potential measurements show two distinct regimes of weak and strong complexation, which appear successively as the pH is increased and are separated by a well-defined limit. Weak complexes observed by neutron scattering and contrast matching have an open, non-compact structure, while strong complexes are condensed.

Cosmology and the weak interaction

NASA Technical Reports Server (NTRS)

Schramm, David N.

1989-01-01

The weak interaction plays a critical role in modern Big Bang cosmology. Two of its most publicized comological connections are emphasized: big bang nucleosynthesis and dark matter. The first of these is connected to the cosmological prediction of neutrine flavors, N(sub nu) is approximately 3 which in now being confirmed. The second is interrelated to the whole problem of galacty and structure formation in the universe. The role of the weak interaction both for dark matter candidates and for the problem of generating seeds to form structure is demonstrated.

Modeling approaches in avian conservation and the role of field biologists

USGS Publications Warehouse

Beissinger, Steven R.; Walters, J.R.; Catanzaro, D.G.; Smith, Kimberly G.; Dunning, J.B.; Haig, Susan M.; Noon, Barry; Stith, Bradley M.

2006-01-01

This review grew out of our realization that models play an increasingly important role in conservation but are rarely used in the research of most avian biologists. Modelers are creating models that are more complex and mechanistic and that can incorporate more of the knowledge acquired by field biologists. Such models require field biologists to provide more specific information, larger sample sizes, and sometimes new kinds of data, such as habitat-specific demography and dispersal information. Field biologists need to support model development by testing key model assumptions and validating models. The best conservation decisions will occur where cooperative interaction enables field biologists, modelers, statisticians, and managers to contribute effectively. We begin by discussing the general form of ecological models—heuristic or mechanistic, "scientific" or statistical—and then highlight the structure, strengths, weaknesses, and applications of six types of models commonly used in avian conservation: (1) deterministic single-population matrix models, (2) stochastic population viability analysis (PVA) models for single populations, (3) metapopulation models, (4) spatially explicit models, (5) genetic models, and (6) species distribution models. We end by considering their unique attributes, determining whether the assumptions that underlie the structure are valid, and testing the ability of the model to predict the future correctly.

Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: panmixia or complex stock structure?

PubMed Central

Damalas, Dimitrios; Martinsohn, Jann; Zanzi, Antonella; Mariani, Stefano; Sperone, Emilio; Micarelli, Primo; Garibaldi, Fulvio; Megalofonou, Persefoni; Bargelloni, Luca; Franch, Rafaella; Macias, David; Prodöhl, Paulo; Fitzpatrick, Séan; Stagioni, Marco; Tinti, Fausto; Cariani, Alessia

2017-01-01

Background The blue shark (Prionace glauca, Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as “Critically Endangered”, unlike its open-ocean counterpart. Methods Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Results Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4–0.1 million of years. Discussion The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour. PMID:29230359

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus).

PubMed

Johansson, M L; Banks, M A; Glunt, K D; Hassel-Finnegan, H M; Buonaccorsi, V P

2008-07-01

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

USGS Publications Warehouse

Sonsthagen, Sarah A.; Jay, Chadwick V.; Fischbach, Anthony S.; Sage, George K.; Talbot, Sandra L.

2012-01-01

Pacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST=0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST=0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST=0.019; mtDNA ΦST=0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST=0.019–0.035; mtDNA ΦST=0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

A population genomics insight into the Mediterranean origins of wine yeast domestication.

PubMed

Almeida, Pedro; Barbosa, Raquel; Zalar, Polona; Imanishi, Yumi; Shimizu, Kiminori; Turchetti, Benedetta; Legras, Jean-Luc; Serra, Marta; Dequin, Sylvie; Couloux, Arnaud; Guy, Julie; Bensasson, Douda; Gonçalves, Paula; Sampaio, José Paulo

2015-11-01

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts. © 2015 John Wiley & Sons Ltd.

Origin of 12 micrometer Emission Across Galaxy Populations from Wise and ADSS Surveys

NASA Technical Reports Server (NTRS)

Donso, E.; Yan, Lin; Tsai, C.; Eisenhardt, P; Stern, D.; Assef, R. J.; Leisawitz, D.; Jarrett, T. H.; Stanford, S. A.

2012-01-01

We cross-matched Wide-field Infrared Survey Explorer sources brighter than 1 mJy at 12 micron with the Sloan Digital Sky Survey galaxy spectroscopic catalog to produce a sample of approx. 10(exp 5) galaxies at z = 0.08, the largest of its kind. This sample is dominated (70%) by star-forming (SF) galaxies from the blue sequence, with total IR luminosities in the range approx 10(exp 8)-10(exp 12) Solar L. We identify which stellar populations are responsible for most of the 12 micron emission. We find that most (approx 80%) of the 12 micron emission in SF galaxies is produced by stellar populations younger than 0.6 Gyr. In contrast, the 12 micron emission in weak active galactic nuclei (AGNs; L [O iii] < 10(exo 7) solar L ) is produced by older stars, with ages of approx 1-3 Gyr. We find that L(sub 12 micron) linearly correlates with stellar mass for SF galaxies. At fixed 12 micron luminosity, weak AGNs deviate toward higher masses since they tend to be hosted by massive, early-type galaxies with older stellar populations. SF galaxies and weak AGNs follow different L(sub 12 micron) - SFR (star formation rate) relations, with weak AGNs showing excess 12 micron emission at low SFR (0.02-1 solar M /yr). This is likely due to dust grains heated by older stars. While the specific star formation rate (SSFR) of SF galaxies is nearly constant, the SSFR of weak AGNs decreases by approx 3 orders of magnitude, reflecting the very different star formation efficiencies between SF galaxies and massive, early-type galaxies. Stronger type II AGNs in our sample (L(sub [O iii]) > 10(exp 7) solar L ), act as an extension of massive SF galaxies, connecting the SF and weak AGN sequences. This suggests a picture where galaxies form stars normally until an AGN (possibly after a starburst episode) starts to gradually quench the SF activity. We also find that 4.6-12 micron color is a useful first-order indicator of SF activity in a galaxy when no other data are available.

Genetic Structure of Wild Bonobo Populations: Diversity of Mitochondrial DNA and Geographical Distribution

PubMed Central

Higuchi, Shoko; Sakamaki, Tetsuya; Hart, John A.; Hart, Terese B.; Tokuyama, Nahoko; Reinartz, Gay E.; Guislain, Patrick; Dupain, Jef; Cobden, Amy K.; Mulavwa, Mbangi N.; Yangozene, Kumugo; Darroze, Serge; Devos, Céline; Furuichi, Takeshi

2013-01-01

Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species’ range. In 136 effective samples from different individuals (range: 7–37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation. PMID:23544084

Identification of interfaces involved in weak interactions with application to F-actin-aldolase rafts.

PubMed

Hu, Guiqing; Taylor, Dianne W; Liu, Jun; Taylor, Kenneth A

2018-03-01

Macromolecular interactions occur with widely varying affinities. Strong interactions form well defined interfaces but weak interactions are more dynamic and variable. Weak interactions can collectively lead to large structures such as microvilli via cooperativity and are often the precursors of much stronger interactions, e.g. the initial actin-myosin interaction during muscle contraction. Electron tomography combined with subvolume alignment and classification is an ideal method for the study of weak interactions because a 3-D image is obtained for the individual interactions, which subsequently are characterized collectively. Here we describe a method to characterize heterogeneous F-actin-aldolase interactions in 2-D rafts using electron tomography. By forming separate averages of the two constituents and fitting an atomic structure to each average, together with the alignment information which relates the raw motif to the average, an atomic model of each crosslink is determined and a frequency map of contact residues is computed. The approach should be applicable to any large structure composed of constituents that interact weakly and heterogeneously. Copyright © 2017 Elsevier Inc. All rights reserved.

Global Equity and Justice Issues for Young People During the First Three Decades of Life.

PubMed

Petersen, Anne; Koller, Silvia H; Motti-Stefanidi, Frosso; Verma, Suman

This chapter takes a global perspective on equity and justice during development from childhood into adulthood. Globally, the population of young people is booming with the most rapid growth among young people in the poorest countries. While already faced with significant issues related to development and thriving, this population boom also exacerbates equity and justice for these children. Given this urgent situation, this chapter builds from the large body of minority world research, as well as the emergent majority world research, to argue that in order to turn the youth bulge into a demographic dividend, researchers must utilize a positive development framing rather than the more dominant problem-focused framing in studying these issues. The structural challenges confronting young people growing up in contexts marked by poverty; weak systems and institutions, especially those serving education, health, and justice; weak political and governance systems; and continual conflict must also be addressed by global and national governmental bodies. This chapter will emphasize the strengths and opportunities of the majority world, highlighting some of the strong, emergent examples of programs that support and develop the strengths of young people. We conclude with a discussion of appropriate support required from the minority and majority worlds that would further strengthen young people globally and enable them to become leaders of a more just, equitable world. © 2016 Elsevier Inc. All rights reserved.

The Frequency of Intrinsic X-Ray Weakness among Broad Absorption Line Quasars

NASA Astrophysics Data System (ADS)

Liu, Hezhen; Luo, B.; Brandt, W. N.; Gallagher, S. C.; Garmire, G. P.

2018-06-01

We present combined ≈14–37 ks Chandra observations of seven z = 1.6–2.7 broad absorption line (BAL) quasars selected from the Large Bright Quasar Survey (LBQS). These seven objects are high-ionization BAL (HiBAL) quasars, and they were undetected in the Chandra hard band (2–8 keV) in previous observations. The stacking analyses of previous Chandra observations suggested that these seven objects likely contain some candidates for intrinsically X-ray weak BAL quasars. With the new Chandra observations, six targets are detected. We calculate their effective power-law photon indices and hard-band flux weakness, and find that two objects, LBQS 1203+1530 and LBQS 1442–0011, show soft/steep spectral shapes ({{{Γ }}}eff}={2.2}-0.9+0.9 and {1.9}-0.8+0.9) and significant X-ray weakness in the hard band (by factors of ≈15 and 12). We conclude that the two HiBAL quasars are good candidates for intrinsically X-ray weak BAL quasars. The mid-infrared-to-ultraviolet spectral energy distributions of the two candidates are consistent with those of typical quasars. We constrain the fraction of intrinsically X-ray weak active galactic nuclei (AGNs) among HiBAL quasars to be ≈7%–10% (2/29–3/29), and we estimate it is ≈6%–23% (2/35–8/35) among the general BAL quasar population. Such a fraction is considerably larger than that among non-BAL quasars, and we suggest that intrinsically X-ray weak quasars are preferentially observed as BAL quasars. Intrinsically X-ray weak AGNs likely comprise a small minority of the luminous type 1 AGN population, and they should not affect significantly the completeness of these AGNs found in deep X-ray surveys.

Isotropy of Angular Frequencies and Weak Chimeras with Broken Symmetry

NASA Astrophysics Data System (ADS)

Bick, Christian

2017-04-01

The notion of a weak chimeras provides a tractable definition for chimera states in networks of finitely many phase oscillators. Here, we generalize the definition of a weak chimera to a more general class of equivariant dynamical systems by characterizing solutions in terms of the isotropy of their angular frequency vector—for coupled phase oscillators the angular frequency vector is given by the average of the vector field along a trajectory. Symmetries of solutions automatically imply angular frequency synchronization. We show that the presence of such symmetries is not necessary by giving a result for the existence of weak chimeras without instantaneous or setwise symmetries for coupled phase oscillators. Moreover, we construct a coupling function that gives rise to chaotic weak chimeras without symmetry in weakly coupled populations of phase oscillators with generalized coupling.

Weak lensing probe of cubic Galileon model

NASA Astrophysics Data System (ADS)

Dinda, Bikash R.

2018-06-01

The cubic Galileon model containing the lowest non-trivial order action of the full Galileon action can produce the stable late-time cosmic acceleration. This model can have a significant role in the growth of structures. The signatures of the cubic Galileon model in the structure formation can be probed by the weak lensing statistics. Weak lensing convergence statistics is one of the strongest probes to the structure formation and hence it can probe the dark energy or modified theories of gravity models. In this work, we investigate the detectability of the cubic Galileon model from the ΛCDM model or from the canonical quintessence model through the convergence power spectrum and bi-spectrum.

The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin

PubMed Central

Cericola, Fabio; Portis, Ezio; Toppino, Laura; Barchi, Lorenzo; Acciarri, Nazareno; Ciriaci, Tommaso; Sala, Tea; Rotino, Giuseppe Leonardo; Lanteri, Sergio

2013-01-01

A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the “Occidental” and the “Oriental” germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach. PMID:24040032

Matching oceanography and genetics at the basin scale. Seascape connectivity of the Mediterranean shore crab in the Adriatic Sea.

PubMed

Schiavina, M; Marino, I A M; Zane, L; Melià, P

2014-11-01

Investigating the interactions between the physical environment and early life history is crucial to understand the mechanisms that shape the genetic structure of marine populations. Here, we assessed the genetic differentiation in a species with larval dispersal, the Mediterranean shore crab (Carcinus aestuarii) in the Adriatic Sea (central Mediterranean), and we investigated the role of oceanic circulation in shaping population structure. To this end, we screened 11 polymorphic microsatellite loci from 431 individuals collected at eight different sites. We found a weak, yet significant, genetic structure into three major clusters: a northern Adriatic group, a central Adriatic group and one group including samples from southern Adriatic and Ionian seas. Genetic analyses were compared, under a seascape genetics approach, with estimates of potential larval connectivity obtained with a coupled physical-biological model that integrates a water circulation model and a description of biological traits affecting dispersal. The cross-validation of the results of the two approaches supported the view that genetic differentiation reflects an oceanographic subdivision of the Adriatic Sea into three subbasins, with circulation patterns allowing the exchange of larvae through permanent connections linking north Adriatic sites and ephemeral connections like those linking the central Adriatic with northern and southern locations. © 2014 John Wiley & Sons Ltd.

Evolution of a plastic quantitative trait in an age-structured population in a fluctuating environment.

PubMed

Engen, Steinar; Lande, Russell; Saether, Bernt-Erik

2011-10-01

We analyze weak fluctuating selection on a quantitative character in an age-structured population not subject to density regulation. We assume that early in the first year of life before selection, during a critical state of development, environments exert a plastic effect on the phenotype, which remains constant throughout the life of an individual. Age-specific selection on the character affects survival and fecundity, which have intermediate optima subject to temporal environmental fluctuations with directional selection in some age classes as special cases. Weighting individuals by their reproductive value, as suggested by Fisher, we show that the expected response per year in the weighted mean character has the same form as for models with no age structure. Environmental stochasticity generates stochastic fluctuations in the weighted mean character following a first-order autoregressive model with a temporally autocorrelated noise term and stationary variance depending on the amount of phenotypic plasticity. The parameters of the process are simple weighted averages of parameters used to describe age-specific survival and fecundity. The "age-specific selective weights" are related to the stable distribution of reproductive values among age classes. This allows partitioning of the change in the weighted mean character into age-specific components. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

The population structure and diversity of eggplant from Asia and the Mediterranean Basin.

PubMed

Cericola, Fabio; Portis, Ezio; Toppino, Laura; Barchi, Lorenzo; Acciarri, Nazareno; Ciriaci, Tommaso; Sala, Tea; Rotino, Giuseppe Leonardo; Lanteri, Sergio

2013-01-01

A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the "Occidental" and the "Oriental" germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach.

Communication: Charge-population based dispersion interactions for molecules and materials

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

Stöhr, Martin; Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching; Michelitsch, Georg S.

2016-04-21

We introduce a system-independent method to derive effective atomic C{sub 6} coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C{sub 6} coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recentlymore » developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces.« less

Genetic and Ecological Outcomes of Inga vera Subsp. affinis (Leguminosae) Tree Plantations in a Fragmented Tropical Landscape

PubMed Central

Cruz Neto, Oswaldo; Aguiar, Antonio V.; Twyford, Alex D.; Neaves, Linda E.; Pennington, R. Toby; Lopes, Ariadna V.

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = −0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing. PMID:24932729

Genetic and ecological outcomes of Inga vera subsp. affinis (Leguminosae) tree plantations in a fragmented tropical landscape.

PubMed

Cruz Neto, Oswaldo; Aguiar, Antonio V; Twyford, Alex D; Neaves, Linda E; Pennington, R Toby; Lopes, Ariadna V

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = -0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.

CLU rs2279590 polymorphism contributes to Alzheimer's disease susceptibility in Caucasian and Asian populations.

PubMed

Zhang, Shuyan; Zhang, Donghui; Jiang, Yongshuai; Wu, Lina; Shang, Hong; Liu, Jiafeng; Feng, Rennan; Liao, Mingzhi; Zhang, Liangcai; Liu, Yong; Liu, Guiyou; Li, Keshen

2015-03-01

It is reported that CLU rs2279590 polymorphism is significantly associated with Alzheimer's disease (AD) in European ancestry. Recent studies investigated rs2279590 polymorphism in Asian population (Chinese, Japanese and Korean). Four studies showed negative association and two studies showed weak association between rs2279590 and AD. We believe that the weak association or no association may be caused by the relatively small sample size in Asian population. Here, we reinvestigated the association in Asian population. Meanwhile, to investigate the genetic heterogeneity of the rs2279590 polymorphism in Asian and Caucasian populations, we searched the PubMed and AlzGene databases and selected 11 independent studies (6 studies in Asian population and 5 studies in Caucasian population) including 20,655 individuals (8,605 cases and 12,050 controls) for meta-analysis. Our results showed significant association between rs2279590 polymorphism and AD in Asian population with P = 2.00E-04 and P = 2.00E-04 using additive and recessive models, respectively. We observed no significant heterogeneity between Asian and Caucasian populations. We believe that our results may be helpful to understand the mechanisms of CLU in AD pathogenesis and will be useful for future genetic studies in AD.

Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei: Coregoninae).

PubMed

Turgeon, J; Bernatchez, L

2001-11-11

Classical models of the spatial structure of population genetics rely on the assumption of migration-drift equilibrium, which is seldom met in natural populations having only recently colonized their current range (e.g., postglacial). Population structure then depicts historical events, and counfounding effects due to recent secondary contact between recently differentiated lineages can further counfound analyses of association between geographic and genetic distances. Mitochondrial polymorphisms have revealed the existence of two closely related lineages of the lake cisco, Coregonus artedi, whose significantly different but overlaping geographical distributions provided a weak signal of past range fragmentation blurred by putative subsequent extensive secondary contacts. In this study, we analyzed geographical patterns of genetic variation at seven microsatellite loci among 22 populations of lake cisco located along the axis of an area covered by proglacial lakes 12,000-8,000 years ago in North America. The results clearly confirmed the existence of two genetically distinct races characterized by different sets of microsatellite alleles whose frequencies varied clinally across some 3000 km. Equilibrium and nonequilibrium analyses of isolation by distance revealed historical signal of gene flow resulting from the nearly complete admixture of these races following neutral secondary contacts in their historical habitat and indicated that the colonization process occurred by a stepwise expansion of an eastern (Atlantic) race into a previously established Mississippian race. This historical signal of equilibrium contrasted with the current migration-drift disequilibrium within major extant watersheds and was apparently maintained by high effective population sizes and low migration regimes.

Concern With Environmental Deterioration and Attitudes Toward Population Limitation

ERIC Educational Resources Information Center

Barnett, Larry D.

1970-01-01

Analysis of Gallup Poll data of Junuary 1969 reveals weak association between concern about environmental deterioration and the recognition of need for eventual limitation of human population. Suggests that to increase favorable attitudes to population control, role of overpopulation in causing environmental deterioration needs to be presented to…

Optimizing weak lensing mass estimates for cluster profile uncertainty

DOE PAGES

Gruen, D.; Bernstein, G. M.; Lam, T. Y.; ...

2011-09-11

Weak lensing measurements of cluster masses are necessary for calibrating mass-observable relations (MORs) to investigate the growth of structure and the properties of dark energy. However, the measured cluster shear signal varies at fixed mass M 200m due to inherent ellipticity of background galaxies, intervening structures along the line of sight, and variations in the cluster structure due to scatter in concentrations, asphericity and substructure. We use N-body simulated halos to derive and evaluate a weak lensing circular aperture mass measurement M ap that minimizes the mass estimate variance <(M ap - M 200m) 2> in the presence of allmore » these forms of variability. Depending on halo mass and observational conditions, the resulting mass estimator improves on M ap filters optimized for circular NFW-profile clusters in the presence of uncorrelated large scale structure (LSS) about as much as the latter improve on an estimator that only minimizes the influence of shape noise. Optimizing for uncorrelated LSS while ignoring the variation of internal cluster structure puts too much weight on the profile near the cores of halos, and under some circumstances can even be worse than not accounting for LSS at all. As a result, we discuss the impact of variability in cluster structure and correlated structures on the design and performance of weak lensing surveys intended to calibrate cluster MORs.« less

Nonequilibrium mechanisms of weak electrolyte electrification under the action of constant voltage

NASA Astrophysics Data System (ADS)

Stishkov, Yu. K.; Chirkov, V. A.

2016-07-01

The formation of space charge in weak electrolytes, specifically in liquid dielectrics, has been considered. An analytical solution is given to a simplified set of Nernst-Planck equations that describe the formation of nonequilibrium recombination layers in weak electrolytes. This approximate analytical solution is compared with computer simulation data for a complete set of Poisson-Nernst-Planck equations. It has been shown that the current passage in weak electrolytes can be described by a single dimensionless parameter that equals the length of a near-electrode recombination layer divided by the width of the interelectrode gap. The formation mechanism and the structure of charged nonequilibrium near-electrode layers in the nonstationary regime have been analyzed for different injection-to-conduction current ratios. It has been found that almost all charge structures encountered in weak dielectrics can be accounted for by the nonequilibrium dissociation-recombination mechanism of space charge formation.

Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones.

PubMed

Mafessoni, Fabrizio; Lachmann, Michael

2015-12-01

In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a disadvantageous one will quickly disappear from the population. We show that even in simple diploid populations, this is often not true. Dominance and recessivity unexpectedly slow down the evolutionary process for weakly selected alleles. In particular, slightly advantageous dominant and mildly deleterious recessive mutations reach fixation slightly more slowly than neutral ones (at most 5%). This phenomenon determines genetic signatures opposite to those expected under strong selection, such as increased instead of decreased genetic diversity around the selected site. Furthermore, we characterize a new phenomenon: mildly deleterious recessive alleles, thought to represent a wide fraction of newly arising mutations, on average survive in a population slightly longer than neutral ones, before getting lost. Consequently, these mutations are on average slightly older than neutral ones, in contrast with previous expectations. Furthermore, they slightly increase the amount of weakly deleterious polymorphisms, as a consequence of the longer unconditional sojourn times compared to neutral mutations. Copyright © 2015 by the Genetics Society of America.

The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

PubMed

Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

2015-01-01

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Optimally designed gold nanorattles with strong built-in hotspots and weak polarization dependence

NASA Astrophysics Data System (ADS)

Zhang, Xuemin; Wang, Tieqiang; Li, Yunong; Fu, Yu; Guo, Lei

2017-12-01

Localized electromagnetic fields generated by interparticle plasmon coupling suffer greatly from nonreproducibility because they are extremely sensitive to the nanoparticle aggregation status and the incident polarization. Here, we synthesize gold nanorattles that exhibit inherent aggregation-insensitive hotspots due to the intraparticle core-shell plasmon coupling, and investigate the structural effect on the intraparticle coupling strength and its polarization dependence. Through optimizing the structural parameters, we successfully synthesize gold nanorattles with strong built-in hotspots and weak polarization dependence. These aggregation-insensitive and weakly polarization-dependent hotspots make the Raman enhancement from nanorattle aggregates show an unusual weak dependence on the particle aggregation status, which therefore affords the opportunity to fabricate uniform and reproducible surface enhanced Raman scattering substrates.

Noise-induced shifts in the population model with a weak Allee effect

NASA Astrophysics Data System (ADS)

Bashkirtseva, Irina; Ryashko, Lev

2018-02-01

We consider the Truscott-Brindley system of interacting phyto- and zooplankton populations with a weak Allee effect. We add a random noise to the parameter of the prey carrying capacity, and study how the noise affects the dynamic behavior of this nonlinear prey-predator model. Phenomena of the stochastic excitement and noise-induced shifts in zones of the Andronov-Hopf bifurcation and Canard explosion are analyzed on the base of the direct numerical simulation and stochastic sensitivity functions technique. A relationship of these phenomena with transitions between order and chaos is discussed.

Science, population ecology, and the management of the American black duck

USGS Publications Warehouse

Nichols, J.D.

1991-01-01

This essay deals with the relevance of some of the ideas of Romesburg (1981) to population ecology and management of the American black duck (Anas rubripes). Most investigations dealing with the effects of hunting regulations on black duck populations have used the hypothetico-deductive (H-D) approach of specifying a priori hypotheses and associated deduced predictions. These investigations have not used manipulative experimentation, however, but have involved severely constrained analyses of historical data and have thus produced weak inferences. The 1982 lawsuit over black duck hunting regulations, the current uncertainty about appropriate black duck management actions, and the frequent skirmishes in the published literature of black duck population ecology are natural consequences of these weak inferences. I suggest that we attempt to take advantage of management and other manipulations by treating them as an opportunity to learn something via experimentation, as recommended by Macnab (1983) and Walters (1986).

Fixation Probability in a Haploid-Diploid Population

PubMed Central

Bessho, Kazuhiro; Otto, Sarah P.

2017-01-01

Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright–Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species. PMID:27866168

Morphologies of mid-IR variability-selected AGN host galaxies

NASA Astrophysics Data System (ADS)

Polimera, Mugdha; Sarajedini, Vicki; Ashby, Matthew L. N.; Willner, S. P.; Fazio, Giovanni G.

2018-05-01

We use multi-epoch 3.6 and 4.5 μm data from the Spitzer Extended Deep Survey (SEDS) to probe the AGN population among galaxies to redshifts ˜3 via their mid-IR variability. About 1 per cent of all galaxies in our survey contain varying nuclei, 80 per cent of which are likely to be AGN. Twenty-three per cent of mid-IR variables are also X-ray sources. The mid-IR variables have a slightly greater fraction of weakly disturbed morphologies compared to a control sample of normal galaxies. The increased fraction of weakly distorted hosts becomes more significant when we remove the X-ray emitting AGN, while the frequency of strongly disturbed hosts remains similar to the control galaxy sample. These results suggest that mid-IR variability identifies a unique population of obscured, Compton-thick AGN revealing elevated levels of weak distortion among their host galaxies.

High migration rates shape the postglacial history of amphi-Atlantic bryophytes.

PubMed

Désamoré, Aurélie; Patiño, Jairo; Mardulyn, Patrick; Mcdaniel, Stuart F; Zanatta, Florian; Laenen, Benjamin; Vanderpoorten, Alain

2016-11-01

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework. © 2016 John Wiley & Sons Ltd.

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

PubMed Central

Latch, Emily K.; Boarman, William I.; Walde, Andrew; Fleischer, Robert C.

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately. PMID:22132143

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

PubMed

Latch, Emily K; Boarman, William I; Walde, Andrew; Fleischer, Robert C

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.

Propagation Characteristics Of Weakly Guiding Optical Fibers

NASA Technical Reports Server (NTRS)

Manshadi, Farzin

1992-01-01

Report discusses electromagnetic propagation characteristics of weakly guiding optical-fiber structures having complicated shapes with cross-sectional dimensions of order of wavelength. Coupling, power-dividing, and transition dielectric-waveguide structures analyzed. Basic data computed by scalar-wave, fast-Fourier-transform (SW-FFT) technique, based on numerical solution of scalar version of wave equation by forward-marching fast-Fourier-transform method.

Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations.

PubMed

Interlandi, Gianluca; Thomas, Wendy E

2016-07-01

The bacterial adhesin FimH consists of an allosterically regulated mannose-binding lectin domain and a covalently linked inhibitory pilin domain. Under normal conditions, the two domains are bound to each other, and FimH interacts weakly with mannose. However, under tensile force, the domains separate and the lectin domain undergoes conformational changes that strengthen its bond with mannose. Comparison of the crystallographic structures of the low and the high affinity state of the lectin domain reveals conformational changes mainly in the regulatory inter-domain region, the mannose binding site and a large β sheet that connects the two distally located regions. Here, molecular dynamics simulations investigated how conformational changes are propagated within and between different regions of the lectin domain. It was found that the inter-domain region moves towards the high affinity conformation as it becomes more compact and buries exposed hydrophobic surface after separation of the pilin domain. The mannose binding site was more rigid in the high affinity state, which prevented water penetration into the pocket. The large central β sheet demonstrated a soft spring-like twisting. Its twisting motion was moderately correlated to fluctuations in both the regulatory and the binding region, whereas a weak correlation was seen in a direct comparison of these two distal sites. The results suggest a so called "population shift" model whereby binding of the lectin domain to either the pilin domain or mannose locks the β sheet in a rather twisted or flat conformation, stabilizing the low or the high affinity state, respectively. Proteins 2016; 84:990-1008. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

POPULATION DYNAMICS OF CHAFF SCALE, PARLATORIA PERGANDII COMSTOCK IN COMPARATIVE ANALYSIS OF FLUCTUATING POPULATION DENSITIES ON THREE CITRUS VARIETIES IN EL-BEHEIRA GOVERNORATE, EGYPT.

PubMed

Moursi Khadiga, S; Abdel Fattah, S; Rasha; Omar, M A A; Mourad, A K

2015-01-01

Investigation throughout the subsequent years of 2011-2012 and 2012-2013 indicated that chaff scale, P. pegandii is an important economic pest on citrus trees in Abou El-Matamer area, El-Beheira Governorate, Egypt. It has been recorded in relatively high rates all over the year on three citrus varieties called Succari, Baladi and Navel oranges. Field observation and recorded data revealed that the common abundance was recorded for chaff scale on Succari oranges followed by Navel oranges then the least abundant on Baladi oranges. Generally, the calculated data on Succari oranges showed that, the population of P. pergandii reached the maximum during July and there were five highly variation periods in both the growing seasons of 2011-2012 and 2012-2013. The maximal percent of pre and adult females was observed during Spring and early Summer and reached 100% of the total counted individuals during October and December in the first year, but in the second one a higher population was recorded during Summer and early Winter months. The adult males were observed during Summer and Autumn months. Results showed also that the relationship between daily mean temperature and population density of chaff scale was weak, insignificantly negative in the two growing seasons (2011-2012 and 2012-2013) and also insignificantly but positive with relative humidity. That relationship with wind speed indicated weak positive significance in the first year and strong in the second season. The relationship between dew point and insect population was weak of positive significance in both growing seasons.

Expression of the inclusion body myopathy 3 mutation in Drosophila depresses myosin function and stability and recapitulates muscle inclusions and weakness.

PubMed

Wang, Yang; Melkani, Girish C; Suggs, Jennifer A; Melkani, Anju; Kronert, William A; Cammarato, Anthony; Bernstein, Sanford I

2012-06-01

Hereditary myosin myopathies are characterized by variable clinical features. Inclusion body myopathy 3 (IBM-3) is an autosomal dominant disease associated with a missense mutation (E706K) in the myosin heavy chain IIa gene. Adult patients experience progressive muscle weakness. Biopsies reveal dystrophic changes, rimmed vacuoles with cytoplasmic inclusions, and focal disorganization of myofilaments. We constructed a transgene encoding E706K myosin and expressed it in Drosophila (E701K) indirect flight and jump muscles to establish a novel homozygous organism with homogeneous populations of fast IBM-3 myosin and muscle fibers. Flight and jump abilities were severely reduced in homozygotes. ATPase and actin sliding velocity of the mutant myosin were depressed >80% compared with wild-type myosin. Light scattering experiments and electron microscopy revealed that mutant myosin heads bear a dramatic propensity to collapse and aggregate. Thus E706K (E701K) myosin appears far more labile than wild-type myosin. Furthermore, mutant fly fibers exhibit ultrastructural hallmarks seen in patients, including cytoplasmic inclusions containing aberrant proteinaceous structures and disorganized muscle filaments. Our Drosophila model reveals the unambiguous consequences of the IBM-3 lesion on fast muscle myosin and fibers. The abnormalities observed in myosin function and muscle ultrastructure likely contribute to muscle weakness observed in our flies and patients.

Health promotion practices in primary care groups.

PubMed

Heidemann, Ivonete Teresinha Schulter Buss; Alonso da Costa, Maria Fernanda Baeta Neves; Hermida, Patrícia Madalena Vieira; Marçal, Cláudia Cossentino Bruck; Antonini, Fabiano Oliveira; Cypriano, Camilla Costa

2018-04-01

This is a descriptive-exploratory study using a qualitative approach, conducted in ten municipalities in southern Brazil. Data were obtained by talking to 21 nurses from February to November 2012, through semi-structured interviews using questions to probe their health promotion practices. Data were analyzed through thematic analysis focused on health promotion concepts. We identified four themes about health promotion practices of family health nurses in Brazil: a) training of nurses for health promotion practice was weak; b) nurses formed health promotion groups around diseases and life stages; c) nurses formed groups to meet community needs; and d) nurses used health promotion techniques in group work. These family health nurses were somewhat aware of the importance of health promotion, and how to assist the population against various ailments using some health promotion strategies. The main weaknesses were the lack of understanding about health promotion concepts, and the difficulty of understanding the relevance of its practice, probably attributable to limitations in training. We conclude that primary care groups in Brazil's unified health system could do better in applying health promotion concepts in their practice.

Genetic Diversity in Introduced Populations with an Allee Effect

PubMed Central

Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

2014-01-01

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

Floral colour versus phylogeny in structuring subalpine flowering communities.

PubMed

McEwen, Jamie R; Vamosi, Jana C

2010-10-07

The relative number of seeds produced by competing species can influence the community structure; yet, traits that influence seed production, such as pollinator attraction and floral colour, have received little attention in community ecology. Here, we analyse floral colour using reflectance spectra that include near-UV and examined the phylogenetic signal of floral colour. We found that coflowering species within communities tended to be more divergent in floral colour than expected by chance. However, coflowering species were not phylogenetically dispersed, in part due to our finding that floral colour is a labile trait with a weak phylogenetic signal. Furthermore, while we found that locally rare and common species exhibited equivalent floral colour distances from their coflowering neighbours, frequent species (those found in more communities) exhibited higher colour distances from their coflowering neighbours. Our findings support recent studies, which have found that (i) plant lineages exhibit frequent floral colour transitions; and (ii) traits that influence local population dynamics contribute to community structure.

Long-range monostatic remote sensing of geomaterial structure weak vibrations

NASA Astrophysics Data System (ADS)

Heifetz, Alexander; Bakhtiari, Sasan; Gopalsami, Nachappa; Elmer, Thomas W.; Mukherjee, Souvik

2018-04-01

We study analytically and numerically signal sensitivity in remote sensing measurements of weak mechanical vibration of structures made of typical construction geomaterials, such as concrete. The analysis includes considerations of electromagnetic beam atmospheric absorption, reflection, scattering, diffraction and losses. Comparison is made between electromagnetic frequencies of 35GHz (Ka-band), 94GHz (W-band) and 260GHz (WR-3 waveguide band), corresponding to atmospheric transparency windows of the electromagnetic spectrum. Numerical simulations indicate that 94GHz frequency is optimal in terms of signal sensitivity and specificity for long-distance (>1.5km) sensing of weak multi-mode vibrations.

Meeting review. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics.

PubMed

Joost, Stéphane; Vuilleumier, Séverine; Jensen, Jeffrey D; Schoville, Sean; Leempoel, Kevin; Stucki, Sylvie; Widmer, Ivo; Melodelima, Christelle; Rolland, Jonathan; Manel, Stéphanie

2013-07-01

A workshop recently held at the École Polytechnique Fédérale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

Mapping Kainate Activation of Inner Neurons in the Rat Retina

PubMed Central

Nivison-Smith, Lisa; Sun, Daniel; Fletcher, Erica L.; Marc, Robert E.; Kalloniatis, Michael

2014-01-01

Kainate receptors mediate fast, excitatory synaptic transmission for a range of inner neurons in the mammalian retina. However, allocation of functional kainate receptors to known cell types and their sensitivity remains unresolved. Using the cation channel probe 1-amino-4-guanidobutane agmatine (AGB), we investigated kainate sensitivity of neurochemically identified cell populations within the structurally intact rat retina. Most inner retinal neuron populations responded to kainate in a concentration-dependent manner. OFF cone bipolar cells demonstrated the highest sensitivity of all inner neurons to kainate. Immunocytochemical localization of AGB and macromolecular markers confirmed that type 2 bipolar cells were part of this kainate-sensitive population. The majority of amacrine (ACs) and ganglion cells (GCs) showed kainate responses with different sensitivities between major neurochemical classes (γ-aminobutyric acid [GABA]/glycine ACs > glycine ACs > GABA ACs; glutamate [Glu]/weakly GABA GCs > Glu GCs). Conventional and displaced cholinergic ACs were highly responsive to kainate, whereas dopaminergic ACs do not appear to express functional kainate receptors. These findings further contribute to our understanding of neuronal networks in complex multicellular tissues. PMID:23348566

Dispersal capacity predicts both population genetic structure and species richness in reef fishes.

PubMed

Riginos, Cynthia; Buckley, Yvonne M; Blomberg, Simon P; Treml, Eric A

2014-07-01

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.

Evolutionary graph theory: breaking the symmetry between interaction and replacement

PubMed Central

Ohtsuki, Hisashi; Pacheco, Jorge M.; Nowak, Martin A.

2008-01-01

We study evolutionary dynamics in a population whose structure is given by two graphs: the interaction graph determines who plays with whom in an evolutionary game; the replacement graph specifies the geometry of evolutionary competition and updating. First, we calculate the fixation probabilities of frequency dependent selection between two strategies or phenotypes. We consider three different update mechanisms: birth-death, death-birth and imitation. Then, as a particular example, we explore the evolution of cooperation. Suppose the interaction graph is a regular graph of degree h, the replacement graph is a regular graph of degree g and the overlap between the two graphs is a regular graph of degree l. We show that cooperation is favored by natural selection if b/c > hg/l. Here, b and c denote the benefit and cost of the altruistic act. This result holds for death-birth updating, weak selection and large population size. Note that the optimum population structure for cooperators is given by maximum overlap between the interaction and the replacement graph (g = h = l), which means that the two graphs are identical. We also prove that a modified replicator equation can describe how the expected values of the frequencies of an arbitrary number of strategies change on replacement and interaction graphs: the two graphs induce a transformation of the payoff matrix. PMID:17350049

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat.

PubMed

Jighly, Abdulqader; Joukhadar, Reem; Singh, Sukhwinder; Ogbonnaya, Francis C

2018-01-01

Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents ( Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii ; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding.

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat

PubMed Central

Jighly, Abdulqader; Joukhadar, Reem; Singh, Sukhwinder; Ogbonnaya, Francis C.

2018-01-01

Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding. PMID:29467793

Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan

PubMed Central

Marchani, Elizabeth E; Watkins, W Scott; Bulayeva, Kazima; Harpending, Henry C; Jorde, Lynn B

2008-01-01

Background Near the junction of three major continents, the Caucasus region has been an important thoroughfare for human migration. While the Caucasus Mountains have diverted human traffic to the few lowland regions that provide a gateway from north to south between the Caspian and Black Seas, highland populations have been isolated by their remote geographic location and their practice of patrilocal endogamy. We investigate how these cultural and historical differences between highland and lowland populations have affected patterns of genetic diversity. We test 1) whether the highland practice of patrilocal endogamy has generated sex-specific population relationships, and 2) whether the history of migration and military conquest associated with the lowland populations has left Central Asian genes in the Caucasus, by comparing genetic diversity and pairwise population relationships between Daghestani populations and reference populations throughout Europe and Asia for autosomal, mitochondrial, and Y-chromosomal markers. Results We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant. Conclusion The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations. PMID:18637195

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

Tessore, Nicolas; Metcalf, R. Benton; Winther, Hans A.

A number of alternatives to general relativity exhibit gravitational screening in the non-linear regime of structure formation. We describe a set of algorithms that can produce weak lensing maps of large scale structure in such theories and can be used to generate mock surveys for cosmological analysis. By analysing a few basic statistics we indicate how these alternatives can be distinguished from general relativity with future weak lensing surveys.

Figurative language processing in atypical populations: the ASD perspective

PubMed Central

Vulchanova, Mila; Saldaña, David; Chahboun, Sobh; Vulchanov, Valentin

2015-01-01

This paper is intended to provide a critical overview of experimental and clinical research documenting problems in figurative language processing in atypical populations with a focus on the Autistic Spectrum. Research in the comprehension and processing of figurative language in autism invariably documents problems in this area. The greater paradox is that even at the higher end of the spectrum or in the cases of linguistically talented individuals with Asperger syndrome, where structural language competence is intact, problems with extended language persist. If we assume that figurative and extended uses of language essentially depend on the perception and processing of more concrete core concepts and phenomena, the commonly observed failure in atypical populations to understand figurative language remains a puzzle. Various accounts have been offered to explain this issue, ranging from linking potential failure directly to overall structural language competence (Norbury, 2005; Brock et al., 2008) to right-hemispheric involvement (Gold and Faust, 2010). We argue that the dissociation between structural language and figurative language competence in autism should be sought in more general cognitive mechanisms and traits in the autistic phenotype (e.g., in terms of weak central coherence, Vulchanova et al., 2012b), as well as failure at on-line semantic integration with increased complexity and diversity of the stimuli (Coulson and Van Petten, 2002). This perspective is even more compelling in light of similar problems in a number of conditions, including both acquired (e.g., Aphasia) and developmental disorders (Williams Syndrome). This dissociation argues against a simple continuity view of language interpretation. PMID:25741261

Figurative language processing in atypical populations: the ASD perspective.

PubMed

Vulchanova, Mila; Saldaña, David; Chahboun, Sobh; Vulchanov, Valentin

2015-01-01

This paper is intended to provide a critical overview of experimental and clinical research documenting problems in figurative language processing in atypical populations with a focus on the Autistic Spectrum. Research in the comprehension and processing of figurative language in autism invariably documents problems in this area. The greater paradox is that even at the higher end of the spectrum or in the cases of linguistically talented individuals with Asperger syndrome, where structural language competence is intact, problems with extended language persist. If we assume that figurative and extended uses of language essentially depend on the perception and processing of more concrete core concepts and phenomena, the commonly observed failure in atypical populations to understand figurative language remains a puzzle. Various accounts have been offered to explain this issue, ranging from linking potential failure directly to overall structural language competence (Norbury, 2005; Brock et al., 2008) to right-hemispheric involvement (Gold and Faust, 2010). We argue that the dissociation between structural language and figurative language competence in autism should be sought in more general cognitive mechanisms and traits in the autistic phenotype (e.g., in terms of weak central coherence, Vulchanova et al., 2012b), as well as failure at on-line semantic integration with increased complexity and diversity of the stimuli (Coulson and Van Petten, 2002). This perspective is even more compelling in light of similar problems in a number of conditions, including both acquired (e.g., Aphasia) and developmental disorders (Williams Syndrome). This dissociation argues against a simple continuity view of language interpretation.

Sensory complementation and antipredator behavioural compensation in acid-impacted juvenile Atlantic salmon.

PubMed

Elvidge, C K; Macnaughton, C J; Brown, G E

2013-05-01

Prey incorporate multiple forms of publicly available information on predation risk into threat-sensitive antipredator behaviours. Changes in information availability have previously been demonstrated to elicit transient alterations in behavioural patterns, while the effects of long-term deprivation of particular forms of information remain largely unexplored. Damage-released chemical alarm cues from the epidermis of fishes are rendered non-functional under weakly acidic conditions (pH < 6.6), depriving fish of an important source of information on predation risk in acidified waterbodies. We addressed the effects of long-term deprivation on the antipredator responses to different combinations of chemical and visual threat cues via in situ observations of wild, free-swimming 0(+) Atlantic salmon (Salmo salar) fry in four neutral and four weakly acidic nursery streams. In addition, a cross-population transplant experiment and natural interannual variation in acidity enabled the examination of provenance and environment as causes of the observed differences in response. Fish living under weakly acidic conditions demonstrate significantly greater or hypersensitive antipredator responses to visual cues compared to fish under neutral conditions. Under neutral conditions, fish demonstrate complementary (additive or synergistic) effects of paired visual and chemical cues consistent with threat-sensitive responses. Cross-population transplants and interannual comparisons of responses strongly support the conclusion that differences in antipredator responses between neutral and weakly acidic streams result from the loss of chemical information on predation risk, as opposed to population-derived differences in behaviours.

Dissipation in a rotating frame: Master equation, effective temperature, and Lamb shift

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

Verso, Alvise; Ankerhold, Joachim

Motivated by recent realizations of microwave-driven nonlinear resonators in superconducting circuits, the impact of environmental degrees of freedom is analyzed as seen from a rotating frame. A system plus reservoir model is applied to consistently derive in the weak coupling limit the master equation for the reduced density in the moving frame and near the first bifurcation threshold. The concept of an effective temperature is introduced to analyze to what extent a detailed balance relation exists. Explicit expressions are also found for the Lamb-shift. Results for ohmic baths are in agreement with experimental findings, while for structured environments population inversionmore » is predicted that may qualitatively explain recent observations.« less

Differential dynamic microscopy of weakly scattering and polydisperse protein-rich clusters

NASA Astrophysics Data System (ADS)

Safari, Mohammad S.; Vorontsova, Maria A.; Poling-Skutvik, Ryan; Vekilov, Peter G.; Conrad, Jacinta C.

2015-10-01

Nanoparticle dynamics impact a wide range of biological transport processes and applications in nanomedicine and natural resource engineering. Differential dynamic microscopy (DDM) was recently developed to quantify the dynamics of submicron particles in solutions from fluctuations of intensity in optical micrographs. Differential dynamic microscopy is well established for monodisperse particle populations, but has not been applied to solutions containing weakly scattering polydisperse biological nanoparticles. Here we use bright-field DDM (BDDM) to measure the dynamics of protein-rich liquid clusters, whose size ranges from tens to hundreds of nanometers and whose total volume fraction is less than 10-5. With solutions of two proteins, hemoglobin A and lysozyme, we evaluate the cluster diffusion coefficients from the dependence of the diffusive relaxation time on the scattering wave vector. We establish that for weakly scattering populations, an optimal thickness of the sample chamber exists at which the BDDM signal is maximized at the smallest sample volume. The average cluster diffusion coefficient measured using BDDM is consistently lower than that obtained from dynamic light scattering at a scattering angle of 90∘. This apparent discrepancy is due to Mie scattering from the polydisperse cluster population, in which larger clusters preferentially scatter more light in the forward direction.

Social vulnerability as a contributing factor to disasters in Central America: A case study at San Vicente volcano, El Salvador

NASA Astrophysics Data System (ADS)

Bowman, L. J.; Henquinet, K. B.; Gierke, J. S.; Rose, W. I.

2012-12-01

El Salvador's geographic location on the Pacific Ring of Fire at the juncture of the Caribbean and Cocos plates exposes its population to various natural hazards, including volcanic eruptions (e.g., Santa Ana in 2005), earthquakes (e.g., January 13 and February 13, 2001), and landslides and flooding due to tropical rainfall events (e.g., Hurricane Mitch in 1998, Hurricane Stan in 2005). Such hazards can be devastating anywhere, but the condition of social vulnerability in which many Salvadorans currently live exacerbates the impacts of these hazards. Aspects contributing to most rural Salvadorans being marginalized include a colonial history marked by ethnic discrimination and laws prohibiting land ownership, lack of access to desirable land in an agrarian society, a poor education system, global economic policies that foster inequality, political marginalization, a bloody civil conflict, and rampant criminality and violence. In November 2009, an extreme rainfall event triggered landslides and lahars killing over 200 people at San Vicente volcano. This disaster brought to light weaknesses in disaster preparedness and response plans. Despite the existence of recent hazard maps and lahar inundation models (2001), and the occurrence of a similar, deadly event in 1934, the population appeared to be unaware of the risk, and lacked the organization and decision-making protocols to adequately deal with the emergency. Therefore, in the aftermath of the 2009 lahars, much of the focus on disaster risk reduction (DRR) initiatives has been aimed at the communities affected by this most recent event. Our study examines root causes of social vulnerability and assesses the apparent impacts of these interventions on the population, including individual's perceptions regarding these risk-reducing interventions. Two years after the event, though aid abounds, many people remain vulnerable to hazards in this area. Semi-structured interviews were completed with survivors of the 2009 lahars as well as with other community residents, Civil Protection, National Civilian Police, University of El Salvador faculty, the project coordinator and employees from an NGO, and government officials who are closely involved with DRR efforts. Preliminary results of the data indicate a population that varies widely in terms of its hazard awareness, its willingness/ability to adopt behavioral changes, and its awareness of options available to cope with future disasters. The data gathered from practitioners shows that while advancements have been made since the 2009 event, many weaknesses clearly remain (i.e., lack of coordination between aid entities; conflicts between local governments; confusion over stakeholders' responsibilities; conflicting emergency action plans; and the population's distrust of the organizations charged with helping to prepare for, and assist during, future emergencies). Many of these weaknesses intensify social vulnerability and are directly related to the root causes of marginalization. The data indicate that development interventions in the region fail to acknowledge and deal with the weaknesses outlined above, and as a result, many Salvadorans remain unnecessarily vulnerable to future disasters that will inevitably occur due to the natural hazards endemic to the region.

Committee Effectiveness in Higher Education: The Strengths and Weaknesses of Group Decision Making

ERIC Educational Resources Information Center

Bates, Stephen B.

2014-01-01

Focusing on five models of committee effectiveness for purposes of this assessment will lend insight into the strengths and weaknesses of utilizing a structured action plan as a guide to achieving and maintaining optimum committee effectiveness in higher education. In the compilation of the strengths and weaknesses of committee decision making,…

$$\\chi$$EFT studies of few-nucleon systems: a status report

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

Schiavilla, Rocco

2016-06-01

A status report onmore » $$\\chi$$EFT studies of few-nucleon electroweak structure and dynamics is provided, including electromagnetic elastic form factors of few-nucleon systems, the $pp$ weak fusion and muon weak captures on deuteron and $^3$He, and a number of parity-violating processes induced by hadronic weak interactions.« less

Strong and weak second-order topological insulators with hexagonal symmetry and ℤ3 index

NASA Astrophysics Data System (ADS)

Ezawa, Motohiko

2018-06-01

We propose second-order topological insulators (SOTIs) whose lattice structure has a hexagonal symmetry C6. We start with a three-dimensional weak topological insulator constructed on a stacked triangular lattice, which has only side topological surface states. We then introduce an additional mass term which gaps out the side surface states but preserves the hinge states. The resultant system is a three-dimensional SOTI. The bulk topological quantum number is shown to be the Z3 index protected by inversion time-reversal symmetry I T and rotoinversion symmetry I C6 . We obtain three phases: trivial, strong, and weak SOTI phases. We argue the origin of these two types of SOTIs. A hexagonal prism is a typical structure respecting these symmetries, where six topological hinge states emerge at the side. The building block is a hexagon in two dimensions, where topological corner states emerge at the six corners in the SOTI phase. Strong and weak SOTIs are obtained when the interlayer hopping interaction is strong and weak, respectively.

Visualizing an ultra-weak protein-protein interaction in phosphorylation signaling.

PubMed

Xing, Qiong; Huang, Peng; Yang, Ju; Sun, Jian-Qiang; Gong, Zhou; Dong, Xu; Guo, Da-Chuan; Chen, Shao-Min; Yang, Yu-Hong; Wang, Yan; Yang, Ming-Hui; Yi, Ming; Ding, Yi-Ming; Liu, Mai-Li; Zhang, Wei-Ping; Tang, Chun

2014-10-20

Proteins interact with each other to fulfill their functions. The importance of weak protein-protein interactions has been increasingly recognized. However, owing to technical difficulties, ultra-weak interactions remain to be characterized. Phosphorylation can take place via a K(D)≈25 mM interaction between two bacterial enzymes. Using paramagnetic NMR spectroscopy and with the introduction of a novel Gd(III)-based probe, we determined the structure of the resulting complex to atomic resolution. The structure accounts for the mechanism of phosphoryl transfer between the two enzymes and demonstrates the physical basis for their ultra-weak interaction. Further, molecular dynamics (MD) simulations suggest that the complex has a lifetime in the micro- to millisecond regimen. Hence such interaction is termed a fleeting interaction. From mathematical modeling, we propose that an ultra-weak fleeting interaction enables rapid flux of phosphoryl signal, providing a high effective protein concentration. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Supramolecular features of 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino]-2,3-dihydroquinazolin-4(1H)-ones: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Mandal, Arkalekha; Patel, Bhisma K.

2018-03-01

The molecular structures of two isomeric 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino] substituted 2,3-dihydroquinazolin-4(1H)-ones have been determined via single crystal XRD. Both isomers contain chloro substitutions on each of the phenyl rings and as a result a broad spectrum of halogen mediated weak interactions are viable in their crystal structures. The crystal packing of these compounds is stabilized by strong N-H⋯O hydrogen bond and various weak, non-classical hydrogen bonds acting synergistically. Both the molecules contain a chiral center and the weak interactions observed in them are either chiral self-discriminatory or chiral self-recognizing in nature. The weak interactions and spectral features of the compounds have been studied through experimental as well as computational methods including DFT, MEP, NBO and Hiresfeld surface analyses. In addition, the effect of different weak interactions to dictate either chiral self-recognition or self-discrimination in crystal packing has been elucidated.

Evolution of equal division among unequal partners.

PubMed

Debove, Stéphane; Baumard, Nicolas; André, Jean-Baptiste

2015-02-01

One of the hallmarks of human fairness is its insensitivity to power: although strong individuals are often in a position to coerce weak individuals, fairness requires them to share the benefits of cooperation equally. The existence of such egalitarianism is poorly explained by current evolutionary models. We present a model based on cooperation and partner choice that can account for the emergence of a psychological disposition toward fairness, whatever the balance of power between the cooperative partners. We model the evolution of the division of a benefit in an interaction similar to an ultimatum game, in a population made up of individuals of variable strength. The model shows that strong individuals will not receive any advantage from their strength, instead having to share the benefits of cooperation equally with weak individuals at the evolutionary equilibrium, a result that is robust to variations in population size and the proportion of weak individuals. We discuss how this model suggests an explanation for why egalitarian behaviors toward everyone, including the weak, should be more likely to evolve in humans than in any other species. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

ON THE ORIGIN OF THE SUPERGIANT H I SHELL AND PUTATIVE COMPANION IN NGC 6822

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

Cannon, John M.; O'Leary, Erin M.; Weisz, Daniel R.

2012-03-10

We present new Hubble Space Telescope Advanced Camera for Surveys imaging of six positions spanning 5.8 kpc of the H I major axis of the Local Group dIrr NGC 6822, including both the putative companion galaxy and the large H I hole. The resulting deep color-magnitude diagrams show that NGC 6822 has formed >50% of its stars in the last {approx}5 Gyr. The star formation histories of all six positions are similar over the most recent 500 Myr, including low-level star formation throughout this interval and a weak increase in star formation rate during the most recent 50 Myr. Stellarmore » feedback can create the giant H I hole, assuming that the lifetime of the structure is longer than 500 Myr; such long-lived structures have now been observed in multiple systems and may be the norm in galaxies with solid-body rotation. The old stellar populations (red giants and red clump stars) of the putative companion are consistent with those of the extended halo of NGC 6822; this argues against the interpretation of this structure as a bona fide interacting companion galaxy and against its being linked to the formation of the H I hole via an interaction. Since there is no evidence in the stellar population of a companion galaxy, the most likely explanation of the extended H I structure in NGC 6822 is a warped disk inclined to the line of sight.« less

Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae).

PubMed

García-Fernández, Alfredo; Iriondo, Jose M; Escudero, Adrián; Aguilar, Javier Fuertes; Feliner, Gonzalo Nieto

2013-08-01

Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.

Is Small Still Beautiful for the Strengths and Difficulties Questionnaire? Novel Findings Using Exploratory Structural Equation Modeling.

PubMed

Garrido, Luis Eduardo; Barrada, Juan Ramón; Aguasvivas, José Armando; Martínez-Molina, Agustín; Arias, Víctor B; Golino, Hudson F; Legaz, Eva; Ferrís, Gloria; Rojo-Moreno, Luis

2018-06-01

During the present decade a large body of research has employed confirmatory factor analysis (CFA) to evaluate the factor structure of the Strengths and Difficulties Questionnaire (SDQ) across multiple languages and cultures. However, because CFA can produce strongly biased estimations when the population cross-loadings differ meaningfully from zero, it may not be the most appropriate framework to model the SDQ responses. With this in mind, the current study sought to assess the factorial structure of the SDQ using the more flexible exploratory structural equation modeling approach. Using a large-scale Spanish sample composed of 67,253 youths aged between 10 and 18 years ( M = 14.16, SD = 1.07), the results showed that CFA provided a severely biased and overly optimistic assessment of the underlying structure of the SDQ. In contrast, exploratory structural equation modeling revealed a generally weak factorial structure, including questionable indicators with large cross-loadings, multiple error correlations, and significant wording variance. A subsequent Monte Carlo study showed that sample sizes greater than 4,000 would be needed to adequately recover the SDQ loading structure. The findings from this study prevent recommending the SDQ as a screening tool and suggest caution when interpreting previous results in the literature based on CFA modeling.

Observed seasonal and interannual variability of the near-surface thermal structure of the Arabian Sea Warm Pool

NASA Astrophysics Data System (ADS)

Rao, R. R.; Ramakrishna, S. S. V. S.

2017-06-01

The observed seasonal and interannual variability of near-surface thermal structure of the Arabian Sea Warm Pool (ASWP) is examined utilizing a reanalysis data set for the period 1990-2008. During a year, the ASWP progressively builds from February, reaches its peak by May only in the topmost 60 m water column. The ASWP Index showed a strong seasonal cycle with distinct interannual signatures. The years with higher (lower) sea surface temperature (SST) and larger (smaller) spatial extent are termed as strong (weak) ASWP years. The differences in the magnitude and spatial extent of thermal structure between the strong and weak ASWP regimes are seen more prominently in the topmost 40 m water column. The heat content values with respect to 28 °C isotherm (HC28) are relatively higher (lower) during strong (weak) ASWP years. Even the secondary peak in HC28 seen during the preceding November-December showed higher (lower) magnitude during the strong ASWP (weak) years. The influence of the observed variability in the surface wind field, surface net air-sea heat flux, near-surface mixed layer thickness, sea surface height (SSH) anomaly, depth of 20 °C isotherm and barrier layer thickness is examined to explain the observed differences in the near-surface thermal structure of the ASWP between strong and weak regimes. The surface wind speed is much weaker in particular during the preceding October and February-March corresponding to the strong ASWP years when compared to those of the weak ASWP years implying its important role. Both stronger winter cooling during weak ASWP years and stronger pre-monsoon heating during strong ASWP years through the surface air-sea heat fluxes contribute to the observed sharp contrast in the magnitudes of both the regimes of the ASWP. The upwelling Rossby wave during the preceding summer monsoon, post-monsoon and winter seasons is stronger corresponding to the weak ASWP regime when compared to the strong ASWP regime resulting in greater cooling of the near-surface layers during the summer monsoon season of the preceding year. On the other hand, the downwelling Rossby wave is stronger during pre-monsoon months during the strong ASWP regime when compared to weak ASWP regime leading to lesser cooling during strong ASWP regime.

Lake sturgeon population characteristics in Rainy Lake, Minnesota and Ontario

USGS Publications Warehouse

Adams, W.E.; Kallemeyn, L.W.; Willis, D.W.

2006-01-01

Rainy Lake contains a native population of lake sturgeon Acipenser fulvescens that has been largely unstudied. The aims of this study were to document the population characteristics of lake sturgeon in Rainy Lake and to relate environmental factors to year-class strength for this population. Gill-netting efforts throughout the study resulted in the capture of 322 lake sturgeon, including 50 recaptures. Lake sturgeon in Rainy Lake was relatively plump and fast growing compared with a 32-population summary. Population samples were dominated by lake sturgeon between 110 and 150 cm total length. Age–structure analysis of the samples indicated few younger (<10 years) lake sturgeon, but the smallest gill net mesh size used for sampling was 102 mm (bar measure) and would not retain small sturgeon. Few lake sturgeon older than age 50 years were captured, and maximum age of sampled fish was 59 years. Few correlations existed between lake sturgeon year-class indices and both annual and monthly climate variables, except that mean June air temperature was positively correlated with year-class strength. Analysis of Rainy Lake water elevation and resulting lake sturgeon year-class strength indices across years yielded consistent but weak negative correlations between late April and early June, when spawning of lake sturgeon occurs. The baseline data collected in this study should allow Rainy Lake biologists to establish more specific research questions in the future.

A probabilistic cellular automata model for the dynamics of a population driven by logistic growth and weak Allee effect

NASA Astrophysics Data System (ADS)

Mendonça, J. R. G.

2018-04-01

We propose and investigate a one-parameter probabilistic mixture of one-dimensional elementary cellular automata under the guise of a model for the dynamics of a single-species unstructured population with nonoverlapping generations in which individuals have smaller probability of reproducing and surviving in a crowded neighbourhood but also suffer from isolation and dispersal. Remarkably, the first-order mean field approximation to the dynamics of the model yields a cubic map containing terms representing both logistic and weak Allee effects. The model has a single absorbing state devoid of individuals, but depending on the reproduction and survival probabilities can achieve a stable population. We determine the critical probability separating these two phases and find that the phase transition between them is in the directed percolation universality class of critical behaviour.

Population of Nuclei Via 7Li-Induced Binary Reactions

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

Clark, Rodney M.; Phair, Larry W.; Descovich, M.

2005-08-08

The authors have investigated the population of nuclei formed in binary reactions involving {sup 7}Li beams on targets of {sup 160}Gd and {sup 184}W. The {sup 7}Li + {sup 184}W data were taken in the first experiment using the LIBERACE Ge-array in combination with the STARS Si {Delta}E-E telescope system at the 88-Inch Cyclotron of the Lawrence Berkeley National Laboratory. By using the Wilczynski binary transfer model, in combination with a standard evaporation model, they are able to reproduce the experimental results. This is a useful method for predicting the population of neutron-rich heavy nuclei formed in binary reactions involvingmore » beams of weakly bound nuclei formed in binary reactions involving beams of weakly bound nuclei and will be of use in future spectroscopic studies.« less

Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.

PubMed

Santos, Eduarda M; Hamilton, Patrick B; Coe, Tobias S; Ball, Jonathan S; Cook, Alastair C; Katsiadaki, Ioanna; Tyler, Charles R

2013-10-15

Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. Copyright © 2013 Elsevier B.V. All rights reserved.

Microwave Spectrum of the Isopropanol-Water Dimer

NASA Astrophysics Data System (ADS)

Mead, Griffin; Finneran, Ian A.; Carroll, Brandon; Blake, Geoffrey

2016-06-01

Microwave spectroscopy provides a unique opportunity to study model non-covalent interactions. Of particular interest is the hydrogen bonding of water, whose various molecular properties are influenced by both strong and weak intermolecular forces. More specifically, measuring the hydrogen bonded structures of water-alcohol dimers investigates both strong (OH ··· OH) and weak (CH ··· OH) hydrogen bond interactions. Recently, we have measured the pure rotational spectrum of the isopropanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) between 8-18 GHz. Here, we present the spectrum of this dimer and elaborate on the structure's strong and weak hydrogen bonding.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

PubMed Central

Vergara, María; Basto, Mafalda P.; Madeira, María José; Gómez-Moliner, Benjamín J.; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species. PMID:26222680

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

PubMed

Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

PubMed

Men, Qiulei; Xue, Guoxi; Mu, Dan; Hu, Qingling; Huang, Minyi

2017-01-01

Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

Environmental and genetic correlates of allocation to sexual reproduction in the circumpolar plant Bistorta vivipara.

PubMed

Bills, John W; Roalson, Eric H; Busch, Jeremiah W; Eidesen, Pernille B

2015-07-01

• Sexual reproduction often requires more energy and time than clonal reproduction. In marginal arctic conditions, species that can reproduce both sexually and clonally dominate. Plants with this capacity may thrive because they can alter reproduction depending on environmental conditions. Bistorta vivipara is a circumpolar herb that predominately reproduces clonally, but certain environmental conditions promote higher investment in flowers (and possible sexual reproduction). Despite largely reproducing clonally, the herb has high levels of genetic variation, and the processes underlying this paradoxical pattern of variation remain unclear. Here we identified environmental factors associated with sexual investment and examined whether sexual reproduction is associated with higher levels of genetic variation.• We sampled 20 populations of B. vivipara across the high Arctic archipelago of Svalbard. In each population, we measured reproductive traits, environmental variables, and collected samples for genetic analyses. These samples permitted hypotheses to be tested regarding sexual investment and ecological and genetic correlates.• Increased soil nitrogen and organic matter content and decreased elevation were positively associated with investment in flowers. Increased investment in flowers significantly correlated with more genotypes per population. Linkage disequilibrium was consistent with predominant clonality, but several populations showed higher genetic variation and lower differentiation than expected. There was no geographical genetic structure.• In B. vivipara, sexual investment is positively associated with habitat quality. Bistorta vivipara predominantly reproduces clonally, but occasional outcrossing, efficient clonal reproduction, and dispersal by bulbils can explain the considerable genetic variation and weak genetic structure in B. vivipara. © 2015 Botanical Society of America, Inc.

Fixation Probability in a Haploid-Diploid Population.

PubMed

Bessho, Kazuhiro; Otto, Sarah P

2017-01-01

Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species. Copyright © 2017 by the Genetics Society of America.

Transfusion strategy for weak D type 4.0 based on RHD alleles and RH haplotypes in Tunisia

PubMed Central

Ouchari, Mouna; Srivastava, Kshitij; Romdhane, Houda; Yacoub, Saloua Jemni; Flegel, Willy Albert

2017-01-01

Background With more than 460 RHD alleles, this gene is the most complex and polymorphic among all blood group systems. The Tunisian population has the largest known prevalence of weak D type 4.0 alleles, occurring in 1 of 105 RH haplotypes. We aimed to establish a rationale for the transfusion strategy of weak D type 4.0 in Tunisia. Study design and methods Donors were randomly screened for the serological weak D phenotype. The RHD coding sequence and parts of the introns were sequenced. To establish the RH haplotype, the RHCE gene was tested for characteristic single nucleotide positions. Results We determined all RHD alleles and the RH haplotypes coding for the serologic weak D phenotype among 13,431 Tunisian donations. A serologic weak D phenotype was found in 67 individuals (0.50%). Among them, 60 carried a weak D type 4 allele: 53 weak D type 4.0, 6 weak D type 4.2.2 (DAR), and 1 weak D type 4.1. Another 4 donors had 1 variant allele each: DVII, weak D type 1, weak D type 3, and weak D type 100, while 3 donors showed a normal RHD sequence. The weak D type 4.0 was most often linked to RHCE*ceVS.04.01, weak D type 4.2.2 to RHCE*ceAR, and weak D type 4.1 to RHCE*ceVS.02, while the other RHD alleles were linked to one of the common RHCE alleles. Conclusions Among the weak D phenotypes in Tunisia, no novel RHD allele was found and almost 90% were caused by alleles of the weak D type 4 cluster, of which 88% represented the weak D type 4.0 allele. Based on established RH haplotypes for variant RHD and RHCE alleles and the lack of adverse clinical reports, we recommend D positive transfusions for patients with weak D type 4.0 in Tunisia. PMID:29193104

Transfusion strategy for weak D Type 4.0 based on RHD alleles and RH haplotypes in Tunisia.

PubMed

Ouchari, Mouna; Srivastava, Kshitij; Romdhane, Houda; Jemni Yacoub, Saloua; Flegel, Willy Albert

2018-02-01

With more than 460 RHD alleles, this gene is the most complex and polymorphic among all blood group systems. The Tunisian population has the largest known prevalence of weak D Type 4.0 alleles, occurring in one of 105 RH haplotypes. We aimed to establish a rationale for the transfusion strategy of weak D Type 4.0 in Tunisia. Donors were randomly screened for the serologic weak D phenotype. The RHD coding sequence and parts of the introns were sequenced. To establish the RH haplotype, the RHCE gene was tested for characteristic single-nucleotide positions. We determined all RHD alleles and the RH haplotypes coding for the serologic weak D phenotype among 13,431 Tunisian donations. A serologic weak D phenotype was found in 67 individuals (0.50%). Among them, 60 carried a weak D Type 4 allele: 53 weak D Type 4.0, six weak D Type 4.2.2 (DAR), and one weak D Type 4.1. An additional four donors had one variant allele each: DVII, weak D Type 1, weak D Type 3, and weak D type 100, while three donors showed a normal RHD sequence. The weak D Type 4.0 was most often linked to RHCE*ceVS.04.01, weak D Type 4.2.2 to RHCE*ceAR, and weak D Type 4.1 to RHCE*ceVS.02, while the other RHD alleles were linked to one of the common RHCE alleles. Among the weak D phenotypes in Tunisia, no novel RHD allele was found and almost 90% were caused by alleles of the weak D Type 4 cluster, of which 88% represented the weak D Type 4.0 allele. Based on established RH haplotypes for variant RHD and RHCE alleles and the lack of adverse clinical reports, we recommend D+ transfusions for patients with weak D Type 4.0 in Tunisia. © 2017 AABB.

Architecture of the hydrophobic and hydrophilic layers as found from crystal structure analysis of N-benzyl-N,N-dimethylalkylammonium bromides.

PubMed

Hodorowicz, Maciej; Stadnicka, Katarzyna; Czapkiewicz, Jan

2005-10-01

The molecular and crystal structures of N-benzyl-N,N-dimethylalkylammonium bromides monohydrates with chain length n=8-10 have been determined. The crystals are isostructural with the N-benzyl-N,N-dimethyldodecylammonium bromide monohydrate. The structures consist of alternated hydrophobic and hydrophilic layers perpendicular to [001]. The attraction between N+ of the cation head-groups and Br- anions is achieved through weak C_H...Br interactions. The water molecules incorporated into ionic layers are donors for two O_H...Br hydrogen bonds and serve as the acceptors in two weak interactions of C_H...O type. The methylene chains, with the slightly curved general shape, have the extended all-trans conformation. The mutual packing of the chains in the hydrophobic layers is governed by weak C_H...pi interactions.

A Study of Strengths and Weaknesses of Descriptive Assessment from Principals, Teachers and Experts Points of View in Chaharmahal and Bakhteyari Primary Schools

ERIC Educational Resources Information Center

Sharief, Mostafa; Naderi, Mahin; Hiedari, Maryam Shoja; Roodbari, Omolbanin; Jalilvand, Mohammad Reza

2012-01-01

The aim of current study is to determine the strengths and weaknesses of descriptive evaluation from the viewpoint of principals, teachers and experts of Chaharmahal and Bakhtiari province. A descriptive survey was performed. Statistical population includes 208 principals, 303 teachers, and 100 executive experts of descriptive evaluation scheme in…

Do Mexican immigrants "import" social gradients in health to the US?

PubMed

Buttenheim, Alison; Goldman, Noreen; Pebley, Anne R; Wong, Rebeca; Chung, Chang

2010-10-01

Greater educational attainment is consistently associated with lower mortality and better health, a pattern known as the social gradient. However, recent research suggests that Mexican-origin adults in the US have weak or flat gradients, in contrast to steep gradients for non-Hispanic whites. In this study we evaluate one hypothesis for this finding: Is the relative weakness of education gradients in health behaviors observed among Mexican-origin adults in the US due to weak gradients in the sending population? We test this "imported gradients" hypothesis with data from two nationally-representative datasets: the US National Health Interview Survey (NHIS) and the Mexican National Health Survey (ENSA 2000). We compare education gradients in smoking and obesity for recently-arrived Mexican immigrants in the US to the corresponding gradients in high-migration regions of Mexico. Results partially support the imported gradients hypothesis and have implications for health education and promotion programs targeted to immigrant populations to reduce racial and ethnic disparities in health in the US.

Do Mexican immigrants “import” social gradients in health to the US?

PubMed Central

Buttenheim, Alison; Goldman, Noreen; Pebley, Anne R; Wong, Rebeca; Chung, Chang

2011-01-01

Greater educational attainment is consistently associated with lower mortality and better health, a pattern known as the social gradient. However, recent research suggests that Mexican-origin adults in the US have weak or flat gradients, in contrast to steep gradients for non-Hispanic whites. In this study we evaluate one hypothesis for this finding: Is the relative weakness of education gradients in health behaviors observed among Mexican-origin adults in the US due to weak gradients in the sending population? We test this “imported gradients” hypothesis with data from two nationally-representative datasets: the US National Health Interview Survey (NHIS) and the Mexican National Health Survey (ENSA 2000). We compare education gradients in smoking and obesity for recently-arrived Mexican immigrants in the US to the corresponding gradients in high-migration regions of Mexico. Results partially support the imported gradients hypothesis and have implications for health education and promotion programs targeted to immigrant populations to reduce racial and ethnic disparities in health in the US. PMID:20692753

Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima).

PubMed

Nayfa, Maria G; Zenger, Kyall R

2016-08-01

Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G×E effects) among populations in this region. Global Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and Fst analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan.

PubMed

Postaire, B; Gélin, P; Bruggemann, J H; Magalon, H

2017-04-01

Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive F IS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise F ST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.

Extrapolating subsurface geometry by surface expressions in transpressional strike slip fault, deduced from analogue experiments with settings of rheology and convergence angle

NASA Astrophysics Data System (ADS)

Hsieh, Shang Yu; Neubauer, Franz

2015-04-01

The internal structure of major strike-slip faults is still poorly understood, particularly how to extrapolate subsurface structures by surface expressions. Series of brittle analogue experiments by Leever et al., 2011 resulted the convergence angle is the most influential factor for surface structures. Further analogue models with different ductile settings allow a better understanding in extrapolating surface structures to the subsurface geometry of strike-slip faults. Fifteen analogue experiments were constructed to represent strike-slip faults in nature in different geological settings. As key parameters investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressional system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry.

Sex ratio rather than population size affects genetic diversity in Antennaria dioica.

PubMed

Rosche, C; Schrieber, K; Lachmuth, S; Durka, W; Hirsch, H; Wagner, V; Schleuning, M; Hensen, I

2018-03-09

Habitat fragmentation and small population size can lead to genetic erosion in threatened plant populations. Classical theory implies that dioecy can counteract genetic erosion as it decreases the magnitude of inbreeding and genetic drift due to obligate outcrossing. However, in small populations, sex ratios may be strongly male- or female-biased, leading to substantial reductions in effective population size. This may theoretically result in a unimodal relationship between sex ratios and genetic diversity; yet, empirical studies on this relationship are scarce. Using AFLP markers, we studied genetic diversity, structure and differentiation in 14 highly fragmented Antennaria dioica populations from the Central European lowlands. Our analyses focused on the relationship between sex ratio, population size and genetic diversity. Although most populations were small (mean: 35.5 patches), genetic diversity was moderately high. We found evidence for isolation-by-distance, but overall differentiation of the populations was rather weak. Females dominated 11 populations, which overall resulted in a slightly female-biased sex ratio (61.5%). There was no significant relationship between population size and genetic diversity. The proportion of females was not unimodally but positively linearly related to genetic diversity. The high genetic diversity and low genetic differentiation suggest that A. dioica has been widely distributed in the Central European lowlands in the past, while fragmentation occurred only in the last decades. Sex ratio has more immediate consequences on genetic diversity than population size. An increasing proportion of females can increase genetic diversity in dioecious plants, probably due to a higher amount of sexual reproduction. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Uncloaking a cryptic, threatened rail with molecular markers: origins, connectivity and demography of a recently-discovered population

USGS Publications Warehouse

Girard, Philippe; Takekawa, John Y.; Beissinger, Steven R.

2010-01-01

The threatened California Black Rail lives under dense marsh vegetation, is rarely observed, flies weakly and has a highly disjunct distribution. The largest population of rails is found in 8–10 large wetlands in San Francisco Bay (SF Bay), but a population was recently discovered in the foothills of the Sierra Nevada Mountains (Foothills), within a wetland network comprised of over 200 small marshes. Using microsatellite and mitochondrial analyses, our objectives were to determine the origins, connectivity and demography of this recently-discovered population. Analyses of individuals from the Foothills (n = 31), SF Bay (n = 31), the Imperial Valley (n = 6) and the East Coast (n = 3), combined with rigorous power evaluations, provided valuable insights into past history and current dynamics of the species in Northern California that challenge conventional wisdom about the species. The Foothills and SF Bay populations have diverged strongly from the Imperial Valley population, even more strongly than from individuals of the East Coast subspecies. The data also suggest a historical presence of the species in the Foothills. The SF Bay and Foothills populations had similar estimated effective population size over the areas sampled and appeared linked by a strongly asymmetrical migration pattern, with a greater probability of movement from the Foothills to SF Bay than vice versa. Random mating was inferred in the Foothills, but local substructure among marshes and inbreeding were detected in SF Bay, suggesting different dispersal patterns within each location. The unexpected dimensions of Black Rail demography and population structure suggested by these analyses and their potential importance for management are discussed.

Investigating genetic diversity and habitat dynamics in Plantago brutia (Plantaginaceae), implications for the management of narrow endemics in Mediterranean mountain pastures.

PubMed

De Vita, A; Bernardo, L; Gargano, D; Palermo, A M; Peruzzi, L; Musacchio, A

2009-11-01

Many factors have contributed to the richness of narrow endemics in the Mediterranean, including long-lasting human impact on pristine landscapes. The abandonment of traditional land-use practices is causing forest recovery throughout the Mediterranean mountains, by increasing reduction and fragmentation of open habitats. We investigated the population genetic structure and habitat dynamics of Plantago brutia Ten., a narrow endemic in mountain pastures of S Italy. Some plants were cultivated in the botanical garden to explore the species' breeding system. Genetic diversity was evaluated based on inter-simple sequence repeat (ISSR) polymorphisms in 150 individuals from most of known stands. Recent dynamics in the species habitat were checked over a 14-year period. Flower phenology, stigma receptivity and experimental pollinations revealed protogyny and self-incompatibility. With the exception of very small and isolated populations, high genetic diversity was found at the species and population level. amova revealed weak differentiation among populations, and the Mantel test suggested absence of isolation-by-distance. Multivariate analysis of population and genetic data distinguished the populations based on genetic richness, size and isolation. Landscape analyses confirmed recent reduction and isolation of potentially suitable habitats. Low selfing, recent isolation and probable seed exchange may have preserved P. brutia populations from higher loss of genetic diversity. Nonetheless, data related to very small populations suggest that this species may suffer further fragmentation and isolation. To preserve most of the species' genetic richness, future management efforts should consider the large and isolated populations recognised in our analyses.

Determining the structure of Higgs couplings at the CERN LargeHadron Collider.

PubMed

Plehn, Tilman; Rainwater, David; Zeppenfeld, Dieter

2002-02-04

Higgs boson production via weak boson fusion at the CERN Large Hadron Collider has the capability to determine the dominant CP nature of a Higgs boson, via the tensor structure of its coupling to weak bosons. This information is contained in the azimuthal angle distribution of the two outgoing forward tagging jets. The technique is independent of both the Higgs boson mass and the observed decay channel.

Deformation of Aztec Sandstone at Valley of Fire of Nevada: failure modes, sequence of deformation, structural products and their interplay with paleo fluids

NASA Astrophysics Data System (ADS)

Aydin, A.

2014-12-01

The Valley of Fire State Park, 60 km NE of Las Vegas, is a beacon of knowledge for deformation of Aztec Sandstone, a cross-bedded quartz arenite deposited in the Aztec-Navajo-Nugget erg in early Jurassic. It displays great diversity of physical properties, different localization types and micromechanics. The two deformation episodes, the Sevier folding & thrusting and the Basin & Range extension affected the area. The appearance of compaction bands marks the earliest deformation structure and their distribution, orientation, and dimension are controlled by the depositional architecture and loading. The earliest shear structures in the area are the Muddy Mountain, Summit, and Willow Tank thrusts and numerous small-scale bed-parallel faults. They altogether produced several kilometers of E-SE transport and shortening in the late Cretaceous and display numerous shear bands in its damage zone within the Aztec Sandstone. Shear bands also occur along dune boundaries and cross-bed interfaces. These observations indicate that the early deformation of the sandstone was accommodated by strain localization with various kinematics. The younger generation of faults in the area is of mid-Miocene age, and crops out pervasively. It includes a series of small offset normal faults (less than a few ten meters) which can be identified at steep cliff faces. These faults are highly segmented and are surrounded by a dense population of splay fractures. A large number of these splays were later sheared sequentially resulting in a well-defined network of left- and right-lateral strike-slip faults with slip magnitudes up to a few kilometers in the Park. The formation mechanisms of both the normal and strike-slip faults can be characterized as the sliding along planes of initial weaknesses and the accompanying cataclastic deformation. Some of the initial weak planes are associated with the depositional elements such as interdune boundaries and cross-bed interfaces while others are joint zones apparently not physically connected to any observable normal fault or dune boundary fault, but consistent with the earlier extension direction. The specific kinematics of this latter period of faulting is thought to be dictated by the orientation of the depositional and structural weaknesses and the orientation and rotation of the driving stresses.

Weak ferromagnetism in a high-pressure phase of FeTiO3 with polar lattice distortion

NASA Astrophysics Data System (ADS)

Varga, Tamas; Mitchell, John; Fennie, Craig; Streiffer, Stephen; Hong, Seungbum; Park, Moonkyu; Gopalan, Venkatraman; Kumar, Amit; Vlahos, Eftihia; Sanehira, Takeshi; Wang, Yanbin

2009-03-01

Today's challenge in multiferroics is to identify materials in which polarization and magnetization -- normally considered contraindicated properties - are strongly coupled. Recent density functional theory calculations have predicted that the family of compounds MTiO3 (M = Mn, Fe, Ni) are promising candidates where a polar lattice distortion can induce weak ferromagnetism. The crucial insight is that while the equilibrium one-atmosphere structure of these is ilmenite, they must be transformed to a closely related LiNbO3-type structure. We have prepared the corresponding FeTiO3 phase at 18 GPa and 1200 ^oC. It shows a sharp antiferromagnetic (AF) transition at 111.5 K. FeTiO3 also displays ferroelectric domains, and weak ferromagnetism coincident with the AF transition. Possible coupling between its polarization and weak ferromagnetism is discussed based on results of piezoelectric force microscopy (PFM), second harmonic generation (SHG), dielectric, and polarization measurements.

MagnetoSperm: A microrobot that navigates using weak magnetic fields

NASA Astrophysics Data System (ADS)

Khalil, Islam S. M.; Dijkslag, Herman C.; Abelmann, Leon; Misra, Sarthak

2014-06-01

In this work, a propulsion system similar in motion to a sperm-cell is investigated. This system consists of a structure resembling a sperm-cell with a magnetic head and a flexible tail of 42 μm and 280 μm in length, respectively. The thickness, length, and width of this structure are 5.2 μm, 322 μm, and 42 μm, respectively. The magnetic head includes a 200 nm-thick cobalt-nickel layer. The cobalt-nickel layer provides a dipole moment and allows the flexible structure to align along oscillating weak (less than 5 mT) magnetic field lines, and hence generates a propulsion thrust force that overcomes the drag force. The frequency response of this system shows that the propulsion mechanism allows for swimming at an average speed of 158 ± 32 μm/s at alternating weak magnetic field of 45 Hz. In addition, we experimentally demonstrate controlled steering of the flexible structure towards reference positions.

Contagion processes on the static and activity-driven coupling networks

NASA Astrophysics Data System (ADS)

Lei, Yanjun; Jiang, Xin; Guo, Quantong; Ma, Yifang; Li, Meng; Zheng, Zhiming

2016-03-01

The evolution of network structure and the spreading of epidemic are common coexistent dynamical processes. In most cases, network structure is treated as either static or time-varying, supposing the whole network is observed in the same time window. In this paper, we consider the epidemics spreading on a network which has both static and time-varying structures. Meanwhile, the time-varying part and the epidemic spreading are supposed to be of the same time scale. We introduce a static and activity-driven coupling (SADC) network model to characterize the coupling between the static ("strong") structure and the dynamic ("weak") structure. Epidemic thresholds of the SIS and SIR models are studied using the SADC model both analytically and numerically under various coupling strategies, where the strong structure is of homogeneous or heterogeneous degree distribution. Theoretical thresholds obtained from the SADC model can both recover and generalize the classical results in static and time-varying networks. It is demonstrated that a weak structure might make the epidemic threshold low in homogeneous networks but high in heterogeneous cases. Furthermore, we show that the weak structure has a substantive effect on the outbreak of the epidemics. This result might be useful in designing some efficient control strategies for epidemics spreading in networks.

Non-weight bearing-induced muscle weakness: the role of myosin quantity and quality in MHC type II fibers.

PubMed

Kim, Jong-Hee; Thompson, LaDora V

2014-07-15

We tested the hypothesis that non-weight bearing-induced muscle weakness (i.e., specific force) results from decreases in myosin protein quantity (i.e., myosin content per half-sarcomere and the ratio of myosin to actin) and quality (i.e., force per half-sarcomere and population of myosin heads in the strong-binding state during muscle contraction) in single myosin heavy chain (MHC) type II fibers. Fisher-344 rats were assigned to weight-bearing control (Con) or non-weight bearing (NWB). The NWB rats were hindlimb unloaded for 2 wk. Diameter, force, and MHC content were determined in permeabilized single fibers from the semimembranosus muscle. MHC isoform and the ratio of MHC to actin in each fiber were determined by gel electrophoresis and silver staining techniques. The structural distribution of myosin from spin-labeled fiber bundles during maximal isometric contraction was evaluated using electron paramagnetic resonance spectroscopy. Specific force (peak force per cross-sectional area) in MHC type IIB and IIXB fibers from NWB was significantly reduced by 38% and 18%, respectively. MHC content per half-sarcomere was significantly reduced by 21%. Two weeks of hindlimb unloading resulted in a reduced force per half-sarcomere of 52% and fraction of myosin strong-binding during contraction of 34%. The results suggest that reduced myosin and actin content (quantity) and myosin quality concomitantly contribute to non-weight bearing-related muscle weakness. Copyright © 2014 the American Physiological Society.

Neuronal avalanches and coherence potentials

NASA Astrophysics Data System (ADS)

Plenz, D.

2012-05-01

The mammalian cortex consists of a vast network of weakly interacting excitable cells called neurons. Neurons must synchronize their activities in order to trigger activity in neighboring neurons. Moreover, interactions must be carefully regulated to remain weak (but not too weak) such that cascades of active neuronal groups avoid explosive growth yet allow for activity propagation over long-distances. Such a balance is robustly realized for neuronal avalanches, which are defined as cortical activity cascades that follow precise power laws. In experiments, scale-invariant neuronal avalanche dynamics have been observed during spontaneous cortical activity in isolated preparations in vitro as well as in the ongoing cortical activity of awake animals and in humans. Theory, models, and experiments suggest that neuronal avalanches are the signature of brain function near criticality at which the cortex optimally responds to inputs and maximizes its information capacity. Importantly, avalanche dynamics allow for the emergence of a subset of avalanches, the coherence potentials. They emerge when the synchronization of a local neuronal group exceeds a local threshold, at which the system spawns replicas of the local group activity at distant network sites. The functional importance of coherence potentials will be discussed in the context of propagating structures, such as gliders in balanced cellular automata. Gliders constitute local population dynamics that replicate in space after a finite number of generations and are thought to provide cellular automata with universal computation. Avalanches and coherence potentials are proposed to constitute a modern framework of cortical synchronization dynamics that underlies brain function.

An official American Thoracic Society Clinical Practice guideline: the diagnosis of intensive care unit-acquired weakness in adults.

PubMed

Fan, Eddy; Cheek, Fern; Chlan, Linda; Gosselink, Rik; Hart, Nicholas; Herridge, Margaret S; Hopkins, Ramona O; Hough, Catherine L; Kress, John P; Latronico, Nicola; Moss, Marc; Needham, Dale M; Rich, Mark M; Stevens, Robert D; Wilson, Kevin C; Winkelman, Chris; Zochodne, Doug W; Ali, Naeem A

2014-12-15

Profound muscle weakness during and after critical illness is termed intensive care unit-acquired weakness (ICUAW). To develop diagnostic recommendations for ICUAW. A multidisciplinary expert committee generated diagnostic questions. A systematic review was performed, and recommendations were developed using the Grading, Recommendations, Assessment, Development, and Evaluation (GRADE) approach. Severe sepsis, difficult ventilator liberation, and prolonged mechanical ventilation are associated with ICUAW. Physical rehabilitation improves outcomes in heterogeneous populations of ICU patients. Because it may not be feasible to provide universal physical rehabilitation, an alternative approach is to identify patients most likely to benefit. Patients with ICUAW may be such a group. Our review identified only one case series of patients with ICUAW who received physical therapy. When compared with a case series of patients with ICUAW who did not receive structured physical therapy, evidence suggested those who receive physical rehabilitation were more frequently discharged home rather than to a rehabilitative facility, although confidence intervals included no difference. Other interventions show promise, but fewer data proving patient benefit existed, thus precluding specific comment. Additionally, prior comorbidity was insufficiently defined to determine its influence on outcome, treatment response, or patient preferences for diagnostic efforts. We recommend controlled clinical trials in patients with ICUAW that compare physical rehabilitation with usual care and further research in understanding risk and patient preferences. Research that identifies treatments that benefit patients with ICUAW is necessary to determine whether the benefits of diagnostic testing for ICUAW outweigh its burdens.

Access to health care and social protection.

PubMed

Martin, Philippe

2012-06-01

In France, the access to healthcare has been conceived as a social right and is mainly managed through the coverage of the population by the National Health Insurance, which is a part of the whole French social security scheme. This system was based on the so-called Bismarckian model, which implies that it requires full employment and solid family links, as the insured persons are the workers and their dependents. This paper examines the typical problems that this system has to face as far as the right to healthcare is concerned. First, it addresses the need to introduce some universal coverage programs, in order to integrate the excluded population. Then, it addresses the issue of financial sustainability as the structural weakness of the French system--in which healthcare is still mainly provided by private practice physicians and governed by the principle of freedom--leads to conceive and implement complex forms of regulations between the State, the Social security institutions and the healthcare providers.

Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

NASA Astrophysics Data System (ADS)

Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

2018-02-01

The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

Mutation-selection equilibrium in games with multiple strategies.

PubMed

Antal, Tibor; Traulsen, Arne; Ohtsuki, Hisashi; Tarnita, Corina E; Nowak, Martin A

2009-06-21

In evolutionary games the fitness of individuals is not constant but depends on the relative abundance of the various strategies in the population. Here we study general games among n strategies in populations of large but finite size. We explore stochastic evolutionary dynamics under weak selection, but for any mutation rate. We analyze the frequency dependent Moran process in well-mixed populations, but almost identical results are found for the Wright-Fisher and Pairwise Comparison processes. Surprisingly simple conditions specify whether a strategy is more abundant on average than 1/n, or than another strategy, in the mutation-selection equilibrium. We find one condition that holds for low mutation rate and another condition that holds for high mutation rate. A linear combination of these two conditions holds for any mutation rate. Our results allow a complete characterization of nxn games in the limit of weak selection.

Finite element analysis of ROPS for mechanical driving dump truck cab

NASA Astrophysics Data System (ADS)

Wang, Yong; Xie, Heping; Fang, Yuanbin; Feng, Handui; Dong, Lei

2018-02-01

For roll-over protective structures (ROPS) in a mechanical driving dump truck cab, it simulates the lateral, vertical and longitudinal loads of ROPS. It obtains stress and deformation of the cab that occurs to roll. For the relative weak position of ROPS in the cab, the structure of the cab is improved and verified according to the ISO 3164: 1995. The results show that the established finite element model can effectively predict the deformation and stress distribution of ROPS, and optimize the weak structure of the cab, which has important guiding significance for structural design of the cab and ROPS optimization of the mechanical driving dump truck cab.

Population biology of Avena : IX. Gene flow and neighborhood size in relation to microgeographic variation in Avena barbata.

PubMed

Rai, Kedar N; Jain, Subodh K

1982-06-01

Pollen and seed dispersal patterns were analyzed in both natural and experimental populations of Avena barbata. Localized estimates of gene flow rates and plant densities gave estimates of neighborhood size in the range of 40 to 400 plants; the estimates of mean rate and distance of gene flow seemed to vary widely due to variable wind direction, rodent activity, microsite heterogeneity, etc. The relative sizes of neighborhoods in several populations were correlated with the patchy distribution of different genotypes (scored for lemma color and leaf sheath hairiness) within short distances, but patch sizes had a wide range among different sites. Highly localized gene flow patterns seemed to account for the observed pattern of highly patchy variation even when the dispersal curves for both pollen and seed were platykurtic in many cases. Measures of the stability of patches in terms of their size, dispersion in space and genetic structure in time are needed in order to sort out the relative roles of founder effects, random drift (due to small neighborhood size), and highly localized selection. However, our observations suggest that many variables and stochastic processes are involved in such studies so as to allow only weak inference about the underlying role of natural selection, drift and factors of population regulatien.

Genetic diversity of resin yielder Pinus merkusii from West Java - Indonesia revealed by microsatellites marker

NASA Astrophysics Data System (ADS)

Susilowati, A.; Rachmat, H. H.; Siregar, I. Z.; Supriyanto

2018-02-01

Phenotypic observation of resin yielder Pinus merkusii showed higher value of genetic variation and narrow sense heritability values for resin production trait. This result indicated that genetic factor played as dominant aspect. However, further observation using molecular marker would still be needed to overcome the weakness of phenotypic observation. This study was carried out in order to characterize the genetic diversity and genetic differentiation of resin yielder genotype candidate P.merkusii using microsatellite markers and to characterize the genetic structure in the resin yielder populations. Seventy needle and inner bark samples were collected from resin yielder in Cijambu Seedling Seed Orchard (SSO) Sumedang, West Java and further divided into two genotype candidates (lower and high resin yielder). Seven microsatellites loci (pm01, pm04, pm05, pm07, pm08, pm09a, pm12, pde5 and SPAC 11.6) were used for detection of genetic diversity. Results showed that genetic diversity in higher resin candidates was (0.551), slightly different compared lower candidates (0.545). However, cluster analysis determined that higher resin yielder grouped with lower one. Molecular variation was found to be low among populations (21%) and high among individuals within the populations (79%). Private alleles were detected both in higher yielder and also normal population.

Demographic matrix model for informing swallow-wort (Vincetoxicum spp.) biological control

USDA-ARS?s Scientific Manuscript database

Demographic matrix modeling of plant populations can be a powerful tool to identify key life stage transitions that contribute the most to population growth of an invasive plant and hence should be targeted for disruption (weak links) by biological control and/or other control tactics. Therefore, t...

Availability and structure of primary medical care services and population health and health care indicators in England

PubMed Central

Gulliford, Martin C; Jack, Ruth H; Adams, Geoffrey; Ukoumunne, Obioha C

2004-01-01

Background It has been proposed that greater availability of primary medical care practitioners (GPs) contributes to better population health. We evaluated whether measures of the supply and structure of primary medical services are associated with health and health care indicators after adjusting for confounding. Methods Data for the supply and structure of primary medical services and the characteristics of registered patients were analysed for 99 health authorities in England in 1999. Health and health care indicators as dependent variables included standardised mortality ratios (SMR), standardised hospital admission rates, and conceptions under the age of 18 years. Linear regression analyses were adjusted for Townsend score, proportion of ethnic minorities and proportion of social class IV/ V. Results Higher proportions of registered rural patients and patients ≥ 75 years were associated with lower Townsend deprivation scores, with larger partnership sizes and with better health outcomes. A unit increase in partnership size was associated with a 4.2 (95% confidence interval 1.7 to 6.7) unit decrease in SMR for all-cause mortality at 15–64 years (P = 0.001). A 10% increase in single-handed practices was associated with a 1.5 (0.2 to 2.9) unit increase in SMR (P = 0.027). After additional adjustment for percent of rural and elderly patients, partnership size and proportion of single-handed practices, GP supply was not associated with SMR (-2.8, -6.9 to 1.3, P = 0.183). Conclusions After adjusting for confounding with health needs of populations, mortality is weakly associated with the degree of organisation of practices as represented by the partnership size but not with the supply of GPs. PMID:15193157

Exploration of the utility of ancestry informative markers for genetic association studies of African Americans with type 2 diabetes and end stage renal disease.

PubMed

Keene, Keith L; Mychaleckyj, Josyf C; Leak, Tennille S; Smith, Shelly G; Perlegas, Peter S; Divers, Jasmin; Langefeld, Carl D; Freedman, Barry I; Bowden, Donald W; Sale, Michèle M

2008-09-01

Admixture and population stratification are major concerns in genetic association studies. We wished to evaluate the impact of admixture using empirically derived data from genetic association studies of African Americans (AA) with type 2 diabetes (T2DM) and end-stage renal disease (ESRD). Seventy ancestry informative markers (AIMs) were genotyped in 577 AA with T2DM-ESRD, 596 AA controls, 44 Yoruba Nigerian (YRI) and 39 European American (EA) controls. Genotypic data and association results for eight T2DM candidate gene studies in our AA population were included. Ancestral estimates were calculated using FRAPPE, ADMIXMAP and STRUCTURE for all AA samples, using varying numbers of AIMs (25, 50, and 70). Ancestry estimates varied significantly across all three programs with the highest estimates obtained using STRUCTURE, followed by ADMIXMAP; while FRAPPE estimates were the lowest. FRAPPE estimates were similar using varying numbers of AIMs, while STRUCTURE estimates using 25 AIMs differed from estimates using 50 and 70 AIMs. Female T2DM-ESRD cases showed higher mean African proportions as compared to female controls, male cases, and male controls. Age showed a weak but significant correlation with individual ancestral estimates in AA cases (r2 = 0.101; P = 0.019) and in the combined set (r2 = 0.131; P = 3.57 x 10(-5)). The absolute difference between frequencies in parental populations, absolute delta, was correlated with admixture impact for dominant, additive, and recessive genotypic models of association. This study presents exploratory analyses of the impact of admixture on studies of AA with T2DM-ESRD and supports the use of ancestral proportions as a means of reducing confounding effects due to admixture.

Exploration of the utility of ancestry informative markers for genetic association studies of African Americans with type 2 diabetes and end stage renal disease

PubMed Central

Keene, Keith L.; Mychaleckyj, Josyf C.; Leak, Tennille S.; Smith, Shelly G.; Perlegas, Peter S.; Divers, Jasmin; Langefeld, Carl D.; Freedman, Barry I.; Bowden, Donald W.; Sale, Michèle M.

2009-01-01

Admixture and population stratification are major concerns in genetic association studies. We wished to evaluate the impact of admixture using empirically derived data from genetic association studies of African Americans (AA) with type 2 diabetes (T2DM) and end-stage renal disease (ESRD). Seventy ancestry informative markers (AIMs) were genotyped in 577 AA with T2DM-ESRD, 596 AA controls, 44 Yoruba Nigerian (YRI) and 39 European American (EA) controls. Genotypic data and association results for eight T2DM candidate gene studies in our AA population were included. Ancestral estimates were calculated using FRAPPE, ADMIXMAP and STRUCTURE for all AA samples, using varying numbers of AIMs (25, 50, and 70). Ancestry estimates varied significantly across all three programs with the highest estimates obtained using STRUCTURE, followed by ADMIXMAP; while FRAPPE estimates were the lowest. FRAPPE estimates were similar using varying numbers of AIMs, while STRUCTURE estimates using 25 AIMs differed from estimates using 50 and 70 AIMs. Female T2DM-ESRD cases showed higher mean African proportions as compared to female controls, male cases, and male controls. Age showed a weak but significant correlation with individual ancestral estimates in AA cases (r2=0.101; P=0.019) and in the combined set (r2=0.131; P=3.57×10−5). The absolute difference between frequencies in parental populations, absolute δ, was correlated with admixture impact for dominant, additive, and recessive genotypic models of association. This study presents exploratory analyses of the impact of admixture on studies of AA with T2DM-ESRD and supports the use of ancestral proportions as a means of reducing confounding effects due to admixture. PMID:18654799

Population displacements as a risk factor for the emergence of epidemics.

PubMed

Tabbaa, Darem; Seimenis, Aristarco

2013-01-01

Wars and civil conflicts have been terrible experiences since ancient times but, regretfully, they are always present even in the 21st century. Their catastrophic effects are still lived by many populations displaced from their native areas. Conflicts, particularly the civil ones, create disruption in most aspects of national structures and populations, which are forced to move to more or less safer or even distant areas, survive under downgraded conditions. They are usually housed in temporary shelters in overcrowded camps and contaminated environment. Water and food are neither safe nor sufficient. Malnutrition, lack or weak sanitary care and long-term stress lead these populations to being vulnerable to severe infections. Under such conditions there are high rates of morbidity and mortality, with elders and children being the main victims. Public health, animal health, municipalities and other inter-related sectors should work on preparedness plans well in advance in order to provide ways and means to face emergencies. Zoonotic and other communicable disease outbreaks should not be left uncontrolled, as their impact would be an additional burden for the country under unrest. Guidance should be provided on how to best articulate an emergency management plan from the early detection of outbreaks up to their control. These aspects are briefly exposed together with the imperative request for alleviation of suffering and of the multitude of hazards conflict-affected populations have to face.

Experimental research on the structural instability mechanism and the effect of multi-echelon support of deep roadways in a kilometre-deep well

PubMed Central

Peng, Rui; Zhao, Guangming; Li, Yingming; Zhu, Jianming

2018-01-01

We study the structural instability mechanism and effect of a multi-echelon support in very-deep roadways. We conduct a scale model test for analysing the structural failure mechanism and the effect of multi-echelon support of roadways under high horizontal stress. Mechanical bearing structures are classified according to their secondary stress distribution and the strength degradation of the surrounding rock after roadway excavation. A new method is proposed by partitioning the mechanical bearing structure of the surrounding rock into weak, key and main coupling bearing stratums. In the surrounding rock, the main bearing stratum is the plastic reshaping and flowing area. The weak bearing stratum is the peeling layer or the caving part. And the key bearing stratum is the shearing and yielding area. The structural fracture mechanism of roadways is considered in analysing the bearing structure instability of the surrounding rock, and multi-echelon support that considers the structural characteristics of roadway bearings is proposed. Results of the experimental study indicate that horizontal pressure seriously influences the stability of the surrounding rock, as indicated by extension of the weak bearing area and the transfer of the main and key bearing zones. The falling roof, rib spalling, and floor heave indicate the decline of the bearing capacity of surrounding rock, thereby causing roadway structural instability. Multi-echelon support is proposed according to the mechanical bearing structure of the surrounding rock without support. The redesigned support can reduce the scope of the weak bearing area and limit the transfer of the main and key bearing areas. Consequently, kilometre-deep roadway disasters, such as wedge roof caving, floor heave, and rib spalling, can be avoided to a certain degree, and plastic flow in the surrounding rock is relieved. The adverse effect of horizontal stress on the vault, spandrel and arch foot decreases. The stability of the soft rock surrounding the roadways is maintained. PMID:29447180

Highlights from High Energy Neutrino Experiments at CERN

NASA Astrophysics Data System (ADS)

Schlatter, W.-D.

2015-07-01

Experiments with high energy neutrino beams at CERN provided early quantitative tests of the Standard Model. This article describes results from studies of the nucleon quark structure and of the weak current, together with the precise measurement of the weak mixing angle. These results have established a new quality for tests of the electroweak model. In addition, the measurements of the nucleon structure functions in deep inelastic neutrino scattering allowed first quantitative tests of QCD.

Pawlak Algebra and Approximate Structure on Fuzzy Lattice

PubMed Central

Zhuang, Ying; Liu, Wenqi; Wu, Chin-Chia; Li, Jinhai

2014-01-01

The aim of this paper is to investigate the general approximation structure, weak approximation operators, and Pawlak algebra in the framework of fuzzy lattice, lattice topology, and auxiliary ordering. First, we prove that the weak approximation operator space forms a complete distributive lattice. Then we study the properties of transitive closure of approximation operators and apply them to rough set theory. We also investigate molecule Pawlak algebra and obtain some related properties. PMID:25152922

Pawlak algebra and approximate structure on fuzzy lattice.

PubMed

Zhuang, Ying; Liu, Wenqi; Wu, Chin-Chia; Li, Jinhai

2014-01-01

The aim of this paper is to investigate the general approximation structure, weak approximation operators, and Pawlak algebra in the framework of fuzzy lattice, lattice topology, and auxiliary ordering. First, we prove that the weak approximation operator space forms a complete distributive lattice. Then we study the properties of transitive closure of approximation operators and apply them to rough set theory. We also investigate molecule Pawlak algebra and obtain some related properties.

Data Structures in Natural Computing: Databases as Weak or Strong Anticipatory Systems

NASA Astrophysics Data System (ADS)

Rossiter, B. N.; Heather, M. A.

2004-08-01

Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on to idealised machines with von Neumann architectures consisting of fixed instructions. Category theory developed as a formalism to explore the theoretical concept of naturality shows that methods like sketches arising from graph theory as only non-natural models of naturality cannot capture real-world structures for strong anticipatory information systems. Databases need a schema of the natural world. Natural computing databases need the schema itself to be also natural. Natural computing methods including neural computers, evolutionary automata, molecular and nanocomputing and quantum computation have the potential to be strong. At present they are mainly at the stage of weak anticipatory systems.

Structure of Weakly Charged Polyelectrolyte Brushes: Monomer Density Profiles

NASA Astrophysics Data System (ADS)

Borisov, O. V.; Zhulina, E. B.

1997-03-01

The internal structure (the monomer density profiles) of weakly charged polyelectrolyte brushes of different morphologies has been analyzed on the basis of the self-consistent-field approach. In contrast to previous studies based on the local electroneutrality approximation valid for sufficiently strongly charged or densely grafted (“osmotic") brushes we consider the opposite limit of sparse brushes which are unable to retain the counterions inside the brush. We have shown that an exact analytical solution of the SCF-equations is available in the case of a planar brush. In contrast to Gaussian monomer density profile known for “osmotic" polyelectrolyte brushes we have found that weakly charged brushes are characterized by constant monomer density. At the same time free ends of grafted polyions are distributed throughout the brush. Thus, the structural cross-over between polyelectrolyte “mushrooms" and dense brush regimes is established.

Does evolution lead to maximizing behavior?

PubMed

Lehmann, Laurent; Alger, Ingela; Weibull, Jörgen

2015-07-01

A long-standing question in biology and economics is whether individual organisms evolve to behave as if they were striving to maximize some goal function. We here formalize this "as if" question in a patch-structured population in which individuals obtain material payoffs from (perhaps very complex multimove) social interactions. These material payoffs determine personal fitness and, ultimately, invasion fitness. We ask whether individuals in uninvadable population states will appear to be maximizing conventional goal functions (with population-structure coefficients exogenous to the individual's behavior), when what is really being maximized is invasion fitness at the genetic level. We reach two broad conclusions. First, no simple and general individual-centered goal function emerges from the analysis. This stems from the fact that invasion fitness is a gene-centered multigenerational measure of evolutionary success. Second, when selection is weak, all multigenerational effects of selection can be summarized in a neutral type-distribution quantifying identity-by-descent between individuals within patches. Individuals then behave as if they were striving to maximize a weighted sum of material payoffs (own and others). At an uninvadable state it is as if individuals would freely choose their actions and play a Nash equilibrium of a game with a goal function that combines self-interest (own material payoff), group interest (group material payoff if everyone does the same), and local rivalry (material payoff differences). © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations

PubMed Central

Cardone, Antonio; Pant, Harish; Hassan, Sergio A.

2013-01-01

Weak and ultra-weak protein-protein association play a role in molecular recognition, and can drive spontaneous self-assembly and aggregation. Such interactions are difficult to detect experimentally, and are a challenge to the force field and sampling technique. A method is proposed to identify low-population protein-protein binding modes in aqueous solution. The method is designed to identify preferential first-encounter complexes from which the final complex(es) at equilibrium evolves. A continuum model is used to represent the effects of the solvent, which accounts for short- and long-range effects of water exclusion and for liquid-structure forces at protein/liquid interfaces. These effects control the behavior of proteins in close proximity and are optimized based on binding enthalpy data and simulations. An algorithm is described to construct a biasing function for self-adaptive configurational-bias Monte Carlo of a set of interacting proteins. The function allows mixing large and local changes in the spatial distribution of proteins, thereby enhancing sampling of relevant microstates. The method is applied to three binary systems. Generalization to multiprotein complexes is discussed. PMID:24044772

Testing spatial heterogeneity with stock assessment models

PubMed Central

Eero, Margit; Silva, Alexandra; Ulrich, Clara; Pawlowski, Lionel; Holmes, Steven J.; Ibaibarriaga, Leire; De Oliveira, José A. A.; Riveiro, Isabel; Alzorriz, Nekane; Citores, Leire; Scott, Finlay; Uriarte, Andres; Carrera, Pablo; Duhamel, Erwan; Mosqueira, Iago

2018-01-01

This paper describes a methodology that combines meta-population theory and stock assessment models to gain insights about spatial heterogeneity of the meta-population in an operational time frame. The methodology was tested with stochastic simulations for different degrees of connectivity between sub-populations and applied to two case studies, North Sea cod (Gadus morua) and Northeast Atlantic sardine (Sardina pilchardus). Considering that the biological components of a population can be partitioned into discrete spatial units, we extended this idea into a property of additivity of sub-population abundances. If the additivity results hold true for putative sub-populations, then assessment results based on sub-populations will provide information to develop and monitor the implementation of finer scale/local management. The simulation study confirmed that when sub-populations are independent and not too heterogeneous with regards to productivity, the sum of stock assessment model estimates of sub-populations’ SSB is similar to the SSB estimates of the meta-population. It also showed that a strong diffusion process can be detected and that the stronger the connection between SSB and recruitment, the better the diffusion process will be detected. On the other hand it showed that weak to moderate diffusion processes are not easy to identify and large differences between sub-populations productivities may be confounded with weak diffusion processes. The application to North Sea cod and Atlantic sardine exemplified how much insight can be gained. In both cases the results obtained were sufficiently robust to support the regional analysis. PMID:29364901

Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data

PubMed Central

Zhang, Cheng; Ni, Pan; Ahmad, Hafiz Ishfaq; Gemingguli, M; Baizilaitibei, A; Gulibaheti, D; Fang, Yaping; Wang, Haiyang; Asif, Akhtar Rasool; Xiao, Changyi; Chen, Jianhai; Ma, Yunlong; Liu, Xiangdong; Du, Xiaoyong; Zhao, Shuhong

2018-01-01

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

Magnetic Reconnection Dynamics in the Presence of Low-energy Ion Component: PIC Simulations of Hidden Particle Population

NASA Astrophysics Data System (ADS)

Khotyaintsev, Y. V.; Divin, A. V.; Toledo Redondo, S.; Andre, M.; Vaivads, A.; Markidis, S.; Lapenta, G.

2015-12-01

Magnetospheric and astrophysical plasmas are rarely in the state of thermal equilibrium. Plasma distribution functions may contain beams, supra-thermal tails, multiple ion and electron populations which are not thermalized over long time scales due to the lack of collisions between particles. In particular, the equatorial region of the dayside Earth's magnetosphere is often populated by plasma containing hot and cold ion components of comparable densities [Andre and Cully, 2012], and such ion distribution alters properties of the magnetic reconnection regions at the magnetopause [Toledo-Redondo et. al., 2015]. Motivated by these recent findings and also by fact that this region is one of the targets of the recently launched MMS mission, we performed 2D PIC simulations of magnetic reconnection in collisionless plasma with hot and cold ion components. We used a standard Harris current sheet, to which a uniform cold ion background is added. We found that introduction of the cold component modifies the structure of reconnection diffusion region. Diffusion region displays three-scale structure, with the cold Ion Diffusion Region (cIDR) scale appearing in-between the Electron Diffusion Region (EDR) and Ion Diffusion Region (IDR) scales. Structure and strength of the Hall magnetic field depends weakly on cold ion temperature or density, and is rather controlled by the conditions (B, n) upstream the reconnection region. The cold ions are accelerated predominantly transverse to the magnetic field by the Hall electric fields inside the IDR, leading to a large ion pressure anisotropy, which is unstable to ion Weibel-type or mirror-type mode. On the opposite, acceleration of cold ions is mostly field-aligned at the reconnection jet fronts downstream the X-line, producing intense ion phase-space holes there. Despite comparable reconnection rates produced , we find that the overall evolution of reconnection in presence of cold ion population is more dynamic compared to the case with a single hot ion component.

Genetic structure and early effects of inbreeding in fragmented temperate forests of a self-incompatible tree, Embothrium coccineum.

PubMed

Mathiasen, Paula; Rovere, Adriana E; Premoli, Andrea C

2007-02-01

Deforestation of temperate forests has created landscapes of forest remnants in matrices of intense human use. We studied the genetic effects of fragmentation in southern Chile on Embothrium coccineum J.R. et G. Forster, an early colonizing, bird-pollinated tree. We tested the hypothesis that, because of its self-incompatibility and life-history strategy, E. coccineum is less strongly affected by fragmentation. We studied the effects of reduced population size and increased isolation on population genetic structure and early performance of progeny. Samples were collected from spatially isolated trees and six fragments of differing sizes (small, 1 ha; medium, 20 ha; large, >150 ha). Based on isozyme polymorphisms we estimated parameters of genetic diversity, divergence, and inbreeding for adults and greenhouse-grown progeny. We also measured germination, seedling growth, and outcrossing rates on progeny arrays. Genetic variation of adults did not correlate significantly with population size, as expected, given that fragmentation occurred relatively recently. Weak effects of fragmentation were measured on progeny. Only adults yielded significant inbreeding. Similar total genetic diversity was found in adults and progeny. Low but significant genetic differentiation existed among adult and progeny populations. Seedling growth correlated positively with the effective number of alleles, showing deleterious effects of inbreeding on progeny. Seeds from small fragments had the highest outcrossing rates and germination success, indicating that higher pollinator activity in such fragments reduced selfing, thereby buffering genetic erosion and maintaining adaptive variation. The effects of forest fragmentation were detectable in E. coccineum, but these effects will probably not be detrimental to the viability of remnant populations because small, fragmented populations demonstrated higher levels of gene flow and lower inbreeding than larger stands. Pioneer species that are insensitive to forest clearing may be crucial in recovery plans to facilitate the establishment of species intolerant to such disturbance.

Space, time, and host evolution facilitate coexistence of competing bacteriophages: theory and experiment.

PubMed

Coberly, L Caitlin; Wei, Wei; Sampson, Koffi Y; Millstein, Jack; Wichman, Holly A; Krone, Stephen M

2009-04-01

We present a joint experimental/theoretical investigation into the roles of spatial structure and time in the competition between two pathogens for a single host. We suggest a natural mechanism by which competing pathogens can coexist when host evolution and competitive dynamics occur on similar timescales. Our experimental system consisted of a single bacterial host species and two competing bacteriophage strains grown on agar plates, with a serial transfer of samples of the bacteriophage population to fresh host populations after each incubation cycle. The experiments included two incubation times and two transfer protocols that either maintained or disrupted the spatial structure of the viruses at each transfer. The same bacteriophage acted as the dominant competitor under both transfer protocols. A striking difference between the treatments is that the weak competitor was able to persist in the long-incubation experiments but not in the short-incubation experiments. Mathematical and experimental evidence suggest that coexistence is due to the appearance of resistant mutant host cells that provide a transient "spatiotemporal refuge" for the weaker competitor. Our mathematical model is individual based, captures the stochastic spatial dynamics down to the level of individual cells, and helps to explain the differences in behavior under the various experimental conditions.

Warps and waves in the stellar discs of the Auriga cosmological simulations

NASA Astrophysics Data System (ADS)

Gómez, Facundo A.; White, Simon D. M.; Grand, Robert J. J.; Marinacci, Federico; Springel, Volker; Pakmor, Rüdiger

2017-03-01

Recent studies have revealed an oscillating asymmetry in the vertical structure of the Milky Way's disc. Here, we analyse 16 high-resolution, fully cosmological simulations of the evolution of individual Milky Way-sized galaxies, carried out with the magnetohydrodynamic code AREPO. At redshift zero, about 70 per cent of our galactic discs show strong vertical patterns, with amplitudes that can exceed 2 kpc. Half of these are typical 'integral sign' warps. The rest are oscillations similar to those observed in the Milky Way. Such structures are thus expected to be common. The associated mean vertical motions can be as large as 30 km s-1. Cold disc gas typically follows the vertical patterns seen in the stars. These perturbations have a variety of causes: close encounters with satellites, distant fly-bys of massive objects, accretion of misaligned cold gas from halo infall or from mergers. Tidally induced vertical patterns can be identified in both young and old stellar populations, whereas those originating from cold gas accretion are seen mainly in the younger populations. Galaxies with regular or at most weakly perturbed discs are usually, but not always, free from recent interactions with massive companions, although we have one case where an equilibrium compact disc reforms after a merger.

Localized versus itinerant states created by multiple oxygen vacancies in SrTiO3

NASA Astrophysics Data System (ADS)

Jeschke, Harald O.; Shen, Juan; Valentí, Roser

2015-02-01

Oxygen vacancies in strontium titanate surfaces (SrTiO3) have been linked to the presence of a two-dimensional electron gas with unique behavior. We perform a detailed density functional theory study of the lattice and electronic structure of SrTiO3 slabs with multiple oxygen vacancies, with a main focus on two vacancies near a titanium dioxide terminated SrTiO3 surface. We conclude based on total energies that the two vacancies preferably inhabit the first two layers, i.e. they cluster vertically, while in the direction parallel to the surface, the vacancies show a weak tendency towards equal spacing. Analysis of the nonmagnetic electronic structure indicates that oxygen defects in the surface TiO2 layer lead to population of Ti {{t}2g} states and thus itinerancy of the electrons donated by the oxygen vacancy. In contrast, electrons from subsurface oxygen vacancies populate Ti eg states and remain localized on the two Ti ions neighboring the vacancy. We find that both the formation of a bound oxygen-vacancy state composed of hybridized Ti 3eg and 4p states neighboring the oxygen vacancy as well as the elastic deformation after extracting oxygen contribute to the stabilization of the in-gap state.

Subjective wellbeing, suicide and socioeconomic factors: an ecological analysis in Hong Kong.

PubMed

Hsu, C-Y; Chang, S-S; Yip, P S F

2018-04-10

There has recently been an increased interest in mental health indicators for the monitoring of population wellbeing, which is among the targets of Sustainable Development Goals adopted by the United Nations. Levels of subjective wellbeing and suicide rates have been proposed as indicators of population mental health, but prior research is limited. Data on individual happiness and life satisfaction were sourced from a population-based survey in Hong Kong (2011). Suicide data were extracted from Coroner's Court files (2005-2013). Area characteristic variables included local poverty rate and four factors derived from a factor analysis of 21 variables extracted from the 2011 census. The associations between mean happiness and life satisfaction scores and suicide rates were assessed using Pearson correlation coefficient at two area levels: 18 districts and 30 quantiles of large street blocks (LSBs; n = 1620). LSB is a small area unit with a higher level of within-unit homogeneity compared with districts. Partial correlations were used to control for area characteristics. Happiness and life satisfaction demonstrated weak inverse associations with suicide rate at the district level (r = -0.32 and -0.36, respectively) but very strong associations at the LSB quantile level (r = -0.83 and -0.84, respectively). There were generally very weak or weak negative correlations across sex/age groups at the district level but generally moderate to strong correlations at the LSB quantile level. The associations were markedly attenuated or became null after controlling for area characteristics. Subjective wellbeing is strongly associated with suicide at a small area level; socioeconomic factors can largely explain this association. Socioeconomic factors could play an important role in determining the wellbeing of the population, and this could inform policies aimed at enhancing population wellbeing.

Using classical population genetics tools with heterochroneous data: time matters!

PubMed

Depaulis, Frantz; Orlando, Ludovic; Hänni, Catherine

2009-01-01

New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.

Statistical genetics and evolution of quantitative traits

NASA Astrophysics Data System (ADS)

Neher, Richard A.; Shraiman, Boris I.

2011-10-01

The distribution and heritability of many traits depends on numerous loci in the genome. In general, the astronomical number of possible genotypes makes the system with large numbers of loci difficult to describe. Multilocus evolution, however, greatly simplifies in the limit of weak selection and frequent recombination. In this limit, populations rapidly reach quasilinkage equilibrium (QLE) in which the dynamics of the full genotype distribution, including correlations between alleles at different loci, can be parametrized by the allele frequencies. This review provides a simplified exposition of the concept and mathematics of QLE which is central to the statistical description of genotypes in sexual populations. Key results of quantitative genetics such as the generalized Fisher’s “fundamental theorem,” along with Wright’s adaptive landscape, are shown to emerge within QLE from the dynamics of the genotype distribution. This is followed by a discussion under what circumstances QLE is applicable, and what the breakdown of QLE implies for the population structure and the dynamics of selection. Understanding the fundamental aspects of multilocus evolution obtained through simplified models may be helpful in providing conceptual and computational tools to address the challenges arising in the studies of complex quantitative phenotypes of practical interest.

Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil.

PubMed

Hmeljevski, Karina Vanessa; dos Reis, Maurício Sedrez; Forzza, Rafaela Campostrini

2015-01-01

Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F(ij) = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Transgenic mice reveal unexpected diversity of On-Off direction selective retinal ganglion cell subtypes and brain structures involved in motion processing

PubMed Central

Rivlin-Etzion, Michal; Zhou, Kaili; Wei, Wei; Elstrott, Justin; Nguyen, Phong L.; Barres, Ben; Huberman, Andrew D.; Feller, Marla B.

2011-01-01

On-Off direction selective retinal ganglion cells (DSGCs) encode the axis of visual motion. They respond strongly to an object moving in a preferred direction and weakly to an object moving in the opposite, ‘null’, direction. Historically, On-Off DSGCs were classified into 4 subtypes according to their directional preference (anterior, posterior, superior or inferior). Here, we compare two genetically identified populations of On-Off DSGCs: DRD4-DSGCs and TRHR-DSGCs. We find that although both populations are tuned for posterior motion, they can be distinguished by a variety of physiological and anatomical criteria. First, the directional tuning of TRHR-DSGCs is broader than that of DRD4-DSGCs. Second, whereas both populations project similarly to the dorsal lateral geniculate nucleus, they project differently to the ventral lateral geniculate nucleus and the superior colliculus. Moreover, TRHR-DSGCs, but not DRD4-DSGCs, also project to the zona incerta, a thalamic area not previously known to receive direction-tuned visual information. Our findings reveal unexpected diversity among mouse On-Off DSGC subtypes that uniquely process and convey image motion to the brain. PMID:21677160

Cosmology with cosmic shear observations: a review.

PubMed

Kilbinger, Martin

2015-07-01

Cosmic shear is the distortion of images of distant galaxies due to weak gravitational lensing by the large-scale structure in the Universe. Such images are coherently deformed by the tidal field of matter inhomogeneities along the line of sight. By measuring galaxy shape correlations, we can study the properties and evolution of structure on large scales as well as the geometry of the Universe. Thus, cosmic shear has become a powerful probe into the nature of dark matter and the origin of the current accelerated expansion of the Universe. Over the last years, cosmic shear has evolved into a reliable and robust cosmological probe, providing measurements of the expansion history of the Universe and the growth of its structure. We review here the principles of weak gravitational lensing and show how cosmic shear is interpreted in a cosmological context. Then we give an overview of weak-lensing measurements, and present the main observational cosmic-shear results since it was discovered 15 years ago, as well as the implications for cosmology. We then conclude with an outlook on the various future surveys and missions, for which cosmic shear is one of the main science drivers, and discuss promising new weak cosmological lensing techniques for future observations.

Changes in actin structural transitions associated with oxidative inhibition of muscle contraction.

PubMed

Prochniewicz, Ewa; Spakowicz, Daniel; Thomas, David D

2008-11-11

We have used transient phosphorescence anisotropy (TPA) to detect changes in actin structural dynamics associated with oxidative inhibition of muscle contraction. Contractility of skinned rabbit psoas muscle fibers was inhibited by treatment with 50 mM H 2O 2, which induced oxidative modifications in the myosin head and in actin, as previously reported. Using proteins purified from oxidized and unoxidized muscle, we used TPA to measure the effects of weakly (+ATP) and strongly (no ATP) bound myosin heads (S1) on the microsecond dynamics of actin labeled at Cys374 with erythrosine iodoacetamide. Oxidative modification of S1 had no effect on actin dynamics in the absence of ATP (strong binding complex), but restricted the dynamics in the presence of ATP (weakly bound complex). In contrast, oxidative modification of actin did not have a significant effect on the weak-to-strong transitions. Thus, we concluded that (1) the effects of oxidation on the dynamics of actin in the actomyosin complex are predominantly determined by oxidation-induced changes in S1, and (2) changes in weak-to-strong structural transitions in actin and myosin are coupled to each other and are associated with oxidative inhibition of muscle contractility.

Changes in actin structural transitions associated with oxidative inhibition of muscle contraction

PubMed Central

Prochniewicz, Ewa; Spakowicz, Daniel; Thomas, David D.

2011-01-01

We have used transient phosphorescence anisotropy (TPA) to detect changes in actin structural dynamics associated with oxidative inhibition of muscle contraction. Contractility of skinned rabbit psoas muscle fibers was inhibited by treatment with 50 mM H2O2, which induced oxidative modifications in the myosin head and in actin, as previously reported. Using proteins purified from oxidized and unoxidized muscle, we used TPA to measure the effects of weakly (+ATP) and strongly (no ATP) bound myosin heads (S1) on the microsecond dynamics of actin labeled at Cys374 with erythrosine iodoacetamide. Oxidative modification of S1 had no effect on actin dynamics in the absence of ATP (strong binding complex), but restricted the dynamics in the presence of ATP (weakly bound complex). In contrast, oxidative modification of actin did not have a significant effect on the weak-to-strong transitions. Thus, we concluded that (1) the effects of oxidation on the dynamics of actin in the actomyosin complex are predominantly determined by oxidation-induced changes in S1, and (2) changes in weak-to-strong structural transitions in actin and myosin are coupled to each other and are associated with oxidative inhibition of muscle contractility. PMID:18855423

Alleles versus genotypes: Genetic interactions and the dynamics of selection in sexual populations

NASA Astrophysics Data System (ADS)

Neher, Richard

2010-03-01

Physical interactions between amino-acids are essential for protein structure and activity, while protein-protein interactions and regulatory interactions are central to cellular function. As a consequence of these interactions, the combined effect of two mutations can differ from the sum of the individual effects of the mutations. This phenomenon of genetic interaction is known as epistasis. However, the importance of epistasis and its effects on evolutionary dynamics are poorly understood, especially in sexual populations where recombination breaks up existing combinations of alleles to produce new ones. Here, we present a computational model of selection dynamics involving many epistatic loci in a recombining population. We demonstrate that a large number of polymorphic interacting loci can, despite frequent recombination, exhibit cooperative behavior that locks alleles into favorable genotypes leading to a population consisting of a set of competing clones. As the recombination rate exceeds a certain critical value this ``genotype selection'' phase disappears in an abrupt transition giving way to ``allele selection'' - the phase where different loci are only weakly correlated as expected in sexually reproducing populations. Clustering of interacting sets of genes on a chromosome leads to the emergence of an intermediate regime, where localized blocks of cooperating alleles lock into genetic modules. Large populations attain highest fitness at a recombination rate just below critical, suggesting that natural selection might tune recombination rates to balance the beneficial aspect of exploration of genotype space with the breaking up of synergistic allele combinations.

Bifurcation analysis of a discrete-time ratio-dependent predator-prey model with Allee Effect

NASA Astrophysics Data System (ADS)

Cheng, Lifang; Cao, Hongjun

2016-09-01

A discrete-time predator-prey model with Allee effect is investigated in this paper. We consider the strong and the weak Allee effect (the population growth rate is negative and positive at low population density, respectively). From the stability analysis and the bifurcation diagrams, we get that the model with Allee effect (strong or weak) growth function and the model with logistic growth function have somewhat similar bifurcation structures. If the predator growth rate is smaller than its death rate, two species cannot coexist due to having no interior fixed points. When the predator growth rate is greater than its death rate and other parameters are fixed, the model can have two interior fixed points. One is always unstable, and the stability of the other is determined by the integral step size, which decides the species coexistence or not in some extent. If we increase the value of the integral step size, then the bifurcated period doubled orbits or invariant circle orbits may arise. So the numbers of the prey and the predator deviate from one stable state and then circulate along the period orbits or quasi-period orbits. When the integral step size is increased to a critical value, chaotic orbits may appear with many uncertain period-windows, which means that the numbers of prey and predator will be chaotic. In terms of bifurcation diagrams and phase portraits, we know that the complexity degree of the model with strong Allee effect decreases, which is related to the fact that the persistence of species can be determined by the initial species densities.

Formation and Evolution of a Multi-Threaded Prominence

NASA Technical Reports Server (NTRS)

Luna, M.; Karpen, J. T.; DeVore, C. R.

2012-01-01

We investigate the process of formation and subsequent evolution of prominence plasma in a filament channel and its overlying arcade. We construct a three-dimensional time-dependent model of a filament-channel prominence suitable to be compared with observations. We combine this magnetic field structure with one-dimensional independent simulations of many flux tubes. The magnetic structure is a three-dimensional sheared double arcade, and the thermal non-equilibrium process governs the plasma evolution. We have found that the condensations in the corona can be divided into two populations: threads and blobs. Threads are massive condensations that linger in the field line dips. Blobs are ubiquitous small condensations that are produced throughout the filament and overlying arcade magnetic structure, and rapidly fall to the chromosphere. The total prominence mass is in agreement with observations. The threads are the principal contributors to the total mass, whereas the blob contribution is small. The motion of the threads is basically horizontal, while blobs move in all directions along the field. The peak velocities for both populations are comparable, but there is a weak tendency for the velocity to increase with the inclination, and the blobs with motion near vertical have the largest values of the velocity. We have generated synthetic images of the whole structure in an H proxy and in two EUV channels of the AIA instrument aboard SDO. These images show the plasma at cool, warm and hot temperatures. The theoretical differential emission measure of our system agrees very well with observations in the temperature range log T = 4.6-5.7. We conclude that the sheared-arcade magnetic structure and plasma dynamics fit well the abundant observational evidence.

Genetic Structure and Inferences on Potential Source Areas for Bactrocera dorsalis (Hendel) Based on Mitochondrial and Microsatellite Markers

PubMed Central

Shi, Wei; Kerdelhué, Carole; Ye, Hui

2012-01-01

Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan. PMID:22615898

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

NASA Astrophysics Data System (ADS)

Helbo, Alexandra Søgaard; Lay, Fides D.; Jones, Peter A.; Liang, Gangning; Grønbæk, Kirsten

2017-02-01

Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.

The year-class phenomenon and the storage effect in marine fishes

NASA Astrophysics Data System (ADS)

Secor, David H.

2007-02-01

Factors contributing to population growth through strong year-class formation have driven a century of directed research in fisheries science. A central discovery of Hjort's paradigm was that multiple generations overlap and longevity is matched with frequency of strong recruitments. Here, I elaborate on this tenet by examining how intra-population modalities in spawning and early habitat use favour population resiliency. A modern theory that has application is the storage effect [Warner, R.R., Chesson, P.L., 1985. Coexistence mediated by recruitment fluctuations - a field guide to the storage effect. Am. Nat. 125, 769-787], whereby spawning stock biomass accumulates each year so that when early survival conditions are favourable, stored egg production can result in explosive population growth. I review two early life history behaviours that contribute to the storage effect: split cohorts (i.e., seasonal pulses of eggs and larvae) and contingent behaviour (i.e., dispersive and retentive patterns in early dispersal). Episodic and pulsed production of larvae is a common feature for marine fishes, well documented through otolith microstructure and hatch-date analyses. In temperate and boreal fishes, early and late spawned cohorts of larvae and juveniles may have differing fates dependent upon seasonal and inter-annual fluctuations in weather and climate. Often, a coastal fish may spawn for a protracted period, yet only a few days' egg production will result in successful recruitment. In these and other instances, it is clear that diversity in spawning behaviour can confer resilience against temporal variations in early survival conditions. Although many factors contribute to intra-population spawning modalities, size and age structure of adults play an important role. Contingent structure, an idea dating to Hjort (herring contingents) and Gilbert (salmon contingents), has been resurrected to describe the diversity of intra-population modalities observed through otolith microchemical and electronic tagging approaches. Retentive and dispersive behaviours confer resiliency against early survival conditions that vary spatially. Examples of contingent structure are increasingly numerous for diadromous fishes. Here, a nursery habitat associated with a contingent behaviour may make a small contribution in a given year, but over a decade contribute significantly to spawning stock biomass. For flatfish and other marine fishes, contingent structure is probable but not well documented. Proximate factors leading to contingent structure are poorly known, but for diadromous fishes, time of spawning and early life history energetic thresholds is hypothesized to lead to alternative life cycles. Here again time of spawning may lead to the storage effect by hedging against spatial variance in early vital rates. Managing for the storage effect will be promoted by conservation of adult age structure and early habitats upon which both strong and weak year-classes rely.

7-Meth­oxy­indan-1-one

PubMed Central

Chang, Yuan Jay; Chen, Kew-Yu

2012-01-01

In the title compound, C10H10O2, the 1-indanone unit is essentially planar (r.m.s. deviation = 0.028 Å). In the crystal, molecules are linked via C—H⋯O hydrogen bonds, forming layers lying parallel to the ab plane. This two-dimensional structure is stabilized by a weak C—H⋯π inter­action. A second weak C—H⋯π inter­action links the layers, forming a three-dimensional structure. PMID:23284398

On the role of weak interface in crack blunting process in nanoscale layered composites

NASA Astrophysics Data System (ADS)

Li, Yi; Zhou, Qing; Zhang, Shuang; Huang, Ping; Xu, Kewei; Wang, Fei; Lu, Tianjian

2018-03-01

Heterointerface in a nanoscale metallic layered composite could improve its crack resistance. However, the influence of metallic interface structures on crack propagation has not been well understood at atomic scale. By using the method of molecular dynamics (MD) simulation, the crack propagation behavior in Cu-Nb bilayer is compared with that in Cu-Ni bilayer. We find that the weak Cu-Nb interface plays an important role in hindering crack propagation in two ways: (i) dislocation nucleation at the interface releases stress concentration for the crack to propagate; (ii) the easily sheared weak incoherent interface blunts the crack tip. The results are helpful for understanding the interface structure dependent crack resistance of nanoscale bicrystal interfaces.

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals.

PubMed

Pietrow, M; Gagoś, M; Misiak, L E; Kornarzyński, K; Szurkowski, J; Rochowski, P; Grzegorczyk, M

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

NMR characterization of weak interactions between RhoGDI2 and fragment screening hits.

PubMed

Liu, Jiuyang; Gao, Jia; Li, Fudong; Ma, Rongsheng; Wei, Qingtao; Wang, Aidong; Wu, Jihui; Ruan, Ke

2017-01-01

The delineation of intrinsically weak interactions between novel targets and fragment screening hits has long limited the pace of hit-to-lead evolution. Rho guanine-nucleotide dissociation inhibitor 2 (RhoGDI2) is a novel target that lacks any chemical probes for the treatment of tumor metastasis. Protein-observed and ligand-observed NMR spectroscopy was used to characterize the weak interactions between RhoGDI2 and fragment screening hits. We identified three hits of RhoGDI2 using streamlined NMR fragment-based screening. The binding site residues were assigned using non-uniformly sampled C α - and H α -based three dimensional NMR spectra. The molecular docking to the proposed geranylgeranyl binding pocket of RhoGDI2 was guided by NMR restraints of chemical shift perturbations and ligand-observed transferred paramagnetic relaxation enhancement. We further validated the weak RhoGDI2-hit interactions using mutagenesis and structure-affinity analysis. Weak interactions between RhoGDI2 and fragment screening hits were delineated using an integrated NMR approach. Binders to RhoGDI2 as a potential anti-cancer target have been first reported, and their weak interactions were depicted using NMR spectroscopy. Our work highlights the powerfulness and the versatility of the integrative NMR techniques to provide valuable structural insight into the intrinsically weak interactions between RhoGDI2 and the fragment screening hits, which could hardly be conceived using other biochemical techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

Psychotropics and weak opioid analgesics in plasma samples of older hip fracture patients - detection frequencies and consistency with drug records.

PubMed

Waade, Ragnhild Birkeland; Molden, Espen; Martinsen, Mette Irene; Hermann, Monica; Ranhoff, Anette Hylen

2017-07-01

To determine use of psychotropic drugs and weak opioids in hip fracture patients by analysing plasma samples at admission, and compare detected drug frequencies with prescription registry data and drug records. Plasma from 250 hip fracture patients aged ≥65 years sampled at hospital admission were analysed by ultra-performance liquid chromatography-tandem mass spectrometry methods for detection of psychotropic drugs and weak opioid analgesics (alcohol also determined). Odds ratios for drugs detected in plasma of hip fracture patients vs. prescription frequencies of the same drugs in an age-, time- and region-matched reference population were calculated. Moreover, recorded and measured drugs were compared. Psychotropic drugs and/or weak opioid analgesics were detected in 158 (63%) of the patients (median age 84 years; 76% females), while alcohol was found in 19 patients (7.6%). The occurrence of diazepam (odds ratio 1.6; 95% confidence interval 1.1-2.4), nitrazepam (2.3; 1.3-4.1), selective serotonin reuptake inhibitors (1.9; 1.3-2.9) and mirtazapine (2.3; 1.2-4.3) was significantly higher in plasma samples of hip fracture patients than in prescription data from the reference population. Poor consistency between recorded and measured drugs was disclosed for z-hypnotics and benzodiazepines; e.g. diazepam was detected in 29 (11.6%), but only recorded in six (2.4%) of the patients. Plasma analysis shows that use of antidepressants and benzodiazepines in hip fracture patients is significantly more frequent than respective prescription frequencies in the general elderly population. Moreover, consistency between recorded and actual use of psychotropic fall-risk drugs is poor at hospital admission of hip fracture patients. © 2017 The British Pharmacological Society.

Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population.

PubMed

Wei, Xile; Zhang, Danhong; Lu, Meili; Wang, Jiang; Yu, Haitao; Che, Yanqiu

2015-01-01

This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance.

Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods

PubMed Central

Kuchta, Shawn R.; Brown, Ashley D.; Converse, Paul E.; Highton, Richard

2016-01-01

Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8–19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed. PMID:26974148

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill

PubMed Central

González-Martínez, Santiago C.; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G.; Verdú, Miguel; Pausas, Juli G.

2017-01-01

Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. PMID:28159988

SWOT analysis in Sina Trauma and Surgery Research Center.

PubMed

Salamati, Payman; ashraf Eghbali, Ali; Zarghampour, Manijeh

2014-01-01

The present study was conducted with the aim of identifying and evaluating the internal and external factors, affecting the Sina Trauma and Surgery Research Center, affiliated to Tehran University of Medical Sciences and propose some of related strategies to senior managers. We used a combined quantitative and qualitative methodology. Our study population consisted of personnel (18 individuals) at Sina Trauma and Surgery Research Center. Data-collection tools were the group discussions and the questionnaires. Data were analyzed with descriptive statistics and SWOT (Strength, Weakness, Opportunities and Threats) analysis. 18 individuals participated in sessions, consisting of 8 women (44.4%) and 10 men (55.6%). The final scores were 2.45 for internal factors (strength-weakness) and 2.17 for external factors (opportunities-threats). In this study, we proposed 36 strategies (10 weakness-threat strategies, 10 weakness-opportunity strategies, 7 strength-threat strategies, and 9 strength-opportunity strategies). The current status of Sina Trauma and Surgery Research Center is threatened weak. We recommend the center to implement the proposed strategies.

Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes

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

Price, Morgan N.; Arkin, Adam P.

Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (N e) by orders of magnitude. For example, for a well-mixed population with 10 12 individuals and a typical level of homologous recombination (r/m= 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that N e is<10 7. An argument for high N e values for bacteria has been the high genetic diversity withinmore » many bacterial “species,” but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate N e correctly. Given an estimate ofN e, standard population genetics models imply that selection should be sufficient to drive evolution if N e ×s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force ifs is above 10 -7 or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10 -9 per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. In conclusion, we used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10 -7are effectively neutral.« less

Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2015-12-15

Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (N e) by orders of magnitude. For example, for a well-mixed population with 10 12 individuals and a typical level of homologous recombination (r/m= 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that N e is<10 7. An argument for high N e values for bacteria has been the high genetic diversity withinmore » many bacterial “species,” but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate N e correctly. Given an estimate ofN e, standard population genetics models imply that selection should be sufficient to drive evolution if N e ×s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force ifs is above 10 -7 or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10 -9 per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. In conclusion, we used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10 -7are effectively neutral.« less

Socioeconomic Gradients in Health for White and Mexican-Origin Populations

PubMed Central

Goldman, Noreen; Kimbro, Rachel T.; Turra, Cassio M.; Pebley, Anne R.

2006-01-01

Objectives. We assessed whether the few findings to date suggesting weak relationships between education and health-related variables among Hispanics are indicative of a more widespread pattern. Methods. We used logistic regression models to examine education differentials (i.e., education gradients) in health behaviors and outcomes among White and Mexican-origin adults, adolescents, and infants. We gathered information from 3 data sets: the Los Angeles Family and Neighborhood Survey, the Fragile Families and Child Wellbeing Study, and the National Health Interview Survey. Results. In contrast with patterns for Whites, education was weakly associated or not associated with numerous health-related variables among the US Mexican-origin population. Among adults, Mexican immigrants were especially likely to have weaker education gradients than Whites. Conclusions. The weak relationships between education and health observed among individuals of Mexican origin may have been the result of several complex mechanisms: social gradients in health in Mexico that differ from those in the United States, selective immigration according to health and socioeconomic status, and particular patterns of integration of Mexican immigrants into US society. PMID:17077396

Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)

PubMed Central

Shirk, R Y; Hamrick, J L; Zhang, C; Qiang, S

2014-01-01

Genetic diversity, and thus the adaptive potential of invasive populations, is largely based on three factors: patterns of genetic diversity in the species' native range, the number and location of introductions and the number of founding individuals per introduction. Specifically, reductions in genetic diversity (‘founder effects') should be stronger for species with low within-population diversity in their native range and few introductions of few individuals to the invasive range. We test these predictions with Geranium carolinianum, a winter annual herb native to North America and invasive in China. We measure the extent of founder effects using allozymes and microsatellites, and ask whether this is consistent with its colonization history and patterns of diversity in the native range. In the native range, genetic diversity is higher and structure is lower than expected based on life history traits. In China, our results provide evidence for multiple introductions near Nanjing, Jiangsu province, with subsequent range expansion to the west and south. Patterns of genetic diversity across China reveal weak founder effects that are driven largely by low-diversity populations at the expansion front, away from the introduction location. This suggests that reduced diversity in China has resulted from successive founder events during range expansion, and that the loss of genetic diversity in the Nanjing area was mitigated by multiple introductions from diverse source populations. This has implications for the future of G. carolinianum in China, as continued gene flow among populations should eventually increase genetic diversity within the more recently founded populations. PMID:24346497

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

PubMed Central

Winternitz, Jamie C; Wares, John P

2013-01-01

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

Evidence of C-F-P and aromatic π-F-P weak interactions in imidazolium ionic liquids and its consequences

NASA Astrophysics Data System (ADS)

Panja, Sumit Kumar; Srivastava, Nitin; Srivastava, Jyoti; Prasad, Namburi Eswara; Noothalapati, Hemanth; Shigeto, Shinsuke; Saha, Satyen

2018-04-01

A simple change from alkyl group to alkene in side chain of imidazolium cation with same anion resulted in a drastic impact on physical properties (e.g., melting point) from bmimPF6 IL to cmimPF6 IL. The underlying reasons have been elucidated by structural and interaction studies with the help of DSC, SCXRD, vibrational and multi-nuclear NMR spectroscopic techniques. Experiments reveal existence of new weak interactions involving the carbon and π cloud of the imidazolium aromatic ring with fluoride of PF6 anion (i.e., C2-F-P and π-F-P) in cmimPF6 but are absent in structurally similar prototype IL, bmimPF6. Though weak, these interactions helped to form ladder type supramolecular arrangement, resulting in quite high melting point for cmimPF6 IL compared to bmimPF6 IL. These findings emphasize that an IL system can behave uniquely because of the existence of uncommon weak interactions.

A weak-coupling immersed boundary method for fluid-structure interaction with low density ratio of solid to fluid

NASA Astrophysics Data System (ADS)

Kim, Woojin; Lee, Injae; Choi, Haecheon

2018-04-01

We present a weak-coupling approach for fluid-structure interaction with low density ratio (ρ) of solid to fluid. For accurate and stable solutions, we introduce predictors, an explicit two-step method and the implicit Euler method, to obtain provisional velocity and position of fluid-structure interface at each time step, respectively. The incompressible Navier-Stokes equations, together with these provisional velocity and position at the fluid-structure interface, are solved in an Eulerian coordinate using an immersed-boundary finite-volume method on a staggered mesh. The dynamic equation of an elastic solid-body motion, together with the hydrodynamic force at the provisional position of the interface, is solved in a Lagrangian coordinate using a finite element method. Each governing equation for fluid and structure is implicitly solved using second-order time integrators. The overall second-order temporal accuracy is preserved even with the use of lower-order predictors. A linear stability analysis is also conducted for an ideal case to find the optimal explicit two-step method that provides stable solutions down to the lowest density ratio. With the present weak coupling, three different fluid-structure interaction problems were simulated: flows around an elastically mounted rigid circular cylinder, an elastic beam attached to the base of a stationary circular cylinder, and a flexible plate, respectively. The lowest density ratios providing stable solutions are searched for the first two problems and they are much lower than 1 (ρmin = 0.21 and 0.31, respectively). The simulation results agree well with those from strong coupling suggested here and also from previous numerical and experimental studies, indicating the efficiency and accuracy of the present weak coupling.

After the oil boom: The holiday ends in the gulf

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

Zanoyan, V.

1995-11-01

The most unmanageable risk facing American interests in the Persian Gulf is the slow but sure decay of the economic and political structure of the United States` key regional allies. They are the Gulf Cooperation Council (GCC) states: Saudia Arabia, Kuwait, Bahrain, Qatar, Oman, and the United Arab Emirates (UAE). External threats to these friendly governments and the direct risks to the continued flow of oil has blinded Washington to the end of these countries 20-year holiday from politics and economics. The holiday from economics was characterized by, among other syndromes, the lack of binding budget constraints, which reduced andmore » sometimes even eliminated the need to set spending priorities and allocate scarce economic resources. It is no longer possible to cover up structural weaknesses and policy inconsistencies. All major interest groups, including governments, ruling families, merchant families, and the population at large, are under pressure to earn not only their privileges but their keep. The need for Washington to address these new threats is examined.« less

High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

PubMed

Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

2018-02-27

The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

[The absence of stewardship in the Chilean health authority after the 2004 health reform].

PubMed

Herrera, Tania; Sánchez, Sergio

2014-11-26

Stewardship is the most important political function of a health system. It is a government responsibility carried out by the health authority. Among other dimensions, it is also a meta-function that includes conduction and regulation. The Health Authority and Management Act, which came about from the health reform of 2004, separated the functions of service provision and stewardship with the aim of strengthening the role of the health authority. However, the current structure of the health system contains overlapping functions between the different entities that leads to lack of coordination and inconsistencies, and a greater weight on individual health actions at the expense of collective ones. Consequently, a properly funded national health strategy to improve the health of the population is missing. Additionally, the components of citizen participation and governance are weak. It is necessary, therefore, to revisit the Chilean health structure in order to develop one that truly enables the exercise of the health authority’s stewardship role.

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

PubMed

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

Pronounced Fixation, Strong Population Differentiation and Complex Population History in the Canary Islands Blue Tit Subspecies Complex

PubMed Central

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible. PMID:24587269

Competitive or weak cooperative stochastic Lotka-Volterra systems conditioned on non-extinction.

PubMed

Cattiaux, Patrick; Méléard, Sylvie

2010-06-01

We are interested in the long time behavior of a two-type density-dependent biological population conditioned on non-extinction, in both cases of competition or weak cooperation between the two species. This population is described by a stochastic Lotka-Volterra system, obtained as limit of renormalized interacting birth and death processes. The weak cooperation assumption allows the system not to blow up. We study the existence and uniqueness of a quasi-stationary distribution, that is convergence to equilibrium conditioned on non-extinction. To this aim we generalize in two-dimensions spectral tools developed for one-dimensional generalized Feller diffusion processes. The existence proof of a quasi-stationary distribution is reduced to the one for a d-dimensional Kolmogorov diffusion process under a symmetry assumption. The symmetry we need is satisfied under a local balance condition relying the ecological rates. A novelty is the outlined relation between the uniqueness of the quasi-stationary distribution and the ultracontractivity of the killed semi-group. By a comparison between the killing rates for the populations of each type and the one of the global population, we show that the quasi-stationary distribution can be either supported by individuals of one (the strongest one) type or supported by individuals of the two types. We thus highlight two different long time behaviors depending on the parameters of the model: either the model exhibits an intermediary time scale for which only one type (the dominant trait) is surviving, or there is a positive probability to have coexistence of the two species.

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.

PubMed

Middleton, David A

2011-02-01

Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β-strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β-sheet layers. Detection of (14)N-(13)C dipolar couplings may provide potentially useful additional structural constraints on β-sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency-selective, transfer of population in double resonance SSNMR experiment is used to detect a weak (14)N-(13)C dipolar coupling in amyloid-like fibrils of the peptide H(2)N-SNNFGAILSS-COOH, which was uniformly (13)C and (15)N labelled across the four C-terminal amino acids. The (14)N-(13)C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β-spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.

Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells

PubMed Central

Pandey, Rachna; Vischer, Norbert O. E.; Smelt, Jan P. P. M.; van Beilen, Johan W. A.; Ter Beek, Alexander; De Vos, Winnok H.; Manders, Erik M. M.

2016-01-01

ABSTRACT Intracellular pH (pHi) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pHi homeostasis. Unfortunately, accurate pHi quantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pHi at single-cell levels in Bacillus subtilis. Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pHi in individual B. subtilis cells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pHi and an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pHi regulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies. IMPORTANCE This study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives. PMID:27565617

Comparing models of Red Knot population dynamics

USGS Publications Warehouse

McGowan, Conor P.

2015-01-01

Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

2-[2-(3-Chloro­phen­yl)hydrazinyl­idene]-1,3-diphenyl­propane-1,3-dione

PubMed Central

Bustos, Carlos; Alvarez-Thon, Luis; Cárcamo, Juan-Guillermo; Ibañez, Andrés; Sánchez, Christian

2011-01-01

The mol­ecular structure of the title compound, C21H15ClN2O2, features one strong intra­molecular N—H⋯O resonance-assisted hydrogen bond (RAHB). In the crystal, mol­ecules form inversion-related dimers via pairs of weak inter­molecular N—H⋯O contacts. These dimers are further stabilized via three weak C—H⋯O contacts, developing the three-dimensional structure. PMID:21754825

The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

2017-06-01

In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

Special discontinuities in nonlinearly elastic media

NASA Astrophysics Data System (ADS)

Chugainova, A. P.

2017-06-01

Solutions of a nonlinear hyperbolic system of equations describing weakly nonlinear quasitransverse waves in a weakly anisotropic elastic medium are studied. The influence of small-scale processes of dissipation and dispersion is investigated. The small-scale processes determine the structure of discontinuities (shocks) and a set of discontinuities with a stationary structure. Among the discontinuities with a stationary structure, there are special ones that, in addition to relations following from conservation laws, satisfy additional relations required for the existence of their structure. In the phase plane, the structure of such discontinuities is represented by an integral curve joining two saddles. Special discontinuities lead to nonunique self-similar solutions of the Riemann problem. Asymptotics of non-self-similar problems for equations with dissipation and dispersion are found numerically. These asymptotics correspond to self-similar solutions of the problems.

Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.

PubMed

Kwasigroch, Jean Marc; Rooman, Marianne

2006-07-15

Prelude&Fugue are bioinformatics tools aiming at predicting the local 3D structure of a protein from its amino acid sequence in terms of seven backbone torsion angle domains, using database-derived potentials. Prelude(&Fugue) computes all lowest free energy conformations of a protein or protein region, ranked by increasing energy, and possibly satisfying some interresidue distance constraints specified by the user. (Prelude&)Fugue detects sequence regions whose predicted structure is significantly preferred relative to other conformations in the absence of tertiary interactions. These programs can be used for predicting secondary structure, tertiary structure of short peptides, flickering early folding sequences and peptides that adopt a preferred conformation in solution. They can also be used for detecting structural weaknesses, i.e. sequence regions that are not optimal with respect to the tertiary fold. http://babylone.ulb.ac.be/Prelude_and_Fugue.

Catastrophic photometric redshift errors: Weak-lensing survey requirements

DOE PAGES

Bernstein, Gary; Huterer, Dragan

2010-01-11

We study the sensitivity of weak lensing surveys to the effects of catastrophic redshift errors - cases where the true redshift is misestimated by a significant amount. To compute the biases in cosmological parameters, we adopt an efficient linearized analysis where the redshift errors are directly related to shifts in the weak lensing convergence power spectra. We estimate the number N spec of unbiased spectroscopic redshifts needed to determine the catastrophic error rate well enough that biases in cosmological parameters are below statistical errors of weak lensing tomography. While the straightforward estimate of N spec is ~10 6 we findmore » that using only the photometric redshifts with z ≤ 2.5 leads to a drastic reduction in N spec to ~ 30,000 while negligibly increasing statistical errors in dark energy parameters. Therefore, the size of spectroscopic survey needed to control catastrophic errors is similar to that previously deemed necessary to constrain the core of the z s – z p distribution. We also study the efficacy of the recent proposal to measure redshift errors by cross-correlation between the photo-z and spectroscopic samples. We find that this method requires ~ 10% a priori knowledge of the bias and stochasticity of the outlier population, and is also easily confounded by lensing magnification bias. In conclusion, the cross-correlation method is therefore unlikely to supplant the need for a complete spectroscopic redshift survey of the source population.« less

Asymmetric Weakness and West Nile Virus Infection.

PubMed

Kuo, Dick C; Bilal, Saadiyah; Koller, Paul

2015-09-01

Weakness is a common presentation in the emergency department (ED). Asymmetric weakness or weakness that appears not to follow an anatomical pattern is a less common occurrence. Acute flaccid paralysis with no signs of meningoencephalitis is one of the more uncommon presentations of West Nile virus (WNV). Patient may complain of an acute onset of severe weakness, or even paralysis, in one or multiple limbs with no sensory deficits. This weakness is caused by injury to the anterior horn cells of the spinal cord. We present a case of acute asymmetric flaccid paralysis with preserved sensory responses that was eventually diagnosed as neuroinvasive WNV infection. A 31-year-old male with no medical history presented with complaints of left lower and right upper extremity weakness. Computed tomography scan was negative and multiple other studies were performed in the ED. Eventually, he was admitted to the hospital and was found to have decreased motor amplitudes, severely reduced motor neuron recruitment, and denervation on electrodiagnostic study. Cerebrospinal fluid specimen tested positive for WNV immunoglobulin (Ig) G and IgM antibodies. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Acute asymmetric flaccid paralysis with no signs of viremia or meningoencephalitis is an unusual presentation of WNV infection. WNV should be included in the differential for patients with asymmetric weakness, especially in the summer months in areas with large mosquito populations. Copyright © 2015 Elsevier Inc. All rights reserved.

Evidences on weaknesses and strengths from health financing after decentralization: lessons from Latin American countries.

PubMed

Arredondo, Armando; Orozco, Emanuel; De Icaza, Esteban

2005-01-01

The main objective was to identify trends and evidence on health financing after health care decentralization. Evaluative research with a before-after design integrating qualitative and quantitative analysis. Taking into account feasibility, political and technical criteria, three Latin American countries were selected as study populations: Mexico, Nicaragua and Peru. The methodology had two main phases. In the first phase, the study referred to secondary sources of data and documents to obtain information about the following variables: type of decentralization implemented, source of finance, funds of financing, providers, final use of resources and mechanisms for resource allocation. In the second phase, the study referred to primary data collected in a survey of key personnel from the health sectors of each country. The trends and evidence reported in all five financing indicators may identify major weaknesses and strengths in health financing. Weaknesses: a lack of human resources trained in health economics who can implement changes, a lack of financial resource independence between the local and central levels, the negative behavior of the main macro-economic variables, and the difficulty in developing new financing alternatives. Strengths: the sharing between the central level and local levels of responsibility for financing health services, the implementation of new organizational structures for the follow-up of financial changes at the local level, the development and implementation of new financial allocation mechanisms taking as a basis the efficiency and equity principles, new technique of a per-capita adjustment factor corrected at the local health needs, and the increase of financing contributions from households and local levels of government.

Automatic protein structure solution from weak X-ray data

NASA Astrophysics Data System (ADS)

Skubák, Pavol; Pannu, Navraj S.

2013-11-01

Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals

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

Pietrow, M., E-mail: mrk@kft.umcs.lublin.pl; Misiak, L. E.; Gagoś, M.

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra canmore » be used as a probe indicating differences in the solid structures of hydrocarbons.« less

Phase structure of NJL model with weak renormalization group

NASA Astrophysics Data System (ADS)

Aoki, Ken-Ichi; Kumamoto, Shin-Ichiro; Yamada, Masatoshi

2018-06-01

We analyze the chiral phase structure of the Nambu-Jona-Lasinio model at finite temperature and density by using the functional renormalization group (FRG). The renormalization group (RG) equation for the fermionic effective potential V (σ ; t) is given as a partial differential equation, where σ : = ψ bar ψ and t is a dimensionless RG scale. When the dynamical chiral symmetry breaking (DχSB) occurs at a certain scale tc, V (σ ; t) has singularities originated from the phase transitions, and then one cannot follow RG flows after tc. In this study, we introduce the weak solution method to the RG equation in order to follow the RG flows after the DχSB and to evaluate the dynamical mass and the chiral condensate in low energy scales. It is shown that the weak solution of the RG equation correctly captures vacuum structures and critical phenomena within the pure fermionic system. We show the chiral phase diagram on temperature, chemical potential and the four-Fermi coupling constant.

Youth Perceptions of Suicide and Help-Seeking: "They'd Think I Was Weak or "Mental""

ERIC Educational Resources Information Center

Curtis, Cate

2010-01-01

Youth suicide is an issue of international concern and the college population may have a considerably higher rate of suicidal behaviour than the general population, yet seeking help for suicidality is uncommon. This research sought to understand college students' knowledge of suicidal behaviour and attitudes to help-seeking, in a New Zealand…

Biotic resistance: Exclusion of native rodent consumers releases populations of a weak invader

Treesearch

Dean E. Pearson; Teal Potter; John L. Maron

2012-01-01

Biotic resistance is a commonly invoked hypothesis to explain why most exotic plant species naturalize at low abundance. Although numerous studies have documented negative impacts of native consumers on exotic plant performance, longer-term multi-generation studies are needed to understand how native consumer damage to exotics translates to their population-level...

An assessment of mean-field mixed semiclassical approaches: Equilibrium populations and algorithm stability

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

Bellonzi, Nicole; Jain, Amber; Subotnik, Joseph E.

2016-04-21

We study several recent mean-field semiclassical dynamics methods, focusing on the ability to recover detailed balance for long time (equilibrium) populations. We focus especially on Miller and Cotton’s [J. Phys. Chem. A 117, 7190 (2013)] suggestion to include both zero point electronic energy and windowing on top of Ehrenfest dynamics. We investigate three regimes: harmonic surfaces with weak electronic coupling, harmonic surfaces with strong electronic coupling, and anharmonic surfaces with weak electronic coupling. In most cases, recent additions to Ehrenfest dynamics are a strong improvement upon mean-field theory. However, for methods that include zero point electronic energy, we show thatmore » anharmonic potential energy surfaces often lead to numerical instabilities, as caused by negative populations and forces. We also show that, though the effect of negative forces can appear hidden in harmonic systems, the resulting equilibrium limits do remain dependent on any windowing and zero point energy parameters.« less

Pleiotropic Stabilizing Selection Limits the Number of Polymorphic Loci to at Most the Number of Characters

PubMed Central

Hastings, A.; Hom, C. L.

1989-01-01

We demonstrate that, in a model incorporating weak Gaussian stabilizing selection on n additively determined characters, at most n loci are polymorphic at a stable equilibrium. The number of characters is defined to be the number of independent components in the Gaussian selection scheme. We also assume linkage equilibrium, and that either the number of loci is large enough that the phenotypic distribution in the population can be approximated as multivariate Gaussian or that selection is weak enough that the mean fitness of the population can be approximated using only the mean and the variance of the characters in the population. Our results appear to rule out antagonistic pleiotropy without epistasis as a major force in maintaining additive genetic variation in a uniform environment. However, they are consistent with the maintenance of variability by genotype-environment interaction if a trait in different environments corresponds to different characters and the number of different environments exceeds the number of polymorphic loci that affect the trait. PMID:2767424

Variational tricomplex of a local gauge system, Lagrange structure and weak Poisson bracket

NASA Astrophysics Data System (ADS)

Sharapov, A. A.

2015-09-01

We introduce the concept of a variational tricomplex, which is applicable both to variational and nonvariational gauge systems. Assigning this tricomplex with an appropriate symplectic structure and a Cauchy foliation, we establish a general correspondence between the Lagrangian and Hamiltonian pictures of one and the same (not necessarily variational) dynamics. In practical terms, this correspondence allows one to construct the generating functional of a weak Poisson structure starting from that of a Lagrange structure. As a byproduct, a covariant procedure is proposed for deriving the classical BRST charge of the BFV formalism by a given BV master action. The general approach is illustrated by the examples of Maxwell’s electrodynamics and chiral bosons in two dimensions.

[Family characteristics and the labor market in developed countries: a clear distinction between north and south].

PubMed

Barrere-maurisson, M; Marchand, O

1990-09-01

The relationship between family characteristics and the labor market is explored using data concerning 15 OECD countries. Several distinct geographical groupings are identified, including the Mediterranean countries, Scandinavia, North America, and Japan and West Germany. Belgium, France, the Netherlands, and the United Kingdom occupy a middle ground and are less specifically defined. Furthermore, "the statistical map shows a strong relationship which manifests itself in two opposite ways. On the one hand, it shows the link between a traditional family structure and a weak integration of women in the working population (Spain, Ireland), and, on the other hand, it shows a close link between a divided family and the fact women have a paying job, often just part time (Sweden, Denmark)." (SUMMARY IN ENG AND SPA) excerpt

Medicare and Medicaid: Conflicting Incentives for Long-Term Care

PubMed Central

Grabowski, David C

2007-01-01

The structure of Medicare and Medicaid creates conflicting incentives regarding dually eligible beneficiaries without coordinating their care. Both Medicare and Medicaid have an interest in limiting their costs, and neither has an incentive to take responsibility for the management or quality of care. Examples of misaligned incentives are Medicare's cost-sharing rules, cost shifting within home health care and nursing homes, and cost shifting across chronic and acute care settings. Several policy initiatives—capitation, pay-for-performance, and the shift of the dually eligible population's Medicaid costs to the federal government—may address these conflicting incentives, but all have strengths and weaknesses. With the aging baby boom generation and projected federal and state budget shortfalls, this issue will be a continuing focus of policymakers in the coming decades. PMID:18070331

Internal state control of a dense sample of ultracold 23Na87Rb molecules

NASA Astrophysics Data System (ADS)

Ye, Xin; Guo, Mingyang; He, Junyu; Wang, Dajun; Quemener, Goulven; Gonzalez-Martinez, Maykel; Dulieu, Oliver

2017-04-01

We report the optimized production of ultracold 23Na87Rb molecules with completely controlled population distribution among internal states. Starting from a sample of 104 weakly bound Feshbach molecules, we achieved a hyperfine-structure-resolved STIRAP transfer to the ground state with an efficiency up to 95%. By tuning the frequency difference between the Raman lasers and applying an additional microwave signal, we realized the preparation of NaRb samples in different vibrational, rotational, and hyperfine levels. Based on this achievement, some results on molecular collisions with a range of possible loss channels will also be reported. This work was supported by the French ANR/Hong Kong RGC COPOMOL project (Grant No. A-CUHK403/13), the RGC General Research Fund (Grant No. CUHK14301815).

Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins

PubMed Central

Wang, Qian; Diehl, Michael R.; Jana, Biman; Cheung, Margaret S.; Kolomeisky, Anatoly B.; Onuchic, José N.

2017-01-01

Motor proteins are active enzymatic molecules that support important cellular processes by transforming chemical energy into mechanical work. Although the structures and chemomechanical cycles of motor proteins have been extensively investigated, the sensitivity of a motor’s velocity in response to a force is not well-understood. For kinesin, velocity is weakly influenced by a small to midrange external force (weak susceptibility) but is steeply reduced by a large force. Here, we utilize a structure-based molecular dynamic simulation to study the molecular origin of the weak susceptibility for a single kinesin. We show that the key step in controlling the velocity of a single kinesin under an external force is the ATP release from the microtubule-bound head. Only under large loading forces can the motor head release ATP at a fast rate, which significantly reduces the velocity of kinesin. It underpins the weak susceptibility that the velocity will not change at small to midrange forces. The molecular origin of this velocity reduction is that the neck linker of a kinesin only detaches from the motor head when pulled by a large force. This prompts the ATP binding site to adopt an open state, favoring ATP release and reducing the velocity. Furthermore, we show that two load-bearing kinesins are incapable of equally sharing the load unless they are very close to each other. As a consequence of the weak susceptibility, the trailing kinesin faces the challenge of catching up to the leading one, which accounts for experimentally observed weak cooperativity of kinesins motors. PMID:28973894

The Dependence of the Circumnuclear Coma Structure on the Properties of the Nucleus. IV. Structure of the Night-Side Gas Coma of a Strongly Sublimating Nucleus

NASA Astrophysics Data System (ADS)

Crifo, J. F.; Rodionov, A. V.

2000-12-01

The structure of the nightside coma in the vicinity of a strongly active comet nucleus of pure ice is investigated by solving gasdynamic equations for the flow of water vapour sublimated from—or condensed onto—the nucleus surface. To guarantee the physical validity of the solution, both Euler and Navier-Stokes Equations are solved, and the solutions are compared. A spherical nucleus is considered first and then a triaxial ellipsoidal nucleus. The results show that (1) a fluid coma of significant extent and very complicated physical structure is formed; (2) for low heat conduction transfer across the nucleus from the dayside to the nightside surface, a narrow conical weak shock appears near to the antisolar axis; the whole nightside surface acts as a cold trap for the vapor, part of which recondenses onto it; (3) for intermediate heat conduction, part of the nightside surface becomes weakly sublimating, and a different weak shock pattern is formed; and (4) at high heat conduction, the whole nightside surface is weakly sublimating, and the resulting flow pattern becomes similar to that existing in a coma formed by diffusion from the nucleus interior (see Crifo, Rodionov and Bockelée-Morvan, 1999, Icarus138, 83-106). The results are compared to related model results by other authors, and a discussion is made of their relevance to the 1996 observation of the near-nucleus nightside coma of Comet C/1996 B2 Hyakutake.

Resource-driven changes to host population stability alter the evolution of virulence and transmission.

PubMed

Hite, Jessica L; Cressler, Clayton E

2018-05-05

What drives the evolution of parasite life-history traits? Recent studies suggest that linking within- and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to pinpoint the critical factors connecting these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions. First, we dynamically link resources and between-host processes (host density, stability, transmission) to virulence evolution, using a 'non-nested' model. Then, we consider a 'nested' model where population-level processes (transmission and virulence) depend on resource-driven changes to individual-level (within-host) processes (energetics, immune function, parasite production). Contrary to 'non-nested' model predictions, the 'nested' model reveals complex effects of host population dynamics on parasite evolution, including regions of evolutionary bistability; evolution can push parasites towards strongly or weakly stabilizing strategies. This bistability results from dynamic feedbacks between resource-driven changes to host density, host immune function and parasite production. Together, these results highlight how cross-scale feedbacks can provide key insights into the structuring role of parasites and parasite evolution.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'. © 2018 The Author(s).

Psychometric properties of the Turkish version of the Internet Addiction Test (IAT).

PubMed

Boysan, Murat; Kuss, Daria J; Barut, Yaşar; Ayköse, Nafi; Güleç, Mustafa; Özdemir, Osman

2017-01-01

Of many instruments developed to assess Internet addiction, the Internet Addiction Test (IAT), an expanded version of the Internet Addiction Diagnostic Questionnaire (IADQ), has been the most widely used scale in English and non-English speaking populations. In this study, our aim was to investigate the psychometric properties of short and expanded versions of the IAT in a Turkish undergraduate sample. Overall, 455 undergraduate students from Turkey aged between 18 and 30 participated in the study (63.53% were females). Explanatory and confirmatory factor analytic procedures investigated factor structures of the IADQ and IAT. The Internet Addiction Scale (IAS), Coping Inventory for Stressful Situations (CISS), Obsessive Compulsive Inventory-Revised (OCI-R) and Dissociative Experiences Scale (DES) were administered to assess convergent and divergent validities of the IADQ and IAT. Internal consistency and 15-day test-retest reliability were computed. In the factorial analytic investigation, we found a unidimensional factor structure for each measure fit the current data best. Significant but weak to moderate correlations of the IADQ and the IAT with the CISS, OCI-R and DES provided empirical evidence for divergent validity, whereas strong associations with the subscales of the IAS pointed to the convergent validity of Young's Internet addiction construct. Internal consistency of the IADQ was weak (α=0.67) and of the IAT was high (α=0.93). Temporal reliability of both instruments was very high (α=0.81 and α=0.87; respectively). The IAT revealed promising and sound psychometric properties in a Turkish sample. Copyright © 2015 Elsevier Ltd. All rights reserved.

Chromosomal Inversions, Natural Selection and Adaptation in the Malaria Vector Anopheles funestus

PubMed Central

Ayala, Diego; Fontaine, Michael C.; Cohuet, Anna; Fontenille, Didier; Vitalis, Renaud; Simard, Frédéric

2011-01-01

Chromosomal polymorphisms, such as inversions, are presumably involved in the rapid adaptation of populations to local environmental conditions. Reduced recombination between alternative arrangements in heterozygotes may protect sets of locally adapted genes, promoting ecological divergence and potentially leading to reproductive isolation and speciation. Through a comparative analysis of chromosomal inversions and microsatellite marker polymorphisms, we hereby present biological evidence that strengthens this view in the mosquito Anopheles funestus s.s, one of the most important and widespread malaria vectors in Africa. Specimens were collected across a wide range of geographical, ecological, and climatic conditions in Cameroon. We observed a sharp contrast between population structure measured at neutral microsatellite markers and at chromosomal inversions. Microsatellite data detected only a weak signal for population structuring among geographical zones (FST < 0.013, P < 0.01). By contrast, strong differentiation among ecological zones was revealed by chromosomal inversions (FST > 0.190, P < 0.01). Using standardized estimates of FST, we show that inversions behave at odds with neutral expectations strongly suggesting a role of environmental selection in shaping their distribution. We further demonstrate through canonical correspondence analysis that heterogeneity in eco-geographical variables measured at specimen sampling sites explained 89% of chromosomal variance in A. funestus. These results are in agreement with a role of chromosomal inversions in ecotypic adaptation in this species. We argue that this widespread mosquito represents an interesting model system for the study of chromosomal speciation mechanisms and should provide ample opportunity for comparative studies on the evolution of reproductive isolation and speciation in major human malaria vectors. PMID:20837604

Self-administered structured food record for measuring individual energy and nutrient intake in large cohorts: Design and validation.

PubMed

García, Silvia M; González, Claudio; Rucci, Enzo; Ambrosino, Cintia; Vidal, Julia; Fantuzzi, Gabriel; Prestes, Mariana; Kronsbein, Peter

2018-06-05

Several instruments developed to assess dietary intake of groups or populations have strengths and weaknesses that affect their specific application. No self-administered, closed-ended dietary survey was previously used in Argentina to assess current food and nutrient intake on a daily basis. To design and validate a self-administered, structured food record (NutriQuid, NQ) representative of the adult Argentine population's food consumption pattern to measure individual energy and nutrient intake. Records were loaded onto a database using software that checks a regional nutrition information system (SARA program), automatically quantifying energy and nutrient intake. NQ validation included two phases: (1) NQ construct validity comparing records kept simultaneously by healthy volunteers (45-75 years) and a nutritionist who provided meals (reference), and (2) verification of whether NQ reflected target population consumption (calories and nutrients), week consumption differences, respondent acceptability, and ease of data entry/analysis. Data analysis included descriptive statistics, repeated measures ANOVA, intraclass correlation coefficient, nonparametric regression, and cross-classification into quintiles. The first validation (study group vs. reference) showed an underestimation (10%) of carbohydrate, fat, and energy intake. Second validation: 109 volunteers (91% response) completed the NQ for seven consecutive days. Record completion took about 9min/day, and data entry 3-6min. Mean calorie intake was 2240±119kcal/day (42% carbohydrates, 17% protein, and 41% fat). Intake significantly increased in the weekend. NQ is a simple and efficient tool to assess dietary intake in large samples. Copyright © 2018 SEEN y SED. Publicado por Elsevier España, S.L.U. All rights reserved.

Structure of Ion Outflow in the Martian Magnetotail

NASA Astrophysics Data System (ADS)

McFadden, J. P.; Mitchell, D.; Luhmann, J. G.; Connerney, J. E. P.; Jakosky, B. M.

2017-12-01

The Suprathermal And Thermal Ion Composition (STATIC) sensor on the MAVEN spacecraft provides a detailed look at the structure of ion outflow in the Martian magnetotail including ion composition, energization, and flow. Mars' magnetotail contains a mixture of cold (<10 eV) nearly-stationary multi-species ions, tailward-moving cold multi-species ions, suprathermal ions of a few tens of eV, warm (about 100 eV) proton populations, and heavy (primarily O+) pickup ions at energies from 1 to 10 keV which may display several simultaneous peaks in energy flux. The cold tailward-moving ions represent a significant fraction of the Martian ion loss, perhaps comparable to loses from molecular oxygen dissociation. The suprathermal tail that accompanies the cold ions varies greatly and provides clues to ion escape. The warm protons, on first examination, appear to be of sheath origin, displaying a similar energy distribution and accompanied by a tenuous warm population at M/Q=2 (which could be either solar wind alphas or molecular hydrogen ions of ionospheric origin). STATIC produces a weak ghost peak at M/Q=11-12 when observing molecular hydrogen ions, but not alphas, often allowing the instrument to distinguish the source of protons. Measurements show the warm protons are of ionospheric origin in the central tail and transition to sheath plasma in the umbra. Energetic (1-10 keV) pickup oxygen in the magnetotail is produced on the nightside, near the pole where the IMF convection electric field points toward the planet, the same hemisphere where sputtering occurs. When two spectral peaks are observed, these tailward-moving ions differ in direction by relatively small angles (about 20 degrees). These peaks can persist for tens of minutes indicating approximately time-stationary acceleration, and therefore acceleration in potential fields. Magnetotail structure and geometry can be inferred not only from the local magnetic field, but also from the measured electron distributions which indicate source populations and connectivity (closed, open, or interplanetary). This paper will be used to describe the observed tail structure and the inferred acceleration structure.

Allele Age Under Non-Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach.

PubMed

De Sanctis, Bianca; Krukov, Ivan; de Koning, A P Jason

2017-09-19

Determination of the age of an allele based on its population frequency is a well-studied problem in population genetics, for which a variety of approximations have been proposed. We present a new result that, surprisingly, allows the expectation and variance of allele age to be computed exactly (within machine precision) for any finite absorbing Markov chain model in a matter of seconds. This approach makes none of the classical assumptions (e.g., weak selection, reversibility, infinite sites), exploits modern sparse linear algebra techniques, integrates over all sample paths, and is rapidly computable for Wright-Fisher populations up to N e  = 100,000. With this approach, we study the joint effect of recurrent mutation, dominance, and selection, and demonstrate new examples of "selective strolls" where the classical symmetry of allele age with respect to selection is violated by weakly selected alleles that are older than neutral alleles at the same frequency. We also show evidence for a strong age imbalance, where rare deleterious alleles are expected to be substantially older than advantageous alleles observed at the same frequency when population-scaled mutation rates are large. These results highlight the under-appreciated utility of computational methods for the direct analysis of Markov chain models in population genetics.

Psychological effect on single-species population models in a polluted environment.

PubMed

Wei, Fengying; Chen, Lihong

2017-08-01

We formulate and investigate the psychological effect of single-species population models in a polluted environment in this paper. For the deterministic single-species population model, the conditions that guarantee the local extinction and persistence in the mean are derived firstly. We then show that, around the pollution-free equilibrium, the stochastic single-species population is weakly persistent in the mean, and is stochastically permanent under some conditions. As a consequence, some numerical simulations demonstrate the efficiency of the main results. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of suicide mortality in Brazil: spatial distribution and socioeconomic context.

PubMed

Dantas, Ana P; Azevedo, Ulicélia N de; Nunes, Aryelly D; Amador, Ana E; Marques, Marilane V; Barbosa, Isabelle R

2018-01-01

To perform a spatial analysis of suicide mortality and its correlation with socioeconomic indicators in Brazilian municipalities. This is an ecological study with Brazilian municipalities as a unit of analysis. Data on deaths from suicide and contextual variables were analyzed. The spatial distribution, intensity and significance of the clusters were analyzed with the global Moran index, MoranMap and local indicators of spatial association (LISA), seeking to identify patterns through geostatistical analysis. A total of 50,664 deaths from suicide were registered in Brazil between 2010 and 2014. The average suicide mortality rate in Brazil was 5.23/100,000 population. The Brazilian municipalities presenting the highest rates were Taipas do Tocantins, state of Tocantins (79.68 deaths per 100,000 population), Itaporã, state of Mato Grosso do Sul (75.15 deaths per 100,000 population), Mampituba, state of Rio Grande do Sul (52.98 deaths per 100,000 population), Paranhos, state of Mato Grosso do Sul (52.41 deaths per 100,000 population), and Monjolos, state of Minas Gerais (52.08 deaths per 100,000 population). Although weak spatial autocorrelation was observed for suicide mortality (I = 0.2608), there was a formation of clusters in the South. In the bivariate spatial and classical analysis, no correlation was observed between suicide mortality and contextual variables. Suicide mortality in Brazil presents a weak spatial correlation and low or no spatial relationship with socioeconomic factors.

Monitoring of PBDEs concentration in umbilical cord blood and breast milk from Korean population and estimating the effects of various parameters on accumulation in humans.

PubMed

Kim, Un-Jung; Lee, In-Seok; Kim, Hyung Sik; Oh, Jeong-Eun

2011-10-01

In this study, we investigated concentration, congener distribution pattern, and effects of potential environmental factors that affect PBDE accumulation. We also estimated correlation between PBDE concentration and health status or thyroid function by analyzing 90 cord blood and 21 breast milk samples obtained from Korean population. Seven from tri- to hepta-BDEs were analyzed by solid phase extraction-high-resolution gas chromatography/high-resolution mass spectrometry (SPE-HRGC/HRMS). The total concentration of 7 PBDEs in cord blood was 2.786-94.64 ng g(-1) lipid and that in breast milk was 1.076-8.664 ng g(-1) lipid. Tetra-BDE (#47) was the predominant type of PBDE and was present at concentrations of over 40% in both sample types. A weak correlation was observed between the concentration of BDE28 and 153 and thyroid hormone concentration only in the breast milk samples. In children, a weak negative correlation was observed between free thyroxine (FT4) concentration and BDE28 concentration (0.302, p<0.05), while in mothers, a weak positive correlation was observed between thyroid hormone concentration and BDE153 concentration (0.403, p<0.05). No significant correlations between PBDE concentration and work and residential environments were found in this study, but a weak correlation between BDE concentration in cord blood and potential PBDE sources was confirmed by investigating the frequency of oil paint usage (0.510, p<0.001). A weak correlation was also found between PBDE concentration in breast milk during pregnancy and dietary habits such as green tea drinking (0.541, p=0.025) and Trichiuridae intake (0.565, p=0.015). Copyright © 2011 Elsevier Ltd. All rights reserved.

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas.

PubMed

Paterno, Marta; Schiavina, Marcello; Aglieri, Giorgio; Ben Souissi, Jamila; Boscari, Elisa; Casagrandi, Renato; Chassanite, Aurore; Chiantore, Mariachiara; Congiu, Leonardo; Guarnieri, Giuseppe; Kruschel, Claudia; Macic, Vesna; Marino, Ilaria A M; Papetti, Chiara; Patarnello, Tomaso; Zane, Lorenzo; Melià, Paco

2017-04-01

Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus , focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats.

Abnormalities in larvae from the once-largest Pacific herring population in Washington State result primarily from factors independent of spawning location

USGS Publications Warehouse

Hershberger, P.K.; Elder, N.E.; Wittouck, J.; Stick, K.; Kocan, R.M.

2005-01-01

Among larvae from populations of Pacific herring Clupea pallasii in Washington State those from Cherry Point have consistently demonstrated abnormalities indicative of distress, including low weights and lengths at hatch, increased prevalences of skeletal abnormalities, and shorter survival times in food deprivation studies. The biomass of adult, prespawn Pacific herring at Cherry Point declined from 13,606 metric tons in 1973 to a record low 733 metric tons in 2000. However, correlation of larval abnormalities with adult recruitment was weak, indicating that the larval abnormalities did not directly cause the decline. Larval abnormalities originated primarily from factors independent of conditions at the spawning location because they were not reproduced by incubation of foreign zygotes along the Cherry Point shoreline but were reproduced after the development of indigenous zygotes in controlled laboratory conditions. Although the precise cause of the abnormalities was not determined, recent zoographic trends in elevated natural mortality among adult Pacific herring and resulting reduced age structures may be involved. ?? Copyright by the American Fisheries Society 2005.

Weak genetic differentiation in cobia, Rachycentron canadum from Indian waters as inferred from mitochondrial DNA ATPase 6 and 8 genes.

PubMed

Joy, Linu; Mohitha, C; Divya, P R; Gopalakrishnan, A; Basheer, V S; Jena, J K

2016-07-01

Cobia, Rachycentron canadum, is an economically important migratory fish distributed in tropical waters worldwide and is a candidate fish species for aquaculture practices. The genetic stock structure of R. canadum distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 15 haplotypes with mean low nucleotide diversity (π = 0.001) and high haplotype diversity (h = 0.785). AMOVA indicated the genetic differentiation of 90.47% for individuals within the population. This is well supported by co-efficient of genetic differentiation (FST) values obtained for pairwise populations that were low and non-significant with an overall value of 0.002. The parsimony network tree revealed star-like phylogeny and all the haplotypes were connected with each other by single mutational event. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.

Uncondensed atoms in the regime of velocity-selective coherent population trapping

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

Il’ichov, L. V.; Tomilin, V. A., E-mail: 8342tomilin@mail.ru

2016-01-15

We consider the model of a Bose condensate in the regime of velocity-selective coherent population trapping. As a result of interaction between particles, some fraction of atoms is outside the condensate, remaining in the coherent trapping state. These atoms are involved in brief events of intense interaction with external resonant electromagnetic fields. Intense induced and spontaneous transitions are accompanied by the exchange of momenta between atoms and radiation, which is manifested as migration of atoms in the velocity space. The rate of such migration is calculated. A nonlinear kinetic equation for the many-particle statistical operator for uncondensed atoms is derivedmore » under the assumption that correlations of atoms with different momenta are insignificant. The structure of its steady-state solution leads to certain conclusions about the above-mentioned migration pattern taking the Bose statistics into consideration. With allowance for statistical effects, we derive nonlinear integral equations for frequencies controlling the migration. The results of numerical solution of these equations are represented in the weak interatomic interaction approximation.« less

Reconstructing historical habitat data with predictive models Read More: http://www.esajournals.org/doi/abs/10.1890/13-0327.1

USGS Publications Warehouse

Zweig, Christa L.; Kitchens, Wiley M.

2014-01-01

Historical vegetation data are important to ecological studies, as many structuring processes operate at long time scales, from decades to centuries. Capturing the pattern of variability within a system (enough to declare a significant change from past to present) relies on correct assumptions about the temporal scale of the processes involved. Sufficient long-term data are often lacking, and current techniques have their weaknesses. To address this concern, we constructed multistate and artificial neural network models (ANN) to provide fore- and hindcast vegetation communities considered critical foraging habitat for an endangered bird, the Florida Snail Kite (Rostrhamus sociabilis). Multistate models were not able to hindcast due to our data not satisfying a detailed balance requirement for time reversibility in Markovian dynamics. Multistate models were useful for forecasting and providing environmental variables for the ANN. Results from our ANN hindcast closely mirrored the population collapse of the Snail Kite population using only environmental data to inform the model. The parallel between the two gives us confidence in the hindcasting results and their use in future demographic models.

[Epigenetic research of cognitive deficit in schizophrenia: some methodological considerations].

PubMed

Lezheiko, T V; Alfimova, M V

To highlights the problems of assessing cognitive deficits in schizophrenia, relevant to the epigenetic, as well as a wide range of other approaches to the search for biological bases of cognition. The literature on the weaknesses in the evaluation of cognitive functions in patients with schizophrenia are summarized and discussed. The analysis is illustrated by our experience in developing a cognitive battery and a sample to examine relationships between DNA methylation in blood cells and cognitive deficits in schizophrenia. It has been shown that to assess cognitive deficits in patients and to reduce the influence of confounders in epigenetic analysis it is necessary (1) to use a battery with the existing co-normative data in the target population, which allows to evaluate representativeness of control and patients included in the study sample, (2) to verify the theoretically driven battery structure using normative population and a cohort of patients, (3) to balance groups of cases and controls on the number, age and sex, for which an individual matching of cases and controls is best suited, (4) to conduct an additional statistical analysis controlling for education and smoking.

A plague epizootic in the black-tailed prairie dog (Cynomys ludovicianus).

PubMed

Pauli, Jonathan N; Buskirk, Steven W; Williams, Elizabeth S; Edwards, William H

2006-01-01

Plague is the primary cause for the rangewide decline in prairie dog (Cynomys spp.) distribution and abundance, yet our knowledge of plague dynamics in prairie dog populations is limited. Our understanding of the effects of plague on the most widespread species, the black-tailed prairie dog (C. ludovicianus), is particularly weak. During a study on the population biology of black-tailed prairie dogs in Wyoming, USA, plague was detected in a colony under intensive monitoring, providing a unique opportunity to quantify various consequences of plague. The epizootic reduced juvenile abundance by 96% and adult abundance by 95%. Of the survivors, eight of nine adults and one of eight juveniles developed antibodies to Yersinia pestis. Demographic groups appeared equally susceptible to infection, and age structure was unaffected. Survivors occupied three small coteries and exhibited improved body condition, but increased flea infestation compared to a neighboring, uninfected colony. Black-tailed prairie dogs are capable of surviving a plague epizootic and reorganizing into apparently functional coteries. Surviving prairie dogs may be critical in the repopulation of plague-decimated colonies and, ultimately, the evolution of plague resistance.

Dyslexic entrepreneurs: the incidence; their coping strategies and their business skills.

PubMed

Logan, Julie

2009-11-01

This comparative study explores the incidence of dyslexia in entrepreneurs, corporate managers and the general population. It examines the suggestion that dyslexic entrepreneurs develop coping strategies to manage their weaknesses, which are subsequently of benefit in the new venture creation process. Results of this study suggest that there is a significantly higher incidence of dyslexia in entrepreneurs than in the corporate management and general US and UK populations and some of the strategies they adopt to overcome dyslexia (such as delegation of tasks) may be useful in business. The study was undertaken in two parts. First, entrepreneurs and corporate managers completed an online questionnaire, which combined questions about their company, their management or leadership role and their business skills together with questions that were designed to explore the likely incidence of dyslexia. A follow-up study that made use of a semi-structured questionnaire explored business issues and educational experience in more depth with those who had been diagnosed as dyslexic and those who did not have any history of dyslexia or any other learning difficulty.

Medication advertising in Brazil. Can it be regulated?

PubMed

Nascimento, Alvaro César

2009-01-01

The regulation of medication advertising in Brazil has four weak points. Inspection and punishment of irregularities is carried out a posteriori to the infraction being committed (when the population has already been exposed to a sanitary risk). The fines charged by the Brazilian Sanitary Surveillance Agency (Anvisa) have a derisory value compared to investments in advertising. There is no mechanism that prevents fines from being transferred to prices. The phrase 'If symptoms persist, consult your doctor', rather than warning about the risks of self-medication, encourages using at least the first medication without a prescription, advising a visit to the doctor only if symptoms persist. Anvisa data and academic studies reveal that 90% to 100% of advertising shown in the media contains irregularities. Thus, the Anvisa Collegiate Board of Directors Resolution 102/2000, which seeks to regulate the sector, makes up a system that benefits the infractor and keeps the population at risk. This work analyses alternative regulation, looking at advertising's previous compliance statute through the surveillance system; it studies international statutes and proposes an alteration in the structure of the current model, inserting the logic of sanitary risk prevention.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

Structure and morphology of submarine slab slides: clues to origin and behavior

USGS Publications Warehouse

O'Leary, Dennis W.

1991-01-01

Geologic features suggest that some slab slides probably result from long-term strength degradation of weak layers deep in the homoclinal section. Time-dependent strain in clay-rich layers can create potential slide surfaces of low frictional strength. Competent layers are weak in tension and probably fragment in the first instance of, or even prior to, translation, and the allochthonous mass is readily transformed into a high-momentum debris flow. The structure and geomorphology of slab slides provide important clues to their origin and behavior. -from Author

The thermal stability of the nanograin structure in a weak solute segregation system.

PubMed

Tang, Fawei; Song, Xiaoyan; Wang, Haibin; Liu, Xuemei; Nie, Zuoren

2017-02-08

A hybrid model that combines first principles calculations and thermodynamic evaluation was developed to describe the thermal stability of a nanocrystalline solid solution with weak segregation. The dependence of the solute segregation behavior on the electronic structure, solute concentration, grain size and temperature was demonstrated, using the nanocrystalline Cu-Zn system as an example. The modeling results show that the segregation energy changes with the solute concentration in a form of nonmonotonic function. The change in the total Gibbs free energy indicates that at a constant solute concentration and a given temperature, a nanocrystalline structure can remain stable when the initial grain size is controlled in a critical range. In experiments, dense nanocrystalline Cu-Zn alloy bulk was prepared, and a series of annealing experiments were performed to examine the thermal stability of the nanograins. The experimental measurements confirmed the model predictions that with a certain solute concentration, a state of steady nanograin growth can be achieved at high temperatures when the initial grain size is controlled in a critical range. The present work proposes that in weak solute segregation systems, the nanograin structure can be kept thermally stable by adjusting the solute concentration and initial grain size.

Levels and sources of forest fire prevention knowledge of California hunters

Treesearch

William S. Folkman

1963-01-01

Males 30-50 years of age from the smaller urban centers (under 25,000 population) make up the bulk of the California hunter population. They are mainly from the skilled-semiskilled and professional-managerial occupations. Their level of knowledge about forest fire prevention is generally high, but their knowledge is weak in some pertinent areas. Most frequently...

Forward Compton scattering with weak neutral current: Constraints from sum rules

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

Gorchtein, Mikhail; Zhang, Xilin

2015-06-09

We generalize forward real Compton amplitude to the case of the interference of the electromagnetic and weak neutral current, formulate a low-energy theorem, relate the new amplitudes to the interference structure functions and obtain a new set of sum rules. Furthermore, we address a possible new sum rule that relates the product of the axial charge and magnetic moment of the nucleon to the 0th moment of the structure function g5(ν, 0). For the dispersive γ Z-box correction to the proton’s weak charge, the application of the GDH sum rule allows us to reduce the uncertainty due to resonance contributionsmore » by a factor of two. Finally, the finite energy sum rule helps addressing the uncertainty in that calculation due to possible duality violations.« less

On a Nonlinear Model for Tumor Growth: Global in Time Weak Solutions

NASA Astrophysics Data System (ADS)

Donatelli, Donatella; Trivisa, Konstantina

2014-07-01

We investigate the dynamics of a class of tumor growth models known as mixed models. The key characteristic of these type of tumor growth models is that the different populations of cells are continuously present everywhere in the tumor at all times. In this work we focus on the evolution of tumor growth in the presence of proliferating, quiescent and dead cells as well as a nutrient. The system is given by a multi-phase flow model and the tumor is described as a growing continuum Ω with boundary ∂Ω both of which evolve in time. Global-in-time weak solutions are obtained using an approach based on penalization of the boundary behavior, diffusion and viscosity in the weak formulation.

Skill Acquisition: Compilation of Weak-Method Problem Solutions.

ERIC Educational Resources Information Center

Anderson, John R.

According to the ACT theory of skill acquisition, cognitive skills are encoded by a set of productions, which are organized according to a hierarchical goal structure. People solve problems in new domains by applying weak problem-solving procedures to declarative knowledge they have about this domain. From these initial problem solutions,…

The Instrument for the Observation of Teaching Activities (IOTA) and Alternative Approaches to Remediation of Teacher Weaknesses.

ERIC Educational Resources Information Center

Richardson, Donald C.; Hatley, Richard V.

1980-01-01

Comparing the effectiveness of different strategies for remediating teacher weaknesses, as measured by the Instrument for Observation of Teaching Activities (IOTA), 99 elementary and junior high school teachers were observed. The study revealed that combining IOTA feedback with structured inservice workshops focusing on narrow specific weaknesses…

Generation separation in simple structured life cycles: models and 48 years of field data on a tea tortrix moth.

PubMed

Yamanaka, Takehiko; Nelson, William A; Uchimura, Koichiro; Bjørnstad, Ottar N

2012-01-01

Population cycles have fascinated ecologists since the early nineteenth century, and the dynamics of insect populations have been central to understanding the intrinsic and extrinsic biological processes responsible for these cycles. We analyzed an extraordinary long-term data set (every 5 days for 48 years) of a tea tortrix moth (Adoxophyes honmai) that exhibits two dominant cycles: an annual cycle with a conspicuous pattern of four or five single-generation cycles superimposed on it. General theory offers several candidate mechanisms for generation cycles. To evaluate these, we construct and parameterize a series of temperature-dependent, stage-structured models that include intraspecific competition, parasitism, mate-finding Allee effects, and adult senescence, all in the context of a seasonal environment. By comparing the observed dynamics with predictions from the models, we find that even weak larval competition in the presence of seasonal temperature forcing predicts the two cycles accurately. None of the other mechanisms predicts the dynamics. Detailed dissection of the results shows that a short reproductive life span and differential winter mortality among stages are the additional life-cycle characteristics that permit the sustained cycles. Our general modeling approach is applicable to a wide range of organisms with temperature-dependent life histories and is likely to prove particularly useful in temperate systems where insect pest outbreaks are both density and temperature dependent. © 2011 by The University of Chicago.

3D receiver function Kirchhoff depth migration image of Cascadia subduction slab weak zone

NASA Astrophysics Data System (ADS)

Cheng, C.; Allen, R. M.; Bodin, T.; Tauzin, B.

2016-12-01

We have developed a highly computational efficient algorithm of applying 3D Kirchhoff depth migration to telesismic receiver function data. Combine primary PS arrival with later multiple arrivals we are able to reveal a better knowledge about the earth discontinuity structure (transmission and reflection). This method is highly useful compare with traditional CCP method when dipping structure is met during the imaging process, such as subduction slab. We apply our method to the reginal Cascadia subduction zone receiver function data and get a high resolution 3D migration image, for both primary and multiples. The image showed us a clear slab weak zone (slab hole) in the upper plate boundary under Northern California and the whole Oregon. Compare with previous 2D receiver function image from 2D array(CAFE and CASC93), the position of the weak zone shows interesting conherency. This weak zone is also conherent with local seismicity missing and heat rising, which lead us to think about and compare with the ocean plate stucture and the hydralic fluid process during the formation and migration of the subduction slab.

Microstructure and micromechanical elastic properties of weak layers

NASA Astrophysics Data System (ADS)

Köchle, Berna; Matzl, Margret; Proksch, Martin; Schneebeli, Martin

2014-05-01

Weak layers are the mechanically most important stratigraphic layer for avalanches. Yet, there is little known about their exact geometry and their micromechanical properties. To distinguish weak layers or interfaces is essential to assess stability. However, except by destructive mechanical tests, they cannot be easily identified and characterized in the field. We casted natural weak layers and their adjacent layers in the field during two winter seasons and scanned them non-destructively with X-ray computer tomography with a resolution between 10 - 20 µm. Reconstructed three-dimensional models of centimeter-sized layered samples allow for calculating the change of structural properties. We found that structural transitions cannot always by expressed by geometry like density or grain size. In addition, we calculated the Young's modulus and Poisson's ratio of the individual layers with voxel-based finite element simulations. As any material has its characteristic elastic parameters, they may potentially differentiate individual layers, and therefore different microstructures. Our results show that Young's modulus correlates well with density but do not indicate snow's microstructure, in contrast to Poisson's ratio which tends to be lower for strongly anisotropic forms like cup crystals and facets.

The Congenital Heart Surgeons Society Datacenter: unique attributes as a research organization.

PubMed

Caldarone, Christopher A; Williams, William G

2010-01-01

Over the last 25 years, the Congenital Heart Surgeons Society (CHSS) has evolved from an informal club to a mature organization. A central feature of the CHSS has been dedication to evaluating outcomes of congenital heart surgery across a wide array of clinical diagnoses. These research activities have been orchestrated through the CHSS Datacenter, which has developed a unique organizational structure that has strengths and weaknesses in comparison to other research organizational structures (e.g., prospective randomized trials, registries, etc). This review will highlight the unique attributes of the CHSS Datacenter with emphasis on the Datacenter's strengths and weaknesses in comparison to other organizational structures. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Weak correlations between local density and dynamics near the glass transition.

PubMed

Conrad, J C; Starr, F W; Weitz, D A

2005-11-17

We perform experiments on two different dense colloidal suspensions with confocal microscopy to probe the relationship between local structure and dynamics near the glass transition. We calculate the Voronoi volume for our particles and show that this quantity is not a universal probe of glassy structure for all colloidal suspensions. We correlate the Voronoi volume to displacement and find that these quantities are only weakly correlated. We observe qualitatively similar results in a simulation of a polymer melt. These results suggest that the Voronoi volume does not predict dynamical behavior in experimental colloidal suspensions; a purely structural approach based on local single particle volume likely cannot describe the colloidal glass transition.

[Stigmatizing Attitudes towards Cancer Patients--Results of a Representative Population Survey].

PubMed

Ernst, Jochen; Brähler, Elmar; Hinz, Andreas; Friedrich, Michael; Lehmann-Laue, Antje; Mehnert, Anja; Weißflog, Gregor

2016-03-01

To investigate stigmatizing attitudes towards cancer patients in the general population and to examine their association with socio-structural characteristics and perceived causes of disease. We recruited a representative sample from the German general population (n=2420; mean age: 52 years; 54% women). Stigmatizing attitudes were assessed with a 9-item scale. Predictors of stigmatizing attitudes were identified using a regression analysis. Agreement with stigmatization items ranged from 3.6% (item: work together with a cancer patient) to 18.9% (item: use the same dishes as a cancer patient). Perceived causes of disease with a high levels of personal responsibility showed only weak correlations with stigmatizing attitudes (all r<0.31) and were partially statistical significant (e. g. food intake) or not significant (e. g. alcohol). The strongest predictors of stigmatizing attitudes were lack of cancer-related experiences (Beta=-0,26), age <60 years (Beta=0,1) and the assumption that one cannot protect oneself from cancer (Beta=0,11) (all p<0.001). Further predictors were male gender and living in rural area (p<0.01). The results demonstrate a need for further research and the development of valid methodological instruments to assess stigmatization towards cancer patients. © Georg Thieme Verlag KG Stuttgart · New York.

Weak hard X-ray emission from broad absorption line quasars: evidence for intrinsic X-ray weakness

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

Luo, B.; Brandt, W. N.; Scott, A. E.

We report NuSTAR observations of a sample of six X-ray weak broad absorption line (BAL) quasars. These targets, at z = 0.148-1.223, are among the optically brightest and most luminous BAL quasars known at z < 1.3. However, their rest-frame ≈2 keV luminosities are 14 to >330 times weaker than expected for typical quasars. Our results from a pilot NuSTAR study of two low-redshift BAL quasars, a Chandra stacking analysis of a sample of high-redshift BAL quasars, and a NuSTAR spectral analysis of the local BAL quasar Mrk 231 have already suggested the existence of intrinsically X-ray weak BAL quasars,more » i.e., quasars not emitting X-rays at the level expected from their optical/UV emission. The aim of the current program is to extend the search for such extraordinary objects. Three of the six new targets are weakly detected by NuSTAR with ≲ 45 counts in the 3-24 keV band, and the other three are not detected. The hard X-ray (8-24 keV) weakness observed by NuSTAR requires Compton-thick absorption if these objects have nominal underlying X-ray emission. However, a soft stacked effective photon index (Γ{sub eff} ≈ 1.8) for this sample disfavors Compton-thick absorption in general. The uniform hard X-ray weakness observed by NuSTAR for this and the pilot samples selected with <10 keV weakness also suggests that the X-ray weakness is intrinsic in at least some of the targets. We conclude that the NuSTAR observations have likely discovered a significant population (≳ 33%) of intrinsically X-ray weak objects among the BAL quasars with significantly weak <10 keV emission. We suggest that intrinsically X-ray weak quasars might be preferentially observed as BAL quasars.« less

Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management.

PubMed

Adin, A; Weber, J C; Sotelo Montes, C; Vidaurre, H; Vosman, B; Smulders, M J M

2004-05-01

Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes

PubMed Central

Bitbol, Anne-Florence; Schwab, David J.

2014-01-01

Natural selection drives populations towards higher fitness, but crossing fitness valleys or plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We investigate quantitatively the effect of subdividing an asexual population on the time it takes to cross a fitness valley or plateau. We focus on a generic and minimal model that includes only population subdivision into equivalent demes connected by global migration, and does not require significant size changes of the demes, environmental heterogeneity or specific geographic structure. We determine the optimal speedup of valley or plateau crossing that can be gained by subdivision, if the process is driven by the deme that crosses fastest. We show that isolated demes have to be in the sequential fixation regime for subdivision to significantly accelerate crossing. Using Markov chain theory, we obtain analytical expressions for the conditions under which optimal speedup is achieved: valley or plateau crossing by the subdivided population is then as fast as that of its fastest deme. We verify our analytical predictions through stochastic simulations. We demonstrate that subdivision can substantially accelerate the crossing of fitness valleys and plateaus in a wide range of parameters extending beyond the optimal window. We study the effect of varying the degree of subdivision of a population, and investigate the trade-off between the magnitude of the optimal speedup and the width of the parameter range over which it occurs. Our results, obtained for fitness valleys and plateaus, also hold for weakly beneficial intermediate mutations. Finally, we extend our work to the case of a population connected by migration to one or several smaller islands. Our results demonstrate that subdivision with migration alone can significantly accelerate the crossing of fitness valleys and plateaus, and shed light onto the quantitative conditions necessary for this to occur. PMID:25122220

Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp.

PubMed

Cheikh-Ali, Zakaria; Glynou, Kyriaki; Ali, Tahir; Ploch, Sebastian; Kaiser, Marcel; Thines, Marco; Bode, Helge B; Maciá-Vicente, Jose G

2015-10-01

Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp. strains of a particular phylotype, isolated from roots of Microthlaspi perfoliatum growing in different European localities. Exophillic acid and two previously undescribed compounds were isolated from these strains, and their structures were elucidated by spectroscopic methods using MS, 1D and 2D NMR. Bioassays revealed a weak activity of these compounds against disease-causing protozoa and mammalian cells. In addition, 18 related structures were identified by UPLC/MS based on comparisons with the isolated structures. Three Exophiala strains produced derivatives containing a β-d-glucopyranoside moiety, and their colony morphology was distinct from the other two strains, which produced derivatives lacking β-d-glucopyranoside. Whether the chemical/morphological strain types represent variants of the same genotype or independent genetic populations within Exophiala remains to be evaluated. Copyright © 2015 Elsevier Ltd. All rights reserved.

HOW THE FIRST STARS SHAPED THE FAINTEST GAS-DOMINATED DWARF GALAXIES

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

Verbeke, R.; Vandenbroucke, B.; Rijcke, S. De, E-mail: robbert.verbeke@UGent.be

2015-12-20

Low-mass dwarf galaxies are very sensitive test-beds for theories of cosmic structure formation since their weak gravitational fields allow the effects of the relevant physical processes to clearly stand out. Up to now, no unified account has existed of the sometimes seemingly conflicting properties of the faintest isolated dwarfs in and around the Local Group, such as Leo T and the recently discovered Leo P and Pisces A systems. Using new numerical simulations, we show that this serious challenge to our understanding of galaxy formation can be effectively resolved by taking into account the regulating influence of the ultraviolet radiation of themore » first population of stars on a dwarf’s star formation rate while otherwise staying within the standard cosmological paradigm for structure formation. These simulations produce faint, gas-dominated, star-forming dwarf galaxies that lie on the baryonic Tully–Fisher relation and that successfully reproduce a broad range of chemical, kinematical, and structural observables of real late-type dwarf galaxies. Furthermore, we stress the importance of obtaining properties of simulated galaxies in a manner as close as possible to the typically employed observational techniques.« less

A Preliminary Study of Genetic Variation in Populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, Estimated with AFLP Molecular Markers

PubMed Central

Andrade, I. M.; Mayo, S. J.; van den Berg, C.; Fay, M. F.; Chester, M.; Lexer, C.; Kirkup, D.

2007-01-01

Background and Aims This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. Methods Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. Key Results The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (FST = 0·1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0·6903, P = 0·002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise ΦPT = 0·137, P = 0·003) and as diverse (Nei's gene diversity, average He = 0·1832, 0·1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average He = 0·127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11·95 %, P = 0·037). Conclusions The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests. PMID:17823112

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

Cada, Glenn F; Bevelhimer, Mark S

The development of hydrokinetic (HK) energy projects is under consideration at over 150 sites in large rivers in the United States, including the Mississippi, Ohio, Tennessee, and Atchafalaya Rivers. These waterbodies support numerous fish species that might interact with the HK projects in a variety of ways, e.g., by attraction to or avoidance of project structures. Although many fish species inhabit these rivers (about 172 species in the Mississippi River alone), not all of them will encounter the HK projects. Some species prefer low-velocity, backwater habitats rather than the high-velocity, main channel areas that would be the best sites formore » HK. Other, riverbank-oriented species are weak swimmers or too small to inhabit the main channel for significant periods of time. Some larger, main channel fish species are not known to be attracted to structures. Based on a consideration of habitat preferences, size/swim speed, and behavior, fish species that are most likely to be attracted to HK structures in the main channel include carps, suckers, catfish, white bass, striped bass, smallmouth bass, spotted bass, and sauger. Proper siting of the project in order to avoid sensitive fish populations, backwater and fish nursery habitat areas, and fish migration corridors will likely minimize concerns about fish attraction to or avoidance of HK structures.« less

[The regionalized healthcare network in Santa Catarina State, Brazil, from 2011 to 2015: governance system and oral healthcare].

PubMed

Godoi, Heloisa; Andrade, Selma Regina de; Mello, Ana Lúcia Schaefer Ferreira de

2017-09-28

: The objective was to describe the governance system used in structuring the regionalized healthcare network in Santa Catarina State, Brazil, based on the Bipartite Inter-Managerial Commission (CIB), with a focus on structuring of oral healthcare. This was a qualitative, exploratory-descriptive documental study, based on the foundations of governance as an analytical tool through identification of the dimensions actors, norms, nodal points, and processes. Secondary data were collected from the minutes of CIB meetings held from January 2011 to December 2015. The analysis shows weaknesses in CIB governance in Santa Catarina in relation to regionalized structuring of oral healthcare from a network perspective. Structuring of oral healthcare occurs in parallel to that of other thematic networks in the state and shows the expansion of dental services, especially those with medium complexity, as an effect of the prevailing governance process. The relations established between administrators and decision-making processes allowed recognizing this network's "prescription", since there is little negotiation and local demand, limited more to following recommendations and incentives from the federal/state sphere, intermediated by staff from the State Health Secretariat. Thus, setting a policy agenda for oral healthcare for the population of Santa Catarina is weakened, with a peripheral position in relation to other health programs.

Muscular Dystrophy with Ribitol-Phosphate Deficiency: A Novel Post-Translational Mechanism in Dystroglycanopathy

PubMed Central

Kanagawa, Motoi; Toda, Tatsushi

2017-01-01

Muscular dystrophy is a group of genetic disorders characterized by progressive muscle weakness. In the early 2000s, a new classification of muscular dystrophy, dystroglycanopathy, was established. Dystroglycanopathy often associates with abnormalities in the central nervous system. Currently, at least eighteen genes have been identified that are responsible for dystroglycanopathy, and despite its genetic heterogeneity, its common biochemical feature is abnormal glycosylation of alpha-dystroglycan. Abnormal glycosylation of alpha-dystroglycan reduces its binding activities to ligand proteins, including laminins. In just the last few years, remarkable progress has been made in determining the sugar chain structures and gene functions associated with dystroglycanopathy. The normal sugar chain contains tandem structures of ribitol-phosphate, a pentose alcohol that was previously unknown in humans. The dystroglycanopathy genes fukutin, fukutin-related protein (FKRP), and isoprenoid synthase domain-containing protein (ISPD) encode essential enzymes for the synthesis of this structure: fukutin and FKRP transfer ribitol-phosphate onto sugar chains of alpha-dystroglycan, and ISPD synthesizes CDP-ribitol, a donor substrate for fukutin and FKRP. These findings resolved long-standing questions and established a disease subgroup that is ribitol-phosphate deficient, which describes a large population of dystroglycanopathy patients. Here, we review the history of dystroglycanopathy, the properties of the sugar chain structure of alpha-dystroglycan, dystroglycanopathy gene functions, and therapeutic strategies. PMID:29081423

Interactions between propagating rifts and pre-existing linear rheological heterogeneities: insights from 3D analogue experiments of rotational extension

NASA Astrophysics Data System (ADS)

Molnar, Nicolas; Cruden, Alexander

2017-04-01

Propagating rifts are a natural consequence of lithospheric plates that diverge with respect to each other about a pole of rotation. This process of "unzipping" is common in the geological record, but how rifts interact with pre-existing structures (i.e., with a non-homogeneous lithosphere) as they propagate is poorly understood. Here we report on a series of lithospheric-scale three-dimensional analogue experiments of rotational extension with in-built, variably oriented linear weak zones in the lithospheric mantle, designed to investigate the role that inherited structural or thermal weaknesses play in the localisation of strain and rifting. Surface strain and dynamic topography in the analogue models are quantified by high-resolution particle imaging velocimetry and digital photogrammetry, which allows us to characterise the spatio-temporal evolution of deformation as a function of the orientation of the linear heterogeneities in great detail. The results show that the presence of a linear zone of weakness oriented at low angles with respect to the rift axis (i.e., favourably oriented) produces strain localisation in narrow domains, which enhances the "unzipping" process prior to continental break up. Strong strain partitioning is observed when the linear heterogeneity is oriented at high angles with respect to the rift axis (i.e., unfavourably oriented). In these experiments, early sub-parallel V-shaped basins propagate towards the pole of rotation until they are abandoned and strain is transferred entirely to structures developed in the vicinity of the strongly oblique weak lithosphere zone boundary. The modelling also provides insights on how propagating rift branches that penetrate the weak linear zone boundary are aborted when strain is relayed onto structures that develop in rheologically weaker areas. The experimental results are summarised in terms of their evolution, patterns of strain localisation, and dynamic topography as a function of the lithospheric heterogeneity obliquity angle, and compared to ancient and modern examples in nature.

Content Analysis of Standardized-Patients' Descriptive Feedback on Student Performance on the CPX.

PubMed

Lee, Young Hee; Lee, Young-Mee; Kim, Byung Soo

2010-12-01

The goal of this study was to explore what kind of additional information is provided by the descriptive comments other than the rating scales, on the physician-patient interaction (PPI) in the clinical performance examination (CPX) and its feedback role in identifying students' strengths and weaknesses in communication skills. The data were collected from 18 medical schools in Seoul and Gyeonggi region, which participated in the CPX for fourth-year medical students in 2006 and 2007. In total 12,650 examination cases in 2006 and 12,814 cases in 2007 were analyzed. Descriptive comments from the standardized patients (SPs) were analyzed by content analysis, which includes a 4-step process: coding, conceptualizing, categorizing and explanation. Ten categories (41 concepts) for 'strength' and 11 for 'weakness' (40 concepts) in the PPI were extracted. Among them, 10 categories were the same in both strength and weakness: providing adequate interview atmosphere, attentive listening, providing emotional support, non-verbal behaviors, professional attitude, questioning, explanation, reaching agreement, counseling & education and conducting adequate physical examination. For the 'structured and organized interview', only weakness was described. In 'providing emotional support' and 'adequate interview atmosphere', comments on strengths were more frequently mentioned than weaknesses. However, communication skills that were related to non-verbal behaviors were more frequently considered weaknesses rather than strengths. The numbers and content of the SP's comments on students' strengths and weaknesses in the PPI varied depending on the case specificities. The results suggest that the SPs' descriptive comments on student' performance on the CPX can provide additional information versus structured quantitative assessment tools such as performance checklists and rating scales. In particular, this information can be used as valuable feedback to identify the advantages and dicadvantages of the PPI and to enhance students' communication skills.

A powerful and efficient set test for genetic markers that handles confounders

PubMed Central

Listgarten, Jennifer; Lippert, Christoph; Kang, Eun Yong; Xiang, Jing; Kadie, Carl M.; Heckerman, David

2013-01-01

Motivation: Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger datasets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects—one to capture the set association signal and one to capture confounders. We also introduce a computational speedup for two random-effects models that makes this approach feasible even for extremely large cohorts. Using this model with both the likelihood ratio test and score test, we find that the former yields more power while controlling type I error. Application of our approach to richly structured Genetic Analysis Workshop 14 data demonstrates that our method successfully corrects for population structure and family relatedness, whereas application of our method to a 15 000 individual Crohn’s disease case–control cohort demonstrates that it additionally recovers genes not recoverable by univariate analysis. Availability: A Python-based library implementing our approach is available at http://mscompbio.codeplex.com. Contact: jennl@microsoft.com or lippert@microsoft.com or heckerma@microsoft.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23599503

Structural Evolution of a Warm Frontal Precipitation Band During GCPEx

NASA Technical Reports Server (NTRS)

Colle, Brian A.; Naeger, Aaron; Molthan, Andrew; Nesbitt, Stephen

2015-01-01

A warm frontal precipitation band developed over a few hours 50-100 km to the north of a surface warm front. The 3-km WRF was able to realistically simulate band development, although the model is somewhat too weak. Band genesis was associated with weak frontogenesis (deformation) in the presence of weak potential and conditional instability feeding into the band region, while it was closer to moist neutral within the band. As the band matured, frontogenesis increased, while the stability gradually increased in the banding region. Cloud top generating cells were prevalent, but not in WRF (too stable). The band decayed as the stability increased upstream and the frontogenesis (deformation) with the warm front weakened. The WRF may have been too weak and short-lived with the band because too stable and forcing too weak (some micro issues as well).

Short GRBs: Slashing Through the Jungle One Step at a Time

NASA Astrophysics Data System (ADS)

Gehrels, Neil

2008-03-01

We are learning in the Swift era that short and long bursts have very different origins. The short bursts appear to have old-population stellar progenitors and the long bursts certainly have young-population progenitors. However, the going is tough for short bursts, with low event rates and weak afterglows. Hints of sub-populations are emerging in distance range, progenitor type and lightcurve characteristics. This paper will discuss the growing Swift data set on short bursts and where it is leading.

Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

NASA Astrophysics Data System (ADS)

Hsieh, S. Y.; Neubauer, F.; Willingshofer, E.; Sokoutis, D.

2014-12-01

The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry.

Immunochemical and structural analysis of the O polysaccharides of Salmonella zuerich [1,9,27,(46)

PubMed Central

Nghiêm, H O; Himmelspach, K; Mayer, H

1992-01-01

Salmonella zuerich [1,9,27,(46)] has been shown to exhibit two levels of structural heterogeneity. The bacterium carries two distinct O-polysaccharide molecules with and without O:factor 1. Both sets of molecules (1+ and 1-) carry the two O:factors 27 and 46 on the same O chain, but they are expressed unevenly; in contrast to factor 27, O:factor 46 is always weakly expressed. Part of this weak expression was thought to be due to strong inhibition of factor 46 by factor 1. In this study, serological analysis gave more detailed information on the sizes of the different O:factor epitopes. Structural analysis of S. zuerich O polysaccharides showed that they are constructed of the expected chemical sequences characteristic of factors 1, 9, 27, and 46. No modification in the sugar sequence could account for the weak expression of O:factor 46. Factors 27 and 46 are present on oligosaccharides carrying either an alpha-Man (factor 27) or a beta-Man (factor 46) residue. In S. zuerich, the alpha-Man configuration is predominant, corroborating the expression of strong factor 27 and weak factor 46 on the bacteria. Questions raised by the existence of such heterogeneous O polysaccharides on the specificity of the O chain polymerase, as well as the place of S. zuerich in Salmonella evolution, are dicussed in this paper. PMID:1372315

Universality of emergent states in diverse physical systems

NASA Astrophysics Data System (ADS)

Guidry, Mike

2017-12-01

Our physics textbooks are dominated by examples of simple weakly-interacting microscopic states, but most of the real world around us is most effectively described in terms of emergent states that have no clear connection to simple textbook states. Emergent states are strongly-correlated and dominated by properties that emerge as a consequence of interactions and are not part of the description of the corresponding weakly-interacting system. This paper proposes a connection of weakly-interacting textbook states and realistic emergent states through fermion dynamical symmetries having fully-microscopic generators of the emergent states. These imply unique truncation of the Hilbert space for the weakly-interacting system to a collective subspace where the emergent states live. Universality arises because the possible symmetries under commutation of generators, which transcend the microscopic structure of the generators, are highly restricted in character and determine the basic structure of the emergent state, with the microscopic structure of the generators influencing emergent state only parametrically. In support of this idea we show explicit evidence that high-temperature superconductors, collective states in heavy atomic nuclei, and graphene quantum Hall states in strong magnetic fields exhibit a near-universal emergent behavior in their microscopically-computed total energy surfaces, even though these systems share essentially nothing in common at the microscopic level and their emergent states are characterized by fundamentally different order parameters.

Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells.

PubMed

Pandey, Rachna; Vischer, Norbert O E; Smelt, Jan P P M; van Beilen, Johan W A; Ter Beek, Alexander; De Vos, Winnok H; Brul, Stanley; Manders, Erik M M

2016-11-01

Intracellular pH (pH i ) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pH i homeostasis. Unfortunately, accurate pH i quantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pH i at single-cell levels in Bacillus subtilis Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pH i in individual B. subtilis cells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pH i and an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pH i regulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies. This study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Photoemission study of the electronic structure and charge density waves of Na₂Ti₂Sb₂O

DOE PAGES

Tan, S. Y.; Jiang, J.; Ye, Z. R.; ...

2015-04-30

The electronic structure of Na₂Ti₂Sb₂O single crystal is studied by photon energy and polarization dependent angle-resolved photoemission spectroscopy (ARPES). The obtained band structure and Fermi surface agree well with the band structure calculation of Na₂Ti₂Sb₂O in the non-magnetic state, which indicates that there is no magnetic order in Na₂Ti₂Sb₂O and the electronic correlation is weak. Polarization dependent ARPES results suggest the multi-band and multi-orbital nature of Na₂Ti₂Sb₂O. Photon energy dependent ARPES results suggest that the electronic structure of Na₂Ti₂Sb₂O is rather two-dimensional. Moreover, we find a density wave energy gap forms below the transition temperature and reaches 65 meV atmore » 7 K, indicating that Na₂Ti₂Sb₂O is likely a weakly correlated CDW material in the strong electron-phonon interaction regime. (author)« less

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

NASA Astrophysics Data System (ADS)

Prasanna, M. D.; Row, T. N. Guru

2001-05-01

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Coexistence of Weak Ferromagnetism and Ferroelectricity in the High Pressure LiNbO3-Type Phase of FeTiO3

NASA Astrophysics Data System (ADS)

Varga, T.; Kumar, A.; Vlahos, E.; Denev, S.; Park, M.; Hong, S.; Sanehira, T.; Wang, Y.; Fennie, C. J.; Streiffer, S. K.; Ke, X.; Schiffer, P.; Gopalan, V.; Mitchell, J. F.

2009-07-01

We report the magnetic and electrical characteristics of polycrystalline FeTiO3 synthesized at high pressure that is isostructural with acentric LiNbO3 (LBO). Piezoresponse force microscopy, optical second harmonic generation, and magnetometry demonstrate ferroelectricity at and below room temperature and weak ferromagnetism below ˜120K. These results validate symmetry-based criteria and first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LBO structure.

Coexistence of weak ferromagnetism and ferroelectricity in the high pressure LiNbO3-type phase of FeTiO3.

PubMed

Varga, T; Kumar, A; Vlahos, E; Denev, S; Park, M; Hong, S; Sanehira, T; Wang, Y; Fennie, C J; Streiffer, S K; Ke, X; Schiffer, P; Gopalan, V; Mitchell, J F

2009-07-24

We report the magnetic and electrical characteristics of polycrystalline FeTiO_{3} synthesized at high pressure that is isostructural with acentric LiNbO_{3} (LBO). Piezoresponse force microscopy, optical second harmonic generation, and magnetometry demonstrate ferroelectricity at and below room temperature and weak ferromagnetism below approximately 120 K. These results validate symmetry-based criteria and first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LBO structure.

Ion acoustic shock wave in collisional equal mass plasma

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

Adak, Ashish, E-mail: ashish-adak@yahoo.com; Ghosh, Samiran, E-mail: sran-g@yahoo.com; Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in

The effect of ion-ion collision on the dynamics of nonlinear ion acoustic wave in an unmagnetized pair-ion plasma has been investigated. The two-fluid model has been used to describe the dynamics of both positive and negative ions with equal masses. It is well known that in the dynamics of the weakly nonlinear wave, the viscosity mediates wave dissipation in presence of weak nonlinearity and dispersion. This dissipation is responsible for the shock structures in pair-ion plasma. Here, it has been shown that the ion-ion collision in presence of collective phenomena mediated by the plasma current is the source of dissipationmore » that causes the Burgers' term which is responsible for the shock structures in equal mass pair-ion plasma. The dynamics of the weakly nonlinear wave is governed by the Korteweg-de Vries Burgers equation. The analytical and numerical investigations revealed that the ion acoustic wave exhibits both oscillatory and monotonic shock structures depending on the frequency of ion-ion collision parameter. The results have been discussed in the context of the fullerene pair-ion plasma experiments.« less

Spatio-temporal dynamics of pneumonia in bighorn sheep

USGS Publications Warehouse

Cassirer, E. Frances; Plowright, Raina K.; Manlove, Kezia R.; Cross, Paul C.; Dobson, Andrew P.; Potter, Kathleen A.; Hudson, Peter J.

2013-01-01

Bighorn sheep mortality related to pneumonia is a primary factor limiting population recovery across western North America, but management has been constrained by an incomplete understanding of the disease. We analysed patterns of pneumonia-caused mortality over 14 years in 16 interconnected bighorn sheep populations to gain insights into underlying disease processes. 2. We observed four age-structured classes of annual pneumonia mortality patterns: all-age, lamb-only, secondary all-age and adult-only. Although there was considerable variability within classes, overall they differed in persistence within and impact on populations. Years with pneumonia-induced mortality occurring simultaneously across age classes (i.e. all-age) appeared to be a consequence of pathogen invasion into a naïve population and resulted in immediate population declines. Subsequently, low recruitment due to frequent high mortality outbreaks in lambs, probably due to association with chronically infected ewes, posed a significant obstacle to population recovery. Secondary all-age events occurred in previously exposed populations when outbreaks in lambs were followed by lower rates of pneumonia-induced mortality in adults. Infrequent pneumonia events restricted to adults were usually of short duration with low mortality. 3. Acute pneumonia-induced mortality in adults was concentrated in fall and early winter around the breeding season when rams are more mobile and the sexes commingle. In contrast, mortality restricted to lambs peaked in summer when ewes and lambs were concentrated in nursery groups. 4. We detected weak synchrony in adult pneumonia between adjacent populations, but found no evidence for landscape-scale extrinsic variables as drivers of disease. 5. We demonstrate that there was a >60% probability of a disease event each year following pneumonia invasion into bighorn sheep populations. Healthy years also occurred periodically, and understanding the factors driving these apparent fade-out events may be the key to managing this disease. Our data and modelling indicate that pneumonia can have greater impacts on bighorn sheep populations than previously reported, and we present hypotheses about processes involved for testing in future investigations and management.

Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!

PubMed Central

Depaulis, Frantz; Orlando, Ludovic; Hänni, Catherine

2009-01-01

Background New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. Methodology/Principal Findings We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony (∼10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism θ, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22–130 thousand years ago (KYA)). Conclusions/Significance Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale. PMID:19440242

A large sample of shear-selected clusters from the Hyper Suprime-Cam Subaru Strategic Program S16A Wide field mass maps

NASA Astrophysics Data System (ADS)

Miyazaki, Satoshi; Oguri, Masamune; Hamana, Takashi; Shirasaki, Masato; Koike, Michitaro; Komiyama, Yutaka; Umetsu, Keiichi; Utsumi, Yousuke; Okabe, Nobuhiro; More, Surhud; Medezinski, Elinor; Lin, Yen-Ting; Miyatake, Hironao; Murayama, Hitoshi; Ota, Naomi; Mitsuishi, Ikuyuki

2018-01-01

We present the result of searching for clusters of galaxies based on weak gravitational lensing analysis of the ˜160 deg2 area surveyed by Hyper Suprime-Cam (HSC) as a Subaru Strategic Program. HSC is a new prime focus optical imager with a 1.5°-diameter field of view on the 8.2 m Subaru telescope. The superb median seeing on the HSC i-band images of 0.56" allows the reconstruction of high angular resolution mass maps via weak lensing, which is crucial for the weak lensing cluster search. We identify 65 mass map peaks with a signal-to-noise (S/N) ratio larger than 4.7, and carefully examine their properties by cross-matching the clusters with optical and X-ray cluster catalogs. We find that all the 39 peaks with S/N > 5.1 have counterparts in the optical cluster catalogs, and only 2 out of the 65 peaks are probably false positives. The upper limits of X-ray luminosities from the ROSAT All Sky Survey (RASS) imply the existence of an X-ray underluminous cluster population. We show that the X-rays from the shear-selected clusters can be statistically detected by stacking the RASS images. The inferred average X-ray luminosity is about half that of the X-ray-selected clusters of the same mass. The radial profile of the dark matter distribution derived from the stacking analysis is well modeled by the Navarro-Frenk-White profile with a small concentration parameter value of c500 ˜ 2.5, which suggests that the selection bias on the orientation or the internal structure for our shear-selected cluster sample is not strong.

Inertia-Centric Stability Analysis of a Planar Uniform Dust Molecular Cloud with Weak Neutral-Charged Dust Frictional Coupling

NASA Astrophysics Data System (ADS)

K. Karmakar, P.; Borah, B.

2014-05-01

This paper adopts an inertia-centric evolutionary model to study the excitation mechanism of new gravito-electrostatic eigenmode structures in a one-dimensional (1-D) planar self-gravitating dust molecular cloud (DMC) on the Jeans scale. A quasi-neutral multi-fluid consisting of warm electrons, warm ions, neutral gas and identical inertial cold dust grains with partial ionization is considered. The grain-charge is assumed not to vary at the fluctuation evolution time scale. The neutral gas particles form the background, which is weakly coupled with the collapsing grainy plasma mass. The gravitational decoupling of the background neutral particles is justifiable for a higher inertial mass of the grains with higher neutral population density so that the Jeans mode frequency becomes reasonably large. Its physical basis is the Jeans assumption of a self-gravitating uniform medium adopted for fiducially analytical simplification by neglecting the zero-order field. So, the equilibrium is justifiably treated initially as “homogeneous”. The efficacious inertial role of the thermal species amidst weak collisions of the neutral-charged grains is taken into account. A standard multiscale technique over the gravito-electrostatic equilibrium yields a unique pair of Korteweg-de Vries (KdV) equations. It is integrated numerically by the fourth-order Runge-Kutta method with multi-parameter variation for exact shape analyses. Interestingly, the model is conducive for the propagation of new conservative solitary spectral patterns. Their basic physics, parametric features and unique characteristics are discussed. The results go qualitatively in good correspondence with the earlier observations made by others. Tentative applications relevant to space and astrophysical environments are concisely highlighted.

Life stage and species identity affect whether habitat subsidies enhance or simply redistribute consumer biomass.

PubMed

Keller, Danielle A; Gittman, Rachel K; Bouchillon, Rachel K; Fodrie, F Joel

2017-10-01

Quantifying the response of mobile consumers to changes in habitat availability is essential for determining the degree to which population-level productivity is habitat limited rather than regulated by other, potentially density-independent factors. Over landscape scales, this can be explored by monitoring changes in density and foraging as habitat availability varies. As habitat availability increases, densities may: (1) decrease (unit-area production decreases; weak habitat limitation); (2) remain stable (unit-area production remains stable; habitat limitation) or (3) increase (unit-area production increases; strong habitat limitation). We tested the response of mobile estuarine consumers over 5 months to changes in habitat availability in situ by comparing densities and feeding rates on artificial reefs that were or were not adjacent to neighbouring artificial reefs or nearby natural reefs. Using either constructed or natural reefs to manipulate habitat availability, we documented threefold density decreases among juvenile stone crabs as habitat increased (i.e. weak habitat imitation). However, for adult stone crabs, density remained stable across treatments, demonstrating that habitat limitation presents a bottleneck in this species' later life history. Oyster toadfish densities also did not change with increasing habitat availability (i.e. habitat limitation), but densities of other cryptic fishes decreased as habitat availability increased (i.e. weak limitation). Feeding and abundance data suggested that some mobile fishes experience habitat limitation, or, potentially in one case, strong limitation across our habitat manipulations. These findings of significant, community-level habitat limitation provide insight into how global declines in structurally complex estuarine habitats may have reduced the fishery production of coastal ecosystems. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

A Chandra Survey of Milky Way Globular Clusters. I. Emissivity and Abundance of Weak X-Ray Sources

NASA Astrophysics Data System (ADS)

Cheng, Zhongqun; Li, Zhiyuan; Xu, Xiaojie; Li, Xiangdong

2018-05-01

Based on archival Chandra data, we have carried out an X-ray survey of 69, or nearly half the known population of, Milky Way globular clusters (GCs), focusing on weak X-ray sources, mainly cataclysmic variables (CVs) and coronally active binaries (ABs). Using the cumulative X-ray luminosity per unit stellar mass (i.e., X-ray emissivity) as a proxy of the source abundance, we demonstrate a paucity (lower by 41% ± 27% on average) of weak X-ray sources in most GCs relative to the field, which is represented by the Solar Neighborhood and Local Group dwarf elliptical galaxies. We also revisit the mutual correlations among the cumulative X-ray luminosity (L X), cluster mass (M), and stellar encounter rate (Γ), finding {L}{{X}}\\propto {M}0.74+/- 0.13, {L}{{X}}\\propto {{{Γ }}}0.67+/- 0.07 and {{Γ }}\\propto {M}1.28+/- 0.17. The three quantities can further be expressed as {L}{{X}}\\propto {M}0.64+/- 0.12 {{{Γ }}}0.19+/- 0.07, which indicates that the dynamical formation of CVs and ABs through stellar encounters in GCs is less dominant than previously suggested, and that the primordial formation channel has a substantial contribution. Taking these aspects together, we suggest that a large fraction of primordial, soft binaries have been disrupted in binary–single or binary–binary stellar interactions before they could otherwise evolve into X-ray-emitting close binaries, whereas the same interactions also have led to the formation of new close binaries. No significant correlations between {L}{{X}}/{L}K and cluster properties, including dynamical age, metallicity, and structural parameters, are found.

Physiological characteristics of dysphagia following thermal burn injury.

PubMed

Rumbach, Anna F; Ward, Elizabeth C; Cornwell, Petrea L; Bassett, Lynell V; Muller, Michael J

2012-09-01

The study aim was to document the acute physiological characteristics of swallowing impairment following thermal burn injury. A series of 19 participants admitted to a specialised burn centre with thermal burn injury were identified with suspected aspiration risk by a clinical swallow examination (CSE) conducted by a speech-language pathologist and referred to the study. Once medically stable, each then underwent more detailed assessment using both a CSE and fiberoptic evaluation of swallowing (FEES). FEES confirmed six individuals (32%) had no aspiration risk and were excluded from further analyses. Of the remaining 13, CSE confirmed that two had specific oral-phase deficits due to orofacial scarring and contractures, and all 13 had generalised oromotor weakness. FEES revealed numerous pharyngeal-phase deficits, with the major findings evident in greater than 50% being impaired secretion management, laryngotracheal edema, delayed swallow initiation, impaired sensation, inadequate movement of structures within the hypopharynx and larynx, and diffuse pharyngeal residue. Penetration and/or aspiration occurred in 83% (n = 10/12) of thin fluids trials, with a lack of response to the penetration/aspiration noted in 50% (n = 6/12 penetration aspiration events) of the cases. Most events occurred post swallow. Findings support the fact that individuals with dysphagia post thermal burn present with multiple risk factors for aspiration that appear predominantly related to generalised weakness and inefficiency and further impacted by edema and sensory impairments. Generalised oromotor weakness and orofacial contractures (when present) impact oral-stage swallow function. This study has identified a range of factors that may contribute to both oral- and pharyngeal-stage dysfunction in this clinical population and has highlighted the importance of using a combination of clinical and instrumental assessments to fully understand the influence of burn injury on oral intake and swallowing.

Persistence of collective behavior at high spin in the N = 88 nucleus Tb 153

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

Hartley, D. J.; Riley, M. A.; Wang, X.

Excited states in the N = 88 nucleus Tb-153 were observed up to spin similar to 40 in an experiment utilizing the Gammasphere array. The Tb-153 states were populated in a weak alpha 4n evaporation channel of the Cl-37 + Sn-124 reaction. Two previously known sequences were extended to higher spins, and a new decoupled structure was identified. The pi h(11/2) band was observed in the spin region where other N = 88 isotopes exhibit effects of prolate to oblate shape changes leading to band termination along the yrast line, whereas Tb-153 displays a persistent collective behavior. However, minor perturbationsmore » of the very highest state in both signatures of this h(11/2) band are observed, which perhaps signal the start of the transition towards band termination.« less

Existence of solutions of a two-dimensional boundary value problem for a system of nonlinear equations arising in growing cell populations.

PubMed

Jeribi, Aref; Krichen, Bilel; Mefteh, Bilel

2013-01-01

In the paper [A. Ben Amar, A. Jeribi, and B. Krichen, Fixed point theorems for block operator matrix and an application to a structured problem under boundary conditions of Rotenberg's model type, to appear in Math. Slovaca. (2014)], the existence of solutions of the two-dimensional boundary value problem (1) and (2) was discussed in the product Banach space L(p)×L(p) for p∈(1, ∞). Due to the lack of compactness on L1 spaces, the analysis did not cover the case p=1. The purpose of this work is to extend the results of Ben Amar et al. to the case p=1 by establishing new variants of fixed-point theorems for a 2×2 operator matrix, involving weakly compact operators.

The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

PubMed Central

2014-01-01

Background Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown. Results To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia. Conclusions The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia. PMID:24411008

Electronic structure and weak itinerant magnetism in metallic Y 2 Ni 7

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

Singh, David J.

2015-11-03

We describe a density functional study of the electronic structure and magnetism of Y₂Ni₇. The results show itinerant magnetism very similar to that in the weak itinerant ferromagnet Ni₃Al. The electropositive Y atoms in Y₂Ni₇ donate charge to the Ni host mostly in the form of s electrons. The non-spin-polarized state shows a high density of states at the Fermi level, N (E F), due to flat bands. This leads to a ferromagnetic instability. However, there are also several much more dispersive bands crossing E(F), which should promote the conductivity. Spin fluctuation effects appear to be comparable to or weakermore » than Ni₃Al, based on comparison with experimental data. Y₂Ni₇ provides a uniaxial analog to cubic Ni₃Al, for studying weak itinerant ferromagnetism, suggesting detailed measurements of its low temperature physical properties and spin fluctuations, as well as experiments under pressure.« less

Weak-field H3O+ ion cyclotron resonance alters water refractive index.

PubMed

D'Emilia, E; Ledda, M; Foletti, A; Lisi, A; Giuliani, L; Grimaldi, S; Liboff, A R

2017-01-01

Heretofore only observed in living systems, we report that weak-field ion cyclotron resonance (ICR) also occurs in inanimate matter. Weak magnetic field (50 nT) hydronium ICR at the field combination (7.84 Hz, 7.5 µT) markedly changes water structure, as evidenced by finding an altered index of refraction exactly at this combined field. This observation utilizes a novel technique which measures the scattering of a He-Ne laser beam as the sample is exposed to a ramped magnetic field frequency. In addition to the hydronium resonance, we find evidence of ICR coupling to a more massive structure, possibly a tetrahedral combination of three waters and a single hydronium ion. To check our observations, we extended this technique to D 2 O, successfully predicting the specific ICR charge-to-mass ratio for D 3 O + that alters the index of refraction.

Exploratory factor analysis of self-reported symptoms in a large, population-based military cohort

PubMed Central

2010-01-01

Background US military engagements have consistently raised concern over the array of health outcomes experienced by service members postdeployment. Exploratory factor analysis has been used in studies of 1991 Gulf War-related illnesses, and may increase understanding of symptoms and health outcomes associated with current military conflicts in Iraq and Afghanistan. The objective of this study was to use exploratory factor analysis to describe the correlations among numerous physical and psychological symptoms in terms of a smaller number of unobserved variables or factors. Methods The Millennium Cohort Study collects extensive self-reported health data from a large, population-based military cohort, providing a unique opportunity to investigate the interrelationships of numerous physical and psychological symptoms among US military personnel. This study used data from the Millennium Cohort Study, a large, population-based military cohort. Exploratory factor analysis was used to examine the covariance structure of symptoms reported by approximately 50,000 cohort members during 2004-2006. Analyses incorporated 89 symptoms, including responses to several validated instruments embedded in the questionnaire. Techniques accommodated the categorical and sometimes incomplete nature of the survey data. Results A 14-factor model accounted for 60 percent of the total variance in symptoms data and included factors related to several physical, psychological, and behavioral constructs. A notable finding was that many factors appeared to load in accordance with symptom co-location within the survey instrument, highlighting the difficulty in disassociating the effects of question content, location, and response format on factor structure. Conclusions This study demonstrates the potential strengths and weaknesses of exploratory factor analysis to heighten understanding of the complex associations among symptoms. Further research is needed to investigate the relationship between factor analytic results and survey structure, as well as to assess the relationship between factor scores and key exposure variables. PMID:20950474

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

PubMed Central

Laidò, Giovanni; Mangini, Giacomo; Taranto, Francesca; Gadaleta, Agata; Blanco, Antonio; Cattivelli, Luigi; Marone, Daniela; Mastrangelo, Anna M.; Papa, Roberto; De Vita, Pasquale

2013-01-01

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles. PMID:23826256

New T Tauri stars in Chamaeleon I and Chamaeleon II

NASA Technical Reports Server (NTRS)

Hartigan, Patrick

1993-01-01

A new objective prism survey of the entire Chamaeleon I dark cloud and 2/3 of the Chamaeleon II cloud has uncovered 26 new H-alpha emission line objects that were missed by previous H-alpha plate surveys. The new H-alpha emission line objects have similar IR colors and spatial distributions to the known T Tauri stars in these dark clouds, and could represent the very low mass end of the stellar population in these clouds or an older, less active component to the usual classical T Tauri star population. The new H-alpha survey identified 70 percent of the total known Young Stellar Objects (YSOs) in Cha I, compared with 35 percent for IRAS, and 25 percent from the Einstein X-ray survey. Ten of the new objects are weak-lined stars, with H-alpha equivalent widths less than 10 A. Weak-lined T Tauri stars make up about half of the total population of young stars in the Chamaeleon I cloud, a proportion similar to the Taurus-Auriga cloud. Presented are coordinates, finding charts, and optical and IR photometry of the new emission-line objects.

Species invasion shifts the importance of predator dependence.

PubMed

Griffen, Blaine D; Delaney, David G

2007-12-01

The strength of interference between foraging individuals can influence per capita consumption rates, with important consequences for predator and prey populations and system stability. Here we demonstrate how the replacement of a previously established invader, the predatory crab Carcinus maenas, by the recently invading predatory crab Hemigrapsus sanguineus shifts predation from a species that experiences strong predator interference (strong predator dependence) to one that experiences weak predator interference (weak predator dependence). We demonstrate using field experiments that differences in the strength of predator dependence persist for these species both when they forage on a single focal prey species only (the mussel Mytilus edulis) and when they forage more broadly across the entire prey community. This shift in predator dependence with species replacement may be altering the biomass across trophic levels, consistent with theoretical predictions, as we show that H. sanguineus populations are much larger than C. maenas populations throughout their invaded ranges. Our study highlights that predator dependence may differ among predator species and demonstrates that different predatory impacts of two conspicuous invasive predators may be explained at least in part by different strengths of predator dependence.

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Channeling of Branched Flow in Weakly Scattering Anisotropic Media.

PubMed

Degueldre, Henri; Metzger, Jakob J; Schultheis, Erik; Fleischmann, Ragnar

2017-01-13

When waves propagate through weakly scattering but correlated, disordered environments they are randomly focused into pronounced branchlike structures, a phenomenon referred to as branched flow, which has been studied in a wide range of isotropic random media. In many natural environments, however, the fluctuations of the random medium typically show pronounced anisotropies. A prominent example is the focusing of tsunami waves by the anisotropic structure of the ocean floor topography. We study the influence of anisotropy on such natural focusing events and find a strong and nonintuitive dependence on the propagation angle which we explain by semiclassical theory.

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Astrophysics Data System (ADS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-03-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Technical Reports Server (NTRS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-01-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

[Anorexia nervosa in the light of neurocognitive functioning: New theoretical and therapeutic perspectives].

PubMed

Martinez, G; Cook-Darzens, S; Chaste, P; Mouren, M-C; Doyen, C

2014-04-01

Anorexia nervosa is a serious psychiatric disorder, for which very few validated therapeutic strategies exist. The specific sociocognitive style of anorexic patients has already been described in the 1960s: it involves a concrete style with abstraction difficulties. Current neuropsychological tests have contributed to a more precise definition of these difficulties. IS THERE A SPECIFIC COGNITIVE PROFILE?: Contrary to common beliefs, these patients' intellectual performances are not superior to those of the general population. However, detailed comparisons of profiles on the Weschler Scales suggest difficulties in synthesizing information and better abilities in concrete problem solving. The dominant hypothesis concerning the attentional dimension is the existence of a weakness in central coherence, resulting in superior detail processing and a weakness in global integration. This trend appears to be stable even after the normalization of nutritional status. The impairment of set-shifting abilities leads to rigidity, expressed by inflexibility and perseveration, both in reasoning and behaviour. This reduced cognitive flexibility appears to persist after recovery, and may constitute a familial trait. In addition, this likely endophenotype seems to be independent from obsessional traits. Alexithymia is frequently described in anorexic individuals. It is the verbal description of feelings which seems to be particularly impaired. It may explain underlying difficulties in empathy. Indeed, these subjects have lower scores on emotional tests drawn from the theory of mind. These cognitive abnormalities are well documented in pervasive developmental disorders. NEUROANATOMICAL DATA: NEUROIMAGING IN SUPPORT OF LIMBIC AND FRONTO-STRIATAL ABNORMALITIES: Evidence from neuroimaging suggests abnormalities in cortical and subcortical structures, involving the temporal and orbito-frontal lobes. Various functional hypotheses are formulated, involving fronto-striatothalamic circuits, amygdala or insula. IS ANOREXIA NERVOSA A DEVELOPMENTAL DISORDER?: Pervasive developmental disorders are over-represented among anorexic subjects in comparison to the general population. Conversely, restrictive and selective eating disorders are more frequent among individuals presenting an autistic spectrum disorder. In view of the common cognitive and neuroanatomical data that are found in anorexia nervosa and neurodevelopmental disorders, we adhere to the hypothesis that anorexia nervosa may be similar to a neurodevelopmental disorder. Clinical observations suggest that this hypothesis may be especially relevant in the early forms of anorexia nervosa. These cognitive data confirm the potential relevance of new therapeutic modalities such as cognitive remediation. Initial results from its application to anorexia nervosa seem promising. A review of the recent literature highlights the possible existence of a developmental impairment of cortical and subcortical structures, associated with specific abnormalities in cognitive development such as a weakness in central coherence, reduced set-shifting ability and poor social skills. On this basis, cognitive remediation may be a promising therapeutic innovation. Copyright © 2013. Published by Elsevier Masson SAS.

Effect of an atom on a quantum guided field in a weakly driven fiber-Bragg-grating cavity

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

Le Kien, Fam; Hakuta, K.

2010-02-15

We study the interaction of an atom with a quantum guided field in a weakly driven fiber-Bragg-grating (FBG) cavity. We present an effective Hamiltonian and derive the density-matrix equations for the combined atom-cavity system. We calculate the mean photon number, the second-order photon correlation function, and the atomic excited-state population. We show that due to the confinement of the guided cavity field in the fiber cross-section plane and in the space between the FBG mirrors, the presence of the atom in the FBG cavity can significantly affect the mean photon number and the photon statistics even though the cavity finessemore » is moderate, the cavity is long, and the probe field is weak.« less

Weakly superconducting, thin-film structures as radiation detectors.

NASA Technical Reports Server (NTRS)

Kirschman, R. K.

1972-01-01

Measurements were taken with weakly superconducting quantum structures of the Notarys-Mercereau type, representing a thin superconductor film with a short region that is weakened in the sense that its transition temperature is lower than in the remaining portion of the film. The structure acts as a superconducting relaxation oscillator in which the supercurrent increases with time until the critical current of the weakened section is attained, at which moment the supercurrent decays and the cycle repeats. Under applied radiation, a series of constant-voltage steps appears in the current-voltage curve, and the size of the steps varies periodically with the amplitude of applied radiation. Measurements of the response characteristics were made in the frequency range of 10 to 450 MHz.

Computation of Large-Scale Structure Jet Noise Sources With Weak Nonlinear Effects Using Linear Euler

NASA Technical Reports Server (NTRS)

Dahl, Milo D.; Hixon, Ray; Mankbadi, Reda R.

2003-01-01

An approximate technique is presented for the prediction of the large-scale turbulent structure sound source in a supersonic jet. A linearized Euler equations code is used to solve for the flow disturbances within and near a jet with a given mean flow. Assuming a normal mode composition for the wave-like disturbances, the linear radial profiles are used in an integration of the Navier-Stokes equations. This results in a set of ordinary differential equations representing the weakly nonlinear self-interactions of the modes along with their interaction with the mean flow. Solutions are then used to correct the amplitude of the disturbances that represent the source of large-scale turbulent structure sound in the jet.

The role of transvaginal ultrasonography for detecting ovarian cancer in an asymptomatic screening population: a systematic review.

PubMed

Buhling, Kai J; Lezon, S; Eulenburg, C; Schmalfeldt, B

2017-05-01

The purpose of this study was to systematically analyze the effect of transvaginal ultrasonography in an asymptomatic female population as an annual screening procedure with regard to mortality data. Studies were evaluated descriptively on their strengths and weaknesses considering the methods and results. We evaluated 632 international studies by selecting only randomized controlled trials (RCTs). Three RCTs concerning transvaginal ultrasonography were found, performed in Japan, the USA, and Great Britain. Currently, no clear recommendation for the screening for ovarian cancer in an asymptomatic population can be given based on these three studies. The authors could not show a change in mortality using transvaginal ultrasonography for annual screening. An annual palpation does not offer a beneficial effect. The development of new ultrasound machines with higher image resolution in combination with a well-standardized algorithm for ovarian cancer in upcoming years might provide an improvement regarding mortality. The current studies do not show a benefit in screening an asymptomatic population annually with transvaginal ultrasonography, but the most recent publication showed a trend toward lower mortality in patients who underwent screening after 7-14 years of follow-up. Nevertheless, all three heterogeneous RCTs had weaknesses in their methods and therefore they neither contradict the general recommendation for screening in an asymptomatic population nor do they support it.

Atomic diffusion and mixing in old stars. V. A deeper look into the globular cluster NGC 6752

NASA Astrophysics Data System (ADS)

Gruyters, Pieter; Nordlander, Thomas; Korn, Andreas J.

2014-07-01

Context. Abundance trends in heavier elements with evolutionary phase have been shown to exist in the globular cluster NGC 6752 ([Fe / H] = -1.6). These trends are a result of atomic diffusion and additional (non-convective) mixing. Studying such trends can provide us with important constraints on the extent to which diffusion modifies the internal structure and surface abundances of solar-type, metal-poor stars. Aims: Taking advantage of a larger data sample, we investigate the reality and the size of these abundance trends and address questions and potential biases associated with the various stellar populations that make up NGC 6752. Methods: We perform an abundance analysis by combining photometric and spectroscopic data of 194 stars located between the turnoff point and the base of the red giant branch. Stellar parameters are derived from uvby Strömgren photometry. Using the quantitative-spectroscopy package SME, stellar surface abundances for light elements such as Li, Na, Mg, Al, and Si as well as heavier elements such as Ca, Ti, and Fe are derived in an automated way by fitting synthetic spectra to individual lines in the stellar spectra, obtained with the VLT/FLAMES-GIRAFFE spectrograph. Results: Based on uvby Strömgren photometry, we are able to separate three stellar populations in NGC 6752 along the evolutionary sequence from the base of the red giant branch down to the turnoff point. We find weak systematic abundance trends with evolutionary phase for Ca, Ti, and Fe which are best explained by stellar-structure models including atomic diffusion with efficient additional mixing. We derive a new value for the initial lithium abundance of NGC 6752 after correcting for the effect of atomic diffusion and additional mixing which falls slightly below the predicted standard BBN value. Conclusions: We find three stellar populations by combining photometric and spectroscopic data of 194 stars in the globular cluster NGC 6752. Abundance trends for groups of elements, differently affected by atomic diffusion and additional mixing, are identified. Although the statistical significance of the individual trends is weak, they all support the notion that atomic diffusion is operational along the evolutionary sequence of NGC 6752. Based on data collected at the ESO telescopes under programs 079.D-0645(A) and 081.D-0253(A).Full Tables 2 and 8 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/567/A72

Constraining stochastic gravitational wave background from weak lensing of CMB B-modes

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

Shaikh, Shabbir; Mukherjee, Suvodip; Souradeep, Tarun

2016-09-01

A stochastic gravitational wave background (SGWB) will affect the CMB anisotropies via weak lensing. Unlike weak lensing due to large scale structure which only deflects photon trajectories, a SGWB has an additional effect of rotating the polarization vector along the trajectory. We study the relative importance of these two effects, deflection and rotation, specifically in the context of E-mode to B-mode power transfer caused by weak lensing due to SGWB. Using weak lensing distortion of the CMB as a probe, we derive constraints on the spectral energy density (Ω{sub GW}) of the SGWB, sourced at different redshifts, without assuming anymore » particular model for its origin. We present these bounds on Ω{sub GW} for different power-law models characterizing the SGWB, indicating the threshold above which observable imprints of SGWB must be present in CMB.« less

Combating Transnational Terrorism in Kenya

DTIC Science & Technology

2005-06-17

Organizational Structure and Leadership.......................................................................13 Causes of Terrorism...Nongovernmental Organization AU Africa Union viii ILLUSTRATIONS Page Figure 1. Terrorist Organization Structure , Infrastructure, and...acknowledge the wider context that led to the growth of terrorism, which would imply an admission of the erosion of governance structures , notably weak

The effect of sexual selection on adaptation and extinction under increasing temperatures.

PubMed

Parrett, Jonathan M; Knell, Robert J

2018-04-25

Strong sexual selection has been reported to both enhance and hinder the adaptive capacity and persistence of populations when exposed to novel environments. Consequently, how sexual selection influences population adaption and persistence under stress remains widely debated. Here, we present two empirical investigations of the fitness consequences of sexual selection on populations of the Indian meal moth, Plodia interpunctella, exposed to stable or gradually increasing temperatures. When faced with increasing temperatures, strong sexual selection was associated with both increased fecundity and offspring survival compared with populations experiencing weak sexual selection, suggesting sexual selection acts to drive adaptive evolution by favouring beneficial alleles. Strong sexual selection did not, however, delay extinction when the temperature became excessively high. By manipulating individuals' mating opportunities during fitness assays, we were able to assess the effect of multiple mating independently from the effect of population-level sexual selection, and found that polyandry has a positive effect on both fecundity and offspring survival under increasing temperatures in those populations evolving with weak sexual selection. Within stable temperatures, there were some benefits from strong sexual selection but these were not consistent across the entire experiment, possibly reflecting changing costs and benefits of sexual selection under stabilizing and directional selection. These results indicate that sexual selection can provide a buffer against climate change and increase adaptation rates within a continuously changing environment. These positive effects of sexual selection may, however, be too small to protect populations and delay extinction when environmental changes are relatively rapid. © 2018 The Author(s).

Rapid genetic restoration of a keystone species exhibiting delayed demographic response.

PubMed

Cosentino, Bradley J; Schooley, Robert L; Bestelmeyer, Brandon T; McCarthy, Alison J; Sierzega, Kevin

2015-12-01

Genetic founder effects are often expected when animals colonize restored habitat in fragmented landscapes, but empirical data on genetic responses to restoration are limited. We examined the genetic response of banner-tailed kangaroo rats (Dipodomys spectabilis) to landscape-scale grassland restoration in the Chihuahuan Desert of New Mexico, USA. Dipodomys spectabilis is a grassland specialist and keystone species. At sites treated with herbicide to remove shrubs, colonization by D. spectabilis is slow and populations persist at low density for ≥10 years (≥6 generations). Persistence at low density and low gene flow may cause strong founder effects. We compared genetic structure of D. spectabilis populations between treated sites and remnant grasslands, and we examined how the genetic response to restoration depended on treatment age, area, and connectivity to source populations. Allelic richness and heterozygosity were similar between treated sites and remnant grasslands. Allelic richness at treated sites was greatest early in the restoration trajectory, and genetic divergence did not differ between recently colonized and established populations. These results indicated that founder effects during colonization of treated sites were weak or absent. Moreover, our results suggested founder effects were not mitigated by treatment area or connectivity. Dispersal is negatively density-dependent in D. spectabilis, and we hypothesize that high gene flow may occur early in the restoration trajectory when density is low. Our study shows genetic diversity can be recovered more rapidly than demographic components of populations after habitat restoration and that founder effects are not inevitable for animals colonizing restored habitat in fragmented landscapes. © 2015 John Wiley & Sons Ltd.

Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

NASA Astrophysics Data System (ADS)

Hsieh, Shang Yu; Neubauer, Franz; Cloetingh, Sierd; Willingshofer, Ernst; Sokoutis, Dimitrios

2014-05-01

The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011 and references therein). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry. References Leever, K. A., Gabrielsen, R. H., Sokoutis, D., Willingshofer, E., 2011. The effect of convergence angle on the kinematic evolution of strain partitioning in transpressional brittle wedges: Insight from analog modeling and high-resolution digital image analysis. Tectonics, 30(2), TC2013. Molnar, P., Dayem, K.E., 2010. Major intracontinental strike-slip faults and contrasts in lithospheric strength. Geosphere, 6, 444-467.

Electric Field-Dependent Photoluminescence in Multilayer Transition Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Stanev, T. K.; Henning, A.; Sangwan, V. K.; Speiser, N.; Stern, N. P.; Lauhon, L. J.; Hersam, M. C.; Wang, K.; Valencia, D.; Charles, J.; Kubis, T. C.

Owing to interlayer coupling, transition metal dichalcogenides (TMDCs) such as MoS2 exhibit strong layer dependence of optical and electronic phenomena such as the band gap and trion and neutral exciton population dynamics. Here, we systematically measure the effect of layer number on the optical response of multilayer MoS2 in an external electric field, observing field and layer number dependent emission energy and photoluminescence intensity. These effects are studied in few (2-6) and bulk (11 +) layered structures at low temperatures. In MoS2\\ the observed layer dependence arises from several mechanisms, including interlayer charge transfer, band structure, Stark Effect, Fermi level changes, screening, and surface effects, so it can be challenging to isolate how these mechanisms impact the observables. Because it behaves like a stack of weakly interacting monolayers rather than multilayer or bulk, ReS2 provides a comparison to traditional TMDCs to help isolate the underlying physical mechanisms dictating the response of multilayers. This work is supported by the National Science Foundation MRSEC program (DMR-1121262), and the 2-DARE Grant (EFRI-1433510). N.P.S. is an Alfred P. Sloan Research Fellow.

Shape-Coexistence in ^191Tl and ^189Tl.

NASA Astrophysics Data System (ADS)

Reviol, W.; Riedinger, L. L.; Carpenter, M. P.; Fischer, S. M.; Janssens, R. V. F.; Nisius, D.; Moore, E. F.

1997-10-01

The Tl isotopes at A ~ 190 are, like the neighboring Hg and Pb nuclei, recognized for a multiplicity of shapes. These shapes reach from spherical or weakly deformed oblate to well-deformed and superdeformed prolate, as mainly inferred from γ -ray spectroscopic studies. We have previously reported on shape-coexistence phenomena in ^191Tl and ^189Tl(W. Reviol et al., Phys. Scr. T56, 167 (1995), and references therein.). Here, we will focus on new results on the ``normally" deformed states in both nuclei obtained from a recent and an upcoming experiment at GAMMASPHERE. The states in ^191Tl and ^189Tl are populated by the reactions ^159Tb(^36S,4n)^191Tl at E_lab = 165 MeV and ^156Gd(^37Cl,4n)^189Tl at E_lab = 171 MeV, respectively. One of the questions to be addressed is about the main level structure in the positive-parity branch of ^191Tl^2. Whether this structure is oblate-collective in nature, like the [505]9/2^- yrast band, we will try to answer on the basis of the available lifetime data.

Strongly deformed nuclear shapes at ultra-high spin and shape coexistence in N ~ 90 nuclei

DOE PAGES

Riley, M. A.; Aguilar, A.; Evans, A. O.; ...

2009-01-01

The N ~ 90 region of the nuclear chart has featured prominently as the spectroscopy of nuclei at extreme spin has progressed. This talk will present recent discoveries from investigations of high spin behavior in the N ~ 90 Er, Tm and Yb nuclei utilizing the Gammasphere gamma-ray spectrometer. In particular it will include discussion of the beautiful shape evolution and coexistence observed in these nuclei along with the identification of a remarkable new family of band structures. The latter are very weakly populated rotational sequences with high moment of inertia that bypass the classic terminating configurations near spin 40-50h,more » marking a return to collectivity that extends discrete γ-ray spectroscopy to well over 60h. Establishing the nature of the yrast states in these nuclei beyond the oblate band-termination states has been a major goal for the past two decades. Cranking calculations suggest that these new structures most likely represent stable triaxial strongly deformed bands that lie in a valley of favored shell energy in deformation and particle-number space.« less

State of the fight against informal market of medicines in Togo: approaches and limitations.

PubMed

Gnassingbe, A; Flahault, A; Geissbuhler, A; Sprumont, D; Awesso, A

2018-02-01

The extent of medicines sales and consumption in the informal market in Togo raises many ethical and public health issues. In order to report on the situation of public action in the fight against this practice, we conducted a qualitative survey from 15 to 25 February 2016 in the commune of Lomé and in the Maritime Region among the actors of control system and resource people in the general population. This was supplemented by an analysis of Togo's pharmaceutical and health policy documents and a literature review on the illicit drug market issues relating to public health, political science, the social sciences applied to health. In spite of the existence of national and international tools, household poverty, cultural self-medication, ignorance of the population concerning the health risks of informal market medicines, weak political commitment, weakness regulation and enforcement, corruption, constitute obstacles to the success of actions to combat this practice.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

PubMed

Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

2017-04-01

The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Myasthenia Gravis: Unusual Presentations and Diagnostic Pitfalls.

PubMed

Rodolico, Carmelo; Parisi, Daniela; Portaro, Simona; Biasini, Fiammetta; Sinicropi, Stefano; Ciranni, Annamaria; Toscano, Antonio; Messina, Sonia; Musumeci, Olimpia; Vita, Giuseppe; Girlanda, Paolo

2016-08-30

Myasthenia gravis (MG) is an autoimmune disorder presenting with fluctuating, fatigable muscle weakness. Initial symptoms classically involve ocular and proximal limb muscles. Rarely, MG may onset with unusual features, so it can be misdiagnosed with other neuromuscular diseases. To describe unusual and atypical presentations of MG in a large cohort of patients, considering and discussing diagnostic difficulties and pitfalls. We report on 21 out of 508 MG patients, coming to our department in the last 27 years and presenting with atypical or unusual features. The diagnosis was achieved performing a careful clinical examination, a proper neurophysiological assessment, the neostigmine test, the AChR and MuSK antibodies assay and chest CT-scan. Patients with atypical/unusual MG onset were the 4.4% of all MG patients population. We describe seven different clinical categories: asymmetric distal upper limbs weakness, foot drop, isolated triceps brachii weakness and foot drop, post exertional axial weakness with dropped head, acute facial dyplegia, limb-girdle MG and MG with sudden lower limbs weakness and recurrent falls. Atypical and unusual presentations may increase the risk to misdiagnose or delay MG diagnosis. Isolated limb-girdle presentation is the most frequent atypical form in our series.

Two rare species of tylenchids, Discotylenchus biannulatus n. sp. and Labrys chinensis Qing Bert, 2018 (Nematoda: Tylenchidae) from western Iran.

PubMed

Konani, Ehsan; Panahandeh, Yousef; Pourjam, Ebrahim; Álvarez-Ortega, Sergio; Pedram, Majid

2018-04-23

Two rare species of the family Tylenchidae are described and illustrated based on morphological and morphometric characters. Scanning electron microscope (SEM) studies provided details of anterior end structures, helpful in generic identification of the studied populations. Discotylenchus biannulatus n. sp. is characterized by its dorso-ventrally flattened smooth cephalic region having two proximal annuli and a rectangular perioral disc, short longitudinal amphidial slits, lateral field with four incisures, stylet 9-10 μm long, with the conus shorter than half the total stylet length and with posteriorly directed knobs, well-developed median bulb, mono-prodelphic reproductive system with rounded empty spermatheca and short postvulval uterine sac (PUS), and filiform tail with pointed end. It is compared with other species of Discotylenchus having four lines in the lateral field. The Iranian population of Labrys chinensis is characterized by its long and slender (a = 45.2-57.2) body, smooth rounded cephalic region and an offset disc-like apical labial plate, short longitudinal lateral amphidial slits, lateral field with two incisures, moderately developed stylet with the conus less than half the total length and posteriorly directed knobs, median bulb fusiform with distinct but weak valve, gradually joining the isthmus, vulva at 57.2-59.1% with small flaps, elongate conoid tail, uniformly and slightly narrowing toward end with broadly rounded terminus and rare males. The minor morphological differences of the recovered population with the type population are discussed.

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

PubMed

Wear, Emma K; Wilbanks, Elizabeth G; Nelson, Craig E; Carlson, Craig A

2018-03-09

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations.

PubMed

Pericić, Marijana; Lauc, Lovorka Barać; Klarić, Irena Martinović; Rootsi, Siiri; Janićijevic, Branka; Rudan, Igor; Terzić, Rifet; Colak, Ivanka; Kvesić, Ante; Popović, Dan; Sijacki, Ana; Behluli, Ibrahim; Dordevic, Dobrivoje; Efremovska, Ljudmila; Bajec, Dorde D; Stefanović, Branislav D; Villems, Richard; Rudan, Pavao

2005-10-01

The extent and nature of southeastern Europe (SEE) paternal genetic contribution to the European genetic landscape were explored based on a high-resolution Y chromosome analysis involving 681 males from seven populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, and R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly Slavic, paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26) and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-Last Glacial Maximum R1a expansion from east to west, the Younger Dryas-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern Europe and SEE, and a rather weak extent of E3b1 diffusion toward regions nowadays occupied by Slavic-speaking populations.

Thermalization and light cones in a model with weak integrability breaking

DOE PAGES

Bertini, Bruno; Essler, Fabian H. L.; Groha, Stefan; ...

2016-12-09

Here, we employ equation-of-motion techniques to study the nonequilibrium dynamics in a lattice model of weakly interacting spinless fermions. Our model provides a simple setting for analyzing the effects of weak integrability-breaking perturbations on the time evolution after a quantum quench. We establish the accuracy of the method by comparing results at short and intermediate times to time-dependent density matrix renormalization group computations. For sufficiently weak integrability-breaking interactions we always observe prethermalization plateaus, where local observables relax to nonthermal values at intermediate time scales. At later times a crossover towards thermal behavior sets in. We determine the associated time scale,more » which depends on the initial state, the band structure of the noninteracting theory, and the strength of the integrability-breaking perturbation. Our method allows us to analyze in some detail the spreading of correlations and in particular the structure of the associated light cones in our model. We find that the interior and exterior of the light cone are separated by an intermediate region, the temporal width of which appears to scale with a universal power law t 1/3.« less

Crystallographic isomorphism in the structural type of α-HgI{sub 2} by example of KHgI{sub 3} · H{sub 2}O, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4}

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

Borisov, S. V., E-mail: borisov@niic.nsc.ru; Magarill, S. A.; Pervukhina, N. V.

The structure of KHgI{sub 3} · H{sub 2}O is assigned to the family of crystal structures having the three-layer cubic packing of iodine anions with cations in the tetrahedral voids (the structures of α-HgI{sub 2}, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4} among them). Crystallographic analysis shows that the nodes of the three-layer close packing are populated by iodine anions and K cations in the ratio 3/4: 1/4. Transformation of the structure of α-HgI{sub 2} into the structure of KHgI{sub 3} · H{sub 2}O can be formally represented as the replacement of (HgI){sub n}{sup +} fragments by (KH{sub 2}O){sub n}{supmore » +} fragments: (Hg{sub 2}I{sub 4})–(HgI){sup +} + (KH{sub 2}O){sub n}{sup +} = KHgI{sub 3} · H{sub 2}O. Perforated layers of vertex-sharing HgI{sub 4} tetrahedra break down into parallel isolated chains. Channels formed in place of I–Hg–I–Hg–fragments are occupied by–H{sub 2}O–K–-H{sub 2}-O-K-H{sub 2}O-chains weakly bound to neighbors.« less

Liver Enzymes and Bone Mineral Density in the General Population.

PubMed

Breitling, Lutz Philipp

2015-10-01

Liver enzyme serum levels within and just above the normal range are strong predictors of incident morbidity and mortality in the general population. However, despite the close links between hepatic pathology and impaired bone health, the association of liver enzymes with osteoporosis has hardly been investigated. The aim of the present study was to clarify whether serum liver enzyme levels in the general population are associated with bone mineral density. This was an observational, cross-sectional study. Participants and Main Outcome: Data on 13 849 adult participants of the Third National Health and Nutrition Examination Survey were used to quantify the independent associations of γ-glutamyltransferase, alanine transaminase, and aspartate transaminase with femoral neck bone mineral density assessed by dual-energy x-ray absorptiometry. In multiple regression models adjusting for numerous confounding variables, γ-glutamyltransferase showed a weak inverse association with bone mineral density (P = .0063). There also was limited evidence of a nonmonotonous relationship with alanine transaminase, with peak bone mineral density in the second quartile of enzyme activity (P = .0039). No association was found for aspartate transaminase. Although mechanistically plausible associations were found in the present study, the rather weak nature of these patterns renders it unlikely that liver enzyme levels could be of substantial use for osteoporosis risk stratification in the general population.

Scaling of Energy Absorption in Composites to Enhance Survivability

DTIC Science & Technology

2006-08-01

structures very weak in shear, such as the naval-type foam-laminate sandwich plates, has been solved. Various competing formulas have been subject to...for the case of general homogenized orthotropic structures very soft in shear, including layered structures that are loaded tranversely to the

Investigating the Abstractness of Children's Early Knowledge of Argument Structure

ERIC Educational Resources Information Center

McClure, Kathleen; Pine, Julian M.; Lieven, Elena V. M.

2006-01-01

In the current debate about the abstractness of children's early grammatical knowledge, Tomasello & Abbott-Smith (2002) have suggested that children might first develop "weak" or "partial" representations of abstract syntactic structures. This paper attempts to characterize these structures by comparing the development of constructions around…

CLASH: COMPLETE LENSING ANALYSIS OF THE LARGEST COSMIC LENS MACS J0717.5+3745 AND SURROUNDING STRUCTURES

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

Medezinski, Elinor; Lemze, Doron; Ford, Holland

2013-11-01

The galaxy cluster MACS J0717.5+3745 (z = 0.55) is the largest known cosmic lens, with complex internal structures seen in deep X-ray, Sunyaev-Zel'dovich effect, and dynamical observations. We perform a combined weak- and strong-lensing analysis with wide-field BVR{sub c} i'z' Subaru/Suprime-Cam observations and 16-band Hubble Space Telescope observations taken as part of the Cluster Lensing And Supernova survey with Hubble. We find consistent weak distortion and magnification measurements of background galaxies and combine these signals to construct an optimally estimated radial mass profile of the cluster and its surrounding large-scale structure out to 5 Mpc h {sup –1}. We findmore » consistency between strong-lensing and weak-lensing in the region where these independent data overlap, <500 kpc h {sup –1}. The two-dimensional weak-lensing map reveals a clear filamentary structure traced by distinct mass halos. We model the lensing shear field with nine halos, including the main cluster, corresponding to mass peaks detected above 2.5σ{sub κ}. The total mass of the cluster as determined by the different methods is M{sub vir} ≈ (2.8 ± 0.4) × 10{sup 15} M{sub ☉}. Although this is the most massive cluster known at z > 0.5, in terms of extreme value statistics, we conclude that the mass of MACS J0717.5+3745 by itself is not in serious tension with ΛCDM, representing only a ∼2σ departure above the maximum simulated halo mass at this redshift.« less

Activation of preexisting transverse structures in an evolving magmatic rift in East Africa

NASA Astrophysics Data System (ADS)

Muirhead, J. D.; Kattenhorn, S. A.

2018-01-01

Inherited crustal weaknesses have long been recognized as important factors in strain localization and basin development in the East African Rift System (EARS). However, the timing and kinematics (e.g., sense of slip) of transverse (rift-oblique) faults that exploit these weaknesses are debated, and thus the roles of inherited weaknesses at different stages of rift basin evolution are often overlooked. The mechanics of transverse faulting were addressed through an analysis of the Kordjya fault of the Magadi basin (Kenya Rift). Fault kinematics were investigated from field and remote-sensing data collected on fault and joint systems. Our analysis indicates that the Kordjya fault consists of a complex system of predominantly NNE-striking, rift-parallel fault segments that collectively form a NNW-trending array of en echelon faults. The transverse Kordjya fault therefore reactivated existing rift-parallel faults in ∼1 Ma lavas as oblique-normal faults with a component of sinistral shear. In all, these fault motions accommodate dip-slip on an underlying transverse structure that exploits the Aswa basement shear zone. This study shows that transverse faults may be activated through a complex interplay among magma-assisted strain localization, preexisting structures, and local stress rotations. Rather than forming during rift initiation, transverse structures can develop after the establishment of pervasive rift-parallel fault systems, and may exhibit dip-slip kinematics when activated from local stress rotations. The Kordjya fault is shown here to form a kinematic linkage that transfers strain to a newly developing center of concentrated magmatism and normal faulting. It is concluded that recently activated transverse faults not only reveal the effects of inherited basement weaknesses on fault development, but also provide important clues regarding developing magmatic and tectonic systems as young continental rift basins evolve.

Structure effects on reaction mechanisms in collisions induced by radioactive ion beams

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

Pietro, A. Di, E-mail: dipietro@lns.infn.it; Figuera, P.; Scuderi, V.

2006-08-15

The present paper concerns the study of reactions induced by radioactive beams of halo and weakly bound nuclei at energies around and above the Coulomb barrier. The results obtained for the reaction induced by the halo nucleus {sup 6}He on {sup 64}Zn have been compared with the results for the reaction induced by {sup 4}He on the same target. The results of the reaction induced by the weakly bound unstable {sup 13}N on the weakly bound {sup 9}Be have been compared with those for the reaction {sup 10}B + {sup 12}C.

New Turaev braided group categories and weak (co)quasi-Turaev group coalgebras

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

Zhang, Xiaohui, E-mail: zxhhhhh@gmail.com; Wang, Shuanhong, E-mail: shuanhwang2002@yahoo.com

In order to construct a class of new braided crossed G-categories with nontrivial associativity and unit constraints, we study the G-graded monoidal category over a family of algebras (H{sub α}){sub α∈G} and introduce the notion of a weak (co)quasi-Turaev G-(co)algebra. Then we prove that the category of (co)representations of (co)quasitriangular weak (co)quasi-Turaev π-(co)algebras is exactly a braided crossed G-category. In fact, this (co)quasitriangular structure provides a solution to a generalized quantum Yang-Baxter type equation.

What major faults look like, and why this matters for lithospheric dynamics

NASA Astrophysics Data System (ADS)

Fagereng, Ake

2016-04-01

Earthquakes involve seconds to minutes of frictional sliding on a discontinuity, likely of sub-cm thickness, within a damage zone. Earthquakes are separated by an interseismic period of hundreds to thousands of years, during which a number of healing and weakening processes occur within the fault zone. The next earthquake occurs as shear stress exceeds frictional resistance, on the same or a different discontinuity as the previous event, embedded within the fault damage zone. After incremental damage and healing in multiple earthquake cycles, the fault zone rock assemblage evolves to a structure and composition distinctly different from the host rock(s). This presentation presents field geology evidence from a range of settings, to discuss the interplay between the earthquake cycle, long-term deformation, and lithospheric rheology. Classic fault zone models are based on continental transforms, which generally form discrete faults in the upper crust, and wide, anastomosing shear zones in the lower crust. In oceanic crust, transforms are considered frictionally weak, and appear to exploit dyke margins and joint surfaces, but also locally cross-cut these structures in anastomosing networks. In the oceanic lower crust and upper mantle, serpentinisation significantly alters fault structure. In old continental crust, previous deformation events leave a heterogeneous geology affecting active faulting. For example, the amagmatic, southern East African Rift has long been thought to exploit weak Proterozoic 'mobile belts'. However, detailed look at the Bilila-Mtakataka border fault in Malawi indicates that this fault locally exploits weak foliation in existing deformed zones, but also locally forms a new set of anastomosing fault surfaces cross-cutting existing weak foliation. In exhumed lower crust, the Antarctic Maud Belt provides an example of multiple phases of plastic deformation, where the second event is only visible in localised shear zones, likely inherited from the first event. The subduction thrust interface provides an example of fault evolution in underthrust sediments as they deform and dewater. At shallow levels, distributed shear leads to development of scaly cleavage, which in places provides weak, clay surfaces on which earthquakes can propagate to the sea floor. With further deformation, a melange is progressively developed, with increasingly dismembered, sheared lenses of higher viscosity sedimentary rock and slivers of oceanic crust, in a low viscosity, cleaved matrix. The range of examples presented here illustrate how long-term deformation results in weak structures that likely control future deformation. Yet, the rheology of these structures is modulated by strength fluctuations during the earthquake cycle, illustrated by common evidence of episodic fault healing. The take home message from these field studies of fault zones is therefore the heterogeneity of the Earth's crust, the importance of long-term weak zones as a first order control on crustal deformation, and short-term strength fluctuations within these zones as a consequence of, and reason for, the earthquake cycle.