Online evolution reconstruction from a single measurement record with random time intervals for quantum communication

NASA Astrophysics Data System (ADS)

Zhou, Hua; Su, Yang; Wang, Rong; Zhu, Yong; Shen, Huiping; Pu, Tao; Wu, Chuanxin; Zhao, Jiyong; Zhang, Baofu; Xu, Zhiyong

2017-10-01

Online reconstruction of a time-variant quantum state from the encoding/decoding results of quantum communication is addressed by developing a method of evolution reconstruction from a single measurement record with random time intervals. A time-variant two-dimensional state is reconstructed on the basis of recovering its expectation value functions of three nonorthogonal projectors from a random single measurement record, which is composed from the discarded qubits of the six-state protocol. The simulated results prove that our method is robust to typical metro quantum channels. Our work extends the Fourier-based method of evolution reconstruction from the version for a regular single measurement record with equal time intervals to a unified one, which can be applied to arbitrary single measurement records. The proposed protocol of evolution reconstruction runs concurrently with the one of quantum communication, which can facilitate the online quantum tomography.

Hidden Markov models for evolution and comparative genomics analysis.

PubMed

Bykova, Nadezda A; Favorov, Alexander V; Mironov, Andrey A

2013-01-01

The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb.

Amino acid stable isotope applications to deep-sea corals: A molecular geochemistry approach to reconstructing past ocean conditions

NASA Astrophysics Data System (ADS)

McMahon, K.; McCarthy, M. D.; Guilderson, T. P.; Sherwood, O.; Williams, B.; Larsen, T.; Glynn, D. S.

2017-12-01

Future climate change is predicted to alter ocean productivity, food web dynamics, biogeochemical cycling, and the efficacy of the biological pump. Proteinaceous deep-sea corals act as "living sediment traps," providing long-term, high-resolution records of exported surface ocean production and a window into past changes in ocean condition as a historical context for potential future changes. Here, we present recent work developing the application of compound-specific stable isotope analysis of individual amino acids to proteinaceous deep-sea corals to reconstruct past changes in phytoplankton community composition and biogeochemical cycling. We present new calibrations for molecular isotope comparisons between metabolically active coral polyp tissue and bioarchival proteinaceous skeleton. We then applied these techniques to deep-sea corals from the North Pacific Subtropical Gyre (NPSG) to reconstruct centennial to millennial time scale changes in phytoplankton community composition and biogeochemical cycling as a function of regional climate change. This work suggests that the NPSG has undergone multiple major phytoplankton regime shifts over the last millennium between prokaryotic and eukaryotic phytoplankton communities and associated sources of nitrogen fueling production. The most recent regime, which started around the end of the Little Ice Age and the onset of the Industrial era, is unprecedented in the last 1000 years and resulted in a 30-50% increase in diazotrophic cyanobacteria contribution to export production and an associated 17-27% increase in N2-fixation in the NPSG over last century. By offering the first direct phylogenetic context for long-term shifts in isotopic records of exported particulate organic matter, our data represent a major step forward in understanding the evolution of marine plankton community dynamics, food web architecture, biogeochemical cycling, and the climate feedback loops through the biological pump.

Readability of online patient education materials on adult reconstruction Web sites.

PubMed

Polishchuk, Daniil L; Hashem, Jenifer; Sabharwal, Sanjeev

2012-05-01

Recommended readability of patient education materials is sixth-grade level or lower. Readability of 212 patient education materials pertaining to adult reconstruction topics available from the American Academy of Orthopaedic Surgeons, American Association of Hip and Knee Surgeons, and 3 other specialty and private practitioner Web sites was assessed using the Flesch-Kincaid grade formula. The mean Flesch-Kincaid score was 11.1 (range, 3-26.5). Only 5 (2%) articles had a readability level of sixth grade or lower. Readability of most of the articles for patient education on adult reconstruction Web sites evaluated may be too advanced for a substantial portion of patients. Further studies are needed to assess the optimal readability level of health information on the Internet. Copyright © 2012 Elsevier Inc. All rights reserved.

Reconstruction of the first web space in symbrachydactyly using the reverse radial forearm flap.

PubMed

Gülgönen, Ayan; Güdemez, Eftal

2007-02-01

To present a new approach for the reconstruction of severe first web contractures using a distally based reverse radial forearm flap in symbrachydactyly patients. This study included 6 hands in 5 patients. Subjective evaluation included appearance, parent satisfaction (and patient satisfaction when appropriate), and ability to perform daily activities such as thumb-index grasp and pinch at follow-up evaluations. We measured the angle between the first and second rays using a goniometer at maximum radial abduction, and pinch and grasp strengths were evaluated as an objective assessment. The average follow-up period was 2 years. All parents and patients were happy with the aesthetic appearance. They were completely satisfied in their daily living activities. The average first web angle measurement was 56 degrees . An average of 39 degrees of improvement of web measurement was achieved. For the unilateral 4 patients, the average pinch strength measurement was 80% of the normal contralateral hand and the grip strength was 75% of the normal contralateral hand. The reverse radial forearm flap was found to be a safe and simple method in the reconstruction of severe first web contractures in symbrachydactyly patients. This method provided good coverage of appropriate thickness and skin quality, and supple soft tissue that filled the first web space. Therapeutic IV.

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

PubMed

Beauregard-Racine, Julie; Bicep, Cédric; Schliep, Klaus; Lopez, Philippe; Lapointe, François-Joseph; Bapteste, Eric

2011-07-20

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches. We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.

Web 1.0 to Web 3.0 Evolution: Reviewing the Impacts on Tourism Development and Opportunities

NASA Astrophysics Data System (ADS)

Eftekhari, M. Hossein; Barzegar, Zeynab; Isaai, M. T.

The most important event following the establishmenet of the Internet network was the Web introduced by Tim Berners-Lee. Websites give their owners features that allow sharing with which they can publish their content with users and visitors. In the last 5 years, we have seen some changes in the use of web. Users want to participate in content sharing and they like to interact with each other. This is known as Web 2.0. In the last year, Web 2.0 has reached maturity and now we need a smart web which will be accordingly be called Web 3.0. Web 3.0 is based on semantic web definition. Changing the way of using the web has had a clear impact on E-Tourism and its development and also on business models. In this paper, we review the definitions and describe the impacts of web evolution on E-Tourism.

Patient information on breast reconstruction in the era of the world wide web. A snapshot analysis of information available on youtube.com.

PubMed

Tan, M L H; Kok, K; Ganesh, V; Thomas, S S

2014-02-01

Breast cancer patient's expectation and choice of reconstruction is increasing and patients often satisfy their information needs outside clinic time by searching the world wide web. The aim of our study was to analyse the quality of content and extent of information regarding breast reconstruction available on YouTube videos and whether this is an appropriate additional source of information for patients. A snapshot qualitative and quantitative analysis of the first 100 videos was performed after the term 'breast reconstruction' was input into the search window of the video sharing website www.youtube.com on the 1st of September 2011. Qualitative categorical analysis included patient, oncological and reconstruction factors. It was concluded that although videos uploaded onto YouTube do not provide comprehensive information, it is a useful resource that can be utilised in patient education provided comprehensive and validated videos are made available. Copyright © 2013 Elsevier Ltd. All rights reserved.

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

A Web simulation of medical image reconstruction and processing as an educational tool.

PubMed

Papamichail, Dimitrios; Pantelis, Evaggelos; Papagiannis, Panagiotis; Karaiskos, Pantelis; Georgiou, Evangelos

2015-02-01

Web educational resources integrating interactive simulation tools provide students with an in-depth understanding of the medical imaging process. The aim of this work was the development of a purely Web-based, open access, interactive application, as an ancillary learning tool in graduate and postgraduate medical imaging education, including a systematic evaluation of learning effectiveness. The pedagogic content of the educational Web portal was designed to cover the basic concepts of medical imaging reconstruction and processing, through the use of active learning and motivation, including learning simulations that closely resemble actual tomographic imaging systems. The user can implement image reconstruction and processing algorithms under a single user interface and manipulate various factors to understand the impact on image appearance. A questionnaire for pre- and post-training self-assessment was developed and integrated in the online application. The developed Web-based educational application introduces the trainee in the basic concepts of imaging through textual and graphical information and proceeds with a learning-by-doing approach. Trainees are encouraged to participate in a pre- and post-training questionnaire to assess their knowledge gain. An initial feedback from a group of graduate medical students showed that the developed course was considered as effective and well structured. An e-learning application on medical imaging integrating interactive simulation tools was developed and assessed in our institution.

The angular momentum of cosmological coronae and the inside-out growth of spiral galaxies

NASA Astrophysics Data System (ADS)

Pezzulli, Gabriele; Fraternali, Filippo; Binney, James

2017-05-01

Massive and diffuse haloes of hot gas (coronae) are important intermediaries between cosmology and galaxy evolution, storing mass and angular momentum acquired from the cosmic web until eventual accretion on to star-forming discs. We introduce a method to reconstruct the rotation of a galactic corona, based on its angular momentum distribution (AMD). This allows us to investigate in what conditions the angular momentum acquired from tidal torques can be transferred to star-forming discs and explain observed galaxy-scale processes, such as inside-out growth and the build-up of abundance gradients. We find that a simple model of an isothermal corona with a temperature slightly smaller than virial and a cosmologically motivated AMD is in good agreement with galaxy evolution requirements, supporting hot-mode accretion as a viable driver for the evolution of spiral galaxies in a cosmological context. We predict moderately sub-centrifugal rotation close to the disc and slow rotation close to the virial radius. Motivated by the observation that the Milky Way has a relatively hot corona (T ≃ 2 × 106 K), we also explore models with a temperature larger than virial. To be able to drive inside-out growth, these models must be significantly affected by feedback, either mechanical (ejection of low angular momentum material) or thermal (heating of the central regions). However, the agreement with galaxy evolution constraints becomes, in these cases, only marginal, suggesting that our first and simpler model may apply to a larger fraction of galaxy evolution history.

Three-dimensional Reconstruction of Scar Contracture-bearing Axilla and Digital Webs Using the Square Flap Method.

PubMed

Huang, Chenyu; Ogawa, Rei

2014-05-01

Joint scar contractures are characterized by tight bands of soft tissue that bridge the 2 ends of the joint like a web. Classical treatment methods such as Z-plasties are mainly based on 2-dimensional designs. Our square flap method is an alternative surgical method that restores the span of the web in a stereometric fashion, thereby reconstructing joint function. In total, 20 Japanese patients with joint scar contractures on the axillary (n = 10) or first digital web (n = 10) underwent square flap surgery. The maximum range of motion and commissure length were measured before and after surgery. A theoretical stereometric geometrical model of the square flap was established to compare it to the classical single (60 degree), 4-flap (45 degree), and 5-flap (60 degree) Z-plasties in terms of theoretical web reconstruction efficacy. All cases achieved 100% contracture release. The maximum range of motion and web space improved after square flap surgery (P = 0.001). Stereometric geometrical modeling revealed that the standard square flap (α = 45 degree; β = 90 degree) yields a larger flap area, length/width ratio, and postsurgical commissure length than the Z-plasties. It can also be adapted by varying angles α and β, although certain angle thresholds must be met to obtain the stereometric advantages of this method. When used to treat joint scar contractures, the square flap method can fully span the web space in a stereometric manner, thus yielding a close-to-original shape and function. Compared with the classical Z-plasties, it also provides sufficient anatomical blood supply while imposing the least physiological tension on the adjacent skin.

Three-dimensional Reconstruction of Scar Contracture-bearing Axilla and Digital Webs Using the Square Flap Method

PubMed Central

Huang, Chenyu

2014-01-01

Background: Joint scar contractures are characterized by tight bands of soft tissue that bridge the 2 ends of the joint like a web. Classical treatment methods such as Z-plasties are mainly based on 2-dimensional designs. Our square flap method is an alternative surgical method that restores the span of the web in a stereometric fashion, thereby reconstructing joint function. Methods: In total, 20 Japanese patients with joint scar contractures on the axillary (n = 10) or first digital web (n = 10) underwent square flap surgery. The maximum range of motion and commissure length were measured before and after surgery. A theoretical stereometric geometrical model of the square flap was established to compare it to the classical single (60 degree), 4-flap (45 degree), and 5-flap (60 degree) Z-plasties in terms of theoretical web reconstruction efficacy. Results: All cases achieved 100% contracture release. The maximum range of motion and web space improved after square flap surgery (P = 0.001). Stereometric geometrical modeling revealed that the standard square flap (α = 45 degree; β = 90 degree) yields a larger flap area, length/width ratio, and postsurgical commissure length than the Z-plasties. It can also be adapted by varying angles α and β, although certain angle thresholds must be met to obtain the stereometric advantages of this method. Conclusions: When used to treat joint scar contractures, the square flap method can fully span the web space in a stereometric manner, thus yielding a close-to-original shape and function. Compared with the classical Z-plasties, it also provides sufficient anatomical blood supply while imposing the least physiological tension on the adjacent skin. PMID:25289342

Technology Review of Multi-Agent Systems and Tools

DTIC Science & Technology

2005-06-01

over a network, including the Internet. A web services architecture is the logical evolution of object-oriented analysis and design coupled with...the logical evolution of components geared towards the architecture, design, implementation, and deployment of e-business solutions. As in object...querying. The Web Services architecture describes the principles behind the next generation of e- business architectures, presenting a logical evolution

Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

Evolution of the Cosmic Web

NASA Astrophysics Data System (ADS)

Einasto, J.

2017-07-01

In the evolution of the cosmic web dark energy plays an important role. To understand the role of dark energy we investigate the evolution of superclusters in four cosmological models: standard model SCDM, conventional model LCDM, open model OCDM, and a hyper-dark-energy model HCDM. Numerical simulations of the evolution are performed in a box of size 1024 Mpc/h. Model superclusters are compared with superclusters found for Sloan Digital Sky Survey (SDSS). Superclusters are searched using density fields. LCDM superclusters have properties, very close to properties of observed SDSS superclusters. Standard model SCDM has about 2 times more superclusters than other models, but SCDM superclusters are smaller and have lower luminosities. Superclusters as principal structural elements of the cosmic web are present at all cosmological epochs.

Soil life in reconstructed ecosystems: initial soil food web responses after rebuilding a forest soil profile for a climate change experiment

Treesearch

Paul T. Rygiewicz; Vicente J. Monleon; Elaine R. Ingham; Kendall J. Martin; Mark G. Johnson

2010-01-01

Disrupting ecosystem components, while transferring and reconstructing them for experiments can produce myriad responses. Establishing the extent of these biological responses as the system approaches a new equilibrium allows us more reliably to emulate comparable native systems. That is, the sensitivity of analyzing ecosystem processes in a reconstructed system is...

A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.

PubMed

Gerth, Victor E; Vize, Peter D

2005-04-01

The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.

Evolution of the solar irradiance during the Holocene

NASA Astrophysics Data System (ADS)

Vieira, L. E. A.; Solanki, S. K.; Krivova, N. A.; Usoskin, I.

2011-07-01

Context. Long-term records of solar radiative output are vital for understanding solar variability and past climate change. Measurements of solar irradiance are available for only the last three decades, which calls for reconstructions of this quantity over longer time scales using suitable models. Aims: We present a physically consistent reconstruction of the total solar irradiance for the Holocene. Methods: We extend the SATIRE (Spectral And Total Irradiance REconstruction) models to estimate the evolution of the total (and partly spectral) solar irradiance over the Holocene. The basic assumption is that the variations of the solar irradiance are due to the evolution of the dark and bright magnetic features on the solar surface. The evolution of the decadally averaged magnetic flux is computed from decadal values of cosmogenic isotope concentrations recorded in natural archives employing a series of physics-based models connecting the processes from the modulation of the cosmic ray flux in the heliosphere to their record in natural archives. We then compute the total solar irradiance (TSI) as a linear combination of the jth and jth + 1 decadal values of the open magnetic flux. In order to evaluate the uncertainties due to the evolution of the Earth's magnetic dipole moment, we employ four reconstructions of the open flux which are based on conceptually different paleomagnetic models. Results: Reconstructions of the TSI over the Holocene, each valid for a different paleomagnetic time series, are presented. Our analysis suggests that major sources of uncertainty in the TSI in this model are the heritage of the uncertainty of the TSI since 1610 reconstructed from sunspot data and the uncertainty of the evolution of the Earth's magnetic dipole moment. The analysis of the distribution functions of the reconstructed irradiance for the last 3000 years, which is the period that the reconstructions overlap, indicates that the estimates based on the virtual axial dipole moment are significantly lower at earlier times than the reconstructions based on the virtual dipole moment. We also present a combined reconstruction, which represents our best estimate of total solar irradiance for any given time during the Holocene. Conclusions: We present the first physics-based reconstruction of the total solar irradiance over the Holocene, which will be of interest for studies of climate change over the last 11 500 years. The reconstruction indicates that the decadally averaged total solar irradiance ranges over approximately 1.5 W/m2 from grand maxima to grand minima. Appendix A is available in electronic form at http://www.aanda.orgThe TSI data is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/531/A6

Breast reconstruction post mastectomy- Let's Google it. Accessibility, readability and quality of online information.

PubMed

Lynch, Noel P; Lang, Bronagh; Angelov, Sophia; McGarrigle, Sarah A; Boyle, Terence J; Al-Azawi, Dhafir; Connolly, Elizabeth M

2017-04-01

This study evaluated the readability, accessibility and quality of information pertaining to breast reconstruction post mastectomy on the Internet in the English language. Using the Google © search engine the keywords "Breast reconstruction post mastectomy" were searched for. We analyzed the top 75 sites. The Flesch Reading Ease Score and Gunning Fog Index were calculated to assess readability. Web site quality was assessed objectively using the University of Michigan Consumer Health Web site Evaluation Checklist. Accessibility was determined using an automated accessibility tool. In addition, the country of origin, type of organisation producing the site and presence of Health on the Net (HoN) Certification status was recorded. The Web sites were difficult to read and comprehend. The mean Flesch Reading Ease scores were 55.5. The mean Gunning Fog Index scores was 8.6. The mean Michigan score was 34.8 indicating weak quality of websites. Websites with HoN certification ranked higher in the search results (p = 0.007). Website quality was influenced by organisation type (p < 0.0001) with academic/healthcare, not for profit and government sites having higher Michigan scores. 20% of sites met the minimum accessibility criteria. Internet information on breast reconstruction post mastectomy and procedures is poorly written and we suggest that Webpages providing information must be made more readable and accessible. We suggest that health professionals should recommend Web sites that are easy to read and contain high-quality surgical information. Medical information on the Internet should be readable, accessible, reliable and of a consistent quality. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reconstruction of an aquatic food web: Viking Haithabu vs. Medieval Schleswig.

PubMed

von Steinsdorff, Katja; Grupe, Gisela

2006-09-01

In the last two decades, the analysis of stable isotopes of carbonate and collagen from archaeological bone finds became a useful tool in the reconstruction of ancient food webs. Nevertheless there is still only little information available about aquatic food webs, in particular concerning brackish water ecosystems. The Schlei Fjord in Schleswig-Holstein, Germany, is such an ecosystem and was investigated to determine stable isotopic values for nitrogen, carbon and oxygen from bone collagen and carbonate in archaeological bone finds. Wild birds, mammals and fish bones from the Viking settlement Haithabu and the medieval town of Schleswig have been analyzed in this study to determine stable isotope values for marine and limnic species and to investigate possible isotopic gradients for mixing fresh water and salt water ecosystems.

Voids and the Cosmic Web: cosmic depression & spatial complexity

NASA Astrophysics Data System (ADS)

van de Weygaert, Rien

2016-10-01

Voids form a prominent aspect of the Megaparsec distribution of galaxies and matter. Not only do theyrepresent a key constituent of the Cosmic Web, they also are one of the cleanest probesand measures of global cosmological parameters. The shape and evolution of voids are highly sensitive tothe nature of dark energy, while their substructure and galaxy population provides a direct key to thenature of dark matter. Also, the pristine environment of void interiors is an important testing groundfor our understanding of environmental influences on galaxy formation and evolution. In this paper, we reviewthe key aspects of the structure and dynamics ofvoids, with a particular focus on the hierarchical evolution of the void population. We demonstratehow the rich structural pattern of the Cosmic Web is related to the complex evolution and buildupof voids.

The Evolution of Web Searching.

ERIC Educational Resources Information Center

Green, David

2000-01-01

Explores the interrelation between Web publishing and information retrieval technologies and lists new approaches to Web indexing and searching. Highlights include Web directories; search engines; portalisation; Internet service providers; browser providers; meta search engines; popularity based analysis; natural language searching; links-based…

Bioprosthetic Mesh in Abdominal Wall Reconstruction

PubMed Central

Baumann, Donald P.; Butler, Charles E.

2012-01-01

Mesh materials have undergone a considerable evolution over the last several decades. There has been enhancement of biomechanical properties, improvement in manufacturing processes, and development of antiadhesive laminate synthetic meshes. The evolution of bioprosthetic mesh materials has markedly changed our indications and methods for complex abdominal wall reconstruction. The authors review the optimal properties of bioprosthetic mesh materials, their evolution over time, and their indications for use. The techniques to optimize outcomes are described using bioprosthetic mesh for complex abdominal wall reconstruction. Bioprosthetic mesh materials clearly have certain advantages over other implantable mesh materials in select indications. Appropriate patient selection and surgical technique are critical to the successful use of bioprosthetic materials for abdominal wall repair. PMID:23372454

The Czech Provincial Reconstruction Team: Civil-Military Teaming in Logar Province

DTIC Science & Technology

2013-03-01

which authorized ISAF forces to assist Afghan authorities in providing security through ISAF operations across Afghanistan. Alexandr Vondra, the...Ministry of Defense Alexandr Vondra, web site Provincional Reconstruction Team Logar news, the Czech Republic, http://www.mzv.cz/prtlogar/cz...Meade Avenue, Building 50 Fort Leavenworth, 1-3. 4 Handbook Afghanistan Provincial Reconstruction Team No.11-16, Feb.11 published by Center for

WWW.cell Biology Education: Evolution Web Sites

ERIC Educational Resources Information Center

Liu, Dennis

2005-01-01

The debate over teaching evolution has once again reached a fever pitch in the United States. Earnest nineteenth-century clashes between scientific and religious worldviews have given way to the politically charged arguments of creation science and now intelligent design. The Web site of the National Center for Science Education (NCSE;…

The Convergent Evolution of a Chemistry Project: Using Laboratory Posters as a Platform for Web Page Construction.

ERIC Educational Resources Information Center

Rigeman, Sally

1998-01-01

Argues that evolution is a process that occurs within the curriculum as well as within the physical universe. Provides an example that involves student presentations. Discusses the transition from poster presentations to electronic presentations via the World Wide Web. (DDR)

The first metatarsal web space: its applied anatomy and usage in tracing the first dorsal metatarsal artery in thumb reconstruction.

PubMed

Xu, Yong-Qing; Li, Jun; Zhong, Shi-Zhen; Xu, Da-Chuan; Xu, Xiao-Shan; Guo, Yuan-Fa; Wang, Xin-Min; Li, Zhu-Yi; Zhu, Yue-Liang

2004-12-01

To clarify the anatomical relationship of the structures in the first toe webbing space for better dissection of toes in thumb reconstruction. The first dorsal metatarsal artery, the first deep transverse metatarsal ligament and the extensor expansion were observed on 42 adult cadaveric lower extremities. Clinically the method of tracing the first dorsal metatarsal artery around the space of the extensor expansion was used in 36 cases of thumb reconstruction. The distal segments of the first dorsal metatarsal artery of Gilbert types I and II were located superficially to the extensor expansion. The harvesting time of a toe was shortened from 90 minutes to 50 minutes with 100% survival of reconstructed fingers. The distal segment of the first dorsal metatarsal artery lies constantly at the superficial layer of the extensor expansion. Most of the first metatarsal arteries of Gilbert types I and II can be easily located via the combined sequential and reverse dissection around the space of the extensor expansion.

Development of a Web-Based Periscope Simulator for Submarine Officer Training

DTIC Science & Technology

2014-09-01

31 2. The Evolution of Web-Based technology .........................................32...DEVELOPMENT ............................................................................65 A. TECHNOLOGY ...the possibility to deliver 3D simulations using the web browsers and web technology . The objective is to create an effective and efficient WBLE that

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

PubMed Central

McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

PubMed

McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.

Reconstruction and evolutionary history of eutherian chromosomes

PubMed Central

Kim, Jaebum; Auvil, Loretta; Capitanu, Boris; Larkin, Denis M.; Ma, Jian; Lewin, Harris A.

2017-01-01

Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases. PMID:28630326

Readability analysis of healthcare-oriented education resources from the American Academy of Facial Plastic and Reconstructive Surgery.

PubMed

Misra, Poonam; Agarwal, Nitin; Kasabwala, Khushabu; Hansberry, David R; Setzen, Michael; Eloy, Jean Anderson

2013-01-01

Deficient health literacy remains a widespread public issue. As such, the National Institutes of Health (NIH) recommends that all patient resources should be written around a sixth-grade level. The authors evaluate healthcare-oriented resources specified for patient use on the American Academy of Facial Plastic and Reconstructive Surgery (AAFPRS) Web site in order to identify potential areas of improvement and highlight those sections that may serve as paradigms for future revisions. Descriptive and correlational design. Seventeen healthcare-oriented resources specifically for patients were downloaded in February 2012 from the American Academy of Facial Plastic and Reconstructive Surgery Web site. Readability assessments of each article were performed using Readability Studio Professional Edition Version 2012.1. These tests included the Flesch Reading Ease, Flesch-Kincaid Grade Level, SMOG Grading, Coleman-Liau Index, Gunning-Fog Index, the New Fog Count, the New Dale-Chall Readability Formula, FORCAST formula, Raygor Readability Estimate, and the Fry Graph. Patient health education material found on the AAFPRS Web site has been found to be written at an average grade level of 12th grade using 10 different readability scales. Modifications of the patient education section of the AAFPRS Web site can increase the readability of the literature, and allow greater comprehension among a wider audience. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

Soil life in reconstructed ecosystems: Initial soil food web responses after rebuilding a forest soil profile for a climate change experiment

EPA Science Inventory

Disrupting ecosystem components, while transferring and reconstructing them for experiments can produce myriad responses. Establishing the extent of these biological responses as the system approaches a new equilibrium allows us more reliably to emulate comparable native systems....

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants1[W][OA

PubMed Central

Zhang, Peifen; Dreher, Kate; Karthikeyan, A.; Chi, Anjo; Pujar, Anuradha; Caspi, Ron; Karp, Peter; Kirkup, Vanessa; Latendresse, Mario; Lee, Cynthia; Mueller, Lukas A.; Muller, Robert; Rhee, Seung Yon

2010-01-01

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org). PMID:20522724

The Effectiveness of an Online Curriculum on High School Students' Understanding of Biological Evolution

NASA Astrophysics Data System (ADS)

Marsteller, Robert B.; Bodzin, Alec M.

2015-12-01

An online curriculum about biological evolution was designed to promote increased student content knowledge and evidentiary reasoning. A feasibility study was conducted with 77 rural high school biology students who learned with the online biological evolution unit. Data sources included the Biological Evolution Assessment Measure (BEAM), an analysis of discussion forum posts, and a post-implementation perceptions and attitudes questionnaire. BEAM posttest scores were significantly higher than the pretest scores. However, the findings revealed that the students required additional support to develop evidentiary reasoning. Many students perceived that the Web-based curriculum would have been enhanced by increased immediate interaction and feedback. Students required greater scaffolding to support complex, process-oriented tasks. Implications for designing Web-based science instruction with curriculum materials to support students' acquisition of content knowledge and science process skills in a Web-based setting are discussed.

Autonomy and Sensor Webs: The Evolution of Mission Operations

NASA Technical Reports Server (NTRS)

Sherwood, Rob

2008-01-01

Demonstration of these sensor web capabilities will enable fast responding science campaigns that combine spaceborne, airborne, and ground assets. Sensor webs will also require new operations paradigms. These sensor webs will be operated directly by scientists using science goals to control their instruments. We will explore these new operations architectures through a study of existing sensor web prototypes.

Augmenting Research, Education, and Outreach with Client-Side Web Programming.

PubMed

Abriata, Luciano A; Rodrigues, João P G L M; Salathé, Marcel; Patiny, Luc

2018-05-01

The evolution of computing and web technologies over the past decade has enabled the development of fully fledged scientific applications that run directly on web browsers. Powered by JavaScript, the lingua franca of web programming, these 'web apps' are starting to revolutionize and democratize scientific research, education, and outreach. Copyright © 2017 Elsevier Ltd. All rights reserved.

Weaving Silos--A Leadership Challenge: A Cross-Functional Team Approach to Supporting Web-Based Student Services

ERIC Educational Resources Information Center

Kleemann, Gary L.

2005-01-01

The author reviews the evolution of Web services--from information sharing to transactional to relationship building--and the progression from first-generation to fourth-generation Web sites. (Contains 3 figures.)

Infusing Classrooms with Web 2.0 Technologies

ERIC Educational Resources Information Center

Velasco, Richard Carlos L.

2018-01-01

The evolution of digital technologies over the past couple of decades has contributed to a paradigm shift in education where the internet and web-based applications have become ubiquitous in primary and secondary classrooms (Glassman & Kang, 2011). With this shift came the digital phenomena known today as Web 2.0 technologies. Web 2.0…

DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

[Effectiveness of dorsal metacarpal island flap for treating scar contracture of finger web].

PubMed

Qian, Jun; Rui, Yongjun; Zhang, Quanrong; Xue, Mingyu; Zhang, Zhihai

2011-11-01

To investigate the effectiveness of dorsal metacarpal island flap for treating scar contracture of the finger web. Between June 2009 and December 2010, 10 patients with scar contracture of the finger web were treated. There were 6 males and 4 females with an average age of 30 years (range, 14-57 years). Scar contracture was caused by injury in 8 cases, by burn in 1 case, and by operation in 1 case. The locations were the 1st web space in 1 case, the 2nd web space in 3 cases, the 3rd web space in 5 cases, and the 4th web space in 1 case. The disease duration was 3 to 9 months with an average of 5 months. The maximum abduction was 10-20 degrees. After web space scar release, the dorsal metacarpal island flap (3.5 cm x 1.2 cm-4.0 cm x 2.0 cm in size) was used to reconstruct web space (2.0 cm x 1.0 cm-3.0 cm x 1.8 cm in size). The donor site was directly sutured or repaired with local flaps. At 2 days after operation, necrosis occurred in 1 flap, which healed by extractive treatment. The other flaps survived and wound healed by first intention; all the flaps at donor sites survived and incision healed by first intention. Ten patients were followed up 6 to 15 months (mean, 9 months). The reconstructed web space had good appearance, the maximum abduction was 80 degrees in 1 case of the 1st web space scars contracture, and the maximum abduction was 35-45 degrees (mean, 40 degrees) in the other 9 cases. In 8 scar patients causing by injury, no scar contracture recurred during follow-up. It can achieve good results in appearance and function to use dorsal metacarpal island flap for treating scar contracture of the finger web.

Early Cretaceous terrestrial ecosystems in East Asia based on food-web and energy-flow models

USGS Publications Warehouse

Matsukawa, M.; Saiki, K.; Ito, M.; Obata, I.; Nichols, D.J.; Lockley, M.G.; Kukihara, R.; Shibata, K.

2006-01-01

In recent years, there has been global interest in the environments and ecosystems around the world. It is helpful to reconstruct past environments and ecosystems to help understand them in the present and the future. The present environments and ecosystems are an evolving continuum with those of the past and the future. This paper demonstrates the contribution of geology and paleontology to such continua. Using fossils, we can make an estimation of past population density as an ecosystem index based on food-web and energy-flow models. Late Mesozoic nonmarine deposits are distributed widely on the eastern Asian continent and contain various kinds of fossils such as fishes, amphibians, reptiles, dinosaurs, mammals, bivalves, gastropods, insects, ostracodes, conchostracans, terrestrial plants, and others. These fossil organisms are useful for late Mesozoic terrestrial ecosystem reconstruction using food-web and energy-flow models. We chose Early Cretaceous fluvio-lacustrine basins in the Choyr area, southeastern Mongolia, and the Tetori area, Japan, for these analyses and as a potential model for reconstruction of other similar basins in East Asia. The food-web models are restored based on taxa that occurred in these basins. They form four or five trophic levels in an energy pyramid consisting of rich primary producers at its base and smaller biotas higher in the food web. This is the general energy pyramid of a typical ecosystem. Concerning the population densities of vertebrate taxa in 1 km2 in these basins, some differences are recognized between Early Cretaceous and the present. For example, Cretaceous estimates suggest 2.3 to 4.8 times as many herbivores and 26.0 to 105.5 times the carnivore population. These differences are useful for the evaluation of past population densities of vertebrate taxa. Such differences may also be caused by the different metabolism of different taxa. Preservation may also be a factor, and we recognize that various problems occur in past ecosystem reconstructions. Counts of small numbers of confirmed species and estimates of maximum numbers of species present in the basin are used for the analysis and estimation of energy flow. This approach applies the methods of modern ecosystem analysis. ?? 2005 Elsevier Ltd. All rights reserved.

Dynamic Reconstruction Algorithm of Three-Dimensional Temperature Field Measurement by Acoustic Tomography

PubMed Central

Li, Yanqiu; Liu, Shi; Inaki, Schlaberg H.

2017-01-01

Accuracy and speed of algorithms play an important role in the reconstruction of temperature field measurements by acoustic tomography. Existing algorithms are based on static models which only consider the measurement information. A dynamic model of three-dimensional temperature reconstruction by acoustic tomography is established in this paper. A dynamic algorithm is proposed considering both acoustic measurement information and the dynamic evolution information of the temperature field. An objective function is built which fuses measurement information and the space constraint of the temperature field with its dynamic evolution information. Robust estimation is used to extend the objective function. The method combines a tunneling algorithm and a local minimization technique to solve the objective function. Numerical simulations show that the image quality and noise immunity of the dynamic reconstruction algorithm are better when compared with static algorithms such as least square method, algebraic reconstruction technique and standard Tikhonov regularization algorithms. An effective method is provided for temperature field reconstruction by acoustic tomography. PMID:28895930

Phylogeny of lion tamarins (Leontopithecus spp) based on interphotoreceptor retinol binding protein intron sequences.

PubMed

Mundy, N I; Kelly, J

2001-05-01

The evolutionary relationships of the lion tamarins (Leontopithecus) were investigated using nuclear interphotoreceptor retinol binding protein (IRBP) intron sequences. Phylogenetic reconstructions strongly support the monophyly of the genus, and a sister relationship between the golden lion tamarin, Leontopithecus rosalia, and the black lion tamarin, L. chrysopygus, to the exclusion of the golden-headed lion tamarin, L. chrysomelas. The most parsimonious evolutionary reconstruction suggests that the ancestral lion tamarin and the common ancestor of L. rosalia and L. chrysopygus had predominantly black coats. This reconstruction is not consistent with a theory of orthogenetic evolution of coat color that was based on coat color evolution in marmosets and tamarins. An alternative reconstruction that is consistent with metachromism requires that ancestral lion tamarins had agouti hairs. Copyright 2001 Wiley-Liss, Inc.

Monitoring of computing resource use of active software releases at ATLAS

NASA Astrophysics Data System (ADS)

Limosani, Antonio; ATLAS Collaboration

2017-10-01

The LHC is the world’s most powerful particle accelerator, colliding protons at centre of mass energy of 13 TeV. As the energy and frequency of collisions has grown in the search for new physics, so too has demand for computing resources needed for event reconstruction. We will report on the evolution of resource usage in terms of CPU and RAM in key ATLAS offline reconstruction workflows at the TierO at CERN and on the WLCG. Monitoring of workflows is achieved using the ATLAS PerfMon package, which is the standard ATLAS performance monitoring system running inside Athena jobs. Systematic daily monitoring has recently been expanded to include all workflows beginning at Monte Carlo generation through to end-user physics analysis, beyond that of event reconstruction. Moreover, the move to a multiprocessor mode in production jobs has facilitated the use of tools, such as “MemoryMonitor”, to measure the memory shared across processors in jobs. Resource consumption is broken down into software domains and displayed in plots generated using Python visualization libraries and collected into pre-formatted auto-generated Web pages, which allow the ATLAS developer community to track the performance of their algorithms. This information is however preferentially filtered to domain leaders and developers through the use of JIRA and via reports given at ATLAS software meetings. Finally, we take a glimpse of the future by reporting on the expected CPU and RAM usage in benchmark workflows associated with the High Luminosity LHC and anticipate the ways performance monitoring will evolve to understand and benchmark future workflows.

Galaxy evolution in the metric of the cosmic web

NASA Astrophysics Data System (ADS)

Kraljic, K.; Arnouts, S.; Pichon, C.; Laigle, C.; de la Torre, S.; Vibert, D.; Cadiou, C.; Dubois, Y.; Treyer, M.; Schimd, C.; Codis, S.; de Lapparent, V.; Devriendt, J.; Hwang, H. S.; Le Borgne, D.; Malavasi, N.; Milliard, B.; Musso, M.; Pogosyan, D.; Alpaslan, M.; Bland-Hawthorn, J.; Wright, A. H.

2018-02-01

The role of the cosmic web in shaping galaxy properties is investigated in the Galaxy And Mass Assembly (GAMA) spectroscopic survey in the redshift range 0.03 ≤ z ≤ 0.25. The stellar mass, u - r dust corrected colour and specific star formation rate (sSFR) of galaxies are analysed as a function of their distances to the 3D cosmic web features, such as nodes, filaments and walls, as reconstructed by DisPerSE. Significant mass and type/colour gradients are found for the whole population, with more massive and/or passive galaxies being located closer to the filament and wall than their less massive and/or star-forming counterparts. Mass segregation persists among the star-forming population alone. The red fraction of galaxies increases when closing in on nodes, and on filaments regardless of the distance to nodes. Similarly, the star-forming population reddens (or lowers its sSFR) at fixed mass when closing in on filament, implying that some quenching takes place. These trends are also found in the state-of-the-art hydrodynamical simulation HORIZON-AGN. These results suggest that on top of stellar mass and large-scale density, the traceless component of the tides from the anisotropic large-scale environment also shapes galactic properties. An extension of excursion theory accounting for filamentary tides provides a qualitative explanation in terms of anisotropic assembly bias: at a given mass, the accretion rate varies with the orientation and distance to filaments. It also explains the absence of type/colour gradients in the data on smaller, non-linear scales.

The Program Management Challenges of Web 2.0

DTIC Science & Technology

2010-06-01

identifying and keeping abreast of the newly emerging technologies; their fast pace of evolution or modification, changing domain focus areas, their varied...definitive experts. No one knows what the future holds for network-centric materiel development . We are in the early stages of the Information Age and...led to the development and evolution of online Web-based communities and services such as auction houses, knowledge portals, social networking sites

An evolutionary perspective on the history of flap reconstruction in the upper extremity.

PubMed

Fang, Frank; Chung, Kevin C

2014-05-01

Examining the evolution of flap reconstruction of the upper extremity is similar to studying the evolution of biological species. This analogy provides a perspective to appreciate the contributing factors that led to the development of the current arsenal of techniques. It shows the trajectory for the future and provides a glimpse of the factors that that will be influential in the future. Copyright © 2014 Elsevier Inc. All rights reserved.

Reconstructing the evolution of mind.

PubMed

Povinelli, D J

1993-05-01

Since Darwin, the idea of intellectual continuity has gripped comparative psychology. Psychological evolution has been viewed as the accumulation of gradual changes over time, resulting in an unbroken chain of mental capacities throughout the diversity of life. Some researchers have even maintained that no fundamental psychological differences exist among species. An alternative model argues that a rather profound new psychology related to mental state attribution may have evolved recently in the primate order. The author explores recent experimental research from chimpanzees, rhesus monkeys, and children that is consistent with this second model of psychological evolution. Drawing on the fields of developmental, comparative, and social psychology, as well as evolutionary and developmental biology, the author outlines a research agenda aimed at reconstructing the evolution of metacognition.

Web-based volume slicer for 3D electron-microscopy data from EMDB

PubMed Central

Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J.; Patwardhan, Ardan

2016-01-01

We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model.

PubMed

Ingram, T; Harmon, L J; Shurin, J B

2012-09-01

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Understanding Evolution: An Evolution Website for Teachers

ERIC Educational Resources Information Center

Scotchmoor, Judy; Janulaw, Al

2005-01-01

While many states are facing challenges to the teaching of evolution in their science classrooms, the University of California Museum of Paleontology, working with the National Center for Science Education, has developed a useful web-based resource for science teachers of all grade- and experience-levels. Understanding Evolution (UE) was developed…

Evolutionary Biology Digital Dissection Project: Web-Based Laboratory Learning Opportunities for Students

ERIC Educational Resources Information Center

Fabian, Carole Ann

2004-01-01

A university in Buffalo introduced its students to evolution by providing them with information on evidence of evolution, mechanisms for evolution, principles of genetics, selection, adaptation, evolution and sociobiology. This method of teaching with technology enabled students to improve and expand their learning opportunities.

Expanding the Understanding of Evolution

ERIC Educational Resources Information Center

Musante, Susan

2011-01-01

Originally designed for K-12 teachers, the Understanding Evolution (UE) Web site ("www.understandingevolution.org") is a one-stop shop for all of a teacher's evolution education needs, with lesson plans, teaching tips, lists of common evolution misconceptions, and much more. However, during the past five years, the UE project team learned that…

Three dimensional X-ray Diffraction Contrast Tomography Reconstruction of Polycrystalline Strontium Titanate during Sintering and Electron Backscatter Diffraction Validation

NASA Astrophysics Data System (ADS)

Syha, M.; Rheinheimer, W.; Loedermann, B.; Graff, A.; Trenkle, A.; Baeurer, M.; Weygand, D.; Ludwig, W.; Gumbsch, P.

The microstructural evolution of polycrystalline strontium titanate was investigated in three dimensions (3D) using X-ray diffraction contrast tomography (DCT) before and after ex-situ annealing at 1600°C. Post-annealing, the specimen was additionally subjected to phase contrast tomography (PCT) in order to finely resolve the porosities. The resulting microstructure reconstructions were studied with special emphasis on morphology and interface orientation during microstructure evolution. Subsequently, cross-sections of the specimen were studied using electron backscatter diffraction (EBSD). Corresponding cross-sections through the 3D reconstruction were identified and the quality of the reconstruction is validated with special emphasis on the spatial resolution at the grain boundaries, the size and location of pores contained in the material and the accuracy of the orientation determination.

Review of evolution of tunnel position in anterior cruciate ligament reconstruction.

PubMed

Rayan, Faizal; Nanjayan, Shashi Kumar; Quah, Conal; Ramoutar, Darryl; Konan, Sujith; Haddad, Fares S

2015-03-18

Anterior cruciate ligament (ACL) rupture is one of the commonest knee sport injuries. The annual incidence of the ACL injury is between 100000-200000 in the United States. Worldwide around 400000 ACL reconstructions are performed in a year. The goal of ACL reconstruction is to restore the normal knee anatomy and kinesiology. The tibial and femoral tunnel placements are of primordial importance in achieving this outcome. Other factors that influence successful reconstruction are types of grafts, surgical techniques and rehabilitation programmes. A comprehensive understanding of ACL anatomy has led to the development of newer techniques supplemented by more robust biological and mechanical concepts. In this review we are mainly focussing on the evolution of tunnel placement in ACL reconstruction, focusing on three main categories, i.e., anatomical, biological and clinical outcomes. The importance of tunnel placement in the success of ACL reconstruction is well researched. Definite clinical and functional data is lacking to establish the superiority of the single or double bundle reconstruction technique. While there is a trend towards the use of anteromedial portals for femoral tunnel placement, their clinical superiority over trans-tibial tunnels is yet to be established.

Review of evolution of tunnel position in anterior cruciate ligament reconstruction

PubMed Central

Rayan, Faizal; Nanjayan, Shashi Kumar; Quah, Conal; Ramoutar, Darryl; Konan, Sujith; Haddad, Fares S

2015-01-01

Anterior cruciate ligament (ACL) rupture is one of the commonest knee sport injuries. The annual incidence of the ACL injury is between 100000-200000 in the United States. Worldwide around 400000 ACL reconstructions are performed in a year. The goal of ACL reconstruction is to restore the normal knee anatomy and kinesiology. The tibial and femoral tunnel placements are of primordial importance in achieving this outcome. Other factors that influence successful reconstruction are types of grafts, surgical techniques and rehabilitation programmes. A comprehensive understanding of ACL anatomy has led to the development of newer techniques supplemented by more robust biological and mechanical concepts. In this review we are mainly focussing on the evolution of tunnel placement in ACL reconstruction, focusing on three main categories, i.e., anatomical, biological and clinical outcomes. The importance of tunnel placement in the success of ACL reconstruction is well researched. Definite clinical and functional data is lacking to establish the superiority of the single or double bundle reconstruction technique. While there is a trend towards the use of anteromedial portals for femoral tunnel placement, their clinical superiority over trans-tibial tunnels is yet to be established. PMID:25793165

Life span in online communities

NASA Astrophysics Data System (ADS)

Grabowski, A.; Kosiński, R. A.

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users’ activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users’ lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

Life span in online communities.

PubMed

Grabowski, A; Kosiński, R A

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users' activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users' lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

[A group of new experiments on molecular evolution].

PubMed

Zhu, Xin-Yu; Xie, Xiao-Ling; Chen, Pei-Lin

2004-07-01

This paper presents a group of new experiments on molecular evolution. It allows students to get acquaint with the basic process of the reconstruction of phylogenetic tree using DNA or protein sequences, and to acquire the correct viewpoint how to affect the result of reconstruction when different tree-building methods, materials and parameters were used. This group of experiments are also characteristic of the opening and exploring, which accords with the direction and demand of experimental teaching reform.

Simulation of Heterogeneous Atom Probe Tip Shapes Evolution during Field Evaporation Using a Level Set Method and Different Evaporation Models

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

Xu, Zhijie; Li, Dongsheng; Xu, Wei

2015-04-01

In atom probe tomography (APT), accurate reconstruction of the spatial positions of field evaporated ions from measured detector patterns depends upon a correct understanding of the dynamic tip shape evolution and evaporation laws of component atoms. Artifacts in APT reconstructions of heterogeneous materials can be attributed to the assumption of homogeneous evaporation of all the elements in the material in addition to the assumption of a steady state hemispherical dynamic tip shape evolution. A level set method based specimen shape evolution model is developed in this study to simulate the evaporation of synthetic layered-structured APT tips. The simulation results ofmore » the shape evolution by the level set model qualitatively agree with the finite element method and the literature data using the finite difference method. The asymmetric evolving shape predicted by the level set model demonstrates the complex evaporation behavior of heterogeneous tip and the interface curvature can potentially lead to the artifacts in the APT reconstruction of such materials. Compared with other APT simulation methods, the new method provides smoother interface representation with the aid of the intrinsic sub-grid accuracy. Two evaporation models (linear and exponential evaporation laws) are implemented in the level set simulations and the effect of evaporation laws on the tip shape evolution is also presented.« less

From Autotransplantation to Allotransplantation: A Perspective on the Future of Reconstructive Microsurgery.

PubMed

Levin, L Scott

2018-04-28

It has been half a century since Susumu Tamai reported on the first thumb replantation. The evolution of reconstructive microsurgery has continually added new applications of the operating microscope for reconstructive surgery and has had profound impact on countless patients. From the time of Harold Gillies until today, the reconstructive ladder has evolved to a reconstructive elevator with the "penthouse" floor being represented by vascularized composite allotransplantation. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Insights on fluid-rock interaction evolution during deformation from fracture network geochemistry at reservoir-scale

NASA Astrophysics Data System (ADS)

Beaudoin, Nicolas; Koehn, Daniel; Lacombe, Olivier; Bellahsen, Nicolas; Emmanuel, Laurent

2015-04-01

Fluid migration and fluid-rock interactions during deformation is a challenging problematic to picture. Numerous interplays, as between porosity-permeability creation and clogging, or evolution of the mechanical properties of rock, are key features when it comes to monitor reservoir evolution, or to better understand seismic cycle n the shallow crust. These phenomenoms are especially important in foreland basins, where various fluids can invade strata and efficiently react with limestones, altering their physical properties. Stable isotopes (O, C, Sr) measurements and fluid inclusion microthermometry of faults cement and veins cement lead to efficient reconstruction of the origin, temperature and migration pathways for fluids (i.e. fluid system) that precipitated during joints opening or faults activation. Such a toolbox can be used on a diffuse fracture network that testifies the local and/or regional deformation history experienced by the rock at reservoir-scale. This contribution underlines the advantages and limits of geochemical studies of diffuse fracture network at reservoir-scale by presenting results of fluid system reconstruction during deformation in folded structures from various thrust-belts, tectonic context and deformation history. We compare reconstructions of fluid-rock interaction evolution during post-deposition, post-burial growth of basement-involved folds in the Sevier-Laramide American Rocky Mountains foreland, a reconstruction of fluid-rock interaction evolution during syn-depostion shallow detachment folding in the Southern Pyrenean foreland, and a preliminary reconstruction of fluid-rock interactions in a post-deposition, post-burial development of a detachment fold in the Appenines. Beyond regional specification for the nature of fluids, a common behavior appears during deformation as in every fold, curvature-related joints (related either to folding or to foreland flexure) connected vertically the pre-existing stratified fluid system. The lengthscale of the migration and the nature of invading fluids during these connections is different in every studied example, and can be related to the tectonic nature of the fold, along with the burial depth at the time of deformation. Thus, to decipher fluid-fracture relationships provides insights to better reconstruct the mechanisms of deformation at reservoir-scale.

Arachne—A web-based event viewer for MINERνA

NASA Astrophysics Data System (ADS)

Tagg, N.; Brangham, J.; Chvojka, J.; Clairemont, M.; Day, M.; Eberly, B.; Felix, J.; Fields, L.; Gago, A. M.; Gran, R.; Harris, D. A.; Kordosky, M.; Lee, H.; Maggi, G.; Maher, E.; Mann, W. A.; Marshall, C. M.; McFarland, K. S.; McGowan, A. M.; Mislivec, A.; Mousseau, J.; Osmanov, B.; Osta, J.; Paolone, V.; Perdue, G.; Ransome, R. D.; Ray, H.; Schellman, H.; Schmitz, D. W.; Simon, C.; Solano Salinas, C. J.; Tice, B. G.; Walding, J.; Walton, T.; Wolcott, J.; Zhang, D.; Ziemer, B. P.; MinerνA Collaboration

2012-06-01

Neutrino interaction events in the MINERνA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERνA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Arachne - A web-based event viewer for MINERvA

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

Tagg, N.; /Otterbein Coll.; Brangham, J.

2011-11-01

Neutrino interaction events in the MINERvA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERvA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Online 4d Reconstruction Using Multi-Images Available Under Open Access

NASA Astrophysics Data System (ADS)

Ioannides, M.; Hadjiprocopi, A.; Doulamis, N.; Doulamis, A.; Protopapadakis, E.; Makantasis, K.; Santos, P.; Fellner, D.; Stork, A.; Balet, O.; Julien, M.; Weinlinger, G.; Johnson, P. S.; Klein, M.; Fritsch, D.

2013-07-01

The advent of technology in digital cameras and their incorporation into virtually any smart mobile device has led to an explosion of the number of photographs taken every day. Today, the number of images stored online and available freely has reached unprecedented levels. It is estimated that in 2011, there were over 100 billion photographs stored in just one of the major social media sites. This number is growing exponentially. Moreover, advances in the fields of Photogrammetry and Computer Vision have led to significant breakthroughs such as the Structure from Motion algorithm which creates 3D models of objects using their twodimensional photographs. The existence of powerful and affordable computational machinery not only the reconstruction of complex structures but also entire cities. This paper illustrates an overview of our methodology for producing 3D models of Cultural Heritage structures such as monuments and artefacts from 2D data (pictures, video), available on Internet repositories, social media, Google Maps, Bing, etc. We also present new approaches to semantic enrichment of the end results and their subsequent export to Europeana, the European digital library, for integrated, interactive 3D visualisation within regular web browsers using WebGl and X3D. Our main goal is to enable historians, architects, archaeologists, urban planners and affiliated professionals to reconstruct views of historical structures from millions of images floating around the web and interact with them.

Monitoring the Deterioration of Stone at Mindener MUSEUM'S Lapidarium

NASA Astrophysics Data System (ADS)

Pomaska, G.

2013-07-01

Mindener Museum's Lapidarium incorporates a collection of stone work like reliefs, sculptures and inscriptions from different time epochs as advices of the city's history. These gems must be protected against environmental influences and deterioration. In advance of the measures a 3D reconstruction and detailed documentation has to be taken. The framework to establish hard- and software must match the museum's infrastructure. Two major question will be answered. Are low-cost scanning devices like depth cameras and digital of the shelf cameras suitable for the data acquisition? Does the functionality of open source and freeware covers the demand on investigation and analysis in this application? The working chain described in this contribution covers the structure from motion method and the reconstruction with RGB-D cameras. Mesh processing such as cleaning, smoothing, poisson surface reconstruction and texturing will be accomplished with MeshLab. Data acquisition and modelling continues in structure analysis. Therefore the focus lies as well on latest software developments related to 3D printing technologies. Repairing and finishing of meshes is a task for MeshMixer. Netfabb as a tool for positioning, dimensioning and slicing enables virtual handling of the items. On the Sketchfab web site one can publish and share 3D objects with integration into web pages supported by WebGL. Finally if a prototype is needed, the mesh can be uploaded to a 3D printing device provided by an online service.

Working with WebQuests

ERIC Educational Resources Information Center

Raulston, Cassie; Moellinger, Donna

2007-01-01

With the evolution of technology, students can now take online classes that may not be offered in their home schools. While online courses are commonly found in many high schools, WebQuests are used more commonly in elementary schools. Through the exploration of WebQuests, students are able to integrate the Internet into classroom activities. The…

Pragmatic Computing - A Semiotic Perspective to Web Services

NASA Astrophysics Data System (ADS)

Liu, Kecheng

The web seems to have evolved from a syntactic web, a semantic web to a pragmatic web. This evolution conforms to the study of information and technology from the theory of semiotics. The pragmatics, concerning with the use of information in relation to the context and intended purposes, is extremely important in web service and applications. Much research in pragmatics has been carried out; but in the same time, attempts and solutions have led to some more questions. After reviewing the current work in pragmatic web, the paper presents a semiotic approach to website services, particularly on request decomposition and service aggregation.

Web Spam, Social Propaganda and the Evolution of Search Engine Rankings

NASA Astrophysics Data System (ADS)

Metaxas, Panagiotis Takis

Search Engines have greatly influenced the way we experience the web. Since the early days of the web, users have been relying on them to get informed and make decisions. When the web was relatively small, web directories were built and maintained using human experts to screen and categorize pages according to their characteristics. By the mid 1990's, however, it was apparent that the human expert model of categorizing web pages does not scale. The first search engines appeared and they have been evolving ever since, taking over the role that web directories used to play.

Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity.

PubMed

King, Benedict; Lee, Michael S Y

2015-05-01

Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Chromosomal evolution in Rodentia

PubMed Central

Romanenko, S A; Perelman, P L; Trifonov, V A; Graphodatsky, A S

2012-01-01

Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution. PMID:22086076

Reconstruction of oropharyngeal defects after transoral robotic surgery. Review and recommendations of the Commission of Head and Neck Surgery of the Spanish Society of Otolaryngology and Head and Neck Surgery.

PubMed

González García, José Ángel; Pollán Guisasola, Carlos; Chiesa Estomba, Carlos Miguel; Viña Soria, Constanza; Virós Porcuna, David

2018-05-29

Transoral surgery of the oropharynx has seen an important evolution in recent years, expanding the surgical options available (TORS, TOUSS, TOLS). The capacity to resect increasingly extensive lesions and the number of patients who benefit from them. This fact has led to an evolution in the reconstruction of surgical defects after transoral surgery. This article aims to review the possible reconstructive techniques, indications and factors to be taken into account prior to surgery, proposing a protocol to assess the need for transoral reconstruction based on the depth of the defect, the staging, and previous treatment. Copyright © 2018 Sociedad Española de Otorrinolaringología y Cirugía de Cabeza y Cuello. Publicado por Elsevier España, S.L.U. All rights reserved.

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA–transcription factor mixed regulatory circuits (2012 update)

PubMed Central

Bisognin, Andrea; Sales, Gabriele; Coppe, Alessandro; Bortoluzzi, Stefania; Romualdi, Chiara

2012-01-01

MAGIA2 (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post-transcriptional regulators of several key biological and pathological processes. As miRNAs act prevalently through target degradation, their expression profiles are expected to be inversely correlated to those of the target genes. Low specificity of target prediction algorithms makes integration approaches an interesting solution for target prediction refinement. MAGIA2 performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. Nevertheless, miRNAs activity should be viewed as part of a more complex scenario where regulatory elements and their interactors generate a highly connected network and where gene expression profiles are the result of different levels of regulation. The updated MAGIA2 tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators. Two types of circuits are identified: (i) a TF that regulates both a miRNA and its target and (ii) a miRNA that regulates both a TF and its target. PMID:22618880

The Athena Astrophysical MHD Code in Cylindrical Geometry

NASA Astrophysics Data System (ADS)

Skinner, M. A.; Ostriker, E. C.

2011-10-01

We have developed a method for implementing cylindrical coordinates in the Athena MHD code (Skinner & Ostriker 2010). The extension has been designed to alter the existing Cartesian-coordinates code (Stone et al. 2008) as minimally and transparently as possible. The numerical equations in cylindrical coordinates are formulated to maintain consistency with constrained transport, a central feature of the Athena algorithm, while making use of previously implemented code modules such as the eigensystems and Riemann solvers. Angular-momentum transport, which is critical in astrophysical disk systems dominated by rotation, is treated carefully. We describe modifications for cylindrical coordinates of the higher-order spatial reconstruction and characteristic evolution steps as well as the finite-volume and constrained transport updates. Finally, we have developed a test suite of standard and novel problems in one-, two-, and three-dimensions designed to validate our algorithms and implementation and to be of use to other code developers. The code is suitable for use in a wide variety of astrophysical applications and is freely available for download on the web.

Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

PubMed

Christen, Victor; Hartung, Michael; Groß, Anika

2015-01-01

A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

Reconstructing Star Formation Histories to Reveal the Origin and Evolution of the SFR-M* Correlation

NASA Astrophysics Data System (ADS)

Gawiser, Eric

2016-10-01

Correlations have played an important role in advancing our knowledge of astrophysics, from the Schmidt-Kennicutt law to the black hole-bulge mass relation. A surprisingly tight correlation between galaxy star formation rates (SFR) and stellar masses (M*) was discovered in 2007, and models of galaxy formation and evolution can be constrained by studying the evolution of this SFR-M* correlation and its intrinsic scatter. At present, such investigations are weakened by the need to assume a simple parametric form for the star formation history, typically constant or exponentially declining.We propose to use our new dense basis method to reconstruct star-formation histories (SFHs) through SED fitting using multi-band photometry of >10,000 galaxies in the 3D-HST and CANDELS catalogs. Armed with these reconstructed SFHs, we will then:1. Better measure the SFR-M* correlation (aka star-forming sequence) in several redshift bins at 0.5

Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents.

PubMed

Usie, Anabel; Karathia, Hiren; Teixidó, Ivan; Alves, Rui; Solsona, Francesc

2014-01-01

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this 'up-to-dateness' came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains 'up-to-dateness' of the results. http://metres.udl.cat/index.php/downloads, metres.cmb@gmail.com.

SCENERY: a web application for (causal) network reconstruction from cytometry data

PubMed Central

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper

2017-01-01

Abstract Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. PMID:28525568

Internet Librarian '98: Proceedings of the Internet Librarian Conference (2nd, Monterey, California, November 1-5, 1998).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Dengler, M. Heide, Comp.; McHenry, Mare L., Comp.

This proceedings contains 56 papers, presentation summaries, and/or slide presentations pertaining to the Internet, World Wide Web, intranets, and library systems. Topics include: Web databases in medium sized libraries; Dow Jones Intranet Toolkit; the future of online; Web searching and Internet basics; digital archiving; evolution of the online…

A Framework for Synchronous Web-Based Professional Development: Measuring the Impact of Webinar Instruction

ERIC Educational Resources Information Center

Rich, Rachel L.

2011-01-01

Through the evolution and proliferation of the Internet, distance and online education have become more prevalent in modern society. Synchronous web-based professional development continues to gain popularity. Although online education has grown in popularity and breadth, there has been a lack of research about the impact of synchronous web-based…

Inside the Web: A Look at Digital Libraries and the Invisible/Deep Web

ERIC Educational Resources Information Center

Su, Mila C.

2009-01-01

The evolution of the Internet and the World Wide Web continually exceeds expectations with the "swift pace" of technological innovations. Information is added, and just as quickly becomes outdated at a rapid pace. Researchers have found that Digital materials can provide access to primary source materials and connect the researcher to institutions…

Seizing the Digital High Ground: Military Operations and Politics in the Social Media Era

DTIC Science & Technology

2015-04-13

divided on the relative threats and opportunities. Through the analysis of social media’s technological evolution, its impact on crowd behaviour , and... Through the analysis of social media’s technological evolution, its impact on crowd behaviour , and using case studies of the Arab Spring and Islamic... arguments and recommendations proposed. Web 2.0 is a term used to describe the way in which software developers and end-users utilize the World Wide Web as

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.

PubMed

Nakatani, Yoichiro; Takeda, Hiroyuki; Kohara, Yuji; Morishita, Shinichi

2007-09-01

Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

W.E.B. Du Bois and Caste Education: Racial Capitalist Schooling from Reconstruction to Jim Crow

ERIC Educational Resources Information Center

Pierce, Clayton

2017-01-01

This essay provides the first account and examination of caste education in the work of W.E.B. Du Bois. In so doing, I argue that caste education plays a central role in realizing the political and social goals of racial capitalist society for Du Bois. Using Du Bois's caste analytic, I take up and articulate three biopolitical governing strategies…

Selection of trilateral continuums of life history strategies under food web interactions.

PubMed

Fujiwara, Masami

2018-03-14

The study of life history strategies has a long history in ecology and evolution, but determining the underlying mechanisms driving the evolution of life history variation and its consequences for population regulation remains a major challenge. In this study, a food web model with constant environmental conditions was used to demonstrate how multi-species consumer-resource interactions (food-web interactions) can create variation in the duration of the adult stage, age of maturation, and fecundity among species. The model included three key ecological processes: size-dependent species interactions, energetics, and transition among developmental stages. Resultant patterns of life history variation were consistent with previous empirical observations of the life history strategies of aquatic organisms referred to as periodic, equilibrium, and opportunistic strategies (trilateral continuums of life history strategies). Results from the simulation model suggest that these three life history strategies can emerge from food web interactions even when abiotic environmental conditions are held constant.

Evolution of the cosmic web

NASA Astrophysics Data System (ADS)

Cautun, Marius; van de Weygaert, Rien; Jones, Bernard J. T.; Frenk, Carlos S.

2014-07-01

The cosmic web is the largest scale manifestation of the anisotropic gravitational collapse of matter. It represents the transitional stage between linear and non-linear structures and contains easily accessible information about the early phases of structure formation processes. Here we investigate the characteristics and the time evolution of morphological components. Our analysis involves the application of the NEXUS Multiscale Morphology Filter technique, predominantly its NEXUS+ version, to high resolution and large volume cosmological simulations. We quantify the cosmic web components in terms of their mass and volume content, their density distribution and halo populations. We employ new analysis techniques to determine the spatial extent of filaments and sheets, like their total length and local width. This analysis identifies clusters and filaments as the most prominent components of the web. In contrast, while voids and sheets take most of the volume, they correspond to underdense environments and are devoid of group-sized and more massive haloes. At early times the cosmos is dominated by tenuous filaments and sheets, which, during subsequent evolution, merge together, such that the present-day web is dominated by fewer, but much more massive, structures. The analysis of the mass transport between environments clearly shows how matter flows from voids into walls, and then via filaments into cluster regions, which form the nodes of the cosmic web. We also study the properties of individual filamentary branches, to find long, almost straight, filaments extending to distances larger than 100 h-1 Mpc. These constitute the bridges between massive clusters, which seem to form along approximatively straight lines.

PIECE 2.0: an update for the plant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparision and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in ...

High-performance spider webs: integrating biomechanics, ecology and behaviour

PubMed Central

Harmer, Aaron M. T.; Blackledge, Todd A.; Madin, Joshua S.; Herberstein, Marie E.

2011-01-01

Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks. PMID:21036911

A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

PubMed Central

Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

2014-01-01

Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria).

PubMed

Olsson, Sanna; Kaasalainen, Ulla; Rikkinen, Jouko

2012-02-01

In this study we reconstruct the structural evolution of the hyper-variable P6b region of the group I trnLeu intron in a monophyletic group of lichen-symbiotic Nostoc strains and establish it as a useful marker in the phylogenetic analysis of these organisms. The studied cyanobacteria occur as photosynthetic and/or nitrogen-fixing symbionts in lichen species of the diverse Nephroma guild. Phylogenetic analyses and secondary structure reconstructions are used to improve the understanding of the replication mechanisms in the P6b stem-loop and to explain the observed distribution patterns of indels. The variants of the P6b region in the Nostoc clade studied consist of different combinations of five sequence modules. The distribution of indels together with the ancestral character reconstruction performed enables the interpretation of the evolution of each sequence module. Our results indicate that the indel events are usually associated with single nucleotide changes in the P6b region and have occurred several times independently. In spite of their homoplasy, they provide phylogenetic information for closely related taxa. Thus we recognize that features of the P6b region can be used as molecular markers for species identification and phylogenetic studies involving symbiotic Nostoc cyanobacteria.

Three Dimensional Reconstruction Workflows for Lost Cultural Heritage Monuments Exploiting Public Domain and Professional Photogrammetric Imagery

NASA Astrophysics Data System (ADS)

Wahbeh, W.; Nebiker, S.

2017-08-01

In our paper, we document experiments and results of image-based 3d reconstructions of famous heritage monuments which were recently damaged or completely destroyed by the so-called Islamic state in Syria and Iraq. The specific focus of our research is on the combined use of professional photogrammetric imagery and of publicly available imagery from the web for optimally 3d reconstructing those monuments. The investigated photogrammetric reconstruction techniques include automated bundle adjustment and dense multi-view 3d reconstruction using public domain and professional imagery on the one hand and an interactive polygonal modelling based on projected panoramas on the other. Our investigations show that the combination of these two image-based modelling techniques delivers better results in terms of model completeness, level of detail and appearance.

Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

PubMed

Chavalarias, David; Cointet, Jean-Philippe

2013-01-01

We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low.

The evolution of vertebral formulae in Hominoidea.

PubMed

Thompson, Nathan E; Almécija, Sergio

2017-09-01

Primate vertebral formulae have long been investigated because of their link to locomotor behavior and overall body plan. Knowledge of the ancestral vertebral formulae in the hominoid tree of life is necessary to interpret the pattern of evolution among apes, and to critically evaluate the morphological adaptations involved in the transition to hominin bipedalism. Though many evolutionary hypotheses have been proposed based on living and fossil species, the application of quantitative phylogenetic methods for thoroughly reconstructing ancestral vertebral formulae and formally testing patterns of vertebral evolution is lacking. To estimate the most probable scenarios of hominoid vertebral evolution, we utilized an iterative ancestral state reconstruction approach to determine likely ancestral vertebral counts in apes, humans, and other anthropoid out-groups. All available ape and hominin fossil taxa with an inferred regional vertebral count were included in the analysis. Sensitivity iterations were performed both by changing the phylogenetic position of fossil taxa with a contentious placement, and by changing the inferred number of vertebrae in taxa with uncertain morphology. Our ancestral state reconstruction results generally support a short-backed hypothesis of human evolution, with a Pan-Homo last common ancestor possessing a vertebral formulae of 7:13:4:6 (cervical:thoracic:lumbar:sacral). Our results indicate that an initial reduction in lumbar vertebral count and increase in sacral count is a synapomorphy of crown hominoids (supporting an intermediate-backed hypothesis for the origins of the great ape-human clade). Further reduction in lumbar count occurs independently in orangutans and African apes. Our results highlight the complexity and homoplastic nature of vertebral count evolution, and give little support to the long-backed hypothesis of human evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Evolution of the DARWIN System

NASA Technical Reports Server (NTRS)

Walton, Joan D.; Filman, Robert E.; Korsmeyer, David J.; Norvig, Peter (Technical Monitor)

1999-01-01

DARWIN is a web-based system for presenting the results of wind-tunnel testing and computational model analyses to aerospace designers. DARWIN captures the data, maintains the information, and manages derived knowledge (e.g. visualizations, etc.) of large quantities of aerospace data. In addition, it provides tools and an environment for distributed collaborative engineering. We are currently constructing the third version of the DARWIN software system. DARWN's development history has, in some sense, tracked the development of web applications. The 1995 DARWIN reflected the latest web technologies--CGI scripts, Java applets and a three-layer architecture--available at that time. The 1997 version of DARWIN expanded on this base, making extensive use of a plethora of web technologies, including Java/JavaScript and Dynamic HTML. While more powerful, this multiplicity has proven to be a maintenance and development headache. The year 2000 version of DARWIN will provide a more stable and uniform foundation environment, composed primarily of Java mechanisms. In this paper, we discuss this evolution, comparing the strengths and weaknesses of the various architectural approaches and describing the lessons learned about building complex web applications.

Feature saltation and the evolution of mimicry.

PubMed

Gamberale-Stille, Gabriella; Balogh, Alexandra C V; Tullberg, Birgitta S; Leimar, Olof

2012-03-01

In Batesian mimicry, a harmless prey species imitates the warning coloration of an unpalatable model species. A traditional suggestion is that mimicry evolves in a two-step process, in which a large mutation first achieves approximate similarity to the model, after which smaller changes improve the likeness. However, it is not known which aspects of predator psychology cause the initial mutant to be perceived by predators as being similar to the model, leaving open the question of how the crucial first step of mimicry evolution occurs. Using theoretical evolutionary simulations and reconstruction of examples of mimicry evolution, we show that the evolution of Batesian mimicry can be initiated by a mutation that causes prey to acquire a trait that is used by predators as a feature to categorize potential prey as unsuitable. The theory that species gain entry to mimicry through feature saltation allows us to formulate scenarios of the sequence of events during mimicry evolution and to reconstruct an initial mimetic appearance for important examples of Batesian mimicry. Because feature-based categorization by predators entails a qualitative distinction between nonmimics and passable mimics, the theory can explain the occurrence of imperfect mimicry. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces.

PubMed

Fishbein, Mark; Straub, Shannon C K; Boutte, Julien; Hansen, Kimberly; Cronn, Richard C; Liston, Aaron

2018-03-01

Leaf surface traits, such as trichome density and wax production, mediate important ecological processes such as anti-herbivory defense and water-use efficiency. We present a phylogenetic analysis of Asclepias plastomes as a framework for analyzing the evolution of trichome density and presence of epicuticular waxes. We produced a maximum-likelihood phylogeny using plastomes of 103 species of Asclepias. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Asclepias. We resolved the backbone of Asclepias, placing the Sonoran Desert clade and Incarnatae clade as successive sisters to the remaining species. We present novel findings about leaf surface evolution of Asclepias-the ancestor is reconstructed as waxless and sparsely hairy, a macroevolutionary optimal trichome density is supported, and the rate of evolution of trichome density has accelerated. Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are more sensitive to character coding than model selection. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Reconstructing the Cenozoic evolution of the mantle: Implications for mantle plume dynamics under the Pacific and Indian plates

NASA Astrophysics Data System (ADS)

Glišović, Petar; Forte, Alessandro M.

2014-03-01

The lack of knowledge of the initial thermal state of the mantle in the geological past is an outstanding problem in mantle convection. The resolution of this problem also requires the modelling of 3-D mantle evolution that yields maximum consistency with a wide suite of geophysical constraints. Quantifying the robustness of the reconstructed thermal evolution is another major concern. To solve and estimate the robustness of the time-reversed (inverse) problem of mantle convection, we analyse two different numerical techniques: the quasi-reversible (QRV) and the backward advection (BAD) methods. Our investigation extends over the 65 Myr interval encompassing the Cenozoic era using a pseudo-spectral solution for compressible-flow thermal convection in 3-D spherical geometry. We find that the two dominant issues for solving the inverse problem of mantle convection are the choice of horizontally-averaged temperature (i.e., geotherm) and mechanical surface boundary conditions. We find, in particular, that the inclusion of thermal boundary layers that yield Earth-like heat flux at the top and bottom of the mantle has a critical impact on the reconstruction of mantle evolution. We have developed a new regularisation scheme for the QRV method using a time-dependent regularisation function. This revised implementation of the QRV method delivers time-dependent reconstructions of mantle heterogeneity that reveal: (1) the stability of Pacific and African ‘large low shear velocity provinces’ (LLSVP) over the last 65 Myr; (2) strong upward deflections of the CMB topography at 65 Ma beneath: the North Atlantic, the south-central Pacific, the East Pacific Rise (EPR) and the eastern Antarctica; (3) an anchored deep-mantle plume ascending directly under the EPR (Easter and Pitcairn hotspots) throughout the Cenozoic era; and (4) the appearance of the transient Reunion plume head beneath the western edge of the Deccan Plateau at 65 Ma. Our reconstructions of Cenozoic mantle evolution thus suggest that mantle plumes play a key role in driving surface tectonic processes and large-scale volcanism.

Low rank alternating direction method of multipliers reconstruction for MR fingerprinting.

PubMed

Assländer, Jakob; Cloos, Martijn A; Knoll, Florian; Sodickson, Daniel K; Hennig, Jürgen; Lattanzi, Riccardo

2018-01-01

The proposed reconstruction framework addresses the reconstruction accuracy, noise propagation and computation time for magnetic resonance fingerprinting. Based on a singular value decomposition of the signal evolution, magnetic resonance fingerprinting is formulated as a low rank (LR) inverse problem in which one image is reconstructed for each singular value under consideration. This LR approximation of the signal evolution reduces the computational burden by reducing the number of Fourier transformations. Also, the LR approximation improves the conditioning of the problem, which is further improved by extending the LR inverse problem to an augmented Lagrangian that is solved by the alternating direction method of multipliers. The root mean square error and the noise propagation are analyzed in simulations. For verification, in vivo examples are provided. The proposed LR alternating direction method of multipliers approach shows a reduced root mean square error compared to the original fingerprinting reconstruction, to a LR approximation alone and to an alternating direction method of multipliers approach without a LR approximation. Incorporating sensitivity encoding allows for further artifact reduction. The proposed reconstruction provides robust convergence, reduced computational burden and improved image quality compared to other magnetic resonance fingerprinting reconstruction approaches evaluated in this study. Magn Reson Med 79:83-96, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Developing and sustaining a web-based library newsletter.

PubMed

Frisby, Anthony J; Kipnis, Daniel G; Mikita, Elizabeth G

2006-01-01

The JEFFLINE Forum, Scott Library's attempt to revive the traditional library newsletter by employing the technical advantages and increasing presence of the Web, debuted in October 1999. The fifth anniversary of the Forum was a good time to look back at its evolution and to examine some of the challenges inherent in developing and sustaining a library newsletter. By identifying the most successful strategies, and reflecting on the lessons learned along way, the authors hope to continue the evolution of the Forum and help to ensure the viability of the library newsletter.

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles.

PubMed

Griffith, Oliver W; Blackburn, Daniel G; Brandley, Matthew C; Van Dyke, James U; Whittington, Camilla M; Thompson, Michael B

2015-09-01

To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses. © 2015 Wiley Periodicals, Inc.

Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

Evolution Kills: A Web Resource for Instructors of Evolutionary Biology

ERIC Educational Resources Information Center

Vondrasek, Joanna R.; Antonovics, Janis; Taylor, Douglas R.

2004-01-01

We have developed a laboratory course that demonstrates how evolution can be taught as a participatory, investigative science at the undergraduate college or advanced secondary high school level. The course emphasizes the applied importance of evolution to areas such as medicine and agriculture. Because many instructors face budgetary or other…

Increased Learning Observed in Redesigned Introductory Biology Course that Employed Web-enhanced, Interactive Pedagogy

PubMed Central

Lister, Bradford C.; Hanna, Michael H.; Roy, Harry

2007-01-01

Our Introduction to Biology course (BIOL 1010) changed in 2004 from a standard instructor-centered, lecture-homework-exam format to a student-centered format that used Web-enhanced, interactive pedagogy. To measure and compare conceptual learning gains in the traditional course in fall 2003 with a section of the interactive course in fall 2004, we created concept inventories for both evolution and ecology. Both classes were taught by the same instructor who had taught BIOL 1010 since 1976, and each had a similar student composition with comparable biological knowledge. A significant increase in learning gain was observed with the Web-enhanced, interactive pedagogy in evolution (traditional, 0.10; interactive, 0.19; p = 0.024) and ecology (traditional, −0.05; interactive, 0.14; p = 0.000009) when assessment was made unannounced and for no credit in the last week of classes. These results strengthen the case for augmenting or replacing instructor-centered teaching with Web-enhanced, interactive, student-centered teaching. When assessment was made using the final exam in the interactive course, for credit and after studying, significantly greater learning gains were made in evolution (95%, 0.37, p = 0.0001) and ecology (143%, 0.34, p = 0.000003) when compared with learning gains measured without credit or study in the last week of classes. PMID:17785407

The Evolution of WebCT in a Baccalaureate Nursing Program: An Alice in Wonderland Reflection

ERIC Educational Resources Information Center

Donato, Emily; Hudyma, Shirlene; Carter, Lorraine; Schroeder, Catherine

2010-01-01

The use of WebCT in the Laurentian University Bachelor of Science in Nursing program began in 2001 when faculty were eager to explore different modes of delivery for fourth-year courses. Since then, the use of WebCT within the baccalaureate program has increased substantively. This paper outlines the developmental growth of the use of this…

SCENERY: a web application for (causal) network reconstruction from cytometry data.

PubMed

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper; Tsamardinos, Ioannis

2017-07-03

Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Evolution of Complex Microsurgical Midface Reconstruction: A Classification Scheme and Reconstructive Algorithm.

PubMed

Alam, Daniel; Ali, Yaseen; Klem, Christopher; Coventry, Daniel

2016-11-01

Orbito-malar reconstruction after oncological resection represents one of the most challenging facial reconstructive procedures. Until the last few decades, rehabilitation was typically prosthesis based with a limited role for surgery. The advent of microsurgical techniques allowed large-volume tissue reconstitution from a distant donor site, revolutionizing the potential approaches to these defects. The authors report a novel surgery-based algorithm and a classification scheme for complete midface reconstruction with a foundation in the Gillies principles of like-to-like reconstruction and with a significant role of computer-aided virtual planning. With this approach, the authors have been able to achieve significantly better patient outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

Environmental constraints and call evolution in torrent-dwelling frogs.

PubMed

Goutte, Sandra; Dubois, Alain; Howard, Samuel D; Marquez, Rafael; Rowley, Jodi J L; Dehling, J Maximilian; Grandcolas, Philippe; Rongchuan, Xiong; Legendre, Frédéric

2016-04-01

Although acoustic signals are important for communication in many taxa, signal propagation is affected by environmental properties. Strong environmental constraints should drive call evolution, favoring signals with greater transmission distance and content integrity in a given calling habitat. Yet, few empirical studies have verified this prediction, possibly due to a shortcoming in habitat characterization, which is often too broad. Here we assess the potential impact of environmental constraints on the evolution of advertisement call in four groups of torrent-dwelling frogs in the family Ranidae. We reconstruct the evolution of calling site preferences, both broadly categorized and at a finer scale, onto a phylogenetic tree for 148 species with five markers (∼3600 bp). We test models of evolution for six call traits for 79 species with regard to the reconstructed history of calling site preferences and estimate their ancestral states. We find that in spite of existing morphological constraints, vocalizations of torrent-dwelling species are most probably constrained by the acoustic specificities of torrent habitats and particularly their high level of ambient noise. We also show that a fine-scale characterization of calling sites allows a better perception of the impact of environmental constraints on call evolution. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Reconstructive techniques in transoral robotic surgery for head and neck cancer: a North American survey.

PubMed

Konofaos, Petros; Hammond, Sarah; Ver Halen, Jon P; Samant, Sandeep

2013-02-01

Although the use of transoral robotic surgery for tumor extirpation is expanding, little is known about national trends in the reconstruction of resultant defects. An 18-question electronic survey was created by an expert panel of surgeons from the Department of Otolaryngology-Head and Neck Surgery and the Department of Plastic and Reconstructive Surgery at the University of Tennessee. Eligible participants were identified by the American Head and Neck Society Web site and from the Intuitive Surgical, Inc., Web site after review of surgeons trained in transoral robotic surgery techniques. Twenty-three of 27 preselected head and neck surgeons (85.18 percent) completed the survey. All respondents use transoral robotic surgery for head and neck tumor extirpation. The majority of the respondents [n = 17 (77.3 percent)] did not use any means of reconstruction. With respect to methods of reconstruction following transoral robotic surgery defects, the majority [n = 4 (80.0 percent)] used a free flap, a pedicled local flap [n = 3 (60.0 percent)], or a distant flap [n = 3 (60.0 percent)]. The radial forearm flap was the most commonly used free flap by all respondents. In general, the majority of survey respondents allow defects to heal secondarily or close primarily. Based on this survey, consensus indications for pedicled or free tissue transfer following transoral robotic surgery defects were primary head and neck tumors (stage T3 and T4a), pharyngeal defects with exposure of vital structures, and prior irradiation or chemoradiation to the operative site and neck.

The Evolution of Thought

ERIC Educational Resources Information Center

Shadrikov, V. D.

2017-01-01

We investigate the evolution of thought using the method of historical reconstruction, the theory of the cultural and historical determinism of psychological development, data on the relationship between morphological studies, modern findings about child development, and the scientific understanding of neural morphogenesis. We argue for…

Posttraumatic thumb reconstruction.

PubMed

Muzaffar, Arshad R; Chao, James J; Friedrich, Jeffrey B; Freidrich, Jeffrey B

2005-10-01

After reading this article, the reader should be able to: 1. Discuss the critical anatomic features of the thumb as they affect on reconstructive decision making. 2. Define the goals of reconstruction. 3. Discuss an algorithm for thumb reconstruction according to the level of amputation. 4. Understand the role of prosthetics in thumb reconstruction. The function of the thumb is critical to overall hand function. Uniquely endowed with anatomic features that allow circumduction and opposition, the thumb enables activities of pinch, grasp, and fine manipulation that are essential in daily life. Destruction of the thumb secondary to trauma represents a much more significant loss than would result from loss of any other digit. Therefore, significant effort has been focused on thumb reconstruction. Numerous techniques have been described, ranging from simple osteoplastic techniques to complex microsurgical procedures. With an appreciation of the unique anatomic properties of the thumb, the hand surgeon is better able to understand the goals of thumb reconstruction and to develop an algorithm for thumb reconstruction. With such an understanding, an individualized reconstructive plan can be developed for each patient. A great many options are available for posttraumatic thumb reconstruction. Optimal results are obtained by pursuing an organized and logical approach to reconstruction based upon the level of tissue loss. Reconstruction methods depend on the location of the amputation and range from homodigital and heterodigital flaps to partial-toe transfer or a great-toe wrap-around flap to first-web-space deepening using Z-plasties, a dorsal rotation flap, or a distant flap, to distraction osteogenesis, lengthening of the thumb ray, spare parts from another injured digit in the acute setting for pollicization or heterotopic replantation, and microvascular toe transfer. Amputations in the distal third of the thumb are generally well-tolerated. The primary reconstructive issues are the restoration of a padded and sensate soft-tissue cover, as well as aesthetic considerations. First-web-space deepening will generally provide excellent results for amputations at the distal half of the middle third. In the proximal half of the middle third, lengthening of the thumb ray is generally required. Distraction lengthening of the first metacarpal is a useful and reliable technique that provides up to 3 cm of length without requiring complex microsurgical methods. Spare parts from another injured digit may be used in the acute setting for pollicization or heterotopic replantation. Microvascular toe transfer is an excellent option for elective reconstruction. However, other options also are available and may be more appropriate in some cases. Less ideal options include the various types of osteoplastic reconstruction. The reconstruction of posttraumatic thumb defects is a challenging and rewarding surgical endeavor. The value of a functioning thumb is immense, and its reconstruction is worthy of considerable effort. Despite the elegant reconstructive options available, the best results are obtained with replantation or revascularization whenever possible. Finally, the treatment plan always must be derived from a careful assessment of each patient's posttraumatic function and specific reconstructive needs.

D Virtual CH Interactive Information Systems for a Smart Web Browsing Experience for Desktop Pcs and Mobile Devices

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.

2018-05-01

Recently, the diffusion of knowledge on Cultural Heritage (CH) has become an element of primary importance for its valorization. At the same time, the diffusion of surveys based on UAV Unmanned Aerial Vehicles (UAV) technologies and new methods of photogrammetric reconstruction have opened new possibilities for 3D CH representation. Furthermore the recent development of faster and more stable internet connections leads people to increase the use of mobile devices. In the light of all this, the importance of the development of Virtual Reality (VR) environments applied to CH is strategic for the diffusion of knowledge in a smart solution. In particular, the present work shows how, starting from a basic survey and the further photogrammetric reconstruction of a cultural good, is possible to built a 3D CH interactive information system useful for desktop and mobile devices. For this experimentation the Arab-Norman church of the Trinity of Delia (in Castelvetrano-Sicily-Italy) has been adopted as case study. The survey operations have been carried out considering different rapid methods of acquisition (UAV camera, SLR camera and smartphone camera). The web platform to publish the 3D information has been built using HTML5 markup language and WebGL JavaScript libraries (Three.js libraries). This work presents the construction of a 3D navigation system for a web-browsing of a virtual CH environment, with the integration of first person controls and 3D popup links. This contribution adds a further step to enrich the possibilities of open-source technologies applied to the world of CH valorization on web.

The amphioxus genome and the evolution of the chordate karyotype

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

Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E.K.

2008-04-01

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic {approx}520 million base pair genome of the Florida lancelet Branchiostoma floridae, and analyze it in the context of chordate evolution. Whole genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets, and vertebrates), and allow reconstruction of not only the gene complement of the last common chordate ancestor, but also a partial reconstruction of its genomic organization, as well as a description of two genome-wide duplicationsmore » and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.« less

Reconstructing the Initial Relaxation Time of Young Star Clusters in the Large Magellanic Cloud: The Evolution of Star Clusters

NASA Astrophysics Data System (ADS)

Portegies Zwart, S. F.; Chen, H.-C.

2008-06-01

We reconstruct the initial two-body relaxation time at the half mass radius for a sample of young ⪉ 300 Myr star clusters in the Large Magellanic cloud. We achieve this by simulating star clusters with 12288 to 131072 stars using direct N-body integration. The equations of motion of all stars are calculated with high precision direct N-body simulations which include the effects of the evolution of single stars and binaries. We find that the initial relaxation times of the sample of observed clusters in the Large Magellanic Cloud ranges from about 200 Myr to about 2 Gyr. The reconstructed initial half-mass relaxation times for these clusters have a much narrower distribution than the currently observed distribution, which ranges over more than two orders of magnitude.

FMM: a web server for metabolic pathway reconstruction and comparative analysis.

PubMed

Chou, Chih-Hung; Chang, Wen-Chi; Chiu, Chih-Min; Huang, Chih-Chang; Huang, Hsien-Da

2009-07-01

Synthetic Biology, a multidisciplinary field, is growing rapidly. Improving the understanding of biological systems through mimicry and producing bio-orthogonal systems with new functions are two complementary pursuits in this field. A web server called FMM (From Metabolite to Metabolite) was developed for this purpose. FMM can reconstruct metabolic pathways form one metabolite to another metabolite among different species, based mainly on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and other integrated biological databases. Novel presentation for connecting different KEGG maps is newly provided. Both local and global graphical views of the metabolic pathways are designed. FMM has many applications in Synthetic Biology and Metabolic Engineering. For example, the reconstruction of metabolic pathways to produce valuable metabolites or secondary metabolites in bacteria or yeast is a promising strategy for drug production. FMM provides a highly effective way to elucidate the genes from which species should be cloned into those microorganisms based on FMM pathway comparative analysis. Consequently, FMM is an effective tool for applications in synthetic biology to produce both drugs and biofuels. This novel and innovative resource is now freely available at http://FMM.mbc.nctu.edu.tw/.

77 FR 65554 - Subcommittee for Dose Reconstruction Reviews (SDRR), Advisory Board on Radiation and Worker...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-29

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Centers for Disease Control and Prevention Subcommittee... probability of causation guidelines that have been promulgated by the Department of Health and Human Services... reconstruction tools, presentation of the evolution of peer-review procedures, presentation of statistics...

Density perturbation in the models reconstructed from jerk parameter

NASA Astrophysics Data System (ADS)

Sinha, Srijita; Banerjee, Narayan

2018-06-01

The present work deals with the late time evolution of the linear density contrast in the dark energy models reconstructed from the jerk parameter. It is found that the non-interacting models are favoured compared to the models where an interaction is allowed in the dark sector.

Association of Small Computer Users in Education: Proceedings of the ASCUE Summer Conference (31st, North Myrtle Beach, South Carolina, June 7-11, 1998).

ERIC Educational Resources Information Center

Smith, Peter, Ed.

Topics addressed by the papers including in this proceedings include: multimedia in the classroom; World Wide Web site development; the evolution of academic library services; a Web-based literature course; development of a real-time intelligent network environment; serving grades over the Internet; e-mail over a Web browser; using technology to…

The GAENE--Generalized Acceptance of EvolutioN Evaluation: Development of a New Measure of Evolution Acceptance

ERIC Educational Resources Information Center

Smith, Mike U.; Snyder, Scott W.; Devereaux, Randolph S.

2016-01-01

The present study reports the development of a brief, quantitative, web-based, psychometrically sound measure--the Generalized Acceptance of EvolutioN Evaluation (GAENE, pronounced "gene") in a format that is useful in large and small groups, in research, and in classroom settings. The measure was designed to measure only evolution…

The tail of the Ordovician fish Sacabambaspis.

PubMed

Pradel, Alan; Sansom, Ivan J; Gagnier, Pierre-Yves; Cespedes, Ricardo; Janvier, Philippe

2007-02-22

The tail of the earliest known articulated fully skeletonized vertebrate, the arandaspid Sacabambaspis from the Ordovician of Bolivia, is redescribed on the basis of further preparation of the only specimen in which it is most extensively preserved. The first, but soon discarded, reconstruction, which assumed the presence of a long horizontal notochordal lobe separating equal sized dorsal and ventral fin webs, appears to have considerable merit. Although the ventral web is significantly smaller than the dorsal one, the presence of a very long notochordal lobe bearing a small terminal web is confirmed. The discrepancy in the size of the ventral and dorsal webs rather suggests that the tail was hypocercal, a condition that would better accord with the caudal morphology of the living agnathans and the other jawless stem gnathostomes.

The dorsal transposition flap for congenital contractures of the first web space: a 20-year experience.

PubMed

Friedman, R; Wood, V E

1997-07-01

Fifty-four dorsal transposition flaps were performed in 38 patients (46 hands) for severe congenital thumb web-space contractures. At an average follow-up interval of 6 years, complications or unsatisfactory results had occurred in 100% of symbrachydactyly patients and in 27% of all other patients. Postoperative first web-space angle was augmented an average of 59 degrees with a distal flap two-point discrimination of 8 mm. Mean postoperative pinch and grip strengths were 58% and 72%, respectively, of the normal contralateral hand. Parental satisfaction with the functional results was high, and the aesthetic results were generally acceptable. With the exception of symbrachydactyly patients, the dorsal transposition flap remains an excellent reconstructive option for severe congenital contractures of the thumb web space.

3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons.

PubMed

Wanner, Adrian A; Genoud, Christel; Friedrich, Rainer W

2016-11-08

Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25×9.25×25 nm 3 . Skeletons of 1,022 neurons, 98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. The reconstructions allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services (http://www.neurodata.io). Raw data and reconstructions can be visualized in PyKNOSSOS.

3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons

PubMed Central

Wanner, Adrian A.; Genoud, Christel; Friedrich, Rainer W.

2016-01-01

Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25×9.25×25 nm3. Skeletons of 1,022 neurons, 98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. The reconstructions allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services (http://www.neurodata.io). Raw data and reconstructions can be visualized in PyKNOSSOS. PMID:27824337

The study of early human embryos using interactive 3-dimensional computer reconstructions.

PubMed

Scarborough, J; Aiton, J F; McLachlan, J C; Smart, S D; Whiten, S C

1997-07-01

Tracings of serial histological sections from 4 human embryos at different Carnegie stages were used to create 3-dimensional (3D) computer models of the developing heart. The models were constructed using commercially available software developed for graphic design and the production of computer generated virtual reality environments. They are available as interactive objects which can be downloaded via the World Wide Web. This simple method of 3D reconstruction offers significant advantages for understanding important events in morphological sciences.

Assessing Greek Public Hospitals' Websites.

PubMed

Tsirintani, Maria; Binioris, Spyros

2015-01-01

Following a previous (2011) survey, this study assesses the web pages of Greek public hospitals according to specific criteria, which are included in the same web page evaluation model. Our purpose is to demonstrate the evolution of hospitals' web pages and document e-health applications trends. Using descriptive methods we found that public hospitals have made significant steps towards establishing and improving their web presence but there is still a lot of work that needs to be carried out in order to take advantage of the benefits of new technologies in the e-health ecosystem.

Variability analysis of the reconstructed daily global solar radiation under all-sky and cloud-free conditions in Madrid during the period 1887-1950

NASA Astrophysics Data System (ADS)

Antón, M.; Román, R.; Sanchez-Lorenzo, A.; Calbó, J.; Vaquero, J. M.

2017-07-01

This study focuses on the analysis of the daily global solar radiation (GSR) reconstructed from sunshine duration measurements at Madrid (Spain) from 1887 to 1950. Additionally, cloud cover information recorded simultaneously by human observations for the study period was also analyzed and used to select cloud-free days. First, the day-to-day variability of reconstructed GSR data was evaluated, finding a strong relationship between GSR and cloudiness. The second step was to analyze the long-term evolution of the GSR data which exhibited two clear trends with opposite sign: a marked negative trend of - 36 kJ/m2 per year for 1887-1915 period and a moderate positive trend of + 13 kJ/m2 per year for 1916-1950 period, both statistically significant at the 95% confidence level. Therefore, there is evidence of "early dimming" and "early brightening" periods in the reconstructed GSR data for all-sky conditions in Madrid from the late 19th to the mid-20th centuries. Unlike the long-term evolution of GSR data, cloud cover showed non-statistically significant trends for the two analyzed sub-periods, 1887-1915 and 1916-1950. Finally, GSR trends were analyzed exclusively under cloud-free conditions in summer by means of the determination of the clearness index for those days with all cloud cover observations equal to zero oktas. The long-term evolution of the clearness index was in accordance with the "early dimming" and "early brightening" periods, showing smaller trends but still statistically significant. This result points out that aerosol load variability could have had a non-negligible influence on the long-term evolution of GSR even as far as from the late 19th century.

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

PubMed

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

Evolution of Venomous Cartilaginous and Ray-Finned Fishes.

PubMed

Smith, W Leo; Stern, Jennifer H; Girard, Matthew G; Davis, Matthew P

2016-11-01

Venom and its associated delivery systems have evolved in numerous animal groups ranging from jellyfishes to spiders, lizards, shrews, and the male platypus. Building off new data and previously published anatomical and molecular studies, we explore the evolution of and variation within venomous fishes. We show the results of the first multi-locus, ordinal-level phylogenetic analysis of cartilaginous (Chondrichthyes) and ray-finned (Actinopterygii) fishes that hypothesizes 18 independent evolutions of this specialization. Ancestral-states reconstruction indicates that among the 2386-2962 extant venomous fishes, envenomed structures have evolved four times in cartilaginous fishes, once in eels (Anguilliformes), once in catfishes (Siluriformes), and 12 times in spiny-rayed fishes (Acanthomorpha). From our anatomical studies and phylogenetic reconstruction, we show that dorsal spines are the most common envenomed structures (∼95% of venomous fish species and 15 independent evolutions). In addition to envenomed spines, fishes have also evolved venomous fangs (2% of venomous fish species, two independent evolutions), cleithral spines (2% of venomous fish species, one independent evolution), and opercular or subopercular spines (1% of venomous fish species, three independent evolutions). © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

The SNAP Platform: Social Networking for Academic Purposes

ERIC Educational Resources Information Center

Kirkwood, Keith

2010-01-01

Purpose: This paper aims to introduce an enterprise-wide Web 2.0 learning support platform--SNAP, developed at Victoria University in Melbourne, Australia. Design/methodology/approach: Pointing to the evolution of the social web, the paper discusses the potential for the development of e-learning platforms that employ constructivist, connectivist,…

Spider Webs and Silks.

ERIC Educational Resources Information Center

Vollrath, Fritz

1992-01-01

Compares the attributes of the silk from spiders with those of the commercially harvested silk from silkworms. Discusses the evolution, design, and effectiveness of spider webs; the functional mechanics of the varieties of silk that can be produced by the same spider; and the composite, as well as molecular, structure of spider silk thread. (JJK)

Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.

PubMed

Cui, Rongfeng; Schumer, Molly; Kruesi, Karla; Walter, Ronald; Andolfatto, Peter; Rosenthal, Gil G

2013-08-01

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Global vegetation distribution and terrestrial climate evolution at the Eocene-Oligocene transition

NASA Astrophysics Data System (ADS)

Pound, Matthew; Salzmann, Ulrich

2016-04-01

The Eocene - Oligocene transition (EOT; ca. 34-33.5 Ma) is widely considered to be the biggest step in Cenozoic climate evolution. Geochemical marine records show both surface and bottom water cooling, associated with the expansion of Antarctic glaciers and a reduction in the atmospheric CO2 concentration. However, the global response of the terrestrial biosphere to the EOT is less well understood and not uniform when comparing different regions. We present new global vegetation and terrestrial climate reconstructions of the Priabonian (late Eocene; 38-33.9 Ma) and Rupelian (early Oligocene; 33.9-28.45 Ma) by synthesising 215 pollen and spore localities. Using presence/absence data of pollen and spores with multivariate statistics has allowed the reconstruction of palaeo-biomes without relying on modern analogues. The reconstructed palaeo-biomes do not show the equator-ward shift at the EOT, which would be expected from a global cooling. Reconstructions of mean annual temperature, cold month mean temperature and warm month mean temperature do not show a global cooling of terrestrial climate across the EOT. Our new reconstructions differ from previous global syntheses by being based on an internally consistent statistically defined classification of palaeo-biomes and our terrestrial based climate reconstructions are in stark contrast to some marine based climate estimates. Our results raise new questions on the nature and extent of terrestrial global climate change at the EOT.

Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (mammalia, carnivora).

PubMed

Finarelli, John A; Goswami, Anjali

2013-12-01

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead-up to extant taxa; they represent now-extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC-based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant-only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep-time organismal evolution in the absence of deep-time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies. © 2013 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Owl Pellet Paleontology

ERIC Educational Resources Information Center

McAlpine, Lisa K.

2013-01-01

In this activity for the beginning of a high school Biology 1 evolution unit, students are challenged to reconstruct organisms found in an owl pellet as a model for fossil reconstruction. They work in groups to develop hypotheses about what animal they have found, what environment it inhabited, and what niche it filled. At the end of the activity,…

Optimized satellite image compression and reconstruction via evolution strategies

NASA Astrophysics Data System (ADS)

Babb, Brendan; Moore, Frank; Peterson, Michael

2009-05-01

This paper describes the automatic discovery, via an Evolution Strategy with Covariance Matrix Adaptation (CMA-ES), of vectors of real-valued coefficients representing matched forward and inverse transforms that outperform the 9/7 Cohen-Daubechies-Feauveau (CDF) discrete wavelet transform (DWT) for satellite image compression and reconstruction under conditions subject to quantization error. The best transform evolved during this study reduces the mean squared error (MSE) present in reconstructed satellite images by an average of 33.78% (1.79 dB), while maintaining the average information entropy (IE) of compressed images at 99.57% in comparison to the wavelet. In addition, this evolved transform achieves 49.88% (3.00 dB) average MSE reduction when tested on 80 images from the FBI fingerprint test set, and 42.35% (2.39 dB) average MSE reduction when tested on a set of 18 digital photographs, while achieving average IE of 104.36% and 100.08%, respectively. These results indicate that our evolved transform greatly improves the quality of reconstructed images without substantial loss of compression capability over a broad range of image classes.

Monochromatic-beam-based dynamic X-ray microtomography based on OSEM-TV algorithm.

PubMed

Xu, Liang; Chen, Rongchang; Yang, Yiming; Deng, Biao; Du, Guohao; Xie, Honglan; Xiao, Tiqiao

2017-01-01

Monochromatic-beam-based dynamic X-ray computed microtomography (CT) was developed to observe evolution of microstructure inside samples. However, the low flux density results in low efficiency in data collection. To increase efficiency, reducing the number of projections should be a practical solution. However, it has disadvantages of low image reconstruction quality using the traditional filtered back projection (FBP) algorithm. In this study, an iterative reconstruction method using an ordered subset expectation maximization-total variation (OSEM-TV) algorithm was employed to address and solve this problem. The simulated results demonstrated that normalized mean square error of the image slices reconstructed by the OSEM-TV algorithm was about 1/4 of that by FBP. Experimental results also demonstrated that the density resolution of OSEM-TV was high enough to resolve different materials with the number of projections less than 100. As a result, with the introduction of OSEM-TV, the monochromatic-beam-based dynamic X-ray microtomography is potentially practicable for the quantitative and non-destructive analysis to the evolution of microstructure with acceptable efficiency in data collection and reconstructed image quality.

Comparative analysis of gene regulatory networks: from network reconstruction to evolution.

PubMed

Thompson, Dawn; Regev, Aviv; Roy, Sushmita

2015-01-01

Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequence to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: cosmic flows and cosmic web from luminous red galaxies

NASA Astrophysics Data System (ADS)

Ata, Metin; Kitaura, Francisco-Shu; Chuang, Chia-Hsun; Rodríguez-Torres, Sergio; Angulo, Raul E.; Ferraro, Simone; Gil-Marín, Hector; McDonald, Patrick; Hernández Monteagudo, Carlos; Müller, Volker; Yepes, Gustavo; Autefage, Mathieu; Baumgarten, Falk; Beutler, Florian; Brownstein, Joel R.; Burden, Angela; Eisenstein, Daniel J.; Guo, Hong; Ho, Shirley; McBride, Cameron; Neyrinck, Mark; Olmstead, Matthew D.; Padmanabhan, Nikhil; Percival, Will J.; Prada, Francisco; Rossi, Graziano; Sánchez, Ariel G.; Schlegel, David; Schneider, Donald P.; Seo, Hee-Jong; Streblyanska, Alina; Tinker, Jeremy; Tojeiro, Rita; Vargas-Magana, Mariana

2017-06-01

We present a Bayesian phase-space reconstruction of the cosmic large-scale matter density and velocity fields from the Sloan Digital Sky Survey-III Baryon Oscillations Spectroscopic Survey Data Release 12 CMASS galaxy clustering catalogue. We rely on a given Λ cold dark matter cosmology, a mesh resolution in the range of 6-10 h-1 Mpc, and a lognormal-Poisson model with a redshift-dependent non-linear bias. The bias parameters are derived from the data and a general renormalized perturbation theory approach. We use combined Gibbs and Hamiltonian sampling, implemented in the argo code, to iteratively reconstruct the dark matter density field and the coherent peculiar velocities of individual galaxies, correcting hereby for coherent redshift space distortions. Our tests relying on accurate N-body-based mock galaxy catalogues show unbiased real space power spectra of the non-linear density field up to k ˜ 0.2 h Mpc-1, and vanishing quadrupoles down to r ˜ 20 h-1 Mpc. We also demonstrate that the non-linear cosmic web can be obtained from the tidal field tensor based on the Gaussian component of the reconstructed density field. We find that the reconstructed velocities have a statistical correlation coefficient compared to the true velocities of each individual light-cone mock galaxy of r ˜ 0.68 including about 10 per cent of satellite galaxies with virial motions (about r = 0.75 without satellites). The power spectra of the velocity divergence agree well with theoretical predictions up to k ˜ 0.2 h Mpc-1. This work will be especially useful to improve, for example, baryon acoustic oscillation reconstructions, kinematic Sunyaev-Zeldovich, integrated Sachs-Wolfe measurements or environmental studies.

Comparison of 3d Reconstruction Services and Terrestrial Laser Scanning for Cultural Heritage Documentation

NASA Astrophysics Data System (ADS)

Rasztovits, S.; Dorninger, P.

2013-07-01

Terrestrial Laser Scanning (TLS) is an established method to reconstruct the geometrical surface of given objects. Current systems allow for fast and efficient determination of 3D models with high accuracy and richness in detail. Alternatively, 3D reconstruction services are using images to reconstruct the surface of an object. While the instrumental expenses for laser scanning systems are high, upcoming free software services as well as open source software packages enable the generation of 3D models using digital consumer cameras. In addition, processing TLS data still requires an experienced user while recent web-services operate completely automatically. An indisputable advantage of image based 3D modeling is its implicit capability for model texturing. However, the achievable accuracy and resolution of the 3D models is lower than those of laser scanning data. Within this contribution, we investigate the results of automated web-services for image based 3D model generation with respect to a TLS reference model. For this, a copper sculpture was acquired using a laser scanner and using image series of different digital cameras. Two different webservices, namely Arc3D and AutoDesk 123D Catch were used to process the image data. The geometric accuracy was compared for the entire model and for some highly structured details. The results are presented and interpreted based on difference models. Finally, an economical comparison of the generation of the models is given considering the interactive and processing time costs.

Propeller Perforator Flaps in Distal Lower Leg: Evolution and Clinical Applications

PubMed Central

2012-01-01

Simple or complex defects in the lower leg, and especially in its distal third, continue to be a challenging task for reconstructive surgeons. A variety of flaps were used in the attempt to achieve excellence in form and function. After a long evolution of the reconstructive methods, including random pattern flaps, axial pattern flaps, musculocutaneous flaps and fasciocutaneous flaps, the reappraisal of the works of Manchot and Salmon by Taylor and Palmer opened the era of perforator flaps. This era began in 1989, when Koshima and Soeda, and separately Kroll and Rosenfield described the first applications of such flaps. Perforator flaps, whether free or pedicled, gained a high popularity due to their main advantages: decreasing donor-site morbidity and improving aesthetic outcome. The use as local perforator flaps in lower leg was possible due to a better understanding of the cutaneous circulation, leg vascular anatomy, angiosome and perforasome concepts, as well as innovations in flaps design. This review will describe the evolution, anatomy, flap design, and technique of the main distally pedicled propeller perforator flaps used in the reconstruction of defects in the distal third of the lower leg and foot. PMID:22783507

Using a dynamical advection to reconstruct a part of the SSH evolution in the context of SWOT, application to the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Rogé, Marine; Morrow, Rosemary; Ubelmann, Clément; Dibarboure, Gérald

2017-08-01

The main oceanographic objective of the future SWOT mission is to better characterize the ocean mesoscale and sub-mesoscale circulation, by observing a finer range of ocean topography dynamics down to 20 km wavelength. Despite the very high spatial resolution of the future satellite, it will not capture the time evolution of the shorter mesoscale signals, such as the formation and evolution of small eddies. SWOT will have an exact repeat cycle of 21 days, with near repeats around 5-10 days, depending on the latitude. Here, we investigate a technique to reconstruct the missing 2D SSH signal in the time between two satellite revisits. We use the dynamical interpolation (DI) technique developed by Ubelmann et al. (2015). Based on potential vorticity (hereafter PV) conservation using a one and a half layer quasi-geostrophic model, it features an active advection of the SSH field. This model has been tested in energetic open ocean regions such as the Gulf Stream and the Californian Current, and has given promising results. Here, we test this model in the Western Mediterranean Sea, a lower energy region with complex small scale physics, and compare the SSH reconstruction with the high-resolution Symphonie model. We investigate an extension of the simple dynamical model including a separated mean circulation. We find that the DI gives a 16-18% improvement in the reconstruction of the surface height and eddy kinetic energy fields, compared with a simple linear interpolation, and a 37% improvement in the Northern Current subregion. Reconstruction errors are higher during winter and autumn but statistically, the improvement from the DI is also better for these seasons.

Mandible reconstruction: History, state of the art and persistent problems.

PubMed

Ferreira, José J; Zagalo, Carlos M; Oliveira, Marta L; Correia, André M; Reis, Ana R

2015-06-01

Mandibular reconstruction has been experiencing an amazing evolution. Several different approaches are used to reconstruct this bone and therefore have a fundamental role in the recovery of oral functions. This review aims to highlight the persistent problems associated with the approaches identified, whether bone grafts or prosthetic devices are used. A brief summary of the historical evolution of the surgical procedures is presented, as well as an insight into possible future pathways. A literature review was conducted from September to December 2012 using the PubMed database. The keyword used was "mandible reconstruction." Articles published in the last three years were included as well as the relevant references from those articles and the "historical articles" were referred. This research resulted in a monograph that this article aims to summarize. Titanium plates, bone grafts, pediculate flaps, free osteomyocutaneous flaps, rapid prototyping, and tissue engineering strategies are some of the identified possibilities. The classical approaches present considerable associated morbidity donor-site-related problems. Research that results in the development of new prosthetics devices is needed. A new prosthetic approach could minimize the identified problems and offer the patients more predictable, affordable, and comfortable solutions. This review, while affirming the evolution and the good results found with the actual approaches, emphasizes the negative aspects that still subsist. Thus, it shows that mandible reconstruction is not a closed issue. On the contrary, it remains as a research field where new findings could have a direct positive impact on patients' life quality. The identification of the persistent problems reveals the characteristics to be considered in a new prosthetic device. This could overcome the current difficulties and result in more comfortable solutions. Medical teams have the responsibility to keep patients informed about the predictable problems related with each elected approach, even understanding that a perfect reconstruction is a secondary goal when compared with maintenance of life. © The International Society for Prosthetics and Orthotics 2014.

High-resolution phylogenic microbial community profiling

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

NAS operational evolution plan : a foundation for capacity enhancement 2001-2010

DOT National Transportation Integrated Search

2001-06-01

This series of World Wide Web slides focuses on the Operational Evolution Plan, which is a 10-year plan for aviation operational improvements to increase capacity and safety in the United States. This plan is unique in that it integrates all actions:...

Higher order reconstruction for MRI in the presence of spatiotemporal field perturbations.

PubMed

Wilm, Bertram J; Barmet, Christoph; Pavan, Matteo; Pruessmann, Klaas P

2011-06-01

Despite continuous hardware advances, MRI is frequently subject to field perturbations that are of higher than first order in space and thus violate the traditional k-space picture of spatial encoding. Sources of higher order perturbations include eddy currents, concomitant fields, thermal drifts, and imperfections of higher order shim systems. In conventional MRI with Fourier reconstruction, they give rise to geometric distortions, blurring, artifacts, and error in quantitative data. This work describes an alternative approach in which the entire field evolution, including higher order effects, is accounted for by viewing image reconstruction as a generic inverse problem. The relevant field evolutions are measured with a third-order NMR field camera. Algebraic reconstruction is then formulated such as to jointly minimize artifacts and noise in the resulting image. It is solved by an iterative conjugate-gradient algorithm that uses explicit matrix-vector multiplication to accommodate arbitrary net encoding. The feasibility and benefits of this approach are demonstrated by examples of diffusion imaging. In a phantom study, it is shown that higher order reconstruction largely overcomes variable image distortions that diffusion gradients induce in EPI data. In vivo experiments then demonstrate that the resulting geometric consistency permits straightforward tensor analysis without coregistration. Copyright © 2011 Wiley-Liss, Inc.

Reconstruction of high temporal resolution Thomson scattering data during a modulated electron cyclotron resonance heating using conditional averaging

NASA Astrophysics Data System (ADS)

Kobayashi, T.; Ida, K.; Itoh, K.; Yoshinuma, M.; Moon, C.; Inagaki, S.; Yamada, I.; Funaba, H.; Yasuhara, R.; Tsuchiya, H.; Ohdachi, S.; Yoshimura, Y.; Igami, H.; Shimozuma, T.; Kubo, S.; Tsujimura, T. I.

2016-04-01

This paper provides a software application of the sampling scope concept for fusion research. The time evolution of Thomson scattering data is reconstructed with a high temporal resolution during a modulated electron cyclotron resonance heating (MECH) phase. The amplitude profile and the delay time profile of the heat pulse propagation are obtained from the reconstructed signal for discharges having on-axis and off-axis MECH depositions. The results are found to be consistent with the MECH deposition.

Reconstruction of high temporal resolution Thomson scattering data during a modulated electron cyclotron resonance heating using conditional averaging

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

Kobayashi, T., E-mail: kobayashi.tatsuya@LHD.nifs.ac.jp; Yoshinuma, M.; Ohdachi, S.

2016-04-15

This paper provides a software application of the sampling scope concept for fusion research. The time evolution of Thomson scattering data is reconstructed with a high temporal resolution during a modulated electron cyclotron resonance heating (MECH) phase. The amplitude profile and the delay time profile of the heat pulse propagation are obtained from the reconstructed signal for discharges having on-axis and off-axis MECH depositions. The results are found to be consistent with the MECH deposition.

Reconstruction of high temporal resolution Thomson scattering data during a modulated electron cyclotron resonance heating using conditional averaging.

PubMed

Kobayashi, T; Ida, K; Itoh, K; Yoshinuma, M; Moon, C; Inagaki, S; Yamada, I; Funaba, H; Yasuhara, R; Tsuchiya, H; Ohdachi, S; Yoshimura, Y; Igami, H; Shimozuma, T; Kubo, S; Tsujimura, T I

2016-04-01

This paper provides a software application of the sampling scope concept for fusion research. The time evolution of Thomson scattering data is reconstructed with a high temporal resolution during a modulated electron cyclotron resonance heating (MECH) phase. The amplitude profile and the delay time profile of the heat pulse propagation are obtained from the reconstructed signal for discharges having on-axis and off-axis MECH depositions. The results are found to be consistent with the MECH deposition.

Content-Based Personalization Services Integrating Folksonomies

NASA Astrophysics Data System (ADS)

Musto, Cataldo; Narducci, Fedelucio; Lops, Pasquale; de Gemmis, Marco; Semeraro, Giovanni

Basic content-based personalization consists in matching up the attributes of a user profile, in which preferences and interests are stored, with the attributes of a content object. The Web 2.0 (r)evolution has changed the game for personalization, from ‘elitary’ Web 1.0, written by few and read by many, to web content generated by everyone (user-generated content - UGC), since the role of people has evolved from passive consumers of information to that of active contributors.

How happy is your web browsing? A model to quantify satisfaction of an Internet user searching for desired information

NASA Astrophysics Data System (ADS)

Banerji, Anirban; Magarkar, Aniket

2012-09-01

We feel happy when web browsing operations provide us with necessary information; otherwise, we feel bitter. How to measure this happiness (or bitterness)? How does the profile of happiness grow and decay during the course of web browsing? We propose a probabilistic framework that models the evolution of user satisfaction, on top of his/her continuous frustration at not finding the required information. It is found that the cumulative satisfaction profile of a web-searching individual can be modeled effectively as the sum of a random number of random terms, where each term is a mutually independent random variable, originating from ‘memoryless’ Poisson flow. Evolution of satisfaction over the entire time interval of a user’s browsing was modeled using auto-correlation analysis. A utilitarian marker, a magnitude of greater than unity of which describes happy web-searching operations, and an empirical limit that connects user’s satisfaction with his frustration level-are proposed too. The presence of pertinent information in the very first page of a website and magnitude of the decay parameter of user satisfaction (frustration, irritation etc.) are found to be two key aspects that dominate the web user’s psychology. The proposed model employed different combinations of decay parameter, searching time and number of helpful websites. The obtained results are found to match the results from three real-life case studies.

Higher Education on the Web.

ERIC Educational Resources Information Center

Lee, John

2001-01-01

The investment in information technology has doubled for colleges over the last 10 years, and the next big evolution, the development of Web-based learning, is well underway. Most colleges and universities have a strategic plan for distance education or are developing one. The effort is led by community colleges and private universities, both of…

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

USDA-ARS?s Scientific Manuscript database

Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

BioTapestry now provides a web application and improved drawing and layout tools

PubMed Central

Paquette, Suzanne M.; Leinonen, Kalle; Longabaugh, William J.R.

2016-01-01

Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows. PMID:27134726

Signal conflict in spider webs driven by predators and prey

PubMed Central

Blackledge, T. A.

1998-01-01

Variation in the sensory physiologies of organisms can bias the receptions of signals, driving the direction of signal evolution. Sensory drive in the evolution of signals may be particularly important for organisms that confront trade-offs in signal design between the need for conspicuousness to allow effective transfer of information and the need for crypsis of the signal to unintended receivers. Several genera of orb-weaving spiders include conspicuous silk designs, stabilimenta, in the centre of their webs. Stabilimenta can be highly visible signals to predators, warning them of the presence of a noxious, sticky silk web. However, stabilimenta can also be used by prey as a signal in avoidance of webs, creating a trade-off in signal visibility. I argue that the derived spectral properties of stabilimentum silk have resulted in part from this conflict. The innate colour preferences of insects, their ability to learn colours, and the spectral properties of flowers all suggest that the reflectance spectra of stabilimenta renders them relatively cryptic to many insect prey, while maintaining their visibility to vertebrate predators.

BioTapestry now provides a web application and improved drawing and layout tools.

PubMed

Paquette, Suzanne M; Leinonen, Kalle; Longabaugh, William J R

2016-01-01

Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows.

Evolution of health web certification through the HONcode experience.

PubMed

Boyer, Célia; Baujard, Vincent; Geissbuhler, Antoine

2011-01-01

Today, the Web is a media with increasing pervasiveness around the world. Its use is constantly growing and the medical field is no exception. With this large amount of information, the problem is no longer about finding information but assessing the credibility of the publishers as well as the relevance and accuracy of the documents retrieved from the web. This problem is particularly relevant in the medical area which has a direct impact on the well-being of citizens and in the Web 2.0 context where information publishing is easier than ever. To address the quality of the medical Internet, the HONcode certification proposed by the Health On the Net Foundation (HON) is certainly the most successful initiative. The aims of this paper are to present certification activity through the HONcode experience and to show that certification is more complex than a simple code of conduct. Therefore, we first present the HONcode, its application and its current evolutions. Following that, we give some quantitative results and describe how the final user can access the certified information.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

PubMed

Kwon, Daehong; Lee, Daehwan; Kim, Juyeon; Lee, Jongin; Sim, Mikang; Kim, Jaebum

2018-05-09

Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.

Visualization on the Web of 20 Years of Crop Rotation and Wildlife Co-Evolutions

NASA Astrophysics Data System (ADS)

Plumejeaud-Perreau, Christine; Poitevin, Cyril; Bretagnolle, Vincent

2018-05-01

The accumulation of evidences of the effects of intensive agricultural practices against wildlife fauna and flora, and biodiversity in general, has been largely published in scientific papers (Tildman, 1999). However, data serving as sup-port to their conclusions are often kept hidden behind research institutions. This paper presents a data visualization sys-tem opened on the Web allowing citizens to get a comprehensive access to data issued from such kind of research institution, collected for more than 20 years. The Web Information System has been thought in order to ease the comparison of data issues from various databases describing the same object, the agricultural landscape, at different scales and through different observation devices. An interactive visualization is proposed in order to check co-evolution of fauna and flora together with agricultural practices. It mixes aerial orthoimagery produced since 1950 with vectorial data showing the evolutions of agricultural parcels with those of a few sentinel species such as the Montagu's harrier. This is made through a composition of maps, charts and time lines, and specific tools for comparison. A particular concern is given to the observation effort bias in order to show meaningful statistical aggregates.

Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

PubMed

Tonnabel, Jeanne; Mignot, Agnès; Douzery, Emmanuel J P; Rebelo, Anthony G; Schurr, Frank M; Midgley, Jeremy; Illing, Nicola; Justy, Fabienne; Orcel, Denis; Olivieri, Isabelle

2014-10-01

Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life-history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life-history strategies. We found that species with longer seed-dispersal distances tended to evolve lower pollen-dispersal distance, that insect-pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed-bank evolved toward reduced fire-survival ability of adults. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria.

PubMed

Puttick, Mark N; Thomas, Gavin H

2015-12-22

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns. © 2015 The Authors.

Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria

PubMed Central

Puttick, Mark N.; Thomas, Gavin H.

2015-01-01

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns. PMID:26674947

Technique of nonvascularized toe phalangeal transfer and distraction lengthening in the treatment of multiple digit symbrachydactyly.

PubMed

Netscher, David T; Lewis, Eric V

2008-06-01

A combination of nonvascularized multiple toe phalangeal transfers, web space deepening, and distraction lengthening may provide excellent function in the child born with the oligodactylous type of symbrachydactyly. These techniques may reconstruct multiple digits, maintaining a wide and stable grip span with good prehension to the thumb. We detail the techniques of each of these 3 stages in reconstruction and describe appropriate patient selection. Potential complications are discussed. However, with strict attention to technical details, these complications can be minimized.

Enquire within: cultural evolution and cognitive science.

PubMed

Heyes, Cecilia

2018-04-05

Cultural evolution and cognitive science need each other. Cultural evolution needs cognitive science to find out whether the conditions necessary for Darwinian evolution are met in the cultural domain. Cognitive science needs cultural evolution to explain the origins of distinctively human cognitive processes. Focusing on the first question, I argue that cultural evolutionists can get empirical traction on third-way cultural selection by rooting the distinction between replication and reconstruction, two modes of cultural inheritance, in the distinction between System 1 and System 2 cognitive processes. This move suggests that cultural epidemiologists are right in thinking that replication has higher fidelity than reconstruction, and replication processes are not genetic adaptations for culture, but wrong to assume that replication is rare. If replication is not rare, an important requirement for third-way cultural selection, one-shot fidelity , is likely to be met. However, there are other requirements, overlooked by dual-inheritance theorists when they conflate strong (Darwinian) and weak (choice) senses of 'cultural selection', including dumb choices and recurrent fidelity In a second excursion into cognitive science, I argue that these requirements can be met by metacognitive social learning strategies , and trace the origins of these distinctively human cognitive processes to cultural evolution. Like other forms of cultural learning, they are not cognitive instincts but cognitive gadgets.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

The molecular origin and evolution of dim-light vision in mammals.

PubMed

Bickelmann, Constanze; Morrow, James M; Du, Jing; Schott, Ryan K; van Hazel, Ilke; Lim, Steve; Müller, Johannes; Chang, Belinda S W

2015-11-01

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The role of capture spiral silk properties in the diversification of orb webs.

PubMed

Tarakanova, Anna; Buehler, Markus J

2012-12-07

Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification.

Reconstruction of the mandible and the maxilla: the evolution of surgical technique.

PubMed

Genden, Eric M

2010-01-01

The upper and lower jaws play an essential role in mastication, articulation, and cosmetic form. The mandible provides support for tongue position and elevation of the larynx during swallowing, while the maxilla provides support for the nasal structures as well as an opposing structure to the mandible during mastication. The evolution of mandibular and maxillary reconstruction dates back to the early 19th century. Before the introduction of free tissue transfer, a variety of local flaps, regional flaps, and prosthetics were introduced, yet each was met with eventual failure. Since the introduction of free tissue transfer, mandibular and maxillary reconstruction has become as much of an art as it has a science. Whether the mandibular or the palatomaxillary defects are a result of trauma, congenital deformity, or tumor extirpation, the resultant effect often disrupts both form and function. With these considerations taken together, jaw reconstruction is a unique undertaking in which the artistic reconstruction of the facial skeleton is met with the science of reestablishing the mechanics of mastication. The site, size, and associated soft-tissue defects represent the 3 most important factors in determining the impact of a given defect on function and aesthetics. There is also an inherent difference between defects that are sustained in a controlled fashion, such as during cancer ablation, and those that result from trauma. The consideration of these complexities in jaw reconstruction is reflected in the wide variety of approaches and techniques that have evolved over the past century.

Post-launch analysis of the deployment dynamics of a space web sounding rocket experiment

NASA Astrophysics Data System (ADS)

Mao, Huina; Sinn, Thomas; Vasile, Massimiliano; Tibert, Gunnar

2016-10-01

Lightweight deployable space webs have been proposed as platforms or frames for a construction of structures in space where centrifugal forces enable deployment and stabilization. The Suaineadh project was aimed to deploy a 2 × 2m2 space web by centrifugal forces in milli-gravity conditions and act as a test bed for the space web technology. Data from former sounding rocket experiments, ground tests and simulations were used to design the structure, the folding pattern and control parameters. A developed control law and a reaction wheel were used to control the deployment. After ejection from the rocket, the web was deployed but entanglements occurred since the web did not start to deploy at the specified angular velocity. The deployment dynamics was reconstructed from the information recorded in inertial measurement units and cameras. The nonlinear torque of the motor used to drive the reaction wheel was calculated from the results. Simulations show that if the Suaineadh started to deploy at the specified angular velocity, the web would most likely have been deployed and stabilized in space by the motor, reaction wheel and controller used in the experiment.

The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs.

PubMed

Nenzén, Hedvig K; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.

The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs

PubMed Central

Nenzén, Hedvig K.; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities. PMID:25207754

Femtosecond movies of water near interfaces at sub-Angstrom resolution

NASA Astrophysics Data System (ADS)

Coridan, Robert; Hwee Lai, Ghee; Schmidt, Nathan; Abbamonte, Peter; Wong, Gerard C. L.

2010-03-01

The behavior of liquid water near interfaces with nanoscopic variations in chemistry influences a broad range of phenomena in biology. Using inelastic x-ray scattering (IXS) data from 3rd-generation synchrotron x-ray sources, we reconstruct the Greens function of liquid water, which describes the å-scale spatial and femtosecond-scale temporal evolution of density fluctuations. We extend this response function formalism to reconstruct the evolution of hydration structures near dynamic surfaces with different charge distributions, in order to define more precisely the molecular signature of hydrophilicity and hydrophobicity. Moreover, we investigate modifications to surface hydration structures and dynamics as the size of hydrophilic and hydrophobic patches are varied.

Addressing Female Genital Mutilation/Cutting (FGM/C) in the Era of Clitoral Reconstruction: Plastic Surgery.

PubMed

Sigurjonsson, Hannes; Jordal, Malin

2018-01-01

The aim of this review is to give an overview of the recent evidence on clitoral reconstruction and other relevant reconstructive plastic surgery measures after female genital mutilation/cutting (FGM/C). Recent publications present refinements and modifications of the surgical technique of clitoral reconstruction along with reconstruction of the labia majora and clitoral hood. Novel approaches with reposition of the clitoral nerve, anchoring of the labia majora, fat grafting, and full thickness mucosa grafts have been introduced. The current evidence on outcomes of clitoral reconstruction shows potential benefits. However, there is a risk of postoperative complications and a negative outcome. Experts in the field advocate for a multidisciplinary approach including psychosexual counseling and health education with or without subsequent clitoral reconstructive surgery. The evolution of reconstructive treatment for women with FGM/C is expanding, however at a slow rate. The scarcity of evidence on clitoral reconstruction halters availability of clinical guidelines and consensus regarding best practice. Clitoral reconstruction should be provided by multidisciplinary referral centers in a research setting with long-term follow-up on outcomes of postoperative morbidity and possible benefits.

ClonEvol: clonal ordering and visualization in cancer sequencing.

PubMed

Dang, H X; White, B S; Foltz, S M; Miller, C A; Luo, J; Fields, R C; Maher, C A

2017-12-01

Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones throughout metastatic progression observed in the tumors of a published breast cancer patient. ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine. ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

With the evolution of web based technologies, especially HTML5 [1], it becomes possible to create web-based control system user interfaces (UI) that are cross-browser and cross-device compatible. This article describes two technologies that facilitate this goal. The first one is the WebOPI [2], which can seamlessly display CSS BOY [3] Operator Interfaces (OPI) in web browsers without modification to the original OPI file. The WebOPI leverages the powerful graphical editing capabilities of BOY and provides the convenience of re-using existing OPI files. On the other hand, it uses generic JavaScript and a generic communication mechanism between the web browser andmore » web server. It is not optimized for a control system, which results in unnecessary network traffic and resource usage. Our second technology is the WebSocket-based Process Data Access (WebPDA) [4]. It is a protocol that provides efficient control system data communication using WebSocket [5], so that users can create web-based control system UIs using standard web page technologies such as HTML, CSS and JavaScript. WebPDA is control system independent, potentially supporting any type of control system.« less

Monitoring of the data processing and simulated production at CMS with a web-based service: the Production Monitoring Platform (pMp)

NASA Astrophysics Data System (ADS)

Franzoni, G.; Norkus, A.; Pol, A. A.; Srimanobhas, N.; Walker, J.

2017-10-01

Physics analysis at the Compact Muon Solenoid requires both the production of simulated events and processing of the data collected by the experiment. Since the end of the LHC Run-I in 2012, CMS has produced over 20 billion simulated events, from 75 thousand processing requests organised in one hundred different campaigns. These campaigns emulate different configurations of collision events, the detector, and LHC running conditions. In the same time span, sixteen data processing campaigns have taken place to reconstruct different portions of the Run-I and Run-II data with ever improving algorithms and calibrations. The scale and complexity of the events simulation and processing, and the requirement that multiple campaigns must proceed in parallel, demand that a comprehensive, frequently updated and easily accessible monitoring be made available. The monitoring must serve both the analysts, who want to know which and when datasets will become available, and the central production teams in charge of submitting, prioritizing, and running the requests across the distributed computing infrastructure. The Production Monitoring Platform (pMp) web-based service, has been developed in 2015 to address those needs. It aggregates information from multiple services used to define, organize, and run the processing requests. Information is updated hourly using a dedicated elastic database and the monitoring provides multiple configurable views to assess the status of single datasets as well as entire production campaigns. This contribution will describe the pMp development, the evolution of its functionalities, and one and half year of operational experience.

3D Studies of the Solar Corona and its Evolution with SOHO/EIT

NASA Astrophysics Data System (ADS)

Portier-Fozzani, F.

This thesis deals with 3D evolution of coronal structures based upon the ultraviolet telescope of SOHO : EIT. Anaglyphs and incertainties on a complete stereovision reconstruction are described. Stereoscopic methods for loop reconstruction were successfully made to find 3D parameters. With dynamical stereoscopy, physical conditions were derived for 30 loops of temperature around 1MK. A method which is able to derive twist variation were also built. Emerging loops were found highly twisted and they detwist as they grow. According to helicity conservation, this correspond to a transfert of twist into expansion. Long time twist evolution of magnetic flux tubes are followed in relation with flares as relaxation. Interaction between magnetic field lines were analysed. An example of reconnection between open and closed field line were observed. Other interactions were found with multi-wavelength observations : coronal holes borders (and thus CH) are better defined when an active region nearby is growing. Other imaging techniques were used to better take profit as possible of SOHO/EIT. A multiscale vision model (MVM) was applied with success to show small coronal structures evolutions hidden by the noise level.

Deconstruction and Reconstruction of Legal Education in China: Legitimacy and Diffusion of an Academic Discipline from 1949 to 2012

ERIC Educational Resources Information Center

Liu, Zixi; Ting, Kwok-Fai

2017-01-01

Using documentary data, we investigate the evolution of legal education in China from 1949 to 2012. During this period, legal education evolved from an illegitimate practice to a legitimate practice over three distinct periods of nullification, reconstruction, and rationalization. Textual data suggest that the legitimization of legal education has…

Reconstructing a School's Past Using Oral Histories and GIS Mapping.

ERIC Educational Resources Information Center

Alibrandi, Marsha; Beal, Candy; Thompson, Ann; Wilson, Anna

2000-01-01

Describes an interdisciplinary project that incorporated language arts, social studies, instructional technology, and science where middle school students were involved in oral history, Geographic Information System (GIS) mapping, architectural research, the science of dendrochronology, and the creation of an archival school Web site. (CMK)

Spatiotemporal evolution of Calophaca (fabaceae) reveals multiple dispersals in central Asian mountains.

PubMed

Zhang, Ming-Li; Wen, Zhi-Bin; Fritsch, Peter W; Sanderson, Stewart C

2015-01-01

The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried out in order to confirm its taxonomic status and reconstruct its evolutionary history. We employed BEAST Bayesian inference for dating, and S-DIVA and BBM for ancestral area reconstruction, to study its spatiotemporal evolution. Our results show that Calophacais monophyletic and nested within Caragana. The divergence time of Calophaca is estimated at ca. 8.0 Ma, most likely driven by global cooling and aridification, influenced by rapid uplift of the Qinghai Tibet Plateau margins. According to ancestral area reconstructions, the genus most likely originated in the Pamir Mountains, a global biodiversity hotspot and hypothesized Tertiary refugium of many Central Asian plant lineages. Dispersals from this location are inferred to the western Tianshan Mountains, then northward to the Tarbagatai Range, eastward to East Asia, and westward to the Caucasus, Russia, and Europe. The spatiotemporal evolution of Calophaca provides a case contributing to an understanding of the flora and biodiversity of the Central Asian mountains and adjacent regions.

Growth and structure of the World Wide Web: Towards realistic modeling

NASA Astrophysics Data System (ADS)

Tadić, Bosiljka

2002-08-01

We simulate evolution of the World Wide Web from the dynamic rules incorporating growth, bias attachment, and rewiring. We show that the emergent double-hierarchical structure with distinct distributions of out- and in-links is comparable with the observed empirical data when the control parameter (average graph flexibility β) is kept in the range β=3-4. We then explore the Web graph by simulating (a) Web crawling to determine size and depth of connected components, and (b) a random walker that discovers the structure of connected subgraphs with dominant attractor and promoter nodes. A random walker that adapts its move strategy to mimic local node linking preferences is shown to have a short access time to "important" nodes on the Web graph.

Reconstruction of disease transmission rates: Applications to measles, dengue, and influenza.

PubMed

Lange, Alexander

2016-07-07

Transmission rates are key in understanding the spread of infectious diseases. Using the framework of compartmental models, we introduce a simple method to reconstruct time series of transmission rates directly from incidence or disease-related mortality data. The reconstruction employs differential equations, which model the time evolution of infective stages and strains. Being sensitive to initial values, the method produces asymptotically correct solutions. The computations are fast, with time complexity being quadratic. We apply the reconstruction to data of measles (England and Wales, 1948-1967), dengue (Thailand, 1982-1999), and influenza (U.S., 1910-1927). The Measles example offers comparison with earlier work. Here we re-investigate reporting corrections, include and exclude demographic information. The dengue example deals with the failure of vector-control measures in reducing dengue hemorrhagic fever (DHF) in Thailand. Two competing mechanisms have been held responsible: strain interaction and demographic transitions. Our reconstruction reveals that both explanations are possible, showing that the increase in DHF cases is consistent with decreasing transmission rates resulting from reduced vector counts. The flu example focuses on the 1918/1919 pandemic, examining the transmission rate evolution for an invading strain. Our analysis indicates that the pandemic strain could have circulated in the population for many months before the pandemic was initiated by an event of highly increased transmission. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

PubMed Central

Mannige, Ranjan V.; Brooks, Charles L.; Shakhnovich, Eugene I.

2012-01-01

Despite progresses in ancestral protein sequence reconstruction, much needs to be unraveled about the nature of the putative last common ancestral proteome that served as the prototype of all extant lifeforms. Here, we present data that indicate a steady decline (oil escape) in proteome hydrophobicity over species evolvedness (node number) evident in 272 diverse proteomes, which indicates a highly hydrophobic (oily) last common ancestor (LCA). This trend, obtained from simple considerations (free from sequence reconstruction methods), was corroborated by regression studies within homologous and orthologous protein clusters as well as phylogenetic estimates of the ancestral oil content. While indicating an inherent irreversibility in molecular evolution, oil escape also serves as a rare and universal reaction-coordinate for evolution (reinforcing Darwin's principle of Common Descent), and may prove important in matters such as (i) explaining the emergence of intrinsically disordered proteins, (ii) developing composition- and speciation-based “global” molecular clocks, and (iii) improving the statistical methods for ancestral sequence reconstruction. PMID:23300421

The Inference of Gene Trees with Species Trees

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

2015-01-01

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

Eocene to mid-Pliocene landscape evolution in Scandinavia inferred from offshore sediment volumes and pre-glacial topography using inverse modelling

NASA Astrophysics Data System (ADS)

Pedersen, Vivi K.; Braun, Jean; Huismans, Ritske S.

2018-02-01

The origin of high topography in Scandinavia is highly debated, both in terms of its age and the underlying mechanism for its formation. Traditionally, the current high topography is assumed to have formed by several Cenozoic (mainly Neogene) phases of surface uplift and dissection of an old peneplain surface. These same surface uplift events are suggested to explain the increased deposition observed in adjacent offshore basins on the Norwegian shelf and in the North Sea. However, more recently it has been suggested that erosion and isostatic rock uplift of existing topography may also explain the recent evolution of topography in Scandinavia. For this latter view, the increased sedimentation towards the present is assumed to be a consequence of a climate related increase in erosion. In this study we explore whether inverse modelling of landscape evolution can give new insight into Eocene to mid-Pliocene (54-4 Ma) landscape evolution in the Scandinavian region. We do this by combining a highly efficient forward-in-time landscape evolution model (FastScape) with an optimization scheme suitable for non-linear inverse problems (the neighbourhood algorithm - NA). To limit our approach to the fluvial regime, we exclude the most recent mid-Pliocene-Quaternary time period where glacial erosion processes are expected to dominate landscape evolution. The "goodness" of our landscape evolution models is evaluated using i) sediment fluxes based on decompacted offshore sediment volumes and ii) maximum pre-glacial topography from a mid-Pliocene landscape, reconstructed using geophysical relief and offshore sediment volumes from the mid-Pliocene-Quaternary. We find several tested scenarios consistent with the offshore sediment record and the maximum elevation for our reconstructed pre-glacial (mid-Pliocene) landscape reconstruction, including: I) substantial initial topography ( 2 km) at 54 Ma and no induced tectonic rock uplift, II) the combination of some initial topography ( 1.1 km) at 54 Ma and minor continued rock uplift (< 0.04 mm/yr) until 4 Ma, and III) a two-phased tectonic rock uplift of an initially low topography ( 0.1 km). However, out of these, only scenario I (no tectonic rock uplift) matches large-scale characteristics of our reconstructed pre-glacial (mid-Pliocene) topography well. Our preferred model for Eocene to mid-Pliocene landscape evolution in Scandinavia is therefore one where high topography ( 2 km) has existed throughout the time interval from 54 to 4 Ma. We do not find several phases of peneplain surface uplift necessary to explain offshore sediment volumes and large-scale topographic patterns. On the contrary, extensive peneplain dissection seems inconsistent with the low rates of erosion we infer based on the offshore sediment volumes.

The Evolution of a National Distance Guidance Service: Trends and Challenges

ERIC Educational Resources Information Center

Watts, A. G.; Dent, Gareth

2008-01-01

Three trends in the evolution of the UK Learndirect advice service are identified: the partial migration from telephone to web-based services; the trend within the telephone service from information/advice-oriented interventions to more guidance-oriented interventions; and the move from a mainly learning-oriented service to a more career-oriented…

Designing a Resource Evolution Support System for Open Knowledge Communities

ERIC Educational Resources Information Center

Yang, Xianmin; Yu, Shengquan

2015-01-01

The continuous generation and evolution of digital learning resources is important for promoting open learning and meeting the personalized needs of learners. In the Web 2.0 era, open and collaborative authoring is becoming a popular method by which to create vast personalized learning resources in open knowledge communities (OKCs). However, the…

A synthetic computational environment: To control the spread of respiratory infections in a virtual university

NASA Astrophysics Data System (ADS)

Ge, Yuanzheng; Chen, Bin; liu, Liang; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2018-02-01

Individual-based computational environment provides an effective solution to study complex social events by reconstructing scenarios. Challenges remain in reconstructing the virtual scenarios and reproducing the complex evolution. In this paper, we propose a framework to reconstruct a synthetic computational environment, reproduce the epidemic outbreak, and evaluate management interventions in a virtual university. The reconstructed computational environment includes 4 fundamental components: the synthetic population, behavior algorithms, multiple social networks, and geographic campus environment. In the virtual university, influenza H1N1 transmission experiments are conducted, and gradually enhanced interventions are evaluated and compared quantitatively. The experiment results indicate that the reconstructed virtual environment provides a solution to reproduce complex emergencies and evaluate policies to be executed in the real world.

Web-based recruitment and survey methodology to capture followers of popular diets: the adhering to dietary approaches for personal taste (ADAPT) feasibility survey

USDA-ARS?s Scientific Manuscript database

Background: Although there is interest in popular diets such as vegan/vegetarian, Paleo, and other whole food diets, existing cohort studies lack specific data for these subgroups. With the evolution of new technologies, such as electronic data capture and web-based surveys, their application to nut...

Bayesian reconstruction of gravitational wave bursts using chirplets

NASA Astrophysics Data System (ADS)

Millhouse, Margaret; Cornish, Neil; Littenberg, Tyson

2017-01-01

The BayesWave algorithm has been shown to accurately reconstruct unmodeled short duration gravitational wave bursts and to distinguish between astrophysical signals and transient noise events. BayesWave does this by using a variable number of sine-Gaussian (Morlet) wavelets to reconstruct data in multiple interferometers. While the Morlet wavelets can be summed together to produce any possible waveform, there could be other wavelet functions that improve the performance. Because we expect most astrophysical gravitational wave signals to evolve in frequency, modified Morlet wavelets with linear frequency evolution - called chirplets - may better reconstruct signals with fewer wavelets. We compare the performance of BayesWave using Morlet wavelets and chirplets on a variety of simulated signals.

Distinct spinning patterns gain differentiated loading tolerance of silk thread anchorages in spiders with different ecology.

PubMed

Wolff, Jonas O; van der Meijden, Arie; Herberstein, Marie E

2017-07-26

Building behaviour in animals extends biological functions beyond bodies. Many studies have emphasized the role of behavioural programmes, physiology and extrinsic factors for the structure and function of buildings. Structure attachments associated with animal constructions offer yet unrealized research opportunities. Spiders build a variety of one- to three-dimensional structures from silk fibres. The evolution of economic web shapes as a key for ecological success in spiders has been related to the emergence of high performance silks and thread coating glues. However, the role of thread anchorages has been widely neglected in those models. Here, we show that orb-web (Araneidae) and hunting spiders (Sparassidae) use different silk application patterns that determine the structure and robustness of the joint in silk thread anchorages. Silk anchorages of orb-web spiders show a greater robustness against different loading situations, whereas the silk anchorages of hunting spiders have their highest pull-off resistance when loaded parallel to the substrate along the direction of dragline spinning. This suggests that the behavioural 'printing' of silk into attachment discs along with spinneret morphology was a prerequisite for the evolution of extended silk use in a three-dimensional space. This highlights the ecological role of attachments in the evolution of animal architectures. © 2017 The Author(s).

Religion, Race, and Reconstruction: The Public School in the Politics of the 1870s. SUNY Series, Religion and American Public Life.

ERIC Educational Resources Information Center

McAfee, Ward M.

This book examines the impact of public education on the national culture in the context of educational reform and Reconstruction during the 1870s. Chapter 1, "Prologue to the Seventies," traces the evolution of the American public school through the social, economic, and industrial changes of the early 19th Century, culminating with the…

The role of capture spiral silk properties in the diversification of orb webs

PubMed Central

Tarakanova, Anna; Buehler, Markus J.

2012-01-01

Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification. PMID:22896566

Cryptic Diversity of African Tigerfish (Genus Hydrocynus) Reveals Palaeogeographic Signatures of Linked Neogene Geotectonic Events

PubMed Central

Goodier, Sarah A. M.; Cotterill, Fenton P. D.; O'Ryan, Colleen; Skelton, Paul H.; de Wit, Maarten J.

2011-01-01

The geobiotic history of landscapes can exhibit controls by tectonics over biotic evolution. This causal relationship positions ecologically specialized species as biotic indicators to decipher details of landscape evolution. Phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, including fishes, can reveal key events of drainage evolution, notably where geochronological resolution is insufficient. Where geochronological resolution is insufficient, phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, notably fishes, can reveal key events of drainage evolution. This study evaluates paleo-environmental causes of mitochondrial DNA (mtDNA) based phylogeographic records of tigerfishes, genus Hydrocynus, in order to reconstruct their evolutionary history in relation to landscape evolution across Africa. Strong geographical structuring in a cytochrome b (cyt-b) gene phylogeny confirms the established morphological diversity of Hydrocynus and reveals the existence of five previously unknown lineages, with Hydrocynus tanzaniae sister to a clade comprising three previously unknown lineages (Groups B, C and D) and H. vittatus. The dated phylogeny constrains the principal cladogenic events that have structured Hydrocynus diversity from the late Miocene to the Plio-Pleistocene (ca. 0–16 Ma). Phylogeographic tests reveal that the diversity and distribution of Hydrocynus reflects a complex history of vicariance and dispersals, whereby range expansions in particular species testify to changes to drainage basins. Principal divergence events in Hydrocynus have interfaced closely with evolving drainage systems across tropical Africa. Tigerfish evolution is attributed to dominant control by pulses of geotectonism across the African plate. Phylogenetic relationships and divergence estimates among the ten mtDNA lineages illustrates where and when local tectonic events modified Africa's Neogene drainage. Haplotypes shared amongst extant Hydrocynus populations across northern Africa testify to recent dispersals that were facilitated by late Neogene connections across the Nilo-Sahelian drainage. These events in tigerfish evolution concur broadly with available geological evidence and reveal prominent control by the African Rift System, evident in the formative events archived in phylogeographic records of tigerfish. PMID:22194910

Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

PubMed Central

Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

2011-01-01

Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

Preventing the collapse of the Baltic cod stock through an ecosystem-based management approach

PubMed Central

Lindegren, Martin; Möllmann, Christian; Nielsen, Anders; Stenseth, Nils C.

2009-01-01

Worldwide a number of fish stocks have collapsed because of overfishing and climate-induced ecosystem changes. Developing ecosystem-based fisheries management (EBFM) to prevent these catastrophic events in the future requires ecological models incorporating both internal food-web dynamics and external drivers such as fishing and climate. Using a stochastic food-web model for a large marine ecosystem (i.e., the Baltic Sea) hosting a commercially important cod stock, we were able to reconstruct the history of the stock. Moreover we demonstrate that in hindsight the collapse could only have been avoidable by adapting fishing pressure to environmental conditions and food-web interactions. The modeling approach presented here represents a significant advance for EBFM, the application of which is important for sustainable resource management in the future. PMID:19706557

Integrated Approach to Reconstruction of Microbial Regulatory Networks

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

Rodionov, Dmitry A; Novichkov, Pavel S

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated inmore » RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.« less

Image processing pipeline for synchrotron-radiation-based tomographic microscopy.

PubMed

Hintermüller, C; Marone, F; Isenegger, A; Stampanoni, M

2010-07-01

With synchrotron-radiation-based tomographic microscopy, three-dimensional structures down to the micrometer level can be visualized. Tomographic data sets typically consist of 1000 to 1500 projections of 1024 x 1024 to 2048 x 2048 pixels and are acquired in 5-15 min. A processing pipeline has been developed to handle this large amount of data efficiently and to reconstruct the tomographic volume within a few minutes after the end of a scan. Just a few seconds after the raw data have been acquired, a selection of reconstructed slices is accessible through a web interface for preview and to fine tune the reconstruction parameters. The same interface allows initiation and control of the reconstruction process on the computer cluster. By integrating all programs and tools, required for tomographic reconstruction into the pipeline, the necessary user interaction is reduced to a minimum. The modularity of the pipeline allows functionality for new scan protocols to be added, such as an extended field of view, or new physical signals such as phase-contrast or dark-field imaging etc.

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

PubMed Central

Szöllősi, Gergely J.; Boussau, Bastien; Abby, Sophie S.; Tannier, Eric; Daubin, Vincent

2012-01-01

The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record. PMID:23043116

Testing the hypothesis on cognitive evolution of modern humans' learning ability: current status of past-climatic approaches.

NASA Astrophysics Data System (ADS)

Yoneda, Minoru; Abe-Ouchi, Ayako; Kawahata, Hodaka; Yokoyama, Yusuke; Oguchi, Takashi

2014-05-01

The impact of climate change on human evolution is important and debating topic for many years. Since 2010, we have involved in a general joint project entitled "Replacement of Neanderthal by Modern Humans: Testing Evolutional Models of Learning", which based on a theoretical prediction that the cognitive ability related to individual and social learning divide fates of ancient humans in very unstable Late Pleistocene climate. This model predicts that the human populations which experienced a series of environmental changes would have higher rate of individual learners, while detailed reconstructions of global climate change have reported fluent and drastic change based on ice cores and stalagmites. However, we want to understand the difference between anatomically modern human which survived and the other archaic extinct humans including European Neanderthals and Asian Denisovans. For this purpose the global synchronized change is not useful for understanding but the regional difference in the amplitude and impact of climate change is the information required. Hence, we invited a geophysicist busing Global Circulation Model to reconstruct the climatic distribution and temporal change in a continental scale. At the same time, some geochemists and geographers construct a database of local climate changes recorded in different proxies. At last, archaeologists and anthropologists tried to interpret the emergence and disappearance of human species in Europe and Asia on the reconstructed past climate maps using some tools, such as Eco-cultural niche model. Our project will show the regional difference in climate change and related archaeological events and its impact on the evolution of learning ability of modern humans.

Reconstructing the temporal ordering of biological samples using microarray data.

PubMed

Magwene, Paul M; Lizardi, Paul; Kim, Junhyong

2003-05-01

Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

Brief communication: 3-D reconstruction of a collapsed rock pillar from Web-retrieved images and terrestrial lidar data - the 2005 event of the west face of the Drus (Mont Blanc massif)

NASA Astrophysics Data System (ADS)

Guerin, Antoine; Abellán, Antonio; Matasci, Battista; Jaboyedoff, Michel; Derron, Marc-Henri; Ravanel, Ludovic

2017-07-01

In June 2005, a series of major rockfall events completely wiped out the Bonatti Pillar located in the legendary Drus west face (Mont Blanc massif, France). Terrestrial lidar scans of the west face were acquired after this event, but no pre-event point cloud is available. Thus, in order to reconstruct the volume and the shape of the collapsed blocks, a 3-D model has been built using photogrammetry (structure-from-motion (SfM) algorithms) based on 30 pictures collected on the Web. All these pictures were taken between September 2003 and May 2005. We then reconstructed the shape and volume of the fallen compartment by comparing the SfM model with terrestrial lidar data acquired in October 2005 and November 2011. The volume is calculated to 292 680 m3 (±5.6 %). This result is close to the value previously assessed by Ravanel and Deline (2008) for this same rock avalanche (265 000 ± 10 000 m3). The difference between these two estimations can be explained by the rounded shape of the volume determined by photogrammetry, which may lead to a volume overestimation. However it is not excluded that the volume calculated by Ravanel and Deline (2008) is slightly underestimated, the thickness of the blocks having been assessed manually from historical photographs.

Automated 3D reconstruction of interiors with multiple scan views

NASA Astrophysics Data System (ADS)

Sequeira, Vitor; Ng, Kia C.; Wolfart, Erik; Goncalves, Joao G. M.; Hogg, David C.

1998-12-01

This paper presents two integrated solutions for realistic 3D model acquisition and reconstruction; an early prototype, in the form of a push trolley, and a later prototype in the form of an autonomous robot. The systems encompass all hardware and software required, from laser and video data acquisition, processing and output of texture-mapped 3D models in VRML format, to batteries for power supply and wireless network communications. The autonomous version is also equipped with a mobile platform and other sensors for the purpose of automatic navigation. The applications for such a system range from real estate and tourism (e.g., showing a 3D computer model of a property to a potential buyer or tenant) or as tool for content creation (e.g., creating 3D models of heritage buildings or producing broadcast quality virtual studios). The system can also be used in industrial environments as a reverse engineering tool to update the design of a plant, or as a 3D photo-archive for insurance purposes. The system is Internet compatible: the photo-realistic models can be accessed via the Internet and manipulated interactively in 3D using a common Web browser with a VRML plug-in. Further information and example reconstructed models are available on- line via the RESOLV web-page at http://www.scs.leeds.ac.uk/resolv/.

Insect form vision as one potential shaping force of spider web decoration design.

PubMed

Cheng, R-C; Yang, E-C; Lin, C-P; Herberstein, M E; Tso, I-M

2010-03-01

Properties of prey sensory systems are important factors shaping the design of signals generated by organisms exploiting them. In this study we assessed how prey sensory preference affected the exploiter signal design by investigating the evolutionary relationship and relative attractiveness of linear and cruciate form web decorations built by Argiope spiders. Because insects have an innate preference for bilaterally symmetrical patterns, we hypothesized that cruciate form decorations were evolved from linear form due to their higher visual attractiveness to insects. We first reconstructed a molecular phylogeny of the Asian members of the genus Argiope using mitochondrial markers to infer the evolutionary relationship of two decoration forms. Results of ancestral character state reconstruction showed that the linear form was ancestral and the cruciate form derived. To evaluate the luring effectiveness of two decoration forms, we performed field experiments in which the number and orientation of decoration bands were manipulated. Decoration bands arranged in a cruciate form were significantly more attractive to insects than those arranged in a linear form, no matter whether they were composed of silks or dummies. Moreover, dummy decoration bands arranged in a cruciate form attracted significantly more insects than those arranged in a vertical/horizontal form. Such results suggest that pollinator insects' innate preference for certain bilateral or radial symmetrical patterns might be one of the driving forces shaping the arrangement pattern of spider web decorations.

Early post-metamorphic, Carboniferous blastoid reveals the evolution and development of the digestive system in echinoderms.

PubMed

Rahman, Imran A; Waters, Johnny A; Sumrall, Colin D; Astolfo, Alberto

2015-10-01

Inferring the development of the earliest echinoderms is critical to uncovering the evolutionary assembly of the phylum-level body plan but has long proven problematic because early ontogenetic stages are rarely preserved as fossils. Here, we use synchrotron tomography to describe a new early post-metamorphic blastoid echinoderm from the Carboniferous (approx. 323 Ma) of China. The resulting three-dimensional reconstruction reveals a U-shaped tubular structure in the fossil interior, which is interpreted as the digestive tract. Comparisons with the developing gut of modern crinoids demonstrate that crinoids are an imperfect analogue for many extinct groups. Furthermore, consideration of our findings in a phylogenetic context allows us to reconstruct the evolution and development of the digestive system in echinoderms more broadly; there was a transition from a straight to a simple curved gut early in the phylum's evolution, but additional loops and coils of the digestive tract (as seen in crinoids) were not acquired until much later. © 2015 The Author(s).

Constructing Palaeo-DEMs in landscape evolution: example of the Geren catchment, Turkey

NASA Astrophysics Data System (ADS)

van Gorp, Wouter; Schoorl, Jeroen M.; Veldkamp, Tom; Maddy, Darrel; Demir, Tuncer; Aytac, Serdar

2017-04-01

How to reconstruct the past landscape and how does this influence your modelling results? This is an important paradigma in the soilscape and landscape evolution modelling community. Here an example of Turkey will be presented where a 300 ka LEM simulation requested to the thoroughly think about the initial landscape as an important input. What information can be used to know the morphology of a landscape 300 ka ago? The Geren catchment, a tributary of the upstream Gediz river near Kula, Turkey, has been influenced by base level changes during the Late Pleistocene and Holocene. Different lavaflows have blocked the Gediz and Geren river several times over in the timespan of the last 300 ka -200 Ka and in the recent Holocene. The heavily dissected Geren catchment shows a landscape evolution which is more complex than just a reaction on these base level changes. The steps and inputs of the palaeo DEM reconstruction will be presented and the modelling results will be presented. Keywords: Digital Elevation Model, Palaeo DEMs, Numerical modelling

Reconstruction of DNA sequences using genetic algorithms and cellular automata: towards mutation prediction?

PubMed

Mizas, Ch; Sirakoulis, G Ch; Mardiris, V; Karafyllidis, I; Glykos, N; Sandaltzopoulos, R

2008-04-01

Change of DNA sequence that fuels evolution is, to a certain extent, a deterministic process because mutagenesis does not occur in an absolutely random manner. So far, it has not been possible to decipher the rules that govern DNA sequence evolution due to the extreme complexity of the entire process. In our attempt to approach this issue we focus solely on the mechanisms of mutagenesis and deliberately disregard the role of natural selection. Hence, in this analysis, evolution refers to the accumulation of genetic alterations that originate from mutations and are transmitted through generations without being subjected to natural selection. We have developed a software tool that allows modelling of a DNA sequence as a one-dimensional cellular automaton (CA) with four states per cell which correspond to the four DNA bases, i.e. A, C, T and G. The four states are represented by numbers of the quaternary number system. Moreover, we have developed genetic algorithms (GAs) in order to determine the rules of CA evolution that simulate the DNA evolution process. Linear evolution rules were considered and square matrices were used to represent them. If DNA sequences of different evolution steps are available, our approach allows the determination of the underlying evolution rule(s). Conversely, once the evolution rules are deciphered, our tool may reconstruct the DNA sequence in any previous evolution step for which the exact sequence information was unknown. The developed tool may be used to test various parameters that could influence evolution. We describe a paradigm relying on the assumption that mutagenesis is governed by a near-neighbour-dependent mechanism. Based on the satisfactory performance of our system in the deliberately simplified example, we propose that our approach could offer a starting point for future attempts to understand the mechanisms that govern evolution. The developed software is open-source and has a user-friendly graphical input interface.

Advantages of Computer Simulation in Enhancing Students' Learning about Landform Evolution: A Case Study Using the Grand Canyon

ERIC Educational Resources Information Center

Luo, Wei; Pelletier, Jon; Duffin, Kirk; Ormand, Carol; Hung, Wei-chen; Shernoff, David J.; Zhai, Xiaoming; Iverson, Ellen; Whalley, Kyle; Gallaher, Courtney; Furness, Walter

2016-01-01

The long geological time needed for landform development and evolution poses a challenge for understanding and appreciating the processes involved. The Web-based Interactive Landform Simulation Model--Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is an educational tool designed to help students better understand such processes,…

Standards opportunities around data-bearing Web pages.

PubMed

Karger, David

2013-03-28

The evolving Web has seen ever-growing use of structured data, thanks to the way it enhances information authoring, querying, visualization and sharing. To date, however, most structured data authoring and management tools have been oriented towards programmers and Web developers. End users have been left behind, unable to leverage structured data for information management and communication as well as professionals. In this paper, I will argue that many of the benefits of structured data management can be provided to end users as well. I will describe an approach and tools that allow end users to define their own schemas (without knowing what a schema is), manage data and author (not program) interactive Web visualizations of that data using the Web tools with which they are already familiar, such as plain Web pages, blogs, wikis and WYSIWYG document editors. I will describe our experience deploying these tools and some lessons relevant to their future evolution.

Standards, Efficiency, and the Evolution of Web Design

ERIC Educational Resources Information Center

Mitchell, Erik

2010-01-01

The author recently created a presentation using HTML5 based on a tutorial put together by Marcin Wichary. The example presentation is part proof-of-concept, part instructional piece, and it is part of a larger site on HTML5 and how one can use it to create rich Web-based applications. The more he delved into HTML5, the more he found that it was…

Web Content Accessibility Guidelines 2.0: A Further Step towards Accessible Digital Information

ERIC Educational Resources Information Center

Ribera, Mireia; Porras, Merce; Boldu, Marc; Termens, Miquel; Sule, Andreu; Paris, Pilar

2009-01-01

Purpose: The purpose of this paper is to explain the changes in the Web Content Accessibility Guidelines (WCAG) 2.0 compared with WCAG 1.0 within the context of its historical development. Design/methodology/approach: In order to compare WCAG 2.0 with WCAG 1.0 a diachronic analysis of the evolution of these standards is done. Known authors and…

The New Challenges for E-learning: The Educational Semantic Web

ERIC Educational Resources Information Center

Aroyo, Lora; Dicheva, Darina

2004-01-01

The big question for many researchers in the area of educational systems now is what is the next step in the evolution of e-learning? Are we finally moving from a scattered intelligence to a coherent space of collaborative intelligence? How close we are to the vision of the Educational Semantic Web and what do we need to do in order to realize it?…

The Life and Times of a Learning Technology System: The Impact of Change and Evolution

ERIC Educational Resources Information Center

Pahl, Claus

2013-01-01

With the inception of the web now being more than 20 years ago, many web-based learning technology systems (LTS) have had a long life and have undergone many changes, both affecting content and infrastructure technologies. A change factor model can capture the various factors causing LTS to change. Methods for change-aware design of LTS have been…

Embedding the Form Generator in a Content Management System

NASA Astrophysics Data System (ADS)

Delgado, A.; Wicenec, A.; Delmotte, N.; Tejero, A.

2008-08-01

Given the tremendous amount of data generated by ESO's telescopes and the rapid evolution of the World Wide Web, the ESO archive web interface needs to offer more flexible services and advanced functionalities to a growing community of users all over the world. To achieve this endeavour, a query form generator is being developed inside a Content Management System. We present here a progress report.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).

Evolution of System Architectures: Where Do We Need to Fail Next?

NASA Astrophysics Data System (ADS)

Bermudez, Luis; Alameh, Nadine; Percivall, George

2013-04-01

Innovation requires testing and failing. Thomas Edison was right when he said "I have not failed. I've just found 10,000 ways that won't work". For innovation and improvement of standards to happen, service Architectures have to be tested and tested. Within the Open Geospatial Consortium (OGC), testing of service architectures has occurred for the last 15 years. This talk will present an evolution of these service architectures and a possible future path. OGC is a global forum for the collaboration of developers and users of spatial data products and services, and for the advancement and development of international standards for geospatial interoperability. The OGC Interoperability Program is a series of hands-on, fast paced, engineering initiatives to accelerate the development and acceptance of OGC standards. Each initiative is organized in threads that provide focus under a particular theme. The first testbed, OGC Web Services phase 1, completed in 2003 had four threads: Common Architecture, Web Mapping, Sensor Web and Web Imagery Enablement. The Common Architecture was a cross-thread theme, to ensure that the Web Mapping and Sensor Web experiments built on a base common architecture. The architecture was based on the three main SOA components: Broker, Requestor and Provider. It proposed a general service model defining service interactions and dependencies; categorization of service types; registries to allow discovery and access of services; data models and encodings; and common services (WMS, WFS, WCS). For the latter, there was a clear distinction on the different services: Data Services (e.g. WMS), Application services (e.g. Coordinate transformation) and server-side client applications (e.g. image exploitation). The latest testbed, OGC Web Service phase 9, completed in 2012 had 5 threads: Aviation, Cross-Community Interoperability (CCI), Security and Services Interoperability (SSI), OWS Innovations and Compliance & Interoperability Testing & Evaluation (CITE). Compared to the first testbed, OWS-9 did not have a separate common architecture thread. Instead the emphasis was on brokering information models, securing them and making data available efficiently on mobile devices. The outcome is an architecture based on usability and non-intrusiveness while leveraging mediation of information models from different communities. This talk will use lessons learned from the evolution from OGC Testbed phase 1 to phase 9 to better understand how global and complex infrastructures evolve to support many communities including the Earth System Science Community.

Metabolism and evolution: A comparative study of reconstructed genome-level metabolic networks

NASA Astrophysics Data System (ADS)

Almaas, Eivind

2008-03-01

The availability of high-quality annotations of sequenced genomes has made it possible to generate organism-specific comprehensive maps of cellular metabolism. Currently, more than twenty such metabolic reconstructions are publicly available, with the majority focused on bacteria. A typical metabolic reconstruction for a bacterium results in a complex network containing hundreds of metabolites (nodes) and reactions (links), while some even contain more than a thousand. The constrain-based optimization approach of flux-balance analysis (FBA) is used to investigate the functional characteristics of such large-scale metabolic networks, making it possible to estimate an organism's growth behavior in a wide variety of nutrient environments, as well as its robustness to gene loss. We have recently completed the genome-level metabolic reconstruction of Yersinia pseudotuberculosis, as well as the three Yersinia pestis biovars Antiqua, Mediaevalis, and Orientalis. While Y. pseudotuberculosis typically only causes fever and abdominal pain that can mimic appendicitis, the evolutionary closely related Y. pestis strains are the aetiological agents of the bubonic plague. In this presentation, I will discuss our results and conclusions from a comparative study on the evolution of metabolic function in the four Yersiniae networks using FBA and related techniques, and I will give particular focus to the interplay between metabolic network topology and evolutionary flexibility.

Surgeon motivations behind the timing of breast reconstruction in patients requiring postmastectomy radiation therapy.

PubMed

Lee, Ming; Reinertsen, Erik; McClure, Evan; Liu, Shuling; Kruper, Laura; Tanna, Neil; Brian Boyd, J; Granzow, Jay W

2015-11-01

Although postmastectomy radiation therapy (PMRT) has been shown to reduce breast cancer burden and improve survival, PMRT may negatively influence outcomes after reconstruction. The goal of this study was to compare current opinions of plastic and reconstructive surgeons (PRS) and surgical oncologists (SO) regarding the optimal timing of breast reconstruction for patients requiring PMRT. Members of the American Society of Plastic Surgeons (ASPS), the American Society of Breast Surgeons (ASBS), and the Society of Surgical Oncology (SSO) were asked to participate in an anonymous web-based survey. Responses were solicited in accordance to the Dillman method, and they were analyzed using standard descriptive statistics. A total of 330 members of the ASPS and 348 members of the ASBS and SSO participated in our survey. PRS and SO differed in patient-payor mix (p < 0.01) and practice setting (p < 0.01), but they did not differ by urban versus rural setting (p = 0.65) or geographic location (p = 0.30). Although PRS favored immediate reconstruction versus SO, overall timing did not significantly differ between the two specialists (p = 0.14). The primary rationale behind delayed breast reconstruction differed significantly between PRS and SO (p < 0.01), with more PRS believing that the reconstructive outcome is significantly and adversely affected by radiation. Both PRS and SO cited "patient-driven desire to have immediate reconstruction" (p = 0.86) as the primary motivation for immediate reconstruction. Although the optimal timing of reconstruction is controversial between PRS and SO, our study suggests that the timing of reconstruction in PMRT patients is ultimately driven by patient preferences and the desire of PRS to optimize aesthetic outcomes. Copyright © 2015 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Reconstructive transoral laser microsurgery for posterior glottic web with stenosis.

PubMed

Atallah, Ihab; Manjunath, M Krishniah; Omari, Ahmad Al; Righini, Christian Adrien; Castellanos, Paul F

2017-03-01

To demonstrate that reconstructive transoral laser microsurgical (R-TLM) techniques can be used for the treatment of symptomatic laryngeal posterior glottic web-based stenosis (PGWS) in a large cohort of patients utilizing a postcricoid mucosal advancement flap (PCMAF). Retrospective cohort review. A consecutive series of patients with PGWS who underwent R-TLM using a PCMAF were reviewed for outcomes. After laser excision of the PGWS scar and mobilization of fixed cricoarytenoid joints, a PCMAF was raised using microinstruments and a scanning free-beam CO 2 laser. The flap was advanced and attached over the scar bed using a technique with multiple novel features that make it easy to adopt. Fifty-two patients were treated. Of the cases, 42.3% had a tracheostomy at presentation with grade II to IV PGWS, and 46% of cases had grade III to IV PGWS. In all cases, R-TLM was the only treatment approach. No open reconstructions were performed. No airway stents were used. Patients without tracheostomy, regardless of the grade of stenosis, did not require a tracheostomy to undergo this operation. All tracheostomy patients were successfully decannulated. All patients without a tracheostomy had significant improvement of their respiratory symptoms on the Dyspnea Index (mean Δ = 14.75, P value <.01). RTLM using the PCMAF is a feasible, safe, and effective alternative to open approaches for airway reconstruction for PGWS. This novel transoral technique includes a much simpler endoscopic suturing alternative to knot tying among other new features. It is reproducible and reliable for laryngologists familiar with laryngeal microsurgery. 4. Laryngoscope, 127:685-690, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

From GCode to STL: Reconstruct Models from 3D Printing as a Service

NASA Astrophysics Data System (ADS)

Baumann, Felix W.; Schuermann, Martin; Odefey, Ulrich; Pfeil, Markus

2017-12-01

The authors present a method to reverse engineer 3D printer specific machine instructions (GCode) to a point cloud representation and then a STL (Stereolithography) file format. GCode is a machine code that is used for 3D printing among other applications, such as CNC routers. Such code files contain instructions for the 3D printer to move and control its actuator, in case of Fused Deposition Modeling (FDM), the printhead that extrudes semi-molten plastics. The reverse engineering method presented here is based on the digital simulation of the extrusion process of FDM type 3D printing. The reconstructed models and pointclouds do not accommodate for hollow structures, such as holes or cavities. The implementation is performed in Python and relies on open source software and libraries, such as Matplotlib and OpenCV. The reconstruction is performed on the model’s extrusion boundary and considers mechanical imprecision. The complete reconstruction mechanism is available as a RESTful (Representational State Transfer) Web service.

North Pacific region in the Paleogene and Neogene as an example of a semiclosed marine system

NASA Astrophysics Data System (ADS)

Gladenkov, Yu. B.

2015-07-01

Scenarios of different geological events in the Paleogene and Neogene evolution of the North Pacific ecosystem are considered with definition of five large stages in its development. The formation of biotic communities of large semiclosed systems in paratropical and boreal paleoenvironmemts, rates of their evolution, and influence of migration on their development are reconstructed.

Discrepancies between subgeneric classification and molecular phylogeny of Ceratitis (Diptera: Tephritidae), can the evolution of host use provide some clues?

PubMed

Erbout, Nathalie; Virgilio, Massimiliano; Lens, Luc; Barr, Norman; De Meyer, Marc

2011-08-01

Using molecular data from three protein encoding genes and 49 taxa (98 specimens from 20 African countries), we provide an extended phylogeny of Ceratitis and investigate the evolution of stenophagy across clades. Bayesian tree reconstructions support previously proposed monophyletic lineages (Pardalaspis, Pterandrus section A, Pterandrus section B+Ceratitis sensu stricto) and reveal the occurrence of two new monophyletic groups including Ceratalaspis/Hoplolophomyia (viz. Cl(A), and Cl(B)+H). The reconstruction of ancestral character states shows that stenophagy evolved repeatedly and independently in five different clades (Podocarpus, Solanum, Strychnos, Tabernaemontana and Vepris feeders). The evolution of feeding preferences is closely related to the phylogenetic patterns of Ceratalaspis/Hoplolophomyia whose sections include either polyphagous species (Cl(A)) or stenophagous taxa (Cl(B)+H) that are further subdivided in Vepris and Solanum feeders. The evolution of stenophagy in the genus Ceratits appears as the result of a process leading to the exploitation of "unconventional" fruits (viz. toxic and/or not fleshy) and involving either metabolic adaptation to toxic plant compounds and/or the capability of penetrating fruits with thick cuticles. Copyright © 2011 Elsevier Inc. All rights reserved.

A Hybrid Approach to Data Assimilation for Reconstructing the Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Quan; Liu, Lijun

2017-11-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation approach that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics the best.

Adaptive evolution of Mediterranean pines.

PubMed

Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

2013-09-01

Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

A Hybrid Forward-Adjoint Data Assimilation Method for Reconstructing the Temporal Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Q.; Liu, L.

2017-12-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation method that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics to the best.

Landscapes of human evolution: models and methods of tectonic geomorphology and the reconstruction of hominin landscapes.

PubMed

Bailey, Geoffrey N; Reynolds, Sally C; King, Geoffrey C P

2011-03-01

This paper examines the relationship between complex and tectonically active landscapes and patterns of human evolution. We show how active tectonics can produce dynamic landscapes with geomorphological and topographic features that may be critical to long-term patterns of hominin land use, but which are not typically addressed in landscape reconstructions based on existing geological and paleoenvironmental principles. We describe methods of representing topography at a range of scales using measures of roughness based on digital elevation data, and combine the resulting maps with satellite imagery and ground observations to reconstruct features of the wider landscape as they existed at the time of hominin occupation and activity. We apply these methods to sites in South Africa, where relatively stable topography facilitates reconstruction. We demonstrate the presence of previously unrecognized tectonic effects and their implications for the interpretation of hominin habitats and land use. In parts of the East African Rift, reconstruction is more difficult because of dramatic changes since the time of hominin occupation, while fossils are often found in places where activity has now almost ceased. However, we show that original, dynamic landscape features can be assessed by analogy with parts of the Rift that are currently active and indicate how this approach can complement other sources of information to add new insights and pose new questions for future investigation of hominin land use and habitats. Copyright © 2010 Elsevier Ltd. All rights reserved.

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

PubMed Central

Csuros, Miklos; Rogozin, Igor B.; Koonin, Eugene V.

2011-01-01

Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6–7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing. PMID:21935348

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

NASA Astrophysics Data System (ADS)

Novosad, Philip; Reader, Andrew J.

2016-06-01

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [11C]SCH23390 data, showing promising results.

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.

PubMed

Novosad, Philip; Reader, Andrew J

2016-06-21

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [(18)F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [(11)C]SCH23390 data, showing promising results.

Cosmological reconstruction and stability in F(T,TG) gravity

NASA Astrophysics Data System (ADS)

Sharif, M.; Nazir, Kanwal

This study investigates the reconstruction scheme and stability of some well-known cosmological models in F(T,TG) gravity, where T and TG represent the torsion scalar and Gauss-Bonnet invariant torsion term, respectively. For this purpose, we consider isotropic homogeneous universe model and develop the corresponding field equations. It is found that we can reproduce cosmological evolution for power-law, de Sitter solutions, phantom/nonphantom era and Λ cold dark matter by applying reconstruction scheme in this gravity. Finally, we discuss stability of the reconstructed power-law and de Sitter solutions as well as two well-known F(T,TG) models. It is concluded that all these models provide stable solutions for suitable choices of the constants except power-law solutions.

Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia).

PubMed

Datzmann, Thomas; von Helversen, Otto; Mayer, Frieder

2010-06-04

Bats of the family Phyllostomidae show a unique diversity in feeding specializations. This taxon includes species that are highly specialized on insects, blood, small vertebrates, fruits or nectar, and pollen. Feeding specialization is accompanied by morphological, physiological and behavioural adaptations. Several attempts were made to resolve the phylogenetic relationships within this family in order to reconstruct the evolutionary transitions accompanied by nutritional specialization. Nevertheless, the evolution of nectarivory remained equivocal. Phylogenetic reconstructions, based on a concatenated nuclear-and mitochondrial data set, revealed a paraphyletic relationship of nectarivorous phyllostomid bats. Our phylogenetic reconstructions indicate that the nectarivorous genera Lonchophylla and Lionycteris are closer related to mainly frugivorous phyllostomids of the subfamilies Rhinophyllinae, Stenodermatinae, Carolliinae, and the insectivorous Glyphonycterinae rather than to nectarivorous bats of the Glossophaginae. This suggests an independent origin of morphological adaptations to a nectarivorous lifestyle within Lonchophyllinae and Glossophaginae. Molecular clock analysis revealed a relatively short time frame of about ten million years for the divergence of subfamilies. Our study provides strong support for diphyly of nectarivorous phyllostomids. This is remarkable, since their morphological adaptations to nutrition, like elongated rostrums and tongues, reduced teeth and the ability to use hovering flight while ingestion, closely resemble each other. However, more precise examinations of their tongues (e.g. type and structure of papillae and muscular innervation) revealed levels of difference in line with an independent evolution of nectarivory in these bats.

Holocene warming in western continental Eurasia driven by glacial retreat and greenhouse forcing

NASA Astrophysics Data System (ADS)

Baker, Jonathan L.; Lachniet, Matthew S.; Chervyatsova, Olga; Asmerom, Yemane; Polyak, Victor J.

2017-06-01

The global temperature evolution during the Holocene is poorly known. Whereas proxy data suggest that warm conditions prevailed in the Early to mid-Holocene with subsequent cooling, model reconstructions show long-term warming associated with ice-sheet retreat and rising greenhouse gas concentrations. One reason for this contradiction could be the under-representation of indicators for winter climate in current global proxy reconstructions. Here we present records of carbon and oxygen isotopes from two U-Th-dated stalagmites from Kinderlinskaya Cave in the southern Ural Mountains that document warming during the winter season from 11,700 years ago to the present. Our data are in line with the global Holocene temperature evolution reconstructed from transient model simulations. We interpret Eurasian winter warming during the Holocene as a response to the retreat of Northern Hemisphere ice sheets until about 7,000 years ago, and to rising atmospheric greenhouse gas concentrations and winter insolation thereafter. We attribute negative δ18O anomalies 11,000 and 8,200 years ago to enhanced meltwater forcing of North Atlantic Ocean circulation, and a rapid decline of δ13C during the Early Holocene with stabilization after about 10,000 years ago to afforestation at our study site. We conclude that winter climate dynamics dominated Holocene temperature evolution in the continental interior of Eurasia, in contrast to regions more proximal to the ocean.

Spatiotemporal Evolution of Calophaca (Fabaceae) Reveals Multiple Dispersals in Central Asian Mountains

PubMed Central

Zhang, Ming-Li; Wen, Zhi-Bin; Fritsch, Peter W.; Sanderson, Stewart C.

2015-01-01

Background The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried out in order to confirm its taxonomic status and reconstruct its evolutionary history. Methodology/Principal Finding We employed BEAST Bayesian inference for dating, and S-DIVA and BBM for ancestral area reconstruction, to study its spatiotemporal evolution. Our results show that Calophacais monophyletic and nested within Caragana. The divergence time of Calophaca is estimated at ca. 8.0 Ma, most likely driven by global cooling and aridification, influenced by rapid uplift of the Qinghai Tibet Plateau margins. Conclusions/Significance According to ancestral area reconstructions, the genus most likely originated in the Pamir Mountains, a global biodiversity hotspot and hypothesized Tertiary refugium of many Central Asian plant lineages. Dispersals from this location are inferred to the western Tianshan Mountains, then northward to the Tarbagatai Range, eastward to East Asia, and westward to the Caucasus, Russia, and Europe. The spatiotemporal evolution of Calophaca provides a case contributing to an understanding of the flora and biodiversity of the Central Asian mountains and adjacent regions. PMID:25849146

Pairing Quaternary paleoecology and modern ROV exploration to produce novel reconstructions of marine ecosystem responses to millennial-scale climate change

NASA Astrophysics Data System (ADS)

Myhre, S. E.; Pak, D. K.; Borreggine, M. J.; Hill, T. M.; Kennett, J.; Nicholson, C.; Deutsch, C. A.

2017-12-01

One of the most interesting problems for 21st Century marine ecology is understanding the potential physical, chemical, and biological scale of future climate-forced oceanographic changes. These fundamental questions can be informed through the examination of micro- and macrofauna from Quaternary sedimentary sequences, combined with modern observations of continental margin ecosystems. Here we examine Remotely Operated Vehicle (ROV) exploratory videos and sedimentary push cores, to identify biological assemblages, including mollusc, echinoderm, ostracod, and foraminifera density, diversity, and community structure from Santa Barbara Basin in the California Borderland. ROV explorations, from 380-500 meters below sea level (mbsl), describe the zonation of benthic fauna and the distribution of chemosynthetic trophic webs, which are consequences of gradations in the oxygen minimum zone and the ventilating sill depth (475 mbsl). Such observations reveal the modern vertical distribution of chemosynthetic bacterial communities and shallower, diverse communities associated with detrital food webs. Biological assemblages from 16.1-3.4 ka (from core MV0811-15JC, collected at 418 mbsl) produce a suite of paleoceanographic indicators, such as dissolved oxygen concentrations (foraminifera), chemosynthetic trophic webs (molluscs), and water masses (ostracods). These assemblages demonstrate how continental margin ecosystems reorganize vertically (through the water column) and geographically through climate events, for example through the loss of cryophilic species, the ephemeral occurrence of chemosynthetic communities, and the trace fossil evidence (through predation scarring on mollusc shells) of higher trophic web interactions. Together with ROV seafloor observations, these communities can reconstruct step-by-step vertical changes in the zonation of the continental margin, and can identify intervals of zonation change in relation to both Santa Barbara Basin ventilation and the regional California Borderland oxygen minimum zone.

Enhancing Eight Grade Students' Scientific Conceptual Change and Scientific Reasoning through a Web-Based Learning Program

ERIC Educational Resources Information Center

Liao, Ya-Wen; She, Hsiao-Ching

2009-01-01

This study reports the impacts of the Scientific Concept Construction and Reconstruction (SCCR) digital learning system on eighth grade students' concept construction, conceptual change, and scientific reasoning involving the topic of "atoms". A two-factorial experimental design was carried out to investigate the effects of the approach…

Bridging Scientific Reasoning and Conceptual Change through Adaptive Web-Based Learning

ERIC Educational Resources Information Center

She, Hsiao-Ching; Liao, Ya-Wen

2010-01-01

This study reports an adaptive digital learning project, Scientific Concept Construction and Reconstruction (SCCR), and examines its effects on 108 8th grade students' scientific reasoning and conceptual change through mixed methods. A one-group pre-, post-, and retention quasi-experimental design was used in the study. All students received tests…

4D reconstruction of the past

NASA Astrophysics Data System (ADS)

Doulamis, Anastasios; Ioannides, Marinos; Doulamis, Nikolaos; Hadjiprocopis, Andreas; Fritsch, Dieter; Balet, Olivier; Julien, Martine; Protopapadakis, Eftychios; Makantasis, Kostas; Weinlinger, Guenther; Johnsons, Paul S.; Klein, Michael; Fellner, Dieter; Stork, Andre; Santos, Pedro

2013-08-01

One of the main characteristics of the Internet era we are living in, is the free and online availability of a huge amount of data. This data is of varied reliability and accuracy and exists in various forms and formats. Often, it is cross-referenced and linked to other data, forming a nexus of text, images, animation and audio enabled by hypertext and, recently, by the Web3.0 standard. Search engines can search text for keywords using algorithms of varied intelligence and with limited success. Searching images is a much more complex and computationally intensive task but some initial steps have already been made in this direction, mainly in face recognition. This paper aims to describe our proposed pipeline for integrating data available on Internet repositories and social media, such as photographs, animation and text to produce 3D models of archaeological monuments as well as enriching multimedia of cultural / archaeological interest with metadata and harvesting the end products to EUROPEANA. Our main goal is to enable historians, architects, archaeologists, urban planners and affiliated professionals to reconstruct views of historical monuments from thousands of images floating around the web.

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

New parasites and predators follow the introduction of two fish species to a subarctic lake: implications for food-web structure and functioning.

PubMed

Amundsen, Per-Arne; Lafferty, Kevin D; Knudsen, Rune; Primicerio, Raul; Kristoffersen, Roar; Klemetsen, Anders; Kuris, Armand M

2013-04-01

Introduced species can alter the topology of food webs. For instance, an introduction can aid the arrival of free-living consumers using the new species as a resource, while new parasites may also arrive with the introduced species. Food-web responses to species additions can thus be far more complex than anticipated. In a subarctic pelagic food web with free-living and parasitic species, two fish species (arctic charr Salvelinus alpinus and three-spined stickleback Gasterosteus aculeatus) have known histories as deliberate introductions. The effects of these introductions on the food web were explored by comparing the current pelagic web with a heuristic reconstruction of the pre-introduction web. Extinctions caused by these introductions could not be evaluated by this approach. The introduced fish species have become important hubs in the trophic network, interacting with numerous parasites, predators and prey. In particular, five parasite species and four predatory bird species depend on the two introduced species as obligate trophic resources in the pelagic web and could therefore not have been present in the pre-introduction network. The presence of the two introduced fish species and the arrival of their associated parasites and predators increased biodiversity, mean trophic level, linkage density, and nestedness; altering both the network structure and functioning of the pelagic web. Parasites, in particular trophically transmitted species, had a prominent role in the network alterations that followed the introductions.

New parasites and predators follow the introduction of two fish species to a subarctic lake: implications for food-web structure and functioning

USGS Publications Warehouse

Amundsen, Per-Arne; Lafferty, Kevin D.; Knudsen, Rune; Primicerio, Raul; Kristoffersen, Roar; Klemetsen, Anders; Kuris, Armand M.

2012-01-01

Introduced species can alter the topology of food webs. For instance, an introduction can aid the arrival of free-living consumers using the new species as a resource, while new parasites may also arrive with the introduced species. Food-web responses to species additions can thus be far more complex than anticipated. In a subarctic pelagic food web with free-living and parasitic species, two fish species (arctic charr Salvelinus alpinus and three-spined stickleback Gasterosteus aculeatus) have known histories as deliberate introductions. The effects of these introductions on the food web were explored by comparing the current pelagic web with a heuristic reconstruction of the pre-introduction web. Extinctions caused by these introductions could not be evaluated by this approach. The introduced fish species have become important hubs in the trophic network, interacting with numerous parasites, predators and prey. In particular, five parasite species and four predatory bird species depend on the two introduced species as obligate trophic resources in the pelagic web and could therefore not have been present in the pre-introduction network. The presence of the two introduced fish species and the arrival of their associated parasites and predators increased biodiversity, mean trophic level, linkage density, and nestedness; altering both the network structure and functioning of the pelagic web. Parasites, in particular trophically transmitted species, had a prominent role in the network alterations that followed the introductions.

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

[Reconstruction of severe contracture of the first web space and wrist by incorporating pedicled retrograde flap of forearm transplantation].

PubMed

Chen, Jianchong; Wu, Zuhuang; Zhu, Jianxian; Huang, Yongxin; Xie, Baogen

2011-10-01

To summarize the therapeutic effectiveness of incorporating pedicled retrograde flap of forearm transplantation for reconstructing severe contracture of the first web space and wrist. Between November 2005 and February 2010, 26 patients with severe contracture of the first web and wrist were treated. There were 18 males and 8 females with an average age of 27 years (range, 12-45 years). The locations were the right sides in 15 cases and the left sides in 11 cases. The injury reason included hot water scald in 7 cases, explosion hurt in 5 cases, traffic accident in 3 cases, hot pressing in 5 cases, and flame burns in 6 cases. The duration of scar contracture ranged from 6 to 26 months with an average of 11 months. According to the evaluation standard by GU Yudong et al., all had severe contracture of the first web space, and concomitant injuries included adduction deformity thumb, limitation of the thumb extension and opposition function, and carpometacarpal flexion joint deformity. After scar contracture was released, the defect size ranged from 5.8 cm x 4.5 cm to 11.3 cm x 7.2 cm, which were repaired by the incorporating pedicled retrograde flap of forearm of 6.5 cm x 5.0 cm to 12.5 cm x 8.0 cm at size. The donor sites were directly sutured or repaired with skin graft. Blister and partial necrosis occurred at the distal end of the flaps in 2 cases, which were cured after dressing change. The other flaps survived and wounds healed by first intention. Incisions at donor sites healed by first intention. Twenty-six patients were followed up 6 to 24 months (mean, 15 months). The patients had functional recovery in thumb adduction and opposition at different degrees. At 6 months after operation, according to the Swanson et al. AMA system for total thumb activity, the total thumb function was improved significantly, and according to Jensen et al. measurement, the width and angle of the first web space were significantly increased, all showing significant differences (P < 0.05). Incorporating pedicled retrograde flap of forearm transplantation for repairing severe contracture of the first web space and wrist could augment the first web space and improve the wrist flexible function.

A long time ago, where were the galaxies far, far away?

NASA Astrophysics Data System (ADS)

Sirko, Edwin

How did the universe get from then to now ? I examine this broad cosmological problem from two perspectives: forward and backward. In the forward perspective, I implement a method of generating initial conditions for N -body simulations that accurately models real-space statistical properties, such as the mass variance in spheres and the correlation function. The method requires running ensembles of simulations because the power in the DC mode is no longer assumed to be zero. For moderately sized boxes, I demonstrate that the new method corrects the previously widely ignored underestimate in the mass variance in spheres and the shape of the correlation function. In the backward perspective, I use reconstruction techniques to transform a simulated or observed cosmological density field back in time to the early universe. A simple reconstruction technique is used to sharpen the baryon acoustic peak in the correlation function in simulations. At z = 0.3, one can reduce the sample variance error bar on the acoustic scale by at least a factor of 2 and in principle by nearly a factor of 4. This has significant implications for future observational surveys aiming to measure the cosmological distance scale. Another reconstruction technique, Monge-Ampere-Kantorovich reconstruction, is used on evolved N -body simulations to calibrate its effectiveness in recovering the linear power spectrum. A new "memory model" parametrizes the evolution of Fourier modes into two parameters that describe the amount of memory a given mode retains and how much the mode has been scrambled by nonlinear evolution. Reconstruction is spectacularly successful in restoring the memory of Fourier modes and reducing the scrambling; however, the success of reconstruction is not so obvious when considering the power spectrum alone. I apply reconstruction to a volume-limited sample of galaxies from the Sloan Digital Sky Survey and conclude that linear bias is not a good model in the range 0.01 h Mpc -1 [Special characters omitted.] k [Special characters omitted.] 0.5 h Mpc -1 . The most impressive success of reconstruction applied to real data is that the confidence interval on the normalization of the power spectrum is typically halved when using the reconstructed instead of the nonlinear power spectrum.

Reconstructing the evolution of first-row transition metal minerals by GeoDeepDive

NASA Astrophysics Data System (ADS)

Liu, C.; Peters, S. E.; Ross, I.; Golden, J. J.; Downs, R. T.; Hazen, R. M.

2016-12-01

Terrestrial mineralogy evolves as a consequence of a range of physical, chemical, and biological processes [1]. Evolution of the first-row transition metal minerals could mirror the evolution of Earth's oxidation state and life, since these elements mostly are redox-sensitive and/or play critical roles in biology. The fundamental building blocks to reconstruct mineral evolution are the mineral species, locality, and age data, which are typically dispersed in sentences in scientific and technical publications. These data can be tracked down in a brute-force way, i.e., human retrieval, reading, and recording all relevant literature. Alternatively, they can be extracted automatically by GeoDeepDive. In GeoDeepDive, scientific and technical articles from publishers, including Elsevier, Wiley, USGS, SEPM, GSA and Canada Science Publishing, have been parsed into a Javascript database with NLP tags. Sentences containing data of mineral names, locations, and ages can be recognized and extracted by user-developed applications. In a preliminary search for cobalt mineral ages, we successfully extracted 678 citations with >1000 mentions of cobalt minerals, their locations, and ages. The extracted results are in agreement with brute-force search results. What is more, GeoDeepDive provides 40 additional data points that were not recovered by the brute-force approach. The extracted mineral locality-age data suggest that the evolution of Co minerals is controlled by global supercontinent cycles, i.e., more Co minerals form during episodes of supercontinent assembly. Mineral evolution of other first-row transition elements is being investigated through GeoDeepDive. References: [1] Hazen et al. (2008) Mineral evolution. American Mineralogist, 93, 1693-1720

Influence of evolution on the stability of ecological communities.

PubMed

Loeuille, Nicolas

2010-12-01

In randomly assembled communities, diversity is known to have a destabilizing effect. Evolution may affect this result, but our theoretical knowledge of its role is mostly limited to models of small food webs. In the present article, I introduce evolution in a two-species Lotka-Volterra model in which I vary the interaction type and the cost constraining evolution. Regardless of the cost type, evolution tends to stabilize the dynamics more often in trophic interactions than for mutualism or competition. I then use simulations to study the effect of evolution in larger communities that contain all interaction types. Results suggest that evolution usually stabilizes the dynamics. This stabilizing effect is stronger when evolution affects trophic interactions, but happens for all interaction types. Stabilization decreases with diversity and evolution becomes destabilizing in very diverse communities. This suggests that evolution may not counteract the destabilizing effect of diversity observed in random communities. © 2010 Blackwell Publishing Ltd/CNRS.

Evidence for fast dynamo action in a chaotic web

NASA Technical Reports Server (NTRS)

Gilbert, A. D.; Childress, S.

1990-01-01

The evolution of a magnetic field in a chaotic web is studied. The model flow possessing the web is closely related to the nearly integrable ABC flow with A = B and C much less than 1. The magnetic diffusivity is taken to be zero and the field is followed using the Cauchy solution. It is found that the flow folds the magnetic field constructively, in the sense that the average magnetic field in a chaotic region grows exponentially in time. This is suggestive of fast dynamo action, although the effect of diffusion of the strong streamwise magnetic field remains to be assessed.

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication.

PubMed

Xiang, Yezi; Huang, Chien-Hsun; Hu, Yi; Wen, Jun; Li, Shisheng; Yi, Tingshuang; Chen, Hongyi; Xiang, Jun; Ma, Hong

2017-02-01

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

AWARE: Adaptive Software Monitoring and Dynamic Reconfiguration for Critical Infrastructure Protection

DTIC Science & Technology

2015-04-29

in which we applied these adaptation patterns to an adaptive news web server intended to tolerate extremely heavy, unexpected loads. To address...collection of existing models used as benchmarks for OO-based refactoring and an existing web -based repository called REMODD to provide users with model...invariant properties. Specifically, we developed Avida- MDE (based on the Avida digital evolution platform) to support the automatic generation of software

Quantitative complete tooth variation among east Asians and Native Americans: developmental biology as a tool for the assessment of human divergence.

PubMed

Shields, E D

1996-01-01

The quantification of total tooth structure derived from X-rays of Vietnamese, Southern Chinese, Mongolians, Western Eskimos, and Peruvian pre-Inca (Huari Empire) populations was used to examine dental divergence and the morphogenetics of change. Multivariate derived distances between the samples helped identify a quasicontinuous web of ethnic groups with two binary clusters ensconced within the web. One cluster was composed of Mongolians, Western Eskimos, and pre-Inca, and the other group consisted of the Southern Chinese and Vietnamese. Mongolians entered the quasicontinuum from a divergent angle (externally influenced) from that of the Southeast Asians. The Chinese and pre-Inca formed the polar samples of the distance superstructure. The pre-Inca sample was the most isolated, its closest neighbor being the Western Eskimos. Univariate and multivariate analyses suggested that the pre-Inca, whose ancestors arrived in America perhaps approximately 30,000 years ago, was the least derived sample. Clearly, microevolutionary change occurred among the samples, but the dental phenotype was resistant to environmental developmental perturbations. An assessment of dental divergence and developmental biology suggested that the overall dental phenotype is a complex multigenic morphological character, and that the observed variation evolved through total genomic drift. The quantified dental phenotype is greater than its highly multigenic algorithm and its development homeostasis is tightly controlled, or canalized, by the deterministic organization of a complex nonlinear epigenetic milieu. The overall dental phenotype quantified here was selectively neutral and a good character to help reconstruct the sequence of human evolution, but if the outlying homeostatic threshold was or will be exceeded in antecedents and descendants, respectively, evolutionary saltation occurs.

Species-level phylogeny, fruit evolution and diversification history of Geranium (Geraniaceae).

PubMed

Marcussen, Thomas; Meseguer, Andrea S

2017-05-01

The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms. Here, we used a calibrated multispecies coalescent approach to infer the species-level phylogeny and divergence times of the genus based on chloroplast (rbcL, trnL-trnF) and nuclear (ITS) DNA sequences. Our sampling represents most of the morphological variation described in the genus. We reconstruct the evolution of the seed discharge mechanism using ancestral state reconstruction (ASR) techniques on the multispecies coalescent tree, and assess the association between fruit type evolution and species diversification using stochastic birth-death and trait-dependent diversification models. Finally, we reconstruct the early biogeographic history of the genus using discrete and continuous biogeographic analyses of species distribution centroids, including fossil evidence and tip dates. Our results show that fruit type is homoplasious and that the classification based on fruit type in Geranium is artificial. The taxonomy and putative apomorphic characters for Geranium are discussed. ASR of the fruit characters suggests that ET may represent the ancestral state in Geranium and from which CP originated twice, IT presumably once, and SE twice. The independent appearance of the SE syndrome is in both cases associated with increases in diversification rates in the genus. The biogeographic analysis centers the origin and early 10Ma diversification of Geranium on the Mediterranean region. The evolution of seed discharge mechanism about 5Ma might have allowed the species of Geranium to increase in geographic range and to ultimately, diversify. Copyright © 2017 Elsevier Inc. All rights reserved.

Punctuated evolution of viscid silk in spider orb webs supported by mechanical behavior of wet cribellate silk

NASA Astrophysics Data System (ADS)

Piorkowski, Dakota; Blackledge, Todd A.

2017-08-01

The origin of viscid capture silk in orb webs, from cribellate silk-spinning ancestors, is a key innovation correlated with significant diversification of web-building spiders. Ancestral cribellate silk consists of dry nanofibrils surrounding a stiff, axial fiber that adheres to prey through van der Waals interactions, capillary forces, and physical entanglement. In contrast, viscid silk uses chemically adhesive aqueous glue coated onto a highly compliant and extensible flagelliform core silk. The extensibility of the flagelliform fiber accounts for half of the total work of adhesion for viscid silk and is enabled by water in the aqueous coating. Recent cDNA libraries revealed the expression of flagelliform silk proteins in cribellate orb-weaving spiders. We hypothesized that the presence of flagelliform proteins in cribellate silk could have allowed for a gradual shift in mechanical performance of cribellate axial silk, whose effect was masked by the dry nature of its adhesive. We measured supercontraction and mechanical performance of cribellate axial silk, in wet and dry states, for two species of cribellate orb web-weaving spiders to see if water enabled flagelliform silk-like performance. We found that compliance and extensibility of wet cribellate silk increased compared to dry state as expected. However, when compared to other silk types, the response to water was more similar to other web silks, like major and minor ampullate silk, than to viscid silk. These findings support the punctuated evolution of viscid silk mechanical performance.

Floral evolution of Philodendron subgenus Meconostigma (Araceae).

PubMed

de Oliveira, Letícia Loss; Calazans, Luana Silva Braucks; de Morais, Érica Barroso; Mayo, Simon Joseph; Schrago, Carlos Guerra; Sakuragui, Cassia Mônica

2014-01-01

Elucidating the evolutionary patterns of flower and inflorescence structure is pivotal to understanding the phylogenetic relationships of Angiosperms as a whole. The inflorescence morphology and anatomy of Philodendron subgenus Meconostigma, belonging to the monocot family Araceae, has been widely studied but the evolutionary relationships of subgenus Meconostigma and the evolution of its flower characters have hitherto remained unclear. This study examines gynoecium evolution in subgenus Meconostigma in the context of an estimated molecular phylogeny for all extant species of subgenus Meconostigma and analysis of ancestral character reconstructions of some gynoecial structures. The phylogenetic reconstructions of all extant Meconostigma species were conducted under a maximum likelihood approach based on the sequences of two chloroplast (trnk and matK) and two nuclear (ETS and 18S) markers. This topology was used to reconstruct the ancestral states of seven floral characters and to elucidate their evolutionary pattern in the Meconostigma lineage. Our phylogeny shows that Meconostigma is composed of two major clades, one comprising two Amazonian species and the other all the species from the Atlantic Forest and Cerrado biomes with one Amazonian species. The common ancestor of the species of subgenus Meconostigma probably possessed short stylar lobes, long stylar canals, a stylar body, a vascular plexus in the gynoecium and druses in the stylar parenchyma but it is uncertain whether raphide inclusions were present in the parenchyma. The ancestral lineage also probably possessed up to 10 ovary locules. The evolution of these characters seems to have occurred independently in some lineages. We propose that the morphological and anatomical diversity observed in the gynoecial structures of subgenus Meconostigma is the result of an ongoing process of fusion of floral structures leading to a reduction of energy wastage and increase in stigmatic surface.

Can Landscape Evolution Models (LEMs) be used to reconstruct palaeo-climate and sea-level histories?

NASA Astrophysics Data System (ADS)

Leyland, J.; Darby, S. E.

2011-12-01

Reconstruction of palaeo-environmental conditions over long time periods is notoriously difficult, especially where there are limited or no proxy records from which to extract data. Application of landscape evolution models (LEMs) for palaeo-environmental reconstruction involves hindcast modeling, in which simulation scenarios are configured with specific model variables and parameters chosen to reflect a specific hypothesis of environmental change. In this form of modeling, the environmental time series utilized are considered credible when modeled and observed landscape metrics converge. Herein we account for the uncertainties involved in evaluating the degree to which the model simulations and observations converge using Monte Carlo analysis of reduced complexity `metamodels'. The technique is applied to a case study focused on a specific set of gullies found on the southwest coast of the Isle of Wight, UK. A key factor controlling the Holocene evolution of these coastal gullies is the balance between rates of sea-cliff retreat (driven by sea-level rise) and headwards incision caused by knickpoint migration (driven by the rate of runoff). We simulate these processes using a version of the GOLEM model that has been modified to represent sea-cliff retreat. A Central Composite Design (CCD) sampling technique was employed, enabling the trajectories of gully response to different combinations of driving conditions to be modeled explicitly. In some of these simulations, where the range of bedrock erodibility (0.03 to 0.04 m0.2 a-1) and rate of sea-level change (0.005 to 0.0059 m a-1) is tightly constrained, modeled gully forms conform closely to those observed in reality, enabling a suite of climate and sea-level change scenarios which plausibly explain the Holocene evolution of the Isle of Wight gullies to be identified.

Empirical analysis of web-based user-object bipartite networks

NASA Astrophysics Data System (ADS)

Shang, Ming-Sheng; Lü, Linyuan; Zhang, Yi-Cheng; Zhou, Tao

2010-05-01

Understanding the structure and evolution of web-based user-object networks is a significant task since they play a crucial role in e-commerce nowadays. This letter reports the empirical analysis on two large-scale web sites, audioscrobbler.com and del.icio.us, where users are connected with music groups and bookmarks, respectively. The degree distributions and degree-degree correlations for both users and objects are reported. We propose a new index, named collaborative similarity, to quantify the diversity of tastes based on the collaborative selection. Accordingly, the correlation between degree and selection diversity is investigated. We report some novel phenomena well characterizing the selection mechanism of web users and outline the relevance of these phenomena to the information recommendation problem.

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

PubMed Central

2015-01-01

Background Most models of genome evolution concern either genetic sequences, gene content or gene order. They sometimes integrate two of the three levels, but rarely the three of them. Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content. Results We propose a probabilistic evolutionary model for gene neighborhoods, allowing genes to be inserted, duplicated or lost. It uses reconciled phylogenies, which integrate sequence and gene content evolution. We are then able to optimize parameters such as phylogeny branch lengths, or probabilistic laws depicting the diversity of susceptibility of syntenic regions to rearrangements. We reconstruct a structure for ancestral genomes by optimizing a likelihood, keeping track of all evolutionary events at the level of gene content and gene synteny. Ancestral syntenies are associated with a probability of presence. We implemented the model with the restriction that at most one gene duplication separates two gene speciations in reconciled gene trees. We reconstruct ancestral syntenies on a set of 12 drosophila genomes, and compare the evolutionary rates along the branches and along the sites. We compare with a parsimony method and find a significant number of results not supported by the posterior probability. The model is implemented in the Bio++ library. It thus benefits from and enriches the classical models and methods for molecular evolution. PMID:26452018

Metabolic evolution and the self-organization of ecosystems.

PubMed

Braakman, Rogier; Follows, Michael J; Chisholm, Sallie W

2017-04-11

Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus ' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.

Wire-Cell Tomographic Event Reconstruction for large LArTPCs

NASA Astrophysics Data System (ADS)

Qian, Xin; Viren, Brett; Zhang, Chao; Wire-Cell Team

2016-03-01

Event reconstruction is one of the most challenging tasks in analyzing the data from current and future large liquid argon time projection chambers (LArTPCs). The performance of the event reconstruction holds the key to many potential future discoveries with the LArTPC technology including i) searching for new CP violation in the leptonic sector, ii) determining the neutrino mass hierarchy, and iii) searching for additional light (sterile) neutrino species. In this talk, we introduce a new reconstruction method: Wire-Cell. The principle of Wire-Cell strictly follows the principle of LArTPC, that is, the same amount of ionization electrons are observed by all the wire-planes. Using both time and charge information, 3D image of the event topologies are firstly obtained. Further reconstruction steps including the clustering, tracking, and particle identifications (PID) are then directly applied to the 3D image. The principle, current status, and future development plan of Wire-Cell will be described. The results of Wire-Cell event reconstruction will be shown with an innovative web-based ``BEE'' 3D event display. This work is supported by U.S. Department of Energy, Office of Science, Office of High Energy Physics and Early Career Research program under Contract Number DE-SC0012704.

Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

PubMed

Austerlitz, Frédéric; Heyer, Evelyne

2018-06-01

Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography

Treesearch

Mingli Zhang; Xiaoli Hao; Stewart C. Sanderson; Byalt V. Vyacheslav; Alexander P. Sukhorukov; Xia Zhang

2014-01-01

Reaumuria is an arid adapted genus with a distribution center in Central Asia; its evolution and dispersal is investigated in this paper. Eighteen species of Reaumuria and nine species of two other genera in the Tamaricaceae, Tamarix and Myricaria, were sampled, and four markers ITS, rps16, psbB-psbH, and trnL-trnF were sequenced. The reconstructed phylogenetic tree is...

Species Tree Inference Using a Mixture Model.

PubMed

Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

2015-09-01

Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolution and Reconstruction of Learning Cities for Sustainable Actions

ERIC Educational Resources Information Center

Watson, Connie; Wu, Aimee Tiu

2015-01-01

This chapter describes how the concept of learning cities evolved from the "learning society" and the lifelong education and learning movements, and advances multiple forms of communities of learning.

The cosmic web in CosmoGrid void regions

NASA Astrophysics Data System (ADS)

Rieder, Steven; van de Weygaert, Rien; Cautun, Marius; Beygu, Burcu; Portegies Zwart, Simon

2016-10-01

We study the formation and evolution of the cosmic web, using the high-resolution CosmoGrid ΛCDM simulation. In particular, we investigate the evolution of the large-scale structure around void halo groups, and compare this to observations of the VGS-31 galaxy group, which consists of three interacting galaxies inside a large void. The structure around such haloes shows a great deal of tenuous structure, with most of such systems being embedded in intra-void filaments and walls. We use the Nexus+} algorithm to detect walls and filaments in CosmoGrid, and find them to be present and detectable at every scale. The void regions embed tenuous walls, which in turn embed tenuous filaments. We hypothesize that the void galaxy group of VGS-31 formed in such an environment.

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome.

PubMed

Deakin, Janine E; Edwards, Melanie J; Patel, Hardip; O'Meally, Denis; Lian, Jinmin; Stenhouse, Rachael; Ryan, Sam; Livernois, Alexandra M; Azad, Bhumika; Holleley, Clare E; Li, Qiye; Georges, Arthur

2016-06-10

Squamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it difficult to reconstruct the events that have led to extant squamate karyotypic diversity. The purpose of this study was to anchor the recently sequenced central bearded dragon (Pogona vitticeps) genome to chromosomes to trace the evolution of squamate chromosomes. Assigning sequence to sex chromosomes was of particular interest for identifying candidate sex determining genes. By using two different approaches to map conserved blocks of genes, we were able to anchor approximately 42 % of the dragon genome sequence to chromosomes. We constructed detailed comparative maps between dragon, anole and chicken genomes, and where possible, made broader comparisons across Squamata using cytogenetic mapping information for five other species. We show that squamate macrochromosomes are relatively well conserved between species, supporting findings from previous molecular cytogenetic studies. Macrochromosome diversity between members of the Toxicofera clade has been generated by intrachromosomal, and a small number of interchromosomal, rearrangements. We reconstructed the ancestral squamate macrochromosomes by drawing upon comparative cytogenetic mapping data from seven squamate species and propose the events leading to the arrangements observed in representative species. In addition, we assigned over 8 Mbp of sequence containing 219 genes to the Z chromosome, providing a list of genes to begin testing as candidate sex determining genes. Anchoring of the dragon genome has provided substantial insight into the evolution of squamate genomes, enabling us to reconstruct ancestral macrochromosome arrangements at key positions in the squamate phylogeny, demonstrating that fusions between macrochromosomes or fusions of macrochromosomes and microchromosomes, have played an important role during the evolution of squamate genomes. Assigning sequence to the sex chromosomes has identified NR5A1 as a promising candidate sex determining gene in the dragon.

Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

PubMed Central

Nabholz, Benoit; Lartillot, Nicolas

2013-01-01

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment. PMID:23711670

Structural profile reconstructions and thermal metamorphic evolution in the slate belt of southern Hsuehshan Range in the active Taiwan mountain belt

NASA Astrophysics Data System (ADS)

Wu, Yu; Chen, Chih-Tung; Lee, Jian-Cheng; Shyu, J. Bruce H.

2017-04-01

The fate of passive continental margin in collisional orogens is crucial in understanding tectonic evolution of mountain belts. The active arc-continent collision of Taiwan is considered as a model case in studying mountain building processes, and largely consists of deformed margin basement and cover series. Among the whole orogeny belt, the slate belt of the Hsuehshan Range (HR) is a prominent large-scale pop-up structural on the prowedge part of the orogen, and is composed of metamorphosed Eocene to Miocene sediments which experienced only the Neogene Taiwan orogeny after diagenesis in margin graben. Characterizing the metamorphic history of the HR is essential for reconstructing its geological evolution during the mountain building processes. However, previous studies were mostly focused on northern and central HR, structural investigation coupled with metamorphic documentation in the southern part of HR, which is the most active part of the orogeny belt, is therefore targeted in this work. Since carbonaceous material is common in pelitic protolith of HR slates, the Raman spectrum of carbonaceous material (RSCM) measuring the rock peak temperature is chosen for quantitative thermal metamorphic documentation. In this study, we reconstruct a geological structural profile in western central Taiwan across the prowedge part of the mountain belt containing the southern HR by combining the surface geological data, well log records and published seismic reflection profiles. Although most of the existing data are concentrated in the fold-and-thrust belt, they are now reinforced by new field structural measurements and RSCM samples in the southern HR. In total 27 RSCM samples were collected along 2 transects perpendicular to the average strike with a dense interval about 2 km. The results allow us to map peak temperature distribution across southern HR, and provide new constraints for structural profile reconstruction and reappraisal of the structural evolution of the HR and neighboring fold-and-thrust belt. As shown in the previous thermal metamorphic investigation, we expected that southern HR strata acquired highest temperature during its burial stage than the orogenic stage like their central HR counterparts, thus experiencing mostly retrograde metamorphism in the entire mountain building processes.

Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

PubMed Central

2010-01-01

Background Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question. Results We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass) using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position. Conclusions Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain mass. We find that for our dataset the Bayesian analysis for ancestral state reconstruction is least affected by inclusion of fossil data suggesting that this approach might be preferable for future studies on other taxa with a poor fossil record. PMID:20105283

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

PubMed Central

Baumbach, Jan

2007-01-01

Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at . PMID:17986320

The evolution of vision.

PubMed

Gehring, Walter J

2014-01-01

In this review, the evolution of vision is retraced from its putative origins in cyanobacteria to humans. Circadian oscillatory clocks, phototropism, and phototaxis require the capability to detect light. Photosensory proteins allow us to reconstruct molecular phylogenetic trees. The evolution of animal eyes leading from an ancestral prototype to highly complex image forming eyes can be deciphered on the basis of evolutionary developmental genetic experiments and comparative genomics. As all bilaterian animals share the same master control gene, Pax6, and the same retinal and pigment cell determination genes, we conclude that the different eye-types originated monophyletically and subsequently diversified by divergent, parallel, or convergent evolution. © 2012 Wiley Periodicals, Inc.

Arterial complications, venous thromboembolism and deep venous thrombosis prophylaxis after anterior cruciate ligament reconstruction: A systematic review

PubMed Central

Janssen, Rob Paulus Augustinus; Reijman, Max; Janssen, Daan Martijn; van Mourik, Jan Bernardus Antonius

2016-01-01

AIM To summarize the current knowledge on vascular complications and deep venous thrombosis (DVT) prophylaxis after anterior cruciate ligament (ACL) reconstruction. METHODS A systematic review was conducted according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses statement. MEDLINE, EMBASE, Cochrane, Web of Science, CINAHL, PubMed publisher, and Google scholar medical literature databases were searched up to November 10, 2015. Any arthroscopic surgical method of primary or revision intra-articular ACL reconstruction of all graft types in humans was included. A risk of bias assessment was determined. RESULTS Fourty-seven studies were included in the review. Pseudaneurysms were the most frequently reported arterial complication after ACL reconstruction, irrespective of graft type or method of graft fixation with an incidence of 0.3%. The time to diagnosis of arterial complications after ACL reconstruction varied from days to mostly weeks but even years. After ACL reconstruction without thromboprophylaxis, the incidence of DVT was 9.7%, of which 2.1% was symptomatic. The incidence of pulmonary embolism was 0.1%. Tourniquet time > 2 h was related to venous thromboembolism. Thromboprophylaxis is indicated in patients with risk factors for venous thromboembolism. CONCLUSION After ACL reconstruction, the incidence of arterial complications, symptomatic DVT and pulmonary embolism was 0.3%, 2.1% and 0.1% respectively. Arterial complications may occur with all types of arthroscopic ACL reconstruction, methods of graft fixation as well as any type of graft. Patients considered to be at moderate or high risk of venous thromboembolism should routinely receive thromboprophylaxis after ACL reconstruction. PMID:27672574

40 CFR 63.5110 - What special definitions are used in this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment used to apply an organic coating to the surface of metal coil. A coil coating line includes a web... emission limitation (including any operating limit) or work practice standard; (2) Fails to meet any term... before July 18, 2000, and it has not subsequently undergone reconstruction as defined in § 63.2. Facility...

Characterizing Interdisciplinarity of Researchers and Research Topics Using Web Search Engines

PubMed Central

Sayama, Hiroki; Akaishi, Jin

2012-01-01

Researchers' networks have been subject to active modeling and analysis. Earlier literature mostly focused on citation or co-authorship networks reconstructed from annotated scientific publication databases, which have several limitations. Recently, general-purpose web search engines have also been utilized to collect information about social networks. Here we reconstructed, using web search engines, a network representing the relatedness of researchers to their peers as well as to various research topics. Relatedness between researchers and research topics was characterized by visibility boost—increase of a researcher's visibility by focusing on a particular topic. It was observed that researchers who had high visibility boosts by the same research topic tended to be close to each other in their network. We calculated correlations between visibility boosts by research topics and researchers' interdisciplinarity at the individual level (diversity of topics related to the researcher) and at the social level (his/her centrality in the researchers' network). We found that visibility boosts by certain research topics were positively correlated with researchers' individual-level interdisciplinarity despite their negative correlations with the general popularity of researchers. It was also found that visibility boosts by network-related topics had positive correlations with researchers' social-level interdisciplinarity. Research topics' correlations with researchers' individual- and social-level interdisciplinarities were found to be nearly independent from each other. These findings suggest that the notion of “interdisciplinarity" of a researcher should be understood as a multi-dimensional concept that should be evaluated using multiple assessment means. PMID:22719935

Characterizing interdisciplinarity of researchers and research topics using web search engines.

PubMed

Sayama, Hiroki; Akaishi, Jin

2012-01-01

Researchers' networks have been subject to active modeling and analysis. Earlier literature mostly focused on citation or co-authorship networks reconstructed from annotated scientific publication databases, which have several limitations. Recently, general-purpose web search engines have also been utilized to collect information about social networks. Here we reconstructed, using web search engines, a network representing the relatedness of researchers to their peers as well as to various research topics. Relatedness between researchers and research topics was characterized by visibility boost-increase of a researcher's visibility by focusing on a particular topic. It was observed that researchers who had high visibility boosts by the same research topic tended to be close to each other in their network. We calculated correlations between visibility boosts by research topics and researchers' interdisciplinarity at the individual level (diversity of topics related to the researcher) and at the social level (his/her centrality in the researchers' network). We found that visibility boosts by certain research topics were positively correlated with researchers' individual-level interdisciplinarity despite their negative correlations with the general popularity of researchers. It was also found that visibility boosts by network-related topics had positive correlations with researchers' social-level interdisciplinarity. Research topics' correlations with researchers' individual- and social-level interdisciplinarities were found to be nearly independent from each other. These findings suggest that the notion of "interdisciplinarity" of a researcher should be understood as a multi-dimensional concept that should be evaluated using multiple assessment means.

Interactive 3d Landscapes on Line

NASA Astrophysics Data System (ADS)

Fanini, B.; Calori, L.; Ferdani, D.; Pescarin, S.

2011-09-01

The paper describes challenges identified while developing browser embedded 3D landscape rendering applications, our current approach and work-flow and how recent development in browser technologies could affect. All the data, even if processed by optimization and decimation tools, result in very huge databases that require paging, streaming and Level-of-Detail techniques to be implemented to allow remote web based real time fruition. Our approach has been to select an open source scene-graph based visual simulation library with sufficient performance and flexibility and adapt it to the web by providing a browser plug-in. Within the current Montegrotto VR Project, content produced with new pipelines has been integrated. The whole Montegrotto Town has been generated procedurally by CityEngine. We used this procedural approach, based on algorithms and procedures because it is particularly functional to create extensive and credible urban reconstructions. To create the archaeological sites we used optimized mesh acquired with laser scanning and photogrammetry techniques whereas to realize the 3D reconstructions of the main historical buildings we adopted computer-graphic software like blender and 3ds Max. At the final stage, semi-automatic tools have been developed and used up to prepare and clusterise 3D models and scene graph routes for web publishing. Vegetation generators have also been used with the goal of populating the virtual scene to enhance the user perceived realism during the navigation experience. After the description of 3D modelling and optimization techniques, the paper will focus and discuss its results and expectations.

Clusters, voids and reconstructions of the cosmic web

NASA Astrophysics Data System (ADS)

Bos, E. G. Patrick

2016-12-01

The Universe is filled for 95% with dark matter and energy that we cannot see. Of the remaining 5% normal matter we can only see a small part. However, if we want to study the Universe as a whole, we will have to get to know it for 100%. We have to uncover indirectly where dark matter is hiding and what is the nature of dark energy. In this thesis we explore two such methods. The first part describes how we can use the large empty regions between galaxies, "voids", to learn more about dark energy. We converted our theoretical simulations to a model of real observations of galaxies. In this model, we perform the same measurements as we would in real observations. This way, we show that it is indeed possible to unravel the nature of dark energy. The second part is based on our computer code: BARCODE. It unites two models: a physical model of the formation of the Cosmic Web, and a description of the observational effects of (clusters of) galaxies, in particular the effect of redshift on distance measurements. It allows us to back-trace our observations to the primordial conditions. These enable us to trace all (dark) matter, also that which we did not directly observe. The result is a reconstruction of the complete Cosmic Web. In these, we studied "filaments". These objects have not yet been extensively studied. BARCODE will enable further study, e.g. by using it to find observable filaments.

Breast volumetric analysis for aesthetic planning in breast reconstruction: a literature review of techniques

PubMed Central

Rozen, Warren Matthew; Spychal, Robert T.; Hunter-Smith, David J.

2016-01-01

Background Accurate volumetric analysis is an essential component of preoperative planning in both reconstructive and aesthetic breast procedures towards achieving symmetrization and patient-satisfactory outcome. Numerous comparative studies and reviews of individual techniques have been reported. However, a unifying review of all techniques comparing their accuracy, reliability, and practicality has been lacking. Methods A review of the published English literature dating from 1950 to 2015 using databases, such as PubMed, Medline, Web of Science, and EMBASE, was undertaken. Results Since Bouman’s first description of water displacement method, a range of volumetric assessment techniques have been described: thermoplastic casting, direct anthropomorphic measurement, two-dimensional (2D) imaging, and computed tomography (CT)/magnetic resonance imaging (MRI) scans. However, most have been unreliable, difficult to execute and demonstrate limited practicability. Introduction of 3D surface imaging has revolutionized the field due to its ease of use, fast speed, accuracy, and reliability. However, its widespread use has been limited by its high cost and lack of high level of evidence. Recent developments have unveiled the first web-based 3D surface imaging program, 4D imaging, and 3D printing. Conclusions Despite its importance, an accurate, reliable, and simple breast volumetric analysis tool has been elusive until the introduction of 3D surface imaging technology. However, its high cost has limited its wide usage. Novel adjunct technologies, such as web-based 3D surface imaging program, 4D imaging, and 3D printing, appear promising. PMID:27047788

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

Evolution of Mass and Velocity Field in the Cosmic Web: Comparison between Baryonic and Dark Matter

NASA Astrophysics Data System (ADS)

Zhu, Weishan; Feng, Long-Long

2017-03-01

We investigate the evolution of the cosmic web since z = 5 in grid-based cosmological hydrodynamical simulations, focusing on the mass and velocity fields of both baryonic and cold dark matter. The tidal tensor of density is used as the main method for web identification, with λ th = 0.2-1.2. The evolution trends in baryonic and dark matter are similar, although moderate differences are observed. Sheets appear early, and their large-scale pattern may have been set up by z = 3. In terms of mass, filaments supersede sheets as the primary collapsing structures from z ˜ 2-3. Tenuous filaments assembled with each other to form prominent ones at z < 2. In accordance with the construction of the frame of the sheets, the cosmic divergence velocity, v div, was already well-developed above 2-3 Mpc by z = 3. Afterwards, the curl velocity, v curl, grew dramatically along with the rising of filaments, becoming comparable to v div, for <2-3 Mpc at z = 0. The scaling of v curl can be described by the hierarchical turbulence model. The alignment between the vorticity and the eigenvectors of the shear tensor in the baryonic matter field resembles that in the dark matter field, and is even moderately stronger between {\\boldsymbol{ω }} and {{\\boldsymbol{e}}}1, and ω and {{\\boldsymbol{e}}}3. Compared with dark matter, there is slightly less baryonic matter found residing in filaments and clusters, and its vorticity developed more significantly below 2-3 Mpc. These differences may be underestimated because of the limited resolution and lack of star formation in our simulation. The impact of the change of dominant structures in overdense regions at z ˜ 2-3 on galaxy formation and evolution is shortly discussed.

Co-Evolution of User and Organizational Interfaces: A Longitudinal Case Study of WWW Dissemination of National Statistics.

ERIC Educational Resources Information Center

Marchionini, Gary

2002-01-01

Describes how user interfaces for the Bureau of Labor Statistics (BLS) web site evolved over a 5-year period along with the larger organizational interface and how this co-evolution has influenced the institution. Interviews with BLS staff and transaction log analysis are the foci of this study, as well as user information-seeking studies and user…

Temporal evolution of the Green's function reconstruction in the seismic coda

NASA Astrophysics Data System (ADS)

Clerc, V.; Roux, P.; Campillo, M.

2013-12-01

In presence of multiple scattering, the wavefield evolves towards an equipartitioned state, equivalent to ambient noise. CAMPILLO and PAUL (2003) reconstructed the surface wave part of the Green's function between three pairs of stations in Mexico. The data indicate that the time asymmetry between causal and acausal part of the Green's function is less pronounced when the correlation is performed in the later windows of the coda. These results on the correlation of diffuse waves provide another perspective on the reconstruction of Green function which is independent of the source distribution and which suggests that if the time of observation is long enough, a single source could be sufficient. The paper by ROUX et al. (2005) provides a theoretical frame for the reconstruction of the Green's function in a homogeneous middle. In a multiple scattering medium with a single source, scatterers behave as secondary sources according to the Huygens principle. Coda waves are relevant to multiple scattering, a regime which can be approximated by diffusion for long lapse times. We express the temporal evolution of the correlation function between two receivers as a function of the secondary sources. We are able to predict the effect of the persistence of the net flux of energy observed by CAMPILLO and PAUL (2003) in numerical simulations. This method is also effective in order to retrieve the scattering mean free path. We perform a partial reconstruction of the Green's function in a strongly scattering medium in numerical simulations. The prediction of the flux asymmetry allows defining the parts of the coda providing the same information as ambient noise cross correlation.

P-REx: The Piston Reconstruction Experiment for infrared interferometry

NASA Astrophysics Data System (ADS)

Widmann, Felix; Pott, Jörg-Uwe; Velasco, Sergio

2018-03-01

For sensitive infrared interferometry, it is crucial to control the differential piston evolution between the used telescopes. This is classically done by the use of a fringe tracker. In this work, we develop a new method to reconstruct the temporal piston variation from the atmosphere, by using real-time data from adaptive optics (AO) wavefront sensing: the Piston Reconstruction Experiment (P-REx). In order to understand the principle performance of the system in a realistic multilayer atmosphere, it is first extensively tested in simulations. The gained insights are then used to apply P-REx to real data, in order to demonstrate the benefit of using P-REx as an auxiliary system in a real interferometer. All tests show positive results, which encourages further research and eventually a real implementation. Especially, the tests on on-sky data showed that the atmosphere is, under decent observing conditions, sufficiently well structured and stable, in order to apply P-REx. It was possible to conveniently reconstruct the piston evolution in two-thirds of the data sets from good observing conditions (r0 ˜ 30 cm). The main conclusion is that applying the piston reconstruction in a real system would reduce the piston variation from around 10 μm down to 1-2 μm over time-scales of up to two seconds. This suggests an application for mid-infrared interferometry, for example for MATISSE at the very large telescope interferometer or the large binocular telescope interferometer. P-REx therefore provides the possibility to improve interferometric measurements without the need for more complex AO systems than already in regular use at 8-m-class telescopes.

Evolving EO-1 Sensor Web Testbed Capabilities in Pursuit of GEOSS

NASA Technical Reports Server (NTRS)

Mandi, Dan; Ly, Vuong; Frye, Stuart; Younis, Mohamed

2006-01-01

A viewgraph presentation to evolve sensor web capabilities in pursuit of capabilities to support Global Earth Observing System of Systems (GEOSS) is shown. The topics include: 1) Vision to Enable Sensor Webs with "Hot Spots"; 2) Vision Extended for Communication/Control Architecture for Missions to Mars; 3) Key Capabilities Implemented to Enable EO-1 Sensor Webs; 4) One of Three Experiments Conducted by UMBC Undergraduate Class 12-14-05 (1 - 3); 5) Closer Look at our Mini-Rovers and Simulated Mars Landscae at GSFC; 6) Beginning to Implement Experiments with Standards-Vision for Integrated Sensor Web Environment; 7) Goddard Mission Services Evolution Center (GMSEC); 8) GMSEC Component Catalog; 9) Core Flight System (CFS) and Extension for GMSEC for Flight SW; 10) Sensor Modeling Language; 11) Seamless Ground to Space Integrated Message Bus Demonstration (completed December 2005); 12) Other Experiments in Queue; 13) Acknowledgements; and 14) References.

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

WebTag: Web browsing into sensor tags over NFC.

PubMed

Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Alvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

2012-01-01

Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm.

WebTag: Web Browsing into Sensor Tags over NFC

PubMed Central

Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Álvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

2012-01-01

Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm. PMID:23012511

Scrotal reconstruction and testicular prosthetics

PubMed Central

Lucas, Jacob W.; Lester, Kyle M.; Chen, Andrew

2017-01-01

Scrotal surgery encompasses a wide-variety of surgical techniques for an even wider variety of indications. In this manuscript, we review our indications, techniques, and pit-falls for various reconstructive scrotal surgeries as-well-as surgical tips for placement of testicular prostheses. Penoscrotal webbing (PSW) is an abnormal, often-problematic distal insertion of scrotal skin onto the ventral penile shaft. There are several effective and straightforward techniques used to revise this condition, which include simple scrotoplasty, single- or double-Z-plasty, or the VY-flap scrotoplasty. Reconstruction is also commonly indicated following scrotal skin loss caused by infection, trauma, lymphedema, hidradenitis, and cancer. Although initial management of these conditions often involves scrotal skin removal, repair of expansive scrotal skin loss can be technically difficult and can be accomplished by using one of several skin flaps or skin grafting. Split-thickness skin grafting of scrotal defects can be accomplished easily, and provides durable results. PMID:28904904

An experience of the Snow-Littler procedure.

PubMed

Rider, M A; Grindel, S I; Tonkin, M A; Wood, V E

2000-08-01

This paper reviews the results of the Snow-Littler procedure performed in twelve hands with classical central longitudinal deficiency and in one hand with symbrachydactyly, cleft type. There were no instances of major flap necrosis although two flaps showed tip ischaemia. The width of the first web was, in the main, satisfactory but four webspace revisions were performed. Supplementary skin grafting at the time of surgery was necessary in complete and/or complex thumb index syndactylies and in the patient with symbrachydactyly. In eight cases, a transverse metacarpal ligament was reconstructed. In the five other cases, no clinical instability or radiological divergence of the index and ring fingers occurred, in spite of no transverse metacarpal ligament reconstruction. Three de-rotational osteotomies of transposed index fingers were performed in patients who had a transverse metacarpal ligament reconstruction. These results indicated significantly improved appearance and improved function following the Snow-Littler procedure.

Holographic reconstruction of scalar fields in extended Kaluza-Klein cosmology

NASA Astrophysics Data System (ADS)

Korunur, Murat

2018-01-01

In recent years, many studies have been conducted to reconstruct the physical properties of scalar fields by establishing a connection between some energy densities and a scalar field of dark energies. In this paper, using the extended five-dimensional (5D) Kaluza-Klein model, we establish a correspondence among modified holographic dark energy and the tachyon, K-essence and dilaton scalar-field models. We also graphically illustrate the evolution of the equation-of-state parameter versus time.

Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.

PubMed

Franssen, Susanne U; Barton, Nicholas H; Schlötterer, Christian

2017-01-01

The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Repairing severe cicatricial contracture deformity in web-space by kite-like incision combined with full-thickness skin grafting].

PubMed

Liang, Liming; Chai, Jiake; Jia, Xiaoming; Wang, Yirong; Meng, Suyu; Liu, Tao

2012-12-01

To investigate the effectiveness of repairing severe cicatricial contracture deformity in the web-space by kite-like incision combined with full-thickness skin grafting. Between June 2008 and September 2011, 31 patients (87 web-spaces) with severe cicatricial contracture deformities in the web-spaces were treated. There were 24 males and 7 females, aged 5-43 years (median, 22 years). The causes of injuries were flame burn (26 cases), scald (3 cases), electric arc burn (1 case), and chemical burn (1 case). The degree of burn was deep second degree (14 cases) and third degree (17 cases). The interval time from injury to operation was 10 months to 17 years (median, 2.2 years). The kite-like incision was marked on the scar in the web-space. The rhombic scar between the adjacent metacarpophalangeal joints was excised, and cicatricial contracture was released completely. The secondary wound in the web-space was repaired with full-thickness autogeneic skin grafting. The secondary wound at donor site was directly sutured. All full-thickness skin grafts survived well. The incisions at donor sites healed primarily. Of 31 patients, 29 (82 web-spaces) were followed up 6-18 months (mean, 13 months). The sizes and depths of reconstructed web-spaces were similar to those of normal ones. No secondary cicatricial contracture was observed, and the function of fingers recovered well. The short-term effectiveness is satisfactory by kite-like incision combined with full-thickness skin grafting for repairing severe cicatricial contracture deformities in the web-space, while the long-term effectiveness needs further observation.

Diatom genomics: genetic acquisitions and mergers.

PubMed

Nisbet, R Ellen R; Kilian, Oliver; McFadden, Geoffrey I

2004-12-29

Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing

PubMed Central

Zanon, Marco; Davis, Basil A. S.; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O.

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses. PMID:29568303

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing.

PubMed

Zanon, Marco; Davis, Basil A S; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses.

A (historical) remark on the Darwin-Schiaparelli evolution theory.

PubMed

Freguglia, Paolo

2016-01-01

The aim of this paper is a free interpretation and reconstruction of a part of Giovanni Virginio Schiaparelli's essay (1898) where the author presents some ideas about a correspondence between living organisms and geometrical curves. From our analysis we derive a new approach to the ago-antagonist conception of the Darwinian evolution theory which is a continuation of [2]. Copyright: © 2016 by Fabrizio Serra editore, Pisa · Roma.

Skeletal heterochrony is associated with the anatomical specializations of snakes among squamate reptiles.

PubMed

Werneburg, Ingmar; Sánchez-Villagra, Marcelo R

2015-01-01

Snakes possess a derived anatomy, characterized by limb reduction and reorganization of the skull and internal organs. To understand the origin of snakes from an ontogenetic point of view, we conducted comprehensive investigations on the timing of skeletal elements, based on published and new data, and reconstructed the evolution of the ossification sequence among squamates. We included for the first time Varanus, a critical taxon in phylogenetic context. There is comprehensive delay in the onset of ossification of most skeletal elements in snakes when compared to reference developmental events through evolution. We hypothesize that progressing deceleration accompanied limb reduction and reorganization of the snake skull. Molecular and morphological studies have suggested close relationship of snakes to either amphisbaenians, scincids, geckos, iguanids, or varanids. Likewise, alternative hypotheses on habitat for stem snakes have been postulated. Our comprehensive heterochrony analyses detected developmental shifts in ossification for each hypothesis of snake origin. Moreover, we show that reconstruction of ancestral developmental sequences is a valuable tool to understand ontogenetic mechanisms associated with major evolutionary changes and test homology hypotheses. The "supratemporal" of snakes could be homolog to squamosal of other squamates, which starts ossification early to become relatively large in snakes. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

PubMed

Pellicer, Jaume; Kelly, Laura J; Leitch, Ilia J; Zomlefer, Wendy B; Fay, Michael F

2014-03-01

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

PubMed Central

Benítez-Benítez, Carmen; Fernández-Mazuecos, Mario; Martín-Bravo, Santiago

2017-01-01

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5’trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution. PMID:29281689

RootJS: Node.js Bindings for ROOT 6

NASA Astrophysics Data System (ADS)

Beffart, Theo; Früh, Maximilian; Haas, Christoph; Rajgopal, Sachin; Schwabe, Jonas; Wolff, Christoph; Szuba, Marek

2017-10-01

We present rootJS, an interface making it possible to seamlessly integrate ROOT 6 into applications written for Node.js, the JavaScript runtime platform increasingly commonly used to create high-performance Web applications. ROOT features can be called both directly from Node.js code and by JIT-compiling C++ macros. All rootJS methods are invoked asynchronously and support callback functions, allowing non-blocking operation of Node.js applications using them. Last but not least, our bindings have been designed to platform-independent and should therefore work on all systems supporting both ROOT 6 and Node.js. Thanks to rootJS it is now possible to create ROOT-aware Web applications taking full advantage of the high performance and extensive capabilities of Node.js. Examples include platforms for the quality assurance of acquired, reconstructed or simulated data, book-keeping and e-log systems, and even Web browser-based data visualisation and analysis.

Web-Based Learning - Yes We Can!

NASA Astrophysics Data System (ADS)

Schroeder, Ulrik

Web-based Learning has become a matter of fact at universities. We are now at the edge of new developments with Web 2.0 applications and social software is radically changing the way of how we communicate and share in social networks. Can we expect an analogous revolution for university education 2.0? I will give some arguments that I rather expect an incremental evolution than a radical change. First, I take a look at current eLearning implementations and organizational frameworks and give an example from RWTH Aachen University. Against the background of cognitive theories the utilization of Web 2.0 applications are promising to strengthen 21st century learning. But methods and tools must be adapted to the context of institutional learning as well as the formal regulations must be adjusted vice versa.

Sentiment Analysis of Web Sites Related to Vaginal Mesh Use in Pelvic Reconstructive Surgery.

PubMed

Hobson, Deslyn T G; Meriwether, Kate V; Francis, Sean L; Kinman, Casey L; Stewart, J Ryan

2018-05-02

The purpose of this study was to utilize sentiment analysis to describe online opinions toward vaginal mesh. We hypothesized that sentiment in legal Web sites would be more negative than that in medical and reference Web sites. We generated a list of relevant key words related to vaginal mesh and searched Web sites using the Google search engine. Each unique uniform resource locator (URL) was sorted into 1 of 6 categories: "medical", "legal", "news/media", "patient generated", "reference", or "unrelated". Sentiment of relevant Web sites, the primary outcome, was scored on a scale of -1 to +1, and mean sentiment was compared across all categories using 1-way analysis of variance. Tukey test evaluated differences between category pairs. Google searches of 464 unique key words resulted in 11,405 URLs. Sentiment analysis was performed on 8029 relevant URLs (3472 legal, 1625 "medical", 1774 "reference", 666 "news media", 492 "patient generated"). The mean sentiment for all relevant Web sites was +0.01 ± 0.16; analysis of variance revealed significant differences between categories (P < 0.001). Web sites categorized as "legal" and "news/media" had a slightly negative mean sentiment, whereas those categorized as "medical," "reference," and "patient generated" had slightly positive mean sentiments. Tukey test showed differences between all category pairs except the "medical" versus "reference" in comparison with the largest mean difference (-0.13) seen in the "legal" versus "reference" comparison. Web sites related to vaginal mesh have an overall mean neutral sentiment, and Web sites categorized as "medical," "reference," and "patient generated" have significantly higher sentiment scores than related Web sites in "legal" and "news/media" categories.

Web building and silk properties functionally covary among species of wolf spider.

PubMed

Lacava, Mariángeles; Camargo, Arley; Garcia, Luis F; Benamú, Marco A; Santana, Martin; Fang, Jian; Wang, Xungai; Blamires, Sean J

2018-04-15

Although phylogenetic studies have shown covariation between the properties of spider major ampullate (MA) silk and web building, both spider webs and silks are highly plastic so we cannot be sure whether these traits functionally covary or just vary across environments that the spiders occupy. As MaSp2-like proteins provide MA silk with greater extensibility, their presence is considered necessary for spider webs to effectively capture prey. Wolf spiders (Lycosidae) are predominantly non-web building, but a select few species build webs. We accordingly collected MA silk from two web-building and six non-web-building species found in semirural ecosystems in Uruguay to test whether the presence of MaSp2-like proteins (indicated by amino acid composition, silk mechanical properties and silk nanostructures) was associated with web building across the group. The web-building and non-web-building species were from disparate subfamilies so we estimated a genetic phylogeny to perform appropriate comparisons. For all of the properties measured, we found differences between web-building and non-web-building species. A phylogenetic regression model confirmed that web building and not phylogenetic inertia influences silk properties. Our study definitively showed an ecological influence over spider silk properties. We expect that the presence of the MaSp2-like proteins and the subsequent nanostructures improves the mechanical performance of silks within the webs. Our study furthers our understanding of spider web and silk co-evolution and the ecological implications of spider silk properties. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Trends in Anterior Cruciate Ligament Reconstruction in the Last Decade: A Web-Based Analysis.

PubMed

Yucens, Mehmet; Aydemir, Ahmet Nadir

2018-05-31

Anterior cruciate ligament (ACL) injury is known to be one of the most common knee joint injuries. ACL reconstruction can be similar to the native ACL in respect of graft morphology, tension, position, and orientation. ACL reconstruction can be applied with different surgery techniques, graft and fixation devices, and rehabilitation as ACL reconstruction is just as important as surgery. Although commonly known as a sports injury, ACL injuries are increasingly seen in the general population. The aim of this study was to investigate the trends in ACL injury treatment in the last decade especially the graft choice. The abstracts of a total of 2,622 papers which stated ACL in the title were investigated through a search on the Web of Knowledge. Main topics were created as the ACL reconstruction theme. ACL reconstruction was examined in the abstracts with graft choice as the main theme followed by single bundle, double bundle, sports, rehabilitation, revision, complication, skeletally immature, biomechanics and kinematics, fixation devices, meniscus, anesthesia and pain, tunnel, cell, and intra-articular injection. Of the total 2,622 documents, 2,129 were original articles and 181 were reviews. Most of the documents, 436 in number (16.6%), were published in the American Journal of Sports Medicine , followed by the Journal of Knee Surgery , Sports Traumatology , Arthroscopy at 264. Of the total documents published, 36.3% were from the United States followed by 8.5% from Japan. The author with the most publications was F.H. Fu with 94 publications followed by B.R. Bach with 41 publications. The hamstring graft was most used at 187 single use and comprising 52% of the total graft combinations. Most papers were published in 2016. In 2012, single and double bundle grafts were determined to a total of 23. The most common title investigated in papers was biomechanics and kinematics with a total of 241 publications followed by rehabilitation at 208. Throughout the years of the study period, the most common graft choice was hamstring autograft. Biomechanics and kinematics was the most common title investigated as biomechanics and rehabilitation are known to be just as important as surgery for a successful outcome and patient satisfaction. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Information architecture for a planetary 'exploration web'

NASA Technical Reports Server (NTRS)

Lamarra, N.; McVittie, T.

2002-01-01

'Web services' is a common way of deploying distributed applications whose software components and data sources may be in different locations, formats, languages, etc. Although such collaboration is not utilized significantly in planetary exploration, we believe there is significant benefit in developing an architecture in which missions could leverage each others capabilities. We believe that an incremental deployment of such an architecture could significantly contribute to the evolution of increasingly capable, efficient, and even autonomous remote exploration.

Chronic Mycobacterium infection of first dorsal web space after accidental Bacilli Calmette-Guérin injection in a health worker: case report.

PubMed

Vigler, Mordechai; Mulett, Hanan; Hausman, Michael R

2008-11-01

We present a case of inoculation of the first dorsal web space by a nurse practitioner who accidentally stuck herself while preparing Bacilli Calmette-Guérin vaccine for treatment of bladder tumor. We report the evolution and management of this resistant chronic Mycobacterium infection that ultimately required use of a vacuum wound management system followed by a microvascular free tissue transfer.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

PubMed

Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

2018-05-22

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

Morphology controlled synthesis of 2-D Ni-Ni3S2 and Ni3S2 nanostructures on Ni foam towards oxygen evolution reaction

NASA Astrophysics Data System (ADS)

Chaudhari, Nitin Kaduba; Oh, Aram; Sa, Young Jin; Jin, Haneul; Baik, Hionsuck; Kim, Sang Gu; Lee, Suk Joong; Joo, Sang Hoon; Lee, Kwangyeol

2017-03-01

Catalysts for oxygen evolution reactions (OER) are at the heart of key renewable energy technologies, and development of non-precious metal catalysts with high activity and stability remain a great challenge in this field. Among various material candidates, metal sulfides are receiving increasing attention. While morphology-dependent catalytic performances are well established in noble metal-based catalysts, relatively little is known for the morphology‒catalytic performance relationship in metal sulfide catalysts. In this study, uniform spider web-like Ni nanosheets-Ni3S2 and honeycomb-like Ni3S2 structures are deposited on nickel foam (Ni3S2/NF) by a facile one-step hydrothermal synthetic route. When used as an oxygen evolution electrode, the spider web-like Ni-Ni3S2/NF with the large exposed surface area shown excellent catalytic activity and stability with an overpotential of 310 mV to achieve at 10 mA/cm2 and a Tafel slope of 63 mV/dec in alkaline media, which is superior to the honeycomb-like structure without Ni nanosheet. The low Tafel slope of the spider web-like Ni-Ni3S2/NF represents one of the best OER kinetics among nickel sulfide-based OER catalysts. The results point to the fact that performance of the metal sulfide electrocatalysts might be fine-tuned and optimized with morphological controls.

Anatomy assisted PET image reconstruction incorporating multi-resolution joint entropy

NASA Astrophysics Data System (ADS)

Tang, Jing; Rahmim, Arman

2015-01-01

A promising approach in PET image reconstruction is to incorporate high resolution anatomical information (measured from MR or CT) taking the anato-functional similarity measures such as mutual information or joint entropy (JE) as the prior. These similarity measures only classify voxels based on intensity values, while neglecting structural spatial information. In this work, we developed an anatomy-assisted maximum a posteriori (MAP) reconstruction algorithm wherein the JE measure is supplied by spatial information generated using wavelet multi-resolution analysis. The proposed wavelet-based JE (WJE) MAP algorithm involves calculation of derivatives of the subband JE measures with respect to individual PET image voxel intensities, which we have shown can be computed very similarly to how the inverse wavelet transform is implemented. We performed a simulation study with the BrainWeb phantom creating PET data corresponding to different noise levels. Realistically simulated T1-weighted MR images provided by BrainWeb modeling were applied in the anatomy-assisted reconstruction with the WJE-MAP algorithm and the intensity-only JE-MAP algorithm. Quantitative analysis showed that the WJE-MAP algorithm performed similarly to the JE-MAP algorithm at low noise level in the gray matter (GM) and white matter (WM) regions in terms of noise versus bias tradeoff. When noise increased to medium level in the simulated data, the WJE-MAP algorithm started to surpass the JE-MAP algorithm in the GM region, which is less uniform with smaller isolated structures compared to the WM region. In the high noise level simulation, the WJE-MAP algorithm presented clear improvement over the JE-MAP algorithm in both the GM and WM regions. In addition to the simulation study, we applied the reconstruction algorithms to real patient studies involving DPA-173 PET data and Florbetapir PET data with corresponding T1-MPRAGE MRI images. Compared to the intensity-only JE-MAP algorithm, the WJE-MAP algorithm resulted in comparable regional mean values to those from the maximum likelihood algorithm while reducing noise. Achieving robust performance in various noise-level simulation and patient studies, the WJE-MAP algorithm demonstrates its potential in clinical quantitative PET imaging.

HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor

PubMed Central

Clima, Rosanna; Preste, Roberto; Calabrese, Claudia; Diroma, Maria Angela; Santorsola, Mariangela; Scioscia, Gaetano; Simone, Domenico; Shen, Lishuang; Gasparre, Giuseppe; Attimonelli, Marcella

2017-01-01

The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/. PMID:27899581

Examination of an Oligocene Lacustrine Ecosystem Using C and N Stable Isotopes

NASA Astrophysics Data System (ADS)

Schweizer, M. K.; Wooller, M. J.; Toporski, J.; Fogel, M.; Steele, A.

2003-12-01

Stable isotopes of C and N are used to reconstruct the fossil Oligocene (25.8Ma) ecosystem at Lake Enspel, Westerwald, Germany. Enspel was a steep-sided, deep maar lake with anoxic bottom waters. Upon dying, terrestrial and aquatic organisms sank into the sediment where they were colonized by bacteria. These bacteria quickly became fossilized, preserving morphological detail and large amounts of organic matter from the original macroorganism. Carbon and nitrogen are sufficiently preserved in these fossils to permit stable isotope analysis. Stable isotopic signatures identify several trophic levels, including primary producers (terrigenous and aquatic plants, diatoms), primary consumers (tadpoles, some insects), and secondary consumers (carnivores such as fish). Primary producers are associated with depleted d13C and d15N values, primary consumers such as flies are one trophic shift higher, and fish are another shift higher. Signatures for the fish species show heavy-isotope enrichment correlated with increasing length, indicating an increasingly carnivorous diet. This study marks the first attempt to reconstruct a complete fossil ecosystem using stable isotope analysis, and confirms that techniques used to study modern food webs can be applied to extinct webs as well.

The Montaguto earth flow: nine years of observation and analysis

USGS Publications Warehouse

Guerriero, L.; Revellino, R; Grelle, G.; Diodato, N; Guadagno, F.M.; Coe, Jeffrey A.

2016-01-01

This paper summarizes the methods, results, and interpretation of analyses carried out between 2006 and 2015 at the Montaguto earth flow in southern Italy. We conducted a multi-temporal analysis of earth-flow activity to reconstruct the morphological and structural evolution of the flow. Data from field mapping were combined with a geometric reconstruction of the basal slip surface in order to investigate relations between basal-slip surface geometry and deformation styles of earth-flow material. Moreover, we reconstructed the long-term pattern of earth-flow movement using both historical observations and modeled hydrologic and climatic data. Hydrologic and climatic data were used to develop a Landslide Hydrological Climatological (LHC) indicator model.

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

PubMed

Razban, Rostam M; Gilson, Amy I; Durfee, Niamh; Strobelt, Hendrik; Dinkla, Kasper; Choi, Jeong-Mo; Pfister, Hanspeter; Shakhnovich, Eugene I

2018-05-08

Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (p-value<10-10) and -0.46 (p-value<10-10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015). ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary data are available at Bioinformatics. shakhnovich@chemistry.harvard.edu.

Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures.

PubMed

Barriuso, Jorge; Martínez, María Jesús

2017-01-03

Fungal "Versatile carboxylic ester hydrolases" are enzymes with great biotechnological interest. Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling. Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. The properties of the ancestral candidates are discussed on the basis of their three-dimensional structural models, the hydrophobicity of the lid, and the substrate binding intramolecular tunnel, revealing all of them featured properties of these enzymes. The evolutionary history of the putative lipases revealed an increase on the length and hydrophobicity of the lid region, as well as in the size of the substrate binding pocket, during evolution time. These facts suggest the enzymes' specialization towards certain substrates and their subsequent loss of promiscuity. These results bring to light the presence of different pools of lipases in fungi with different habitats and life styles. Despite the consistency of the data gathered from reconstruction of ancestral sequences, the heterologous expression of some of these candidates would be essential to corroborate enzymes' activities.

Tectonic evolution and extension at the Møre Margin - Offshore mid-Norway

NASA Astrophysics Data System (ADS)

Theissen-Krah, S.; Zastrozhnov, D.; Abdelmalak, M. M.; Schmid, D. W.; Faleide, J. I.; Gernigon, L.

2017-11-01

Lithospheric stretching is the key process in forming extensional sedimentary basins at passive rifted margins. This study explores the stretching factors, resulting extension, and structural evolution of the Møre segment on the Mid-Norwegian continental margin. Based on the interpretation of new and reprocessed high-quality seismic, we present updated structural maps of the Møre margin that show very thick post-rift sediments in the central Møre Basin and extensive sill intrusion into the Cretaceous sediments. A major shift in subsidence and deposition occurred during mid-Cretaceous. One transect across the Møre continental margin from the Slørebotn Subbasin to the continent-ocean boundary is reconstructed using the basin modelling software TecMod. We test different initial crustal configurations and rifting events and compare our structural reconstruction results to stretching factors derived both from crustal thinning and the classical backstripping/decompaction approach. Seismic interpretation in combination with structural reconstruction modelling does not support the lower crustal bodies as exhumed and serpentinised mantle. Our extension estimate along this transect is 188 ± 28 km for initial crustal thickness varying between 30 and 40 km.

Evolution of Ge nanoislands on Si(110)-'16 × 2' surface under thermal annealing studied using STM

NASA Astrophysics Data System (ADS)

Gangopadhyay, Subhashis; Yoshimura, Masamichi; Ueda, Kazuyuki

2009-11-01

The initial nucleation of Ge nanoclusters on Si(110) at room temperature (RT), annealing-induced surface roughening and the evolution of three-dimensional Ge nanoislands have been investigated using scanning tunneling microscopy (STM). A few monolayers (ML) of Ge deposited at room temperature lead to the formation of Ge clusters which are homogeneously distributed across the surface. The stripe-like patterns, characteristic of the Si(110)-'16 × 2' surface reconstruction are also retained. Increasing annealing temperatures, however, lead to significant surface diffusion and thus, disruption of the underlying '16 × 2' reconstruction. The annealing-induced removal of the stripe structures (originated from '16 × 2' reconstruction) starts at approximately 300 °C, whereas the terrace structures of Si(110) are thermally stable up to 500 °C. At approximately 650 °C, shallow Ge islands of pyramidal shape with (15,17,1) side facets start to form. Annealing at even higher temperatures enhances Ge island formation. Our findings are explained in terms of partial dewetting of the metastable Ge wetting layer (WL) (formed at room temperature) as well as partial relaxation of lattice strain through three-dimensional (3D) island growth.

Progress towards the use of publicly available data networks to conduct cross-scale historical reconstructions of carbon dynamics in US Drylands

NASA Astrophysics Data System (ADS)

Washington-Allen, R. A.; Landolt, K.; Emanuel, R. E.; Therrell, M. D.; Nagle, N.; Grissino-Mayer, H. D.; Poulter, B.

2016-12-01

Emergent scale properties of water-limited or Dryland ecosystem's carbon flux are unknown at spatial scales from local to global and time scales of 10 - 1000 years or greater. The width of a tree ring is a metric of production that has been correlated with the amount of precipitation. This relationship has been used to reconstruct rainfall and fire histories in the Drylands of the southwestern US. The normalized difference vegetation index (NDVI) is globally measured by selected satellite sensors and is highly correlated with the fraction of solar radiation which is absorbed for photosynthesis by plants (FPAR), as well as with vegetation biomass, net primary productivity (NPP), and tree ring width. Publicly available web-based archives of free NDVI and tree ring data exist and have allowed historical temporal reconstructions of carbon dynamics for the past 300 to 500 years. Climate and tree ring databases have been used to spatially reconstruct drought dynamics for the last 500 years in the western US. In 2007, we hypothesized that NDVI and tree ring width could be used to spatially reconstruct carbon dynamics in US Drylands. In 2015, we succeeded with a 300-year historical spatial reconstruction of NPP in California using a Blue Oak tree ring chronology. Online eddy covariance flux tower measures of NPP are well correlated with satellite measures of NPP. This suggests that net ecosystem exchange (NEE = NPP - soil Respiration) could be historically reconstructed across Drylands. Ongoing research includes 1) scaling historical spatial reconstruction to US Drylands, 2) comparing the use of single versus multiple tree ring species (r2 = 68) and 3) use of the eddy flux tower network, remote sensing, and tree ring data to historically spatially reconstruct Dryland NEE.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing.

PubMed

Adhikari, Badri; Trieu, Tuan; Cheng, Jianlin

2016-11-07

Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data by translating contact counts in Hi-C data into Euclidean distances between chromosomal regions and then satisfying these distances using a structure reconstruction method rigorously tested in the field of protein structure determination. We first evaluate the robustness of the overall reconstruction algorithm on noisy simulated data at various levels of noise by comparing with some of the state-of-the-art reconstruction methods. Then, using simulated data, we validate that Spearman's rank correlation coefficient between pairwise distances in the reconstructed chromosomal structures and the experimental chromosomal contact counts can be used to find optimum conversion rules for transforming interaction frequencies to wish distances. This strategy is then applied to real Hi-C data at chromosome level for optimal transformation of interaction frequencies to wish distances and for ranking and selecting structures. The chromosomal structures reconstructed from a real-world human Hi-C dataset by our method were validated by the known two-compartment feature of the human chromosome organization. We also show that our method is robust with respect to the change of the granularity of Hi-C data, and consistently produces similar structures at different chromosomal resolutions. Chromosome3D is a robust method of reconstructing chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency data. It is available as a web application and as an open source tool at http://sysbio.rnet.missouri.edu/chromosome3d/ .

Reconstruction of Laser-Induced Surface Topography from Electron Backscatter Diffraction Patterns.

PubMed

Callahan, Patrick G; Echlin, McLean P; Pollock, Tresa M; De Graef, Marc

2017-08-01

We demonstrate that the surface topography of a sample can be reconstructed from electron backscatter diffraction (EBSD) patterns collected with a commercial EBSD system. This technique combines the location of the maximum background intensity with a correction from Monte Carlo simulations to determine the local surface normals at each point in an EBSD scan. A surface height map is then reconstructed from the local surface normals. In this study, a Ni sample was machined with a femtosecond laser, which causes the formation of a laser-induced periodic surface structure (LIPSS). The topography of the LIPSS was analyzed using atomic force microscopy (AFM) and reconstructions from EBSD patterns collected at 5 and 20 kV. The LIPSS consisted of a combination of low frequency waviness due to curtaining and high frequency ridges. The morphology of the reconstructed low frequency waviness and high frequency ridges matched the AFM data. The reconstruction technique does not require any modification to existing EBSD systems and so can be particularly useful for measuring topography and its evolution during in situ experiments.

Baryon Acoustic Oscillations reconstruction with pixels

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

Obuljen, Andrej; Villaescusa-Navarro, Francisco; Castorina, Emanuele

2017-09-01

Gravitational non-linear evolution induces a shift in the position of the baryon acoustic oscillations (BAO) peak together with a damping and broadening of its shape that bias and degrades the accuracy with which the position of the peak can be determined. BAO reconstruction is a technique developed to undo part of the effect of non-linearities. We present and analyse a reconstruction method that consists of displacing pixels instead of galaxies and whose implementation is easier than the standard reconstruction method. We show that this method is equivalent to the standard reconstruction technique in the limit where the number of pixelsmore » becomes very large. This method is particularly useful in surveys where individual galaxies are not resolved, as in 21cm intensity mapping observations. We validate this method by reconstructing mock pixelated maps, that we build from the distribution of matter and halos in real- and redshift-space, from a large set of numerical simulations. We find that this method is able to decrease the uncertainty in the BAO peak position by 30-50% over the typical angular resolution scales of 21 cm intensity mapping experiments.« less

The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-08-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

Hubble Tarantula Treasury Project: Unraveling Tarantula's Web. I. Observational Overview and First Results

NASA Technical Reports Server (NTRS)

Sabbi, E.; Anderson, J.; Lennon, D. J.; van der Marel, R. P.; Aloisi, A.; Boyer, Martha L.; Cignoni, M.; De Marchi, G.; De Mink, S. E.; Evans, C. J.;

A tool for optimization of the production and user analysis on the Grid, C. Grigoras for the ALICE Collaboration

NASA Astrophysics Data System (ADS)

Grigoras, Costin; Carminati, Federico; Vladimirovna Datskova, Olga; Schreiner, Steffen; Lee, Sehoon; Zhu, Jianlin; Gheata, Mihaela; Gheata, Andrei; Saiz, Pablo; Betev, Latchezar; Furano, Fabrizio; Mendez Lorenzo, Patricia; Grigoras, Alina Gabriela; Bagnasco, Stefano; Peters, Andreas Joachim; Saiz Santos, Maria Dolores

2011-12-01

With the LHC and ALICE entering a full operation and production modes, the amount of Simulation and RAW data processing and end user analysis computational tasks are increasing. The efficient management of all these tasks, all of which have large differences in lifecycle, amounts of processed data and methods to analyze the end result, required the development and deployment of new tools in addition to the already existing Grid infrastructure. To facilitate the management of the large scale simulation and raw data reconstruction tasks, ALICE has developed a production framework called a Lightweight Production Manager (LPM). The LPM is automatically submitting jobs to the Grid based on triggers and conditions, for example after a physics run completion. It follows the evolution of the job and publishes the results on the web for worldwide access by the ALICE physicists. This framework is tightly integrated with the ALICE Grid framework AliEn. In addition to the publication of the job status, LPM is also allowing a fully authenticated interface to the AliEn Grid catalogue, to browse and download files, and in the near future will provide simple types of data analysis through ROOT plugins. The framework is also being extended to allow management of end user jobs.

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

DOE PAGES

Streubel, Robert; Kronast, Florian; Fischer, Peter; ...

2015-07-03

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

Combining Small-Vertebrate, Marine and Stable-Isotope Data to Reconstruct Past Environments

PubMed Central

Rofes, Juan; Garcia-Ibaibarriaga, Naroa; Aguirre, Mikel; Martínez-García, Blanca; Ortega, Luis; Zuluaga, María Cruz; Bailon, Salvador; Alonso-Olazabal, Ainhoa; Castaños, Jone; Murelaga, Xabier

2015-01-01

Three very different records are combined here to reconstruct the evolution of environments in the Cantabrian Region during the Upper Pleistocene, covering ~35.000 years. Two of these records come from Antoliñako Koba (Bizkaia, Spain), an exceptional prehistoric deposit comprising 9 chrono-cultural units (Aurignacian to Epipaleolithic). The palaeoecological signal of small-vertebrate communities and red deer stable-isotope data (δ13C and δ15N) from this mainland site are contrasted to marine microfaunal evidence (planktonic and benthic foraminifers, ostracods and δ18O data) gathered at the southern Bay of Biscay. Many radiocarbon dates for the Antoliña’s sequence, made it possible to compare the different proxies among them and with other well-known North-Atlantic records. Cooling and warming events regionally recorded, mostly coincide with the climatic evolution of the Upper Pleistocene in the north hemisphere. PMID:26391668

Habitat use affects morphological diversification in dragon lizards

PubMed Central

COLLAR, D C; SCHULTE, J A; O’MEARA, B C; LOSOS, J B

2010-01-01

Habitat use may lead to variation in diversity among evolutionary lineages because habitats differ in the variety of ways they allow for species to make a living. Here, we show that structural habitats contribute to differential diversification of limb and body form in dragon lizards (Agamidae). Based on phylogenetic analysis and ancestral state reconstructions for 90 species, we find that multiple lineages have independently adopted each of four habitat use types: rock-dwelling, terrestriality, semi-arboreality and arboreality. Given these reconstructions, we fit models of evolution to species’ morphological trait values and find that rock-dwelling and arboreality limit diversification relative to terrestriality and semi-arboreality. Models preferred by Akaike information criterion infer slower rates of size and shape evolution in lineages inferred to occupy rocks and trees, and model-averaged rate estimates are slowest for these habitat types. These results suggest that ground-dwelling facilitates ecomorphological differentiation and that use of trees or rocks impedes diversification. PMID:20345808

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

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

Streubel, Robert; Kronast, Florian; Fischer, Peter

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

A Gradualist Scenario for Language Evolution: Precise Linguistic Reconstruction of Early Human (and Neandertal) Grammars

PubMed Central

Progovac, Ljiljana

2016-01-01

In making an argument for the antiquity of language, based on comparative evidence, Dediu and Levinson (2013) express hope that some combinations of structural features will prove so conservative that they will allow deep linguistic reconstruction. I propose that the earliest stages of syntax/grammar as reconstructed in Progovac (2015a), based on a theoretical and data-driven linguistic analysis, provide just such a conservative platform, which would have been commanded also by Neandertals and the common ancestor. I provide a fragment of this proto-grammar, which includes flat verb-noun compounds used for naming and insult (e.g., rattle-snake, cry-baby, scatter-brain), and paratactic (loose) combinations of such flat structures (e.g., Come one, come all; You seek, you find). This flat, binary, paratactic platform is found in all languages, and can be shown to serve as foundation for any further structure building. However, given the degree and nature of variation across languages in elaborating syntax beyond this proto-stage, I propose that hierarchical syntax did not emerge once and uniformly in all its complexity, but rather multiple times, either within Africa, or after dispersion from Africa. If so, then, under the uniregional hypothesis, our common ancestor with Neandertals, H. heidelbergensis, could not have commanded hierarchical syntax, but “only” the proto-grammar. Linguistic reconstructions of this kind are necessary for formulating precise and testable hypotheses regarding language evolution. In addition to the hominin timeline, this reconstruction can also engage, and negotiate between, the fields of neuroscience and genetics, as I illustrate with one specific scenario involving FOXP2 gene. PMID:27877146

Reconstruction of the thermal environment evolution in urban areas from underground temperature distribution.

PubMed

Yamano, Makoto; Goto, Shusaku; Miyakoshi, Akinobu; Hamamoto, Hideki; Lubis, Rachmat Fajar; Monyrath, Vuthy; Taniguchi, Makoto

2009-04-15

It is possible to estimate the ground surface temperature (GST) history of the past several hundred years from temperature profiles measured in boreholes because the temporal variation in GST propagates into the subsurface by thermal diffusion. This "geothermal method" of reconstructing GST histories can be applied to studies of thermal environment evolution in urban areas, including the development of "heat islands." Temperatures in boreholes were logged at 102 sites in Bangkok, Jakarta, Taipei, Seoul and their surrounding areas in 2004 to 2007. The effects of recent surface warming can be recognized in the shapes of most of the obtained temperature profiles. The preliminary results of reconstruction of GST histories through inversion analysis show that GST increased significantly in the last century. Existing temperature profile data for the areas in and around Tokyo and Osaka can also be used to reconstruct GST histories. Because most of these cities are located on alluvial plains in relatively humid areas, it is necessary to use a model with groundwater flow and a layered subsurface structure for reconstruction analysis. Long-term records of subsurface temperatures at multiple depths may demonstrate how the GST variation propagates downward through formations. Time series data provide information on the mechanism of heat transfer (conduction or advection) and the thermal diffusivity. Long-term temperature monitoring has been carried out in a borehole located on the coast of Lake Biwa, Japan. Temperatures at 30 and 40 m below the ground surface were measured for 4 years and 2 years, respectively, with a resolution of 1 mK. The obtained records indicate steady increases at both depths with different rates, which is probably the result of some recent thermal event(s) near the surface. Borehole temperatures have also been monitored at selected sites in Bangkok, Jakarta, and Taiwan.

When parasites become prey: ecological and epidemiological significance of eating parasites

USGS Publications Warehouse

Johnson, Pieter T.J.; Dobson, Andrew P.; Lafferty, Kevin D.; Marcogliese, David J.; Memmott, Jane; Orlofske, Sarah A.; Poulin, Robert; Thieltges, David W.

2010-01-01

Recent efforts to include parasites in food webs have drawn attention to a previously ignored facet of foraging ecology: parasites commonly function as prey within ecosystems. Because of the high productivity of parasites, their unique nutritional composition and their pathogenicity in hosts, their consumption affects both food-web topology and disease risk in humans and wildlife. Here, we evaluate the ecological, evolutionary and epidemiological significance of feeding on parasites, including concomitant predation, grooming, predation on free-living stages and intraguild predation. Combining empirical data and theoretical models, we show that consumption of parasites is neither rare nor accidental, and that it can sharply affect parasite transmission and food web properties. Broader consideration of predation on parasites will enhance our understanding of disease control, food web structure and energy transfer, and the evolution of complex life cycles.

A Query Integrator and Manager for the Query Web

PubMed Central

Brinkley, James F.; Detwiler, Landon T.

2012-01-01

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions. PMID:22531831

Reconstructing the spatial pattern of historical forest land in China in the past 300 years

NASA Astrophysics Data System (ADS)

Yang, Xuhong; Jin, Xiaobin; Xiang, Xiaomin; Fan, Yeting; Shan, Wei; Zhou, Yinkang

2018-06-01

The reconstruction of the historical forest spatial distribution is of a great significance to understanding land surface cover in historical periods as well as its climate and ecological effects. Based on the maximum scope of historical forest land before human intervention, the characteristics of human behaviors in farmland reclamation and deforestation for heating and timber, we create a spatial evolution model to reconstruct the spatial pattern of historical forest land. The model integrates the land suitability for reclamation, the difficulty of deforestation, the attractiveness of timber trading markets and the abundance of forest resources to calibrate the potential scope of historical forest land with the rationale that the higher the probability of deforestation for reclamation and wood, the greater the likelihood that the forest land will be deforested. Compared to the satellite-based forest land distribution in 2000, about 78.5% of our reconstructed historical forest grids are of the absolute error between 25% and -25% while as many as 95.85% of those grids are of the absolute error between 50% and -50%, which indirectly validates the feasibility of our reconstructed model. Then, we simulate the spatial distribution of forest land in China in 1661, 1724, 1820, 1887, 1933 and 1952 with the grid resolution of 1 km × 1 km. Our result shows that (1) the reconstructed historical forest land in China in the past 300 years concentrates in DaXingAnLing, XiaoXingAnLing, ChangBaiShan, HengDuanShan, DaBaShan, WuYiShan, DaBieShan, XueFengShang and etc.; (2) in terms of the spatial evolution, historical forest land shrank gradually in LiaoHe plains, SongHuaJiang-NenJiang plains and SanJiang plains of eastnorth of China, Sichuan basins and YunNan-GuiZhou Plateaus; and (3) these observations are consistent to the proceeding of agriculture reclamation in China in past 300 years towards Northeast China and Southwest China.

Promoting women's human rights: A qualitative analysis of midwives' perceptions about virginity control and hymen 'reconstruction'.

PubMed

Christianson, Monica; Eriksson, Carola

2015-06-01

To explore midwives' perceptions regarding virginity control and hymen 'reconstructions', and how these practices can be debated from a gender perspective. An international group of 266 midwives answered an open-ended question in a Web survey. The great majority came from the Western world, among them, the majority were from Europe. Data were analysed using qualitative content analysis. Three themes emerged: misogynistic practices that cement the gender order, which revealed how the respondents viewed virginity control and hymen 'reconstructions'; raising public awareness and combatting practices that demean women, which were suggested as strategies by which to combat these practices; and promoting agency in women and providing culturally sensitive care, which were considered to improve health care encounters. Virginity control and hymen 'reconstructions' are elements of patriarchy, whereby violence and control are employed to subordinate women. To counter these practices, macro and micro-level activities are needed to expand women's human rights in the private and the public spheres. Political activism, international debates, collaboration between sectors such as health care and law-makers may lead to increased gender equality. A women-centred approach whereby women are empowered with agency will make women more capable of combatting virginity control and hymen 'reconstruction'.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery.

PubMed

Tan, Youri P A; Liverneaux, Philippe; Wong, Jason K F

2018-01-01

Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery

PubMed Central

Tan, Youri P. A.; Liverneaux, Philippe; Wong, Jason K. F.

2018-01-01

Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality. PMID:29740585

Trends in the Evolution of the Public Web, 1998-2002; The Fedora Project: An Open-source Digital Object Repository Management System; State of the Dublin Core Metadata Initiative, April 2003; Preservation Metadata; How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

O'Neill, Edward T.; Lavoie, Brian F.; Bennett, Rick; Staples, Thornton; Wayland, Ross; Payette, Sandra; Dekkers, Makx; Weibel, Stuart; Searle, Sam; Thompson, Dave; Rudner, Lawrence M.

2003-01-01

Includes five articles that examine key trends in the development of the public Web: size and growth, internationalization, and metadata usage; Flexible Extensible Digital Object and Repository Architecture (Fedora) for use in digital libraries; developments in the Dublin Core Metadata Initiative (DCMI); the National Library of New Zealand Te Puna…

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Perturbation theory for BAO reconstructed fields: One-loop results in the real-space matter density field

NASA Astrophysics Data System (ADS)

Hikage, Chiaki; Koyama, Kazuya; Heavens, Alan

2017-08-01

We compute the power spectrum at one-loop order in standard perturbation theory for the matter density field to which a standard Lagrangian baryonic acoustic oscillation (BAO) reconstruction technique is applied. The BAO reconstruction method corrects the bulk motion associated with the gravitational evolution using the inverse Zel'dovich approximation (ZA) for the smoothed density field. We find that the overall amplitude of one-loop contributions in the matter power spectrum substantially decreases after reconstruction. The reconstructed power spectrum thereby approaches the initial linear spectrum when the smoothed density field is close enough to linear, i.e., the smoothing scale Rs≳10 h-1 Mpc . On smaller Rs, however, the deviation from the linear spectrum becomes significant on large scales (k ≲Rs-1 ) due to the nonlinearity in the smoothed density field, and the reconstruction is inaccurate. Compared with N-body simulations, we show that the reconstructed power spectrum at one-loop order agrees with simulations better than the unreconstructed power spectrum. We also calculate the tree-level bispectrum in standard perturbation theory to investigate non-Gaussianity in the reconstructed matter density field. We show that the amplitude of the bispectrum significantly decreases for small k after reconstruction and that the tree-level bispectrum agrees well with N-body results in the weakly nonlinear regime.

Update on orbital reconstruction.

PubMed

Chen, Chien-Tzung; Chen, Yu-Ray

2010-08-01

Orbital trauma is common and frequently complicated by ocular injuries. The recent literature on orbital fracture is analyzed with emphasis on epidemiological data assessment, surgical timing, method of approach and reconstruction materials. Computed tomographic (CT) scan has become a routine evaluation tool for orbital trauma, and mobile CT can be applied intraoperatively if necessary. Concomitant serious ocular injury should be carefully evaluated preoperatively. Patients presenting with nonresolving oculocardiac reflex, 'white-eyed' blowout fracture, or diplopia with a positive forced duction test and CT evidence of orbital tissue entrapment require early surgical repair. Otherwise, enophthalmos can be corrected by late surgery with a similar outcome to early surgery. The use of an endoscope-assisted approach for orbital reconstruction continues to grow, offering an alternative method. Advances in alloplastic materials have improved surgical outcome and shortened operating time. In this review of modern orbital reconstruction, several controversial issues such as surgical indication, surgical timing, method of approach and choice of reconstruction material are discussed. Preoperative fine-cut CT image and thorough ophthalmologic examination are key elements to determine surgical indications. The choice of surgical approach and reconstruction materials much depends on the surgeon's experience and the reconstruction area. Prefabricated alloplastic implants together with image software and stereolithographic models are significant advances that help to more accurately reconstruct the traumatized orbit. The recent evolution of orbit reconstruction improves functional and aesthetic results and minimizes surgical complications.

Coupled Source-to-Sink and Geodynamic Modeling of Extensional Basins: A Case Study of the Gulf of Corinth, Greece.

NASA Astrophysics Data System (ADS)

Smithells, R. A.

2015-12-01

Many studies investigate rift evolution with geodynamic models, giving insight into the architecture and morphology of extensional basins. Recent advances in modeling allow better temporal and spatial resolution in surface processes when coupled with geodynamic processes, allowing modeling the interactions between sediment erosion and deposition with rift development. Here we use a combination of dynamic forward modeling and landscape evolution models to determine feedback and interaction of sediment erosion and deposition with rift development and fault localization. The Gulf of Corinth is an ideal basin to study the effect of surface processes on rifting because it can be considered a closed system for sediment erosion and deposition. It is a young rift, not affected by subsequent overprinting and there is a large amount of data from offshore seismic surveys and onshore fieldwork to constrain its evolution. We reconstruct paleo topography of the catchment area by removing the effects of fault activity and sediment erosion. The reconstructed topography is used to model different scenarios for landscape evolution and the results determine the relative importance of regional and fault related uplift and subsidence on the drainage evolution in the Gulf of Corinth. The landscape models are also used to constrain source area and total amount of sediment eroded from the catchment area. The eroded onshore volume and the amount of sediment deposited offshore are compared in order to reconstruct the source-to-sink balance for the Gulf of Corinth. Our results constrain the evolution of the catchment area and timings of drainage reversals that occurred in the fluvial systems of the Gulf of Corinth. Coupled forward tectonic-surface process modeling is used to investigate feedback between rift formation and the surface processes and to determine its role in developing asymmetry and fault migration in an extensional setting. In this study we investigate the effect of a mature sediment routing system on rift development. Our models show that migrating fault activity may be triggered by migration of sediment deposition filling the accommodation space provided by the associated half grabens. The asymmetric development of the rift can be explained by the preferred erosion and deposition of the southern flank of the Gulf of Corinth.

Time variability in Cenozoic reconstructions of mantle heat flow: plate tectonic cycles and implications for Earth's thermal evolution.

PubMed

Loyd, S J; Becker, T W; Conrad, C P; Lithgow-Bertelloni, C; Corsetti, F A

2007-09-04

The thermal evolution of Earth is governed by the rate of secular cooling and the amount of radiogenic heating. If mantle heat sources are known, surface heat flow at different times may be used to deduce the efficiency of convective cooling and ultimately the temporal character of plate tectonics. We estimate global heat flow from 65 Ma to the present using seafloor age reconstructions and a modified half-space cooling model, and we find that heat flow has decreased by approximately 0.15% every million years during the Cenozoic. By examining geometric trends in plate reconstructions since 120 Ma, we show that the reduction in heat flow is due to a decrease in the area of ridge-proximal oceanic crust. Even accounting for uncertainties in plate reconstructions, the rate of heat flow decrease is an order of magnitude faster than estimates based on smooth, parameterized cooling models. This implies that heat flow experiences short-term fluctuations associated with plate tectonic cyclicity. Continental separation does not appear to directly control convective wavelengths, but rather indirectly affects how oceanic plate systems adjust to accommodate global heat transport. Given that today's heat flow may be unusually low, secular cooling rates estimated from present-day values will tend to underestimate the average cooling rate. Thus, a mechanism that causes less efficient tectonic heat transport at higher temperatures may be required to prevent an unreasonably hot mantle in the recent past.

New generation of integrated geological-geomorphological reconstruction maps in the Rhine-Meuse delta, The Netherlands

NASA Astrophysics Data System (ADS)

Pierik, Harm Jan; Cohen, Kim; Stouthamer, Esther

2016-04-01

Geological-geomorphological reconstructions are important for integrating diverse types of data and improving understanding of landscape formation processes. This works especially well in densely populated Holocene landscapes, where large quantities of raw data are produced by geotechnical, archaeological, soil science and hydrological communities as well as in academic research. The Rhine-Meuse delta, The Netherlands, has a long tradition of integrated digital reconstruction maps and databases. This contributed to improve understanding of delta evolution, especially regarding the channel belt network evolution. In this contribution, we present a new generation of digital map products for the Holocene Rhine-Meuse delta. Our reconstructions expand existing channel belt network maps, with new map layers containing natural levee extent and relative elevation. The maps we present have been based on hundreds of thousands of lithological borehole descriptions, >1000 radiocarbon dates, and further integrate LIDAR data, soil maps and archaeological information. For selected time slices through the Late Holocene, the map products describe the patterns of levee distribution. Additionally, we mapped the palaeo-topography of the levees through the delta, aiming to resolve what parts of the overbank river landscape were the relatively low and high positioned areas in the past landscape. The resulting palaeogeographical maps are integrative products created for a very data-rich research area. They will allow for delta-wide analysis in studying changes in the Late Holocene landscape and the interaction with past habitation.

Time variability in Cenozoic reconstructions of mantle heat flow: Plate tectonic cycles and implications for Earth's thermal evolution

PubMed Central

Loyd, S. J.; Becker, T. W.; Conrad, C. P.; Lithgow-Bertelloni, C.; Corsetti, F. A.

2007-01-01

The thermal evolution of Earth is governed by the rate of secular cooling and the amount of radiogenic heating. If mantle heat sources are known, surface heat flow at different times may be used to deduce the efficiency of convective cooling and ultimately the temporal character of plate tectonics. We estimate global heat flow from 65 Ma to the present using seafloor age reconstructions and a modified half-space cooling model, and we find that heat flow has decreased by ∼0.15% every million years during the Cenozoic. By examining geometric trends in plate reconstructions since 120 Ma, we show that the reduction in heat flow is due to a decrease in the area of ridge-proximal oceanic crust. Even accounting for uncertainties in plate reconstructions, the rate of heat flow decrease is an order of magnitude faster than estimates based on smooth, parameterized cooling models. This implies that heat flow experiences short-term fluctuations associated with plate tectonic cyclicity. Continental separation does not appear to directly control convective wavelengths, but rather indirectly affects how oceanic plate systems adjust to accommodate global heat transport. Given that today's heat flow may be unusually low, secular cooling rates estimated from present-day values will tend to underestimate the average cooling rate. Thus, a mechanism that causes less efficient tectonic heat transport at higher temperatures may be required to prevent an unreasonably hot mantle in the recent past. PMID:17720806

Validation of snow depth reconstruction from lapse-rate webcam images against terrestrial laser scanner measurements in centrel Pyrenees

NASA Astrophysics Data System (ADS)

Revuelto, Jesús; Jonas, Tobias; López-Moreno, Juan Ignacio

2015-04-01

Snow distribution in mountain areas plays a key role in many processes as runoff dynamics, ecological cycles or erosion rates. Nevertheless, the acquisition of high resolution snow depth data (SD) in space-time is a complex task that needs the application of remote sensing techniques as Terrestrial Laser Scanning (TLS). Such kind of techniques requires intense field work for obtaining high quality snowpack evolution during a specific time period. Combining TLS data with other remote sensing techniques (satellite images, photogrammetry…) and in-situ measurements could represent an improvement of the available information of a variable with rapid topographic changes. The aim of this study is to reconstruct daily SD distribution from lapse-rate images from a webcam and data from two to three TLS acquisitions during the snow melting periods of 2012, 2013 and 2014. This information is obtained at Izas Experimental catchment in Central Spanish Pyrenees; a catchment of 33ha, with an elevation ranging from 2050 to 2350m a.s.l. The lapse-rate images provide the Snow Covered Area (SCA) evolution at the study site, while TLS allows obtaining high resolution information of SD distribution. With ground control points, lapse-rate images are georrectified and their information is rasterized into a 1-meter resolution Digital Elevation Model. Subsequently, for each snow season, the Melt-Out Date (MOD) of each pixel is obtained. The reconstruction increases the estimated SD lose for each time step (day) in a distributed manner; starting the reconstruction for each grid cell at the MOD (note the reverse time evolution). To do so, the reconstruction has been previously adjusted in time and space as follows. Firstly, the degree day factor (SD lose/positive average temperatures) is calculated from the information measured at an automatic weather station (AWS) located in the catchment. Afterwards, comparing the SD lose at the AWS during a specific time period (i.e. between two TLS acquisitions) to that melted on each grid cell, a coefficient is obtained for spatially distributing the SD loses. For 2012 and 2013, three TLS acquisition campaigns were available during each melting period. This way the first acquisitions of both melting periods were reserved for validation while the other two were considered for adjusting the reconstruction. Validation has revealed a very good performance of the reconstructed SD distribution when compared with the TLS data (r2 values between 0.74 and 0.8 respectively). When no calibration with TLS data was applied for distributing melt rates; this is, using the distribution coefficients for reconstructing SD of precedent years, rather similar accuracy was reached. With the spatial calibration of 2012 and 2013, the reconstructions for the two TLS acquisition dates in 2014, obtained r2 values that ranged between 0.73 and 0.76. This shows the usefulness of lapse-rate images to estimate not only SCA but also the spatial distribution of the SD when combined with TLS acquisition and punctual information on temperature and SD. In such a way it is shown the effectiveness of combining two remote sensing techniques for obtaining distributed information on snow depth.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa

PubMed Central

Gehrke, Berit; Kandziora, Martha; Pirie, Michael D.

2016-01-01

Background and Aims Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. Methods Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). Key Results It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. Conclusions Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid. PMID:26520565

Phylotranscriptomic analysis of the origin and early diversification of land plants

PubMed Central

Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Carpenter, Eric; Matasci, Naim; Ayyampalayam, Saravanaraj; Barker, Michael S.; Burleigh, J. Gordon; Gitzendanner, Matthew A.; Ruhfel, Brad R.; Wafula, Eric; Graham, Sean W.; Mathews, Sarah; Melkonian, Michael; Soltis, Douglas E.; Soltis, Pamela S.; Miles, Nicholas W.; Rothfels, Carl J.; Pokorny, Lisa; Shaw, A. Jonathan; DeGironimo, Lisa; Stevenson, Dennis W.; Surek, Barbara; Villarreal, Juan Carlos; Roure, Béatrice; Philippe, Hervé; dePamphilis, Claude W.; Chen, Tao; Deyholos, Michael K.; Baucom, Regina S.; Kutchan, Toni M.; Augustin, Megan M.; Wang, Jun; Zhang, Yong; Tian, Zhijian; Yan, Zhixiang; Wu, Xiaolei; Sun, Xiao; Wong, Gane Ka-Shu; Leebens-Mack, James

2014-01-01

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated. PMID:25355905

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

PubMed Central

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

2012-01-01

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

PubMed

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

2012-09-21

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A reconstruction of solar irradiance using a flux transport model

NASA Astrophysics Data System (ADS)

Dasi Espuig, Maria; Jiang, Jie; Krivova, Natalie; Solanki, Sami

2013-04-01

Reconstructions of solar irradiance into the past are of considerable interest for studies of solar influence on climate. Models based on the assumption that irradiance changes are caused by the evolution of the photospheric magnetic field have been the most successful in reproducing the measured irradiance variations. Our SATIRE-S model is one of these. It uses solar full-disc magnetograms as an input, and these are available for less than four decades. Thus, to reconstruct the irradiance back to times when no observed magnetograms are available, we combine the SATIRE-S model with synthetic magnetograms, produced using a surface flux transport model. The model is fed with daily, observed or modelled statistically, records of sunspot positions, areas, and tilt angles. To describe the secular change in the irradiance, we used the concept of overlapping ephemeral region cycles. With this technique TSI can be reconstructed back to 1610.

Model-based adaptive 3D sonar reconstruction in reverberating environments.

PubMed

Saucan, Augustin-Alexandru; Sintes, Christophe; Chonavel, Thierry; Caillec, Jean-Marc Le

2015-10-01

In this paper, we propose a novel model-based approach for 3D underwater scene reconstruction, i.e., bathymetry, for side scan sonar arrays in complex and highly reverberating environments like shallow water areas. The presence of multipath echoes and volume reverberation generates false depth estimates. To improve the resulting bathymetry, this paper proposes and develops an adaptive filter, based on several original geometrical models. This multimodel approach makes it possible to track and separate the direction of arrival trajectories of multiple echoes impinging the array. Echo tracking is perceived as a model-based processing stage, incorporating prior information on the temporal evolution of echoes in order to reject cluttered observations generated by interfering echoes. The results of the proposed filter on simulated and real sonar data showcase the clutter-free and regularized bathymetric reconstruction. Model validation is carried out with goodness of fit tests, and demonstrates the importance of model-based processing for bathymetry reconstruction.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

PubMed

Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

2011-07-01

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

Stratigraphy and Evolution of Delta Channel Deposits, Jezero Crater, Mars

NASA Technical Reports Server (NTRS)

Goudge, T. A.; Mohrig, D.; Cardenas, B. T.; Hughes, C. M.; Fassett, C. I.

2017-01-01

The Jezero impact crater hosted an open-basin lake that was active during the valley network forming era on early Mars. This basin contains a well exposed delta deposit at the mouth of the western inlet valley. The fluvial stratigraphy of this deposit provides a record of the channels that built the delta over time. Here we describe observations of the stratigraphy of the channel deposits of the Jezero western delta to help reconstruct its evolution.

Theory of invasion extinction dynamics in minimal food webs

NASA Astrophysics Data System (ADS)

Haerter, Jan O.; Mitarai, Namiko; Sneppen, Kim

2018-02-01

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.

Theory of invasion extinction dynamics in minimal food webs.

PubMed

Haerter, Jan O; Mitarai, Namiko; Sneppen, Kim

2018-02-01

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

PubMed

Dornburg, Alex; Moore, Jon; Beaulieu, Jeremy M; Eytan, Ron I; Near, Thomas J

2015-01-01

One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often challenged by a lack of fossil evidence that provide insights into historic patterns of abundance and diversity. The greatest diversity of squirrelfishes and soldierfishes (Holocentridae) is in the IAA, yet these fishes also represent some of the most numerous fossil taxa in deposits of the former West Tethyan biodiversity hotspot. We reconstruct the pattern of holocentrid range evolution using time-calibrated phylogenies that include most living species and several fossil lineages, demonstrating the importance of including fossil species as terminal taxa in ancestral area reconstructions. Holocentrids exhibit increased range fragmentation following the West Tethyan hotspot collapse. However, rather than originating within the emerging IAA hotspot, the IAA has acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary time scales. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

[Application of distal palm perforator mini-flap in repair of scar contracture of digital web-spaces].

PubMed

Zhou, Xiao; Xu, Yajun; Rui, Yongjun; Shou, Kuishui; Yao, Qun

2011-02-01

To discuss the effectiveness of distal palm perforator mini-flap in the treatment of scar contracture of digital web-spaces. Between August 2008 and March 2010, 6 cases of scar contracture of digital web-spaces were treated, including 4 males and 2 females and aging 16-68 years (mean, 45 years). The causes were burn injury, twisting injury, and crush injury in 2 cases, respectively. The disease duration was from 3 months to 3 years. The affected digital web-spaces were from index finger to middle finger in 2 cases, from middle finger to ring finger in 3 cases, and from ring finger to small finger in 1 case. The maximum abduction degree of digital web-spaces was 5-10 degrees. The sizes and the depths of reshape of digital web-spaces disappeared. The defect size ranged from 20 mm x 8 mm to 30 mm x 13 mm after opening digital web-spaces. The size of the distal palm perforator mini-flap ranged from 25 mm x 10 mm to 35 mm x 15 mm. The donor sites were sutured directly. All 6 flaps survived and got primary healing. Incisions at donor sites healed by first intention. All patients were followed up 6-12 months. The reconstructed digital web-spaces had good appearance and soft texture. The range of motion of metacarpophalangeal joint was normal. The sizes and the depths of reshape of digital web-spaces were similar to normal ones. The maximum abduction degree of digital web-spaces was 40-60 degrees. There was no scar contracture of incision of palm. The shape of flaps and function of the fingers were satisfactory after 6-12 months of follow-up. It is an ideal method to treat scar contracture of digital web-spaces with distal palm perforator mini-flap.

Reviews Toy: Air swimmers Book: Their Arrows will Darken the Sun: The Evolution and Science of Ballistics Book: Physics Experiments for your Bag Book: Quantum Physics for Poets Equipment: SEP colour wheel kit Equipment: SEP colour mixing kit Software: USB DrDAQ App: iHandy Level Equipment: Photonics Explorer kit Web Watch

NASA Astrophysics Data System (ADS)

2012-01-01

WE RECOMMEND Air swimmers Helium balloon swims like a fish Their Arrows will Darken the Sun: The Evolution and Science of Ballistics Ballistics book hits the spot Physics Experiments for your Bag Handy experiments for your lessons Quantum Physics for Poets Book shows the economic importance of physics SEP colour wheel kit Wheels investigate colour theory SEP colour mixing kit Cheap colour mixing kit uses red, green and blue LEDs iHandy Level iPhone app superbly measures angles Photonics Explorer kit Free optics kit given to schools WORTH A LOOK DrDAQ DrDAQ software gets an upgrade WEB WATCH Websites show range of physics

Evolution of gastropod mitochondrial genome arrangements

PubMed Central

2008-01-01

Background Gastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis), and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods. Results Comparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI) arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group. Conclusion Four main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia). The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P. dolabrata) nor Pulmonata (polyphyletic) nor Opisthobranchia (because of the inclusion S. pectinata) were recovered as monophyletic groups. The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and we propose that at least three major rearrangements have taken place in the evolution of gastropods: one in the ancestor of Caenogastropoda, another in the ancestor of Patellogastropoda, and one more in the ancestor of Heterobranchia. PMID:18302768

Phylogenetic perspectives on reef fish functional traits.

PubMed

Floeter, Sergio R; Bender, Mariana G; Siqueira, Alexandre C; Cowman, Peter F

2018-02-01

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities. © 2017 Cambridge Philosophical Society.

Landscape trajectories during the Lateglacial and the Holocene in the Loir River Valley (France) : the contribution of Geoarchaeology

NASA Astrophysics Data System (ADS)

Piana, Juliene

2015-04-01

A multidisciplinary research has been initiated in the Loir River valley where investigations revealed high-potential fluvial records and landforms for environmental and socio-environmental reconstructions. Investigations provide the opportunity to reconstruct landscape trajectories between climate, environmental and societal changes during the last 16000 years, using geoarchaeological and archaeogeographical approaches: sedimentology, soil micromorphology, geochemistry, archaeology, geomatics, geochronology (AGES Program: Ancient Geomorphological EvolutionS of Loire Basin hydrosystem). In the sector of Vaas (Sarthe, France) the research on the Lateglacial and the Holocene sedimentary sequences from the alluvial plain leads to a general overview of the valley evolution from the end of the Weichselian Upper Pleniglacial to the Present. Joined to archaeological (Protohistoric and Antic sites) and historical data (engineering archives, 18th century cadastral registers) this research highlights the importance of anthropogenic and geomorphological heritages in the current fluvial landscape (microtopography, wetlands, archaeological remains, land use). This knowledge constitutes a basis for skills transfer to planners and managers, in sustainable management of hydrological resources (reducing the vulnerability to flooding and low flows), preservation of biodiversity (wetlands protection) and valorization of landscapes (cultural tourism development).

Morphological characteristics and medium-term evolution of the beaches between Ceuta and Cabo Negro (Morocco)

NASA Astrophysics Data System (ADS)

Anfuso, G.; Martínez Del Pozo, J. A.; Nachite, D.; Benavente, J.; Macias, A.

2007-05-01

This work presents the results of a combined study on the beach morphology and the evolution at short- and medium-term of the littoral between Ceuta and Cabo Negro (Morocco). It is an interesting sector showing a great increase of human occupation and coastal structures. The monitoring program allowed for the reconstruction of the beach morphological behavior and the seasonal changes. The studied beaches presented reflective profiles recording little seasonality, with the most notable morphological changes being strictly related to storms. Surf Similarity and Surf Scaling parameters highlighted the existence of intermediate and reflective beach states, characterized by plunging breakers. Aerial photographs and a satellite image have been geo-referenced and elaborated with GIS tools to reconstruct the short- and medium-term evolution of the littoral and the sediment transport pathways. The littoral showed important erosion at short- and medium-term related to a negative sedimentary budget because of offshore transport. Sand accumulation was recorded close to the main ports, i.e., Marina Smir and Marina Kabila. These port structures constituted impermeable, fixed limits, which divided the studied area into littoral cells. Other free, transit limits were also observed.

Spot distribution and fast surface evolution on Vega

NASA Astrophysics Data System (ADS)

Petit, P.; Hébrard, E. M.; Böhm, T.; Folsom, C. P.; Lignières, F.

2017-11-01

Spectral signatures of surface spots were recently discovered from high cadence observations of the A star Vega. We aim at constraining the surface distribution of these photospheric inhomogeneities and investigating a possible short-term evolution of the spot pattern. Using data collected over five consecutive nights, we employ the Doppler imaging method to reconstruct three different maps of the stellar surface, from three consecutive subsets of the whole time series. The surface maps display a complex distribution of dark and bright spots, covering most of the visible fraction of the stellar surface. A number of surface features are consistently recovered in all three maps, but other features seem to evolve over the time span of observations, suggesting that fast changes can affect the surface of Vega within a few days at most. The short-term evolution is observed as emergence or disappearance of individual spots, and may also show up as zonal flows, with low- and high-latitude belts rotating faster than intermediate latitudes. It is tempting to relate the surface brightness activity to the complex magnetic field topology previously reconstructed for Vega, although strictly simultaneous brightness and magnetic maps will be necessary to assess this potential link.

Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis.

PubMed

Maherali, Hafiz; Oberle, Brad; Stevens, Peter F; Cornwell, William K; McGlinn, Daniel J

2016-11-01

Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The majority of plant species associate with arbuscular mycorrhizal (AM) fungi. By contrast, the minority associate with ectomycorrhizal (EM) fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage in an intermediate, weakly AM symbiosis (AMNM). To understand the processes that maintain the mycorrhizal symbiosis or cause its loss, we reconstructed its evolution using a ∼3,000-species seed plant phylogeny integrated with mycorrhizal state information. Reconstruction indicated that the common ancestor of seed plants most likely associated with AM fungi and that the EM, NM, and AMNM states descended from the AM state. Direct transitions from the AM state to the EM and NM states were infrequent and generally irreversible, implying that natural selection or genetic constraint could promote stasis once a particular state evolved. However, the evolution of the NM state was more frequent via an indirect pathway through the AMNM state, suggesting that weakening of the AM symbiosis is a necessary precursor to mutualism abandonment. Nevertheless, reversions from the AMNM state back to the AM state were an order of magnitude more likely than transitions to the NM state, suggesting that natural selection favors the AM symbiosis over mutualism abandonment.

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns.

PubMed

Schuettpelz, Eric; Pryer, Kathleen M

2006-06-01

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Darwinian perspectives on the evolution of human languages.

PubMed

Pagel, Mark

2017-02-01

Human languages evolve by a process of descent with modification in which parent languages give rise to daughter languages over time and in a manner that mimics the evolution of biological species. Descent with modification is just one of many parallels between biological and linguistic evolution that, taken together, offer up a Darwinian perspective on how languages evolve. Combined with statistical methods borrowed from evolutionary biology, this Darwinian perspective has brought new opportunities to the study of the evolution of human languages. These include the statistical inference of phylogenetic trees of languages, the study of how linguistic traits evolve over thousands of years of language change, the reconstruction of ancestral or proto-languages, and using language change to date historical events.

Skull defect reconstruction based on a new hybrid level set.

PubMed

Zhang, Ziqun; Zhang, Ran; Song, Zhijian

2014-01-01

Skull defect reconstruction is an important aspect of surgical repair. Historically, a skull defect prosthesis was created by the mirroring technique, surface fitting, or formed templates. These methods are not based on the anatomy of the individual patient's skull, and therefore, the prosthesis cannot precisely correct the defect. This study presented a new hybrid level set model, taking into account both the global optimization region information and the local accuracy edge information, while avoiding re-initialization during the evolution of the level set function. Based on the new method, a skull defect was reconstructed, and the skull prosthesis was produced by rapid prototyping technology. This resulted in a skull defect prosthesis that well matched the skull defect with excellent individual adaptation.

Duplication and concerted evolution of MiSp-encoding genes underlie the material properties of minor ampullate silks of cobweb weaving spiders.

PubMed

Vienneau-Hathaway, Jannelle M; Brassfield, Elizabeth R; Lane, Amanda Kelly; Collin, Matthew A; Correa-Garhwal, Sandra M; Clarke, Thomas H; Schwager, Evelyn E; Garb, Jessica E; Hayashi, Cheryl Y; Ayoub, Nadia A

2017-03-14

Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-web weaving spiders are as tough as draglines, due to their higher extensibility despite lower strength. Differences in material properties between silk types result from differences in their component proteins, particularly members of the spidroin (spider fibroin) gene family. However, the extent to which variation in material properties within a single silk type can be explained by variation in spidroin sequences is unknown. Here, we compare the minor ampullate spidroins (MiSp) of orb-weavers and cobweb weavers. Orb-web weavers use minor ampullate silk to form the auxiliary spiral of the orb-web while cobweb weavers use it to wrap prey, suggesting that selection pressures on minor ampullate spidroins (MiSp) may differ between the two groups. We report complete or nearly complete MiSp sequences from five cobweb weaving spider species and measure material properties of minor ampullate silks in a subset of these species. We also compare MiSp sequences and silk properties of our cobweb weavers to published data for orb-web weavers. We demonstrate that all our cobweb weavers possess multiple MiSp loci and that one locus is more highly expressed in at least two species. We also find that the proportion of β-spiral-forming amino acid motifs in MiSp positively correlates with minor ampullate silk extensibility across orb-web and cobweb weavers. MiSp sequences vary dramatically within and among spider species, and have likely been subject to multiple rounds of gene duplication and concerted evolution, which have contributed to the diverse material properties of minor ampullate silks. Our sequences also provide templates for recombinant silk proteins with tailored properties.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

The Great Silk Alternative: Multiple Co-Evolution of Web Loss and Sticky Hairs in Spiders

PubMed Central

Wolff, Jonas O.; Nentwig, Wolfgang; Gorb, Stanislav N.

2013-01-01

Spiders are the most important terrestrial predators among arthropods. Their ecological success is reflected by a high biodiversity and the conquest of nearly every terrestrial habitat. Spiders are closely associated with silk, a material, often seen to be responsible for their great ecological success and gaining high attention in life sciences. However, it is often overlooked that more than half of all Recent spider species have abandoned web building or never developed such an adaptation. These species must have found other, more economic solutions for prey capture and retention, compensating the higher energy costs of increased locomotion activity. Here we show that hairy adhesive pads (scopulae) are closely associated with the convergent evolution of a vagrant life style, resulting in highly diversified lineages of at least, equal importance as the derived web building taxa. Previous studies often highlighted the idea that scopulae have the primary function of assisting locomotion, neglecting the fact that only the distal most pads (claw tufts) are suitable for those purposes. The former observations, that scopulae are used in prey capture, are largely overlooked. Our results suggest the scopulae evolved as a substitute for silk in controlling prey and that the claw tufts are, in most cases, a secondary development. Evolutionary trends towards specialized claw tufts and their composition from a low number of enlarged setae to a dense array of slender ones, as well as the secondary loss of those pads are discussed further. Hypotheses about the origin of the adhesive setae and their diversification throughout evolution are provided. PMID:23650526

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Distributed nuclear medicine applications using World Wide Web and Java technology.

PubMed

Knoll, P; Höll, K; Mirzaei, S; Koriska, K; Köhn, H

2000-01-01

At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

Web-based monitoring tools for Resistive Plate Chambers in the CMS experiment at CERN

NASA Astrophysics Data System (ADS)

Kim, M. S.; Ban, Y.; Cai, J.; Li, Q.; Liu, S.; Qian, S.; Wang, D.; Xu, Z.; Zhang, F.; Choi, Y.; Kim, D.; Goh, J.; Choi, S.; Hong, B.; Kang, J. W.; Kang, M.; Kwon, J. H.; Lee, K. S.; Lee, S. K.; Park, S. K.; Pant, L. M.; Mohanty, A. K.; Chudasama, R.; Singh, J. B.; Bhatnagar, V.; Mehta, A.; Kumar, R.; Cauwenbergh, S.; Costantini, S.; Cimmino, A.; Crucy, S.; Fagot, A.; Garcia, G.; Ocampo, A.; Poyraz, D.; Salva, S.; Thyssen, F.; Tytgat, M.; Zaganidis, N.; Doninck, W. V.; Cabrera, A.; Chaparro, L.; Gomez, J. P.; Gomez, B.; Sanabria, J. C.; Avila, C.; Ahmad, A.; Muhammad, S.; Shoaib, M.; Hoorani, H.; Awan, I.; Ali, I.; Ahmed, W.; Asghar, M. I.; Shahzad, H.; Sayed, A.; Ibrahim, A.; Aly, S.; Assran, Y.; Radi, A.; Elkafrawy, T.; Sharma, A.; Colafranceschi, S.; Abbrescia, M.; Calabria, C.; Colaleo, A.; Iaselli, G.; Loddo, F.; Maggi, M.; Nuzzo, S.; Pugliese, G.; Radogna, R.; Venditti, R.; Verwilligen, P.; Benussi, L.; Bianco, S.; Piccolo, D.; Paolucci, P.; Buontempo, S.; Cavallo, N.; Merola, M.; Fabozzi, F.; Iorio, O. M.; Braghieri, A.; Montagna, P.; Riccardi, C.; Salvini, P.; Vitulo, P.; Vai, I.; Magnani, A.; Dimitrov, A.; Litov, L.; Pavlov, B.; Petkov, P.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Rodozov, M.; Sultanov, G.; Vutova, M.; Stoykova, S.; Hadjiiska, R.; Ibargüen, H. S.; Morales, M. I. P.; Bernardino, S. C.; Bagaturia, I.; Tsamalaidze, Z.; Crotty, I.

2014-10-01

The Resistive Plate Chambers (RPC) are used in the CMS experiment at the trigger level and also in the standard offline muon reconstruction. In order to guarantee the quality of the data collected and to monitor online the detector performance, a set of tools has been developed in CMS which is heavily used in the RPC system. The Web-based monitoring (WBM) is a set of java servlets that allows users to check the performance of the hardware during data taking, providing distributions and history plots of all the parameters. The functionalities of the RPC WBM monitoring tools are presented along with studies of the detector performance as a function of growing luminosity and environmental conditions that are tracked over time.

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

PubMed

Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

2017-10-27

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

Improved Maximum Parsimony Models for Phylogenetic Networks.

PubMed

Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2018-05-01

Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

PubMed Central

Faure, Emmanuel; Savy, Thierry; Rizzi, Barbara; Melani, Camilo; Stašová, Olga; Fabrèges, Dimitri; Špir, Róbert; Hammons, Mark; Čúnderlík, Róbert; Recher, Gaëlle; Lombardot, Benoît; Duloquin, Louise; Colin, Ingrid; Kollár, Jozef; Desnoulez, Sophie; Affaticati, Pierre; Maury, Benoît; Boyreau, Adeline; Nief, Jean-Yves; Calvat, Pascal; Vernier, Philippe; Frain, Monique; Lutfalla, Georges; Kergosien, Yannick; Suret, Pierre; Remešíková, Mariana; Doursat, René; Sarti, Alessandro; Mikula, Karol; Peyriéras, Nadine; Bourgine, Paul

2016-01-01

The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology. PMID:26912388

The Evolution of Ecological Systems.

ERIC Educational Resources Information Center

May, Robert M.

1978-01-01

Discusses the coevaluation of species within ecosystems. This process gives rise to interesting patterns in the total number of species found in a given area, in their relative abundances, and in the overall structure of the local food web. (Author/MA)

[WebSurvCa: web-based estimation of death and survival probabilities in a cohort].

PubMed

Clèries, Ramon; Ameijide, Alberto; Buxó, Maria; Vilardell, Mireia; Martínez, José Miguel; Alarcón, Francisco; Cordero, David; Díez-Villanueva, Ana; Yasui, Yutaka; Marcos-Gragera, Rafael; Vilardell, Maria Loreto; Carulla, Marià; Galceran, Jaume; Izquierdo, Ángel; Moreno, Víctor; Borràs, Josep M

2018-01-19

Relative survival has been used as a measure of the temporal evolution of the excess risk of death of a cohort of patients diagnosed with cancer, taking into account the mortality of a reference population. Once the excess risk of death has been estimated, three probabilities can be computed at time T: 1) the crude probability of death associated with the cause of initial diagnosis (disease under study), 2) the crude probability of death associated with other causes, and 3) the probability of absolute survival in the cohort at time T. This paper presents the WebSurvCa application (https://shiny.snpstats.net/WebSurvCa/), whereby hospital-based and population-based cancer registries and registries of other diseases can estimate such probabilities in their cohorts by selecting the mortality of the relevant region (reference population). Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

PubMed Central

Bazinet, Adam L.; Zwickl, Derrick J.; Cummings, Michael P.

2014-01-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.] PMID:24789072

Revealing the z ~ 2.5 Cosmic Web with 3D Lyα Forest Tomography: a Deformation Tensor Approach

NASA Astrophysics Data System (ADS)

Lee, Khee-Gan; White, Martin

2016-11-01

Studies of cosmological objects should take into account their positions within the cosmic web of large-scale structure. Unfortunately, the cosmic web has only been extensively mapped at low redshifts (z\\lt 1), using galaxy redshifts as tracers of the underlying density field. At z\\gt 1, the required galaxy densities are inaccessible for the foreseeable future, but 3D reconstructions of Lyα forest absorption in closely separated background QSOs and star-forming galaxies already offer a detailed window into z˜ 2-3 large-scale structure. We quantify the utility of such maps for studying the cosmic web by using realistic z = 2.5 Lyα forest simulations matched to observational properties of upcoming surveys. A deformation tensor-based analysis is used to classify voids, sheets, filaments, and nodes in the flux, which are compared to those determined from the underlying dark matter (DM) field. We find an extremely good correspondence, with 70% of the volume in the flux maps correctly classified relative to the DM web, and 99% classified to within one eigenvalue. This compares favorably to the performance of galaxy-based classifiers with even the highest galaxy densities from low-redshift surveys. We find that narrow survey geometries can degrade the recovery of the cosmic web unless the survey is ≳ 60 {h}-1 {Mpc} or ≳ 1 deg on the sky. We also examine halo abundances as a function of the cosmic web, and find a clear dependence as a function of flux overdensity, but little explicit dependence on the cosmic web. These methods will provide a new window on cosmological environments of galaxies at this very special time in galaxy formation, “high noon,” and on overall properties of cosmological structures at this epoch.

[Breast reconstruction by latissimus dorsi flap: Towards an evolution of ideas].

PubMed

Niddam, J; Guihard, T; Cothier-Savey, I; Chaussard, H; Lemasurier, P

2015-12-01

Breast reconstruction with latissimus dorsi flap and fat grafting is a technique widely used in current practice. Some operators still complain at the lack of final results at the first intervention and the need for repeated lipofilling sessions. The objective of this study was to compare the number of reoperations in patients who underwent reconstruction with latissimus dorsi with prosthesis versus without prosthesis. We included all patients operated for breast reconstruction with latissimus dorsi flap, with or without prosthesis between 2008 and 2012 in our center. We noted the number of new surgical interventions in these patients on the reconstructed breast. We also noted the average weight of mastectomy in two groups each year. One hundred and eighty-six patients were included in this study. Ninety-one patients underwent reconstruction with latissimus dorsi and prosthesis, and 95 patients reconstruction by latissimus dorsi and fat graft. It has not been demonstrated significant differences in the number of new surgical procedures between the two groups. The average weight of mastectomies in the autologous group has steadily increased over the five years. There was no significant difference in the average weight of mastectomies between the two groups over the last two years. For breast reconstruction with latissimus dorsi flap, surgical indications changed in our center to the absence of prosthetic implant, whatever the volume of the breast. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Development of a Prognostic Marker for Lung Cancer Using Analysis of Tumor Evolution

DTIC Science & Technology

2016-08-01

construct evolutionary trees , the characteristics of which will be used to predict whether a tumor will metastasize or not. We established a procedure for...of populations, the evolution of tumor cells within a tumor can be diagrammed on a phylogenetic tree . The more diverse a tumor’s phylogenetic tree ...individual tumor cells from the tumors of a training set of patients (half early stage, half late stage). We will reconstruct each tumor’s phylogenetic tree

Fluid Physics of Foam Evolution and Flow

NASA Technical Reports Server (NTRS)

Aref, H.; Thoroddsen, S. T.; Sullivan, J. M.

2003-01-01

The grant supported theoretical, numerical and experimental work focused on the elucidation of the fluid physics of foam structure, evolution and flow. The experimental work concentrated on these subject areas: (a) Measurements of the speed of reconnections within a foam; (b) statistics of bubble rearrangements; and (c) three-dimensional reconstruction of the foam structure. On the numerical simulation and theory side our efforts concentrated on the subjects: (a) simulation techniques for 2D and 3D foams; (b) phase transition in a compressible foam; and (c) TCP structures.

Climatic influences on species: Evidence from the fossil record

USGS Publications Warehouse

Cronin, T. M.; Schneider, C.E.

1990-01-01

The detailed Neogene and Quaternary paleoclimatic reconstructions now available provide a means to test how species respond to environmental change. Paleontologic studies of marine organisms show that climatic change causes evolution (via cladogenesis and anagenesis), ecophenotypic variation, migration, morphologic stasis and extinction. Evolution during climatic change is a rare event relative to the number of climatic cycles that have occurred, but climate-related environmental barriers, usually temperature, may play an important role in the isolation of populations during allopatric speciation.

The use of advanced web-based survey design in Delphi research.

PubMed

Helms, Christopher; Gardner, Anne; McInnes, Elizabeth

2017-12-01

A discussion of the application of metadata, paradata and embedded data in web-based survey research, using two completed Delphi surveys as examples. Metadata, paradata and embedded data use in web-based Delphi surveys has not been described in the literature. The rapid evolution and widespread use of online survey methods imply that paper-based Delphi methods will likely become obsolete. Commercially available web-based survey tools offer a convenient and affordable means of conducting Delphi research. Researchers and ethics committees may be unaware of the benefits and risks of using metadata in web-based surveys. Discussion paper. Two web-based, three-round Delphi surveys were conducted sequentially between August 2014 - January 2015 and April - May 2016. Their aims were to validate the Australian nurse practitioner metaspecialties and their respective clinical practice standards. Our discussion paper is supported by researcher experience and data obtained from conducting both web-based Delphi surveys. Researchers and ethics committees should consider the benefits and risks of metadata use in web-based survey methods. Web-based Delphi research using paradata and embedded data may introduce efficiencies that improve individual participant survey experiences and reduce attrition across iterations. Use of embedded data allows the efficient conduct of multiple simultaneous Delphi surveys across a shorter timeframe than traditional survey methods. The use of metadata, paradata and embedded data appears to improve response rates, identify bias and give possible explanation for apparent outlier responses, providing an efficient method of conducting web-based Delphi surveys. © 2017 John Wiley & Sons Ltd.

Information system for preserving culture heritage in areas affected by heavy industry and mining

NASA Astrophysics Data System (ADS)

Pacina, Jan; Kopecký, Jiří; Bedrníková, Lenka; Handrychová, Barbora; Švarcová, Martina; Holá, Markéta; Pončíková, Edita

2014-05-01

The natural development of the Ústí region (North-West Bohemia, the Czech Republic) has been affected by the human activity during the past hundred years. The heavy industrialization and the brown coal mining have completely changed the land-use in the region. The open-pit coal mines are completely destroying the surrounding landscape, including settlement, communications, hydrological network and the over-all natural development of the region. The other factor affecting the natural development of the landscape, land-use and settlement was the political situation in 1945 (end of the 2nd World War) when the borderland was depopulated. All these factors caused vanishing of more than two hundreds of colonies, villages and towns during this period of time. The task of this project is to prepare and offer for public use a comprehensive information system preserving the cultural heritage in the form of processed old maps, aerial imagery, land-use and georelief reconstructions, local studies, text and photo documents covering the extinct landscape and settlement. Wide range of various maps was used for this area - Müller's map of Bohemia (ca. 1720) followed by the 1st, 2nd and 3rd Military survey of Habsburg empire (1792, 1894, 1938), maps of Stabile cadaster (ca. 1840) and State map derived in the scale 1:5000 (1953, 1972, 1981). All the maps were processed, georeferenced, hand digitized and are further used as base layers for visualization and analysis. The historical aerial imagery was processed in standard ways of photogrammetry and is covering the year 1938, 1953 and the current state. The other important task covered by this project is the georelief reconstruction. We use the old maps and aerial imagery to reconstruct the complete time-line of the georelief development. This time-line is covering the period since 1938 until now. The derived digital terrain models and further on analyzed and printed on a 3D printer. Other reconstruction task are performed using the processed old maps - here we are studying the land-use change, settlement development and the industrialization and brown coal mining effect on the hydrological network structure. The processed data (old maps, aerial photographs, land-use and georelief reconstructions) are published as a web-mapping application built using the ArcGIS API for Flex technology. The application is offering visualization and overlay tools so the user can perform basic landscape and land-use development analyses. The resulting information system will consist of three parts - the web-mapping application, database containing the text and photo information about the vanished towns and villages (spatially linked to the web-mapping application) and other local studies performed on single sites in the region. The local studies are focused on application of data collection methods as UAV (Unmanned Aerial Vehicle), KAP (Kite Aerial Photography) and LIDAR.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis.

PubMed

Jameson Kiesling, Natalie M; Yi, Soojin V; Xu, Ke; Gianluca Sperone, F; Wildman, Derek E

2015-01-01

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification. Copyright © 2014 Elsevier Inc. All rights reserved.

Linking the evolution of body shape and locomotor biomechanics in bird-line archosaurs.

PubMed

Allen, Vivian; Bates, Karl T; Li, Zhiheng; Hutchinson, John R

2013-05-02

Locomotion in living birds (Neornithes) has two remarkable features: feather-assisted flight, and the use of unusually crouched hindlimbs for bipedal support and movement. When and how these defining functional traits evolved remains controversial. However, the advent of computer modelling approaches and the discoveries of exceptionally preserved key specimens now make it possible to use quantitative data on whole-body morphology to address the biomechanics underlying this issue. Here we use digital body reconstructions to quantify evolutionary trends in locomotor biomechanics (whole-body proportions and centre-of-mass position) across the clade Archosauria. We use three-dimensional digital reconstruction to estimate body shape from skeletal dimensions for 17 archosaurs along the ancestral bird line, including the exceptionally preserved, feathered taxa Microraptor, Archaeopteryx, Pengornis and Yixianornis, which represent key stages in the evolution of the avian body plan. Rather than a discrete transition from more-upright postures in the basal-most birds (Avialae) and their immediate outgroup deinonychosauria, our results support hypotheses of a gradual, stepwise acquisition of more-crouched limb postures across much of theropod evolution, although we find evidence of an accelerated change within the clade Maniraptora (birds and their closest relatives, such as deinonychosaurs). In addition, whereas reduction of the tail is widely accepted to be the primary morphological factor correlated with centre-of-mass position and, hence, evolution of hindlimb posture, we instead find that enlargement of the pectoral limb and several associated trends have a much stronger influence. Intriguingly, our support for the onset of accelerated morpho-functional trends within Maniraptora is closely correlated with the evolution of flight. Because we find that the evolution of enlarged forelimbs is strongly linked, via whole-body centre of mass, to hindlimb function during terrestrial locomotion, we suggest that the evolution of avian flight is linked to anatomical novelties in the pelvic limb as well as the pectoral.

On the topology of the world exchange arrangements web

NASA Astrophysics Data System (ADS)

Li, Xiang; Jin, Yu Ying; Chen, Guanrong

2004-11-01

Exchange arrangements among different countries over the world are foundations of the world economy, which generally stand behind the daily economic evolution. As the first study of the world exchange arrangements web (WEAW), we built a bipartite network with countries as one type of nodes and currencies as the other, and found it to have a prominent scale-free feature with a power-law degree distribution. In a further empirical study of the currency section of the WEAW, we calculated the clustering coefficients, average nearest-neighbors degree, and average shortest distance. As an essential economic network, the WEAW is found to be a correlated disassortative network with a hierarchical structure, possessing a more prominent scale-free feature than the world trade web (WTW).

[Design of visualized medical images network and web platform based on MeVisLab].

PubMed

Xiang, Jun; Ye, Qing; Yuan, Xun

2017-04-01

With the trend of the development of "Internet +", some further requirements for the mobility of medical images have been required in the medical field. In view of this demand, this paper presents a web-based visual medical imaging platform. First, the feasibility of medical imaging is analyzed and technical points. CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) images are reconstructed three-dimensionally by MeVisLab and packaged as X3D (Extensible 3D Graphics) files shown in the present paper. Then, the B/S (Browser/Server) system specially designed for 3D image is designed by using the HTML 5 and WebGL rendering engine library, and the X3D image file is parsed and rendered by the system. The results of this study showed that the platform was suitable for multiple operating systems to realize the platform-crossing and mobilization of medical image data. The development of medical imaging platform is also pointed out in this paper. It notes that web application technology will not only promote the sharing of medical image data, but also facilitate image-based medical remote consultations and distance learning.

Teaching neuroscience through Web adventures: adolescents reconstruct the history and science of opioids.

PubMed

Miller, Leslie; Schweingruber, Heidi; Oliver, Robert; Mayes, Janice; Smith, Donna

2002-02-01

New technological and cultural developments surrounding adolescents' use of the World Wide Web offer an opportunity for turning aspects of the Internet gaming phenomenon to the advantage of neuroscience education. Specifically, an experimental project to transmit aspects of problem-based learning and the National Science Standards through an interactive Web adventure is reported here. The Reconstructors is an episodic Web-based adventure series entitled Medicinal Mysteries from History. It is funded by the National Institute on Drug Abuse, and the first series focuses on opioids. It was created with the input of middle school students and teachers. Through the use of multimedia technologies, middle school students enter a futuristic world in which they become "reconstructors," members of an elite scientific unit charged with recovering lost medical knowledge about analgesic drugs. Two of the four episodes have been evaluated through a comprehensive review process involving middle school students, teachers, neuroscience researchers, and clinicians. Analysis of the pretest and posttest scores demonstrated significant knowledge gain that validly can be attributed to use of the game. These data provide evidence that science content can be transmitted through innovative online techniques without sacrificing compelling content or effective pedagogical strategies.

Prevention of Thumb Web Space Contracture With Multiplanar External Fixation.

PubMed

Harper, Carl M; Iorio, Matthew L

2016-09-01

Thumb web space contracture following hand trauma can be disabling with numerous reconstructive procedures existing to correct the resultant deformity. Following marked soft tissue injury to the hand we utilized the Stryker Hoffmann II Micro External Fixator System to link the first and second metacarpals by a multiplanar system using 1.6 or 2.0 mm self-drilling half-pins and 3 mm carbon fiber connecting rods. This facilitated placement of the thumb in maximal palmar abduction as well as allowed adjustment of thumb position throughout the postoperative period. This technique was performed on 5 patients. Two patients were treated with a first web space external fixator for table saw injuries to the radial aspect of the hand. An additional 2 patients were treated with a first web space external fixator following metacarpophalangeal joint capsular release in the setting of thermal burns. A fifth patient underwent second ray amputation, trapeziectomy and trapezoidectomy for squamous cell carcinoma with subsequent stabilization with the external fixator. The external fixator was left in place until soft tissues were healed (average 5.5 wk). The patients were allowed to mobilize their hand in as much as the external fixator allowed, and no device-associated complications were noted. Thumb web space was preserved with passive and supple thumb circumduction and web space abduction/adduction in all patients at an average follow-up of 5 months. The average Quick Dash Score was 35±5 and the average Modern Activity Subjective Survey of 2007 was 30±8.

Complementary molecular information changes our perception of food web structure

PubMed Central

Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

2014-01-01

How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

CF Metadata Conventions: Founding Principles, Governance, and Future Directions

NASA Astrophysics Data System (ADS)

Taylor, K. E.

2016-12-01

The CF Metadata Conventions define attributes that promote sharing of climate and forecasting data and facilitate automated processing by computers. The development, maintenance, and evolution of the conventions have mainly been provided by voluntary community contributions. Nevertheless, an organizational framework has been established, which relies on established rules and web-based discussion to ensure smooth (but relatively efficient) evolution of the standard to accommodate new types of data. The CF standard has been essential to the success of high-profile internationally-coordinated modeling activities (e.g, the Coupled Model Intercomparison Project). A summary of CF's founding principles and the prospects for its future evolution will be discussed.

Topology and evolution of technology innovation networks

NASA Astrophysics Data System (ADS)

Valverde, Sergi; Solé, Ricard V.; Bedau, Mark A.; Packard, Norman

2007-11-01

The web of relations linking technological innovation can be fairly described in terms of patent citations. The resulting patent citation network provides a picture of the large-scale organization of innovations and its time evolution. Here we study the patterns of change of patents registered by the U.S. Patent and Trademark Office. We show that the scaling behavior exhibited by this network is consistent with a preferential attachment mechanism together with a Weibull-shaped aging term. Such an attachment kernel is shared by scientific citation networks, thus indicating a universal type of mechanism linking ideas and designs and their evolution. The implications for evolutionary theory of innovation are discussed.

HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.

PubMed

Clima, Rosanna; Preste, Roberto; Calabrese, Claudia; Diroma, Maria Angela; Santorsola, Mariangela; Scioscia, Gaetano; Simone, Domenico; Shen, Lishuang; Gasparre, Giuseppe; Attimonelli, Marcella

2017-01-04

The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

'The surface management system' (SuMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis

NASA Technical Reports Server (NTRS)

Dickson, J.; Drury, H.; Van Essen, D. C.

2001-01-01

Surface reconstructions of the cerebral cortex are increasingly widely used in the analysis and visualization of cortical structure, function and connectivity. From a neuroinformatics perspective, dealing with surface-related data poses a number of challenges. These include the multiplicity of configurations in which surfaces are routinely viewed (e.g. inflated maps, spheres and flat maps), plus the diversity of experimental data that can be represented on any given surface. To address these challenges, we have developed a surface management system (SuMS) that allows automated storage and retrieval of complex surface-related datasets. SuMS provides a systematic framework for the classification, storage and retrieval of many types of surface-related data and associated volume data. Within this classification framework, it serves as a version-control system capable of handling large numbers of surface and volume datasets. With built-in database management system support, SuMS provides rapid search and retrieval capabilities across all the datasets, while also incorporating multiple security levels to regulate access. SuMS is implemented in Java and can be accessed via a Web interface (WebSuMS) or using downloaded client software. Thus, SuMS is well positioned to act as a multiplatform, multi-user 'surface request broker' for the neuroscience community.

The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

PubMed Central

Rangel, Luiz Thibério; Novaes, Jeniffer; Durham, Alan M.; Madeira, Alda Maria B. N.; Gruber, Arthur

2013-01-01

Parasites of the genus Eimeria infect a wide range of vertebrate hosts, including chickens. We have recently reported a comparative analysis of the transcriptomes of Eimeria acervulina, Eimeria maxima and Eimeria tenella, integrating ORESTES data produced by our group and publicly available Expressed Sequence Tags (ESTs). All cDNA reads have been assembled, and the reconstructed transcripts have been submitted to a comprehensive functional annotation pipeline. Additional studies included orthology assignment across apicomplexan parasites and clustering analyses of gene expression profiles among different developmental stages of the parasites. To make all this body of information publicly available, we constructed the Eimeria Transcript Database (EimeriaTDB), a web repository that provides access to sequence data, annotation and comparative analyses. Here, we describe the web interface, available sequence data sets and query tools implemented on the site. The main goal of this work is to offer a public repository of sequence and functional annotation data of reconstructed transcripts of parasites of the genus Eimeria. We believe that EimeriaTDB will represent a valuable and complementary resource for the Eimeria scientific community and for those researchers interested in comparative genomics of apicomplexan parasites. Database URL: http://www.coccidia.icb.usp.br/eimeriatdb/ PMID:23411718

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

HaploForge: a comprehensive pedigree drawing and haplotype visualization web application.

PubMed

Tekman, Mehmet; Medlar, Alan; Mozere, Monika; Kleta, Robert; Stanescu, Horia

2017-12-15

Haplotype reconstruction is an important tool for understanding the aetiology of human disease. Haplotyping infers the most likely phase of observed genotypes conditional on constraints imposed by the genotypes of other pedigree members. The results of haplotype reconstruction, when visualized appropriately, show which alleles are identical by descent despite the presence of untyped individuals. When used in concert with linkage analysis, haplotyping can help delineate a locus of interest and provide a succinct explanation for the transmission of the trait locus. Unfortunately, the design choices made by existing haplotype visualization programs do not scale to large numbers of markers. Indeed, following haplotypes from generation to generation requires excessive scrolling back and forth. In addition, the most widely used program for haplotype visualization produces inconsistent recombination artefacts for the X chromosome. To resolve these issues, we developed HaploForge, a novel web application for haplotype visualization and pedigree drawing. HaploForge takes advantage of HTML5 to be fast, portable and avoid the need for local installation. It can accurately visualize autosomal and X-linked haplotypes from both outbred and consanguineous pedigrees. Haplotypes are coloured based on identity by descent using a novel A* search algorithm and we provide a flexible viewing mode to aid visual inspection. HaploForge can currently process haplotype reconstruction output from Allegro, GeneHunter, Merlin and Simwalk. HaploForge is licensed under GPLv3 and is hosted and maintained via GitHub. https://github.com/mtekman/haploforge. r.kleta@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Bayesian reconstruction of transmission within outbreaks using genomic variants.

PubMed

De Maio, Nicola; Worby, Colin J; Wilson, Daniel J; Stoesser, Nicole

2018-04-01

Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics. Here we propose a new Bayesian approach to transmission inference, BadTrIP (BAyesian epiDemiological TRansmission Inference from Polymorphisms), that explicitly models evolution of pathogen populations in an outbreak, transmission (including transmission bottlenecks), and sequencing error. BadTrIP enables the inference of host-to-host transmission from pathogen sequencing data and epidemiological data. By assuming that genomic variants are unlinked, our method does not require the computationally intensive and unreliable reconstruction of individual haplotypes. Using simulations we show that BadTrIP is robust in most scenarios and can accurately infer transmission events by efficiently combining information from genetic and epidemiological sources; thanks to its realistic model of pathogen evolution and the inclusion of epidemiological data, BadTrIP is also more accurate than existing approaches. BadTrIP is distributed as an open source package (https://bitbucket.org/nicofmay/badtrip) for the phylogenetic software BEAST2. We apply our method to reconstruct transmission history at the early stages of the 2014 Ebola outbreak, showcasing the power of within-host genomic variants to reconstruct transmission events.

Anomalous structural evolution and √(3)×√(3) reconstruction of a clean Si(111) surface observed after thermal desorption of thallium

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

Kocán, Pavel, E-mail: pavel.kocan@mff.cuni.cz; Krejčí, Ondřej; Tochihara, Hiroshi

2015-03-15

The authors have observed anomalous structural evolution of a clean Si(111) surface, which was prepared first by thallium (Tl) deposition on a Si(111)7 × 7 surface, leading to incomplete formation of a Tl/Si(111)1 × 1 structure at 300 °C and subsequent desorption of Tl at 350 °C. Thus prepared clean Si(111) surfaces exhibit structural changes with increase of temperature: 2×1→(√(3)×√(3))R30°→2×1→5×5→7×7, as observed by low-energy electron diffraction and scanning tunneling microscopy. Among the above structures, the (√(3)×√(3))R30° formed at 450–550 °C is found not to be a simple adatom structure. Instead, by means of ab-initio calculations a new metastable (√(3)×√(3))R30° reconstruction was found, having analogous structural features andmore » formation origin to a 2 × 1 reconstruction known as the Pandey chain model. This new (√(3)×√(3))R30° model is 0.09 eV per surface atom less favorable than the 2 × 1 reconstruction. A reason for the anomalous occurrence of the (√(3)×√(3))R30° structure is explored with an aid of Monte Carlo simulations.« less

Comprehensive evolutionary analysis of the Anthroherpon radiation (Coleoptera, Leiodidae, Leptodirini).

PubMed

Njunjić, Iva; Perrard, Adrien; Hendriks, Kasper; Schilthuizen, Menno; Perreau, Michel; Merckx, Vincent; Baylac, Michel; Deharveng, Louis

2018-01-01

The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa.

PubMed

Gehrke, Berit; Kandziora, Martha; Pirie, Michael D

2016-01-01

Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Exhumation Reconstruction of the Xiangcheng Area, SE Tibetan Plateau. Implication on the Evolution of the Yangtze River in the Cenozoic.

NASA Astrophysics Data System (ADS)

Gourbet, L.; Yang, R.; Fellin, M. G.; Gong, J.; Maden, C.

2016-12-01

Geodynamic processes associated with timing of river incision and river network reorganization on the Tibetan plateau margins remain controversial. In particular, hydrographic network modifications in SE Tibet have been interpreted as related with regional-scale uplift or fault motion. The paleocourse of the upper Yangtze river (Jinsha Sha) and the timing of the establishment of its modern course are highly debated, leading to conflicting models of the plateau evolution. For example, estimated ages for the formation of the Yangtze first bend (where the river shifts from flowing southward to northward) range from the Eocene to the Pliocene. River incision can be reconstructed using low-temperature thermochronometry. However, the lack of suitable rocks along the main riverbed of the Yangtze makes it challenging. To address this problem, we perform a local study of the Xiangcheng area, located in Sichuan, about 150 km upstream of the first bend and drained by tributaries of the upper Yangtze. We combine a tectono-geomorphic analysis to a reconstruction of exhumation rates using (U-Th-Sm)/He thermochronometry. The study area is characterized by the NW-SE trending, active left-lateral Xiangcheng fault, which is attested by crustal-depth seismic activity. Importantly, the courses of two tributaries of the Yangtze are deflected along the Xiangcheng fault, suggesting that the fault partly controls the evolution of the upper Yangtze course. Locally, the fault also exhibits triangular facets, suggesting normal motion probably related to the fault segmentation. Granite samples from the Xiangcheng pluton were collected along three altitudinal profiles and analyzed using zircon and apatite (U-Th-Sm)/He thermochronometry. We will discuss the results and their implications on exhumation and on the Yangtze river history during the Cenozoic.

Decadal Drought and Wetness Reconstructed for Subtropical North America in the Mexican Drought Atlas

NASA Astrophysics Data System (ADS)

Burnette, D. J.; Stahle, D. W.; Cook, E. R.; Villanueva Diaz, J.; Griffin, D.; Cook, B.

2014-12-01

A new drought atlas has been developed for subtropical North America, including the entire Republic of Mexico. This Mexican Drought Atlas (MXDA) is based on 251 tree-ring chronologies, including 82 from Mexico and another 169 from the southern U.S. and western Guatemala. Point-by-point principal components regression was used to reconstruct the self-calibrating Palmer Drought Severity Index (PDSI) for June-August. Calibration and verification statistics were improved over what was previously possible with the North American Drought Atlas, which was based on fewer chronologies only in Mexico. The MXDA will be served on the web with analytical tools for composite, correlation, and congruence analyses. The new PDSI reconstructions provide a more detailed estimation of decadal moisture regimes over the past 2000 years, but are most robust after 1400 AD, when several chronologies are available across Mexico. Droughts previously identified in a subset of chronologies are confirmed and their spatial impact quantified in the new reconstructions. This includes the intense drought of the mid-15th Century described in Aztec legend, the 16th Century megadrought, and "El Año del Hambre", one of the worst famines in Mexican history. We also use the best replicated portion of the MXDA in the 18th and 19th Centuries to reconstruct moisture anomalies during key time periods of Mexican turmoil (e.g., the Mexican War of Independence).

Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes

PubMed Central

2014-01-01

Background Alternative splicing is an important process in higher eukaryotes that allows obtaining several transcripts from one gene. A specific case of alternative splicing is mutually exclusive splicing, in which exactly one exon out of a cluster of neighbouring exons is spliced into the mature transcript. Recently, a new algorithm for the prediction of these exons has been developed based on the preconditions that the exons of the cluster have similar lengths, sequence homology, and conserved splice sites, and that they are translated in the same reading frame. Description In this contribution we introduce Kassiopeia, a database and web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exomes. Currently, Kassiopeia provides access to the mutually exclusive exomes of twelve Drosophila species, the thale cress Arabidopsis thaliana, the flatworm Caenorhabditis elegans, and human. Mutually exclusive spliced exons (MXEs) were predicted based on gene reconstructions from Scipio. Based on the standard prediction values, with which 83.5% of the annotated MXEs of Drosophila melanogaster were reconstructed, the exomes contain surprisingly more MXEs than previously supposed and identified. The user can search Kassiopeia using BLAST or browse the genes of each species optionally adjusting the parameters used for the prediction to reveal more divergent or only very similar exon candidates. Conclusions We developed a pipeline to predict MXEs in the genomes of several model organisms and a web interface, Kassiopeia, for their visualization. For each gene Kassiopeia provides a comprehensive gene structure scheme, the sequences and predicted secondary structures of the MXEs, and, if available, further evidence for MXE candidates from cDNA/EST data, predictions of MXEs in homologous genes of closely related species, and RNA secondary structure predictions. Kassiopeia can be accessed at http://www.motorprotein.de/kassiopeia. PMID:24507667

Continental magnetic anomaly constraints on continental reconstruction

NASA Technical Reports Server (NTRS)

Vonfrese, R. R. B.; Hinze, W. J.; Olivier, R.; Bentley, C. R.

1985-01-01

Crustal magnetic anomalies mapped by the MAGSAT satellite for North and South America, Europe, Africa, India, Australia and Antarctica and adjacent marine areas were adjusted to a common elevation of 400 km and differentially reduced to the radial pole of intensity 60,000 nT. These radially polarized anomalies are normalized for differential inclination, declination and intensity effects of the geomagnetic field, so that in principle they directly reflected the geometric and magnetic polarization attributes of sources which include regional petrologic variations of the crust and upper mantle, and crustal thickness and thermal perturbations. Continental anomalies demonstrate remarkably detailed correlation of regional magnetic sources across rifted margins when plotted on a reconstruction of Pangea. Accordingly, they suggest further fundamental constraints on the geologic evolution of the continents and their reconstructions.

Time rescaling and pattern formation in biological evolution.

PubMed

Igamberdiev, Abir U

2014-09-01

Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

SensorWeb Evolution Using the Earth Observing One (EO-1) Satellite as a Test Platform

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Frye, Stuart; Cappelaere, Pat; Ly, Vuong; Handy, Matthew; Chien, Steve; Grossman, Robert; Tran, Daniel

2012-01-01

The Earth Observing One (EO-1) satellite was launched in November 2000 as a one year technology demonstration mission for a variety of space technologies. After the first year, in addition to collecting science data from its instruments, the EO-1 mission has been used as a testbed for a variety of technologies which provide various automation capabilities and which have been used as a pathfinder for the creation of SensorWebs. A SensorWeb is the integration of variety of space, airborne and ground sensors into a loosely coupled collaborative sensor system that automatically provides useful data products. Typically, a SensorWeb is comprised of heterogeneous sensors tied together with a messaging architecture and web services. This paper provides an overview of the various technologies that were tested and eventually folded into normal operations. As these technologies were folded in, the nature of operations transformed. The SensorWeb software enables easy connectivity for collaboration with sensors, but the side benefit is that it improved the EO-1 operational efficiency. This paper presents the various phases of EO-1 operation over the past 12 years and also presents operational efficiency gains demonstrated by some metrics.

Sensor Web Dynamic Measurement Techniques and Adaptive Observing Strategies

NASA Technical Reports Server (NTRS)

Talabac, Stephen J.

2004-01-01

Sensor Web observing systems may have the potential to significantly improve our ability to monitor, understand, and predict the evolution of rapidly evolving, transient, or variable environmental features and events. This improvement will come about by integrating novel data collection techniques, new or improved instruments, emerging communications technologies and protocols, sensor mark-up languages, and interoperable planning and scheduling systems. In contrast to today's observing systems, "event-driven" sensor webs will synthesize real- or near-real time measurements and information from other platforms and then react by reconfiguring the platforms and instruments to invoke new measurement modes and adaptive observation strategies. Similarly, "model-driven" sensor webs will utilize environmental prediction models to initiate targeted sensor measurements or to use a new observing strategy. The sensor web concept contrasts with today's data collection techniques and observing system operations concepts where independent measurements are made by remote sensing and in situ platforms that do not share, and therefore cannot act upon, potentially useful complementary sensor measurement data and platform state information. This presentation describes NASA's view of event-driven and model-driven Sensor Webs and highlights several research and development activities at the Goddard Space Flight Center.

Adding a Visualization Feature to Web Search Engines: It’s Time

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

Wong, Pak C.

Since the first world wide web (WWW) search engine quietly entered our lives in 1994, the “information need” behind web searching has rapidly grown into a multi-billion dollar business that dominates the internet landscape, drives e-commerce traffic, propels global economy, and affects the lives of the whole human race. Today’s search engines are faster, smarter, and more powerful than those released just a few years ago. With the vast investment pouring into research and development by leading web technology providers and the intense emotion behind corporate slogans such as “win the web” or “take back the web,” I can’t helpmore » but ask why are we still using the very same “text-only” interface that was used 13 years ago to browse our search engine results pages (SERPs)? Why has the SERP interface technology lagged so far behind in the web evolution when the corresponding search technology has advanced so rapidly? In this article I explore some current SERP interface issues, suggest a simple but practical visual-based interface design approach, and argue why a visual approach can be a strong candidate for tomorrow’s SERP interface.« less

Biodiversity and ecosystem functioning in evolving food webs.

PubMed

Allhoff, K T; Drossel, B

2016-05-19

We use computer simulations in order to study the interplay between biodiversity and ecosystem functioning (BEF) during both the formation and the ongoing evolution of large food webs. A species in our model is characterized by its own body mass, its preferred prey body mass and the width of its potential prey body mass spectrum. On an ecological time scale, population dynamics determines which species are viable and which ones go extinct. On an evolutionary time scale, new species emerge as modifications of existing ones. The network structure thus emerges and evolves in a self-organized manner. We analyse the relation between functional diversity and five community level measures of ecosystem functioning. These are the metabolic loss of the predator community, the total biomasses of the basal and the predator community, and the consumption rates on the basal community and within the predator community. Clear BEF relations are observed during the initial build-up of the networks, or when parameters are varied, causing bottom-up or top-down effects. However, ecosystem functioning measures fluctuate only very little during long-term evolution under constant environmental conditions, despite changes in functional diversity. This result supports the hypothesis that trophic cascades are weaker in more complex food webs. © 2016 The Author(s).

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

PubMed Central

Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G.; Gelly, Jean-Christophe

2016-01-01

Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/. PMID:27319297

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.

PubMed

Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G; Gelly, Jean-Christophe

2016-06-20

Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation -with Protein Blocks-, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the 'Hard' category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.

Food web topology and parasites in the pelagic zone of a subarctic lake

USGS Publications Warehouse

Amundsen, Per-Arne; Lafferty, K.D.; Knudsen, R.; Primicerio, R.; Klemetsen, A.; Kuris, A.M.

2009-01-01

Parasites permeate trophic webs with their often complex life cycles, but few studies have included parasitism in food web analyses. Here we provide a highly resolved food web from the pelagic zone of a subarctic lake and explore how the incorporation of parasites alters the topology of the web. 2. Parasites used hosts at all trophic levels and increased both food-chain lengths and the total number of trophic levels. Their inclusion in the network analyses more than doubled the number of links and resulted in an increase in important food-web characteristics such as linkage density and connectance. 3. More than half of the parasite taxa were trophically transmitted, exploiting hosts at multiple trophic levels and thus increasing the degree of omnivory in the trophic web. 4. For trophically transmitted parasites, the number of parasite-host links exhibited a positive correlation with the linkage density of the host species, whereas no such relationship was seen for nontrophically transmitted parasites. Our findings suggest that the linkage density of free-living species affects their exposure to trophically transmitted parasites, which may be more likely to adopt highly connected species as hosts during the evolution of complex life cycles. 5. The study supports a prominent role for parasites in ecological networks and demonstrates that their incorporation may substantially alter considerations of food-web structure and functioning. ?? 2009 British Ecological Society.

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)

PubMed Central

Fernández-Mazuecos, Mario; Blanco-Pastor, José Luis; Gómez, José M.; Vargas, Pablo

2013-01-01

Background and Aims The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ∼30 species and subspecies with highly specialized corollas. Methods A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species. Key Results A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects. Conclusions The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes. PMID:24142920

The role of fusion in ant chromosome evolution: insights from cytogenetic analysis using a molecular phylogenetic approach in the genus mycetophylax.

PubMed

Cardoso, Danon Clemes; das Graças Pompolo, Silvia; Cristiano, Maykon Passos; Tavares, Mara Garcia

2014-01-01

Among insect taxa, ants exhibit one of the most variable chromosome numbers ranging from n = 1 to n = 60. This high karyotype diversity is suggested to be correlated to ants diversification. The karyotype evolution of ants is usually understood in terms of Robertsonian rearrangements towards an increase in chromosome numbers. The ant genus Mycetophylax is a small monogynous basal Attini ant (Formicidae: Myrmicinae), endemic to sand dunes along the Brazilian coastlines. A recent taxonomic revision validates three species, Mycetophylax morschi, M. conformis and M. simplex. In this paper, we cytogenetically characterized all species that belongs to the genus and analyzed the karyotypic evolution of Mycetophylax in the context of a molecular phylogeny and ancestral character state reconstruction. M. morschi showed a polymorphic number of chromosomes, with colonies showing 2n = 26 and 2n = 30 chromosomes. M. conformis presented a diploid chromosome number of 30 chromosomes, while M. simplex showed 36 chromosomes. The probabilistic models suggest that the ancestral haploid chromosome number of Mycetophylax was 17 (Likelihood framework) or 18 (Bayesian framework). The analysis also suggested that fusions were responsible for the evolutionary reduction in chromosome numbers of M. conformis and M. morschi karyotypes whereas fission may determines the M. simplex karyotype. These results obtained show the importance of fusions in chromosome changes towards a chromosome number reduction in Formicidae and how a phylogenetic background can be used to reconstruct hypotheses about chromosomes evolution.

The evolution of floral sonication, a pollen foraging behavior used by bees (Anthophila).

PubMed

Cardinal, Sophie; Buchmann, Stephen L; Russell, Avery L

2018-03-01

Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate ("buzz") flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in bees by generating a time-calibrated phylogeny and reconstructing ancestral states for this pollen extraction behavior. We also test the hypothesis that the ability to sonicate flowers and thereby efficiently access pollen from a diverse assemblage of plant species, led to increased diversification among sonicating bee taxa. We find that floral sonication evolved on average 45 times within bees, possibly first during the Early Cretaceous (100-145 million years ago) in the common ancestor of bees. We find that sonicating lineages are significantly more species rich than nonsonicating sister lineages when comparing sister clades, but a probabilistic structured rate permutation on phylogenies approach failed to support the hypothesis that floral sonication is a key driver of bee diversification. This study provides the evolutionary framework needed to further study how floral sonication by bees may have facilitated the spread and common evolution of angiosperm species with poricidal floral morphology. © 2018 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Dual-TRACER: High resolution fMRI with constrained evolution reconstruction.

PubMed

Li, Xuesong; Ma, Xiaodong; Li, Lyu; Zhang, Zhe; Zhang, Xue; Tong, Yan; Wang, Lihong; Sen Song; Guo, Hua

2018-01-01

fMRI with high spatial resolution is beneficial for studies in psychology and neuroscience, but is limited by various factors such as prolonged imaging time, low signal to noise ratio and scarcity of advanced facilities. Compressed Sensing (CS) based methods for accelerating fMRI data acquisition are promising. Other advanced algorithms like k-t FOCUSS or PICCS have been developed to improve performance. This study aims to investigate a new method, Dual-TRACER, based on Temporal Resolution Acceleration with Constrained Evolution Reconstruction (TRACER), for accelerating fMRI acquisitions using golden angle variable density spiral. Both numerical simulations and in vivo experiments at 3T were conducted to evaluate and characterize this method. Results show that Dual-TRACER can provide functional images with a high spatial resolution (1×1mm 2 ) under an acceleration factor of 20 while maintaining hemodynamic signals well. Compared with other investigated methods, dual-TRACER provides a better signal recovery, higher fMRI sensitivity and more reliable activation detection. Copyright © 2017 Elsevier Inc. All rights reserved.

Lexical evolution rates derived from automated stability measures

NASA Astrophysics Data System (ADS)

Petroni, Filippo; Serva, Maurizio

2010-03-01

Phylogenetic trees can be reconstructed from the matrix which contains the distances between all pairs of languages in a family. Recently, we proposed a new method which uses normalized Levenshtein distances among words with the same meaning and averages over all the items of a given list. Decisions about the number of items in the input lists for language comparison have been debated since the beginning of glottochronology. The point is that words associated with some of the meanings have a rapid lexical evolution. Therefore, a large vocabulary comparison is only apparently more accurate than a smaller one, since many of the words do not carry any useful information. In principle, one should find the optimal length of the input lists, studying the stability of the different items. In this paper we tackle the problem with an automated methodology based only on our normalized Levenshtein distance. With this approach, the program of an automated reconstruction of language relationships is completed.

Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae: ocelot and domestic cat lineages.

PubMed

Masuda, R; Lopez, J V; Slattery, J P; Yuhki, N; O'Brien, S J

1996-12-01

Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group of Felis species but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

PubMed Central

Árnason, Úlfur; Kumar, Vikas

2018-01-01

Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established. PMID:29632892

Adopt-a-Dino

ERIC Educational Resources Information Center

Clary, Renee; Wandersee, James

2011-01-01

This article discusses a creative visualization project to motivate and engage students. Students depict a dinosaur in its ecosystem and include all three elements of the environment: air, land, and water. Students explore scientific content in evolution, natural selection, food webs, ecosystems and geologic time. (Contains 6 figures.)

What is Justice for Juveniles?

ERIC Educational Resources Information Center

Rothwell, Jennifer Truran

1997-01-01

Provides background information and related learning activities for three areas of inquiry involving youth and violence: (1) "Evolution of the Juvenile Justice System"; (2) "The Literature of Crime and Poverty"; (3) "Youth Crime and Public Policy." Includes a list of six recommended Web sites. (MJP)

TMFoldWeb: a web server for predicting transmembrane protein fold class.

PubMed

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

Single stage treatment of ankylosis of the temporomandibular joint using patient-specific total joint replacement and virtual surgical planning.

PubMed

Haq, Jahrad; Patel, Nishma; Weimer, Katherine; Matthews, N Shaun

2014-04-01

Ankylosis of the temporomandibular joint (TMJ) is a debilitating condition that can result in pain, trismus, and a poor quality of life. It can be caused by injury, infection, and rheumatoid disease. Current management includes gap arthroplasty, interpositional arthroplasty, and reconstruction. Traditionally, joints are reconstructed using stock implants, or the procedure is done in two stages with an additional computed tomography (CT) scan between the resective and reconstructive procedures and use of stereolithographic models to aid the design of the definitive prostheses. We describe a technique for the resection of ankylosis and reconstruction of the joint in a single operation using virtually designed custom-made implants. Five patients with ankylosis of the TMJ had a single stage operation with reconstruction between 2010 and 2012. All had preoperative high-resolution CT with contrast angiography. During an international web-based teleconference between the surgeon and the engineer a virtual resection of the ankylosis was done using the reconstructed CT images. The bespoke cutting guides and implants were designed virtually at the same time and were then manufactured precisely using computer-aided design and manufacture (CAD-CAM) over 6 weeks. After release of the ankylosis and reconstruction, the patients underwent an exercise regimen to improve mouth opening. Follow-up was for a minimum of 6 months. Four patients had one operation, and one patient had two. Median/Mean maximum incisal opening increased from 0.6mm before operation to 25 mm afterwards (range 23-27), and there was minimal surgical morbidity. This new method effectively treats ankylosis of the TMJ in a single stage procedure. Fewer operations and hospital stays, and the maintenance of overall clinical outcome are obvious advantages. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Woese on the received view of evolution.

PubMed

Sarkar, Sahotra

2014-01-01

As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.

Complex Homology and the Evolution of Nervous Systems

PubMed Central

Liebeskind, Benjamin J.; Hillis, David M.; Zakon, Harold H.; Hofmann, Hans A.

2016-01-01

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states. PMID:26746806

Phylogeny and biogeography of Maclura (Moraceae) and the origin of an anachronistic fruit.

PubMed

Gardner, Elliot M; Sarraf, Paya; Williams, Evelyn W; Zerega, Nyree J C

2017-12-01

Maclura (ca. 12spp., Moraceae) is a widespread genus of trees and woody climbers found on five continents. Maclura pomifera, the Osage orange, is considered a classic example of an anachronistic fruit. Native to the central USA, the grapefruit-sized Osage oranges are unpalatable and have no known extant native dispersers, leading to speculation that the fruits were adapted to extinct megafauna. Our aim was to reconstruct the phylogeny, estimate divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group. Employing Bayesian and maximum-likelihood methods, we reconstructed the Maclura phylogeny using two nuclear and five chloroplast loci from all Maclura species and outgroups representing all Moraceae tribes. We reconstructed ancestral ranges and syncarp sizes using a family level dated tree, and used Ornstein-Uhlenbeck models to test for significant changes in syncarp size in the Osage orange lineage. Our analyses support a monophyletic Maclura with a Paleocene crown. Subgeneric sections were monophyletic except for the geographically-disjunct Cardiogyne. There was strong support for current species delineations except in the widespread M. cochinchinensis. South America was reconstructed as the ancestral range for Maclura with subsequent colonization of Africa and the northern hemisphere. The clade containing M. pomifera likely diverged in the Oligocene, closely coinciding with crown divergence dates of the mammoth/mastodon and sloth clades that contain possible extinct dispersers. The best fitting model for syncarp size evolution indicated an increase in both syncarp size and the rate of syncarp size evolution in the Osage orange lineage. We conclude that our findings are consistent with the hypothesis that M. pomifera was adapted to dispersal by extinct megafauna. In addition, we consider dispersal rather than vicariance to be most likely responsible for the present distribution of Maclura, as crown divergence post-dated the separation of Africa and South America. We propose revised sectional delimitations based on the phylogeny. This study represents a complete phylogenetic and biogeographic analysis of this globally distributed genus and provides a basis for future work, including a taxonomic revision. Copyright © 2017. Published by Elsevier Inc.

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

PubMed

Fuller, Zachary L; Niño, Elina L; Patch, Harland M; Bedoya-Reina, Oscar C; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M; Miller, Webb

2015-07-10

With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

New tool to assemble repetitive regions using next-generation sequencing data

NASA Astrophysics Data System (ADS)

Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz

2017-08-01

The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

The Knowledge Structure in Amarakośa

NASA Astrophysics Data System (ADS)

Nair, Sivaja S.; Kulkarni, Amba

Amarakośa is the most celebrated and authoritative ancient thesaurus of Sanskrit. It is one of the books which an Indian child learning through Indian traditional educational system memorizes as early as his first year of formal learning. Though it appears as a linear list of words, close inspection of it shows a rich organisation of words expressing various relations a word bears with other words. Thus when a child studies Amarakośa further, the linear list of words unfolds into a knowledge web. In this paper we describe our effort to make the implicit knowledge in Amarakośa explicit. A model for storing such structure is discussed and a web tool is described that answers the queries by reconstructing the links among words from the structured tables dynamically.

A Cenozoic tectonic model for Southeast Asia - microplates and basins

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

Maher, K.A.

1995-04-01

A computer-assisted Cenozoic tectonic model was built for Southeast Asia and used to construct 23 base maps, 2 to 6 million years apart. This close temporal spacing was necessary to constrain all the local geometric shifts in a consistent and geologically feasible fashion. More than a hundred individual blocks were required to adequately treat Cenozoic microplate processes at a basic level. The reconstructions show tectonic evolution to be characterized by long periods of gradual evolution, interrupted by brief, widespread episodes of reorganization in fundamental plate geometries and kinematics. These episodes are triggered by major collisions, or by accumulation of smallermore » changes. The model takes into account difficulties inherent in the region. The Pacific and Indo-Australian plates and their predecessors have driven westward and northward since the late Paleozoic, towards each other and the relatively stationary backstop of Asia. Southeast Asia is therefore the result of a long-lived, complex process of convergent tectonics, making it difficult to reconstruct tectonic evolution as much of the continental margin and sea floor spreading record was erased. In addition, the region has been dominated by small-scale microplate processes with short time scales and internal deformation, taking place in rapidly evolving and more ductile buffer zones between the major rigid plate systems. These plate interaction zones have taken up much of the relative motion between the major plates. Relatively ephemeral crustal blocks appear and die within the buffer zones, or accrete to and disperse from the margins of the major plate systems. However, such microplate evolution is the dominant factor in Cenozoic basin evolution. This detailed testonic model aids in comprehension and prediction of basin development, regional hydrocarbon habitat, and petroleum systems.« less

Parallel and convergent evolution of the dim-light vision gene RH1 in bats (Order: Chiroptera).

PubMed

Shen, Yong-Yi; Liu, Jie; Irwin, David M; Zhang, Ya-Ping

2010-01-21

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

PubMed Central

Shen, Yong-Yi; Liu, Jie; Irwin, David M.; Zhang, Ya-Ping

2010-01-01

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats. PMID:20098620

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

PubMed

Licona-Vera, Yuyini; Ornelas, Juan Francisco

2017-06-05

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

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

Sink- or Source-driven Phanerozoic carbon cycle?

NASA Astrophysics Data System (ADS)

Godderis, Y.; Donnadieu, Y.; Maffre, P.; Carretier, S.

2017-12-01

The Phanerozoic evolution of the atmospheric CO2 level is controlled by the fluxes entering or leaving the exospheric system. Those fluxes (including continental weathering, magmatic degassing, organic carbon burial, oxidation of sedimentary organic carbon) are intertwined, and their relative importance in driving the global carbon cycle evolution may have fluctuated through time. Deciphering the causes of the Phanerozoic climate evolution thus requires a holistic and quantitative approach. Here we focus on the role played by the paleogeographic configuration on the efficiency of the CO2 sink by continental silicate weathering, and on the impact of the magmatic degassing of CO2. We use the spatially resolved numerical model GEOCLIM (geoclimmodel.worpress.com) to compute the response of the silicate weathering and atmospheric CO2 to continental drift for 22 time slices of the Phanerozoic. Regarding the CO2 released by the magmatic activity, we reconstruct several Phanerozoic histories of this flux, based on published indexes. We calculate the CO2 evolution for each degassing scenario, and accounting for the paleogeographic setting. We show that the paleogeographic setting is a main driver of the climate from 540 Ma to about the beginning of the Jurassic. Regarding the role of the magmatic degassing, the various reconstructions do not converge towards a single signal, and thus introduce large uncertainties in the calculated CO2 level over time. Nevertheless, the continental dispersion, which prevails since the Jurassic, promotes the CO2 consumption by weathering and forces atmospheric CO2 to stay low. Warm climates of the "middle" Cretaceous and early Cenozoic require enhanced CO2 degassing by magmatic activity. In summary, the Phanerozoic climate evolution can be hardly assigned to a single process, but is the result of complex and intertwined processes.

Rapid execution of fan beam image reconstruction algorithms using efficient computational techniques and special-purpose processors

NASA Astrophysics Data System (ADS)

Gilbert, B. K.; Robb, R. A.; Chu, A.; Kenue, S. K.; Lent, A. H.; Swartzlander, E. E., Jr.

1981-02-01

Rapid advances during the past ten years of several forms of computer-assisted tomography (CT) have resulted in the development of numerous algorithms to convert raw projection data into cross-sectional images. These reconstruction algorithms are either 'iterative,' in which a large matrix algebraic equation is solved by successive approximation techniques; or 'closed form'. Continuing evolution of the closed form algorithms has allowed the newest versions to produce excellent reconstructed images in most applications. This paper will review several computer software and special-purpose digital hardware implementations of closed form algorithms, either proposed during the past several years by a number of workers or actually implemented in commercial or research CT scanners. The discussion will also cover a number of recently investigated algorithmic modifications which reduce the amount of computation required to execute the reconstruction process, as well as several new special-purpose digital hardware implementations under development in laboratories at the Mayo Clinic.

Reconstruction of Pressure Profile Evolution during Levitated Dipole Experiments

NASA Astrophysics Data System (ADS)

Mauel, M.; Garnier, D.; Boxer, A.; Ellsworth, J.; Kesner, J.

2008-11-01

Magnetic levitation of the LDX superconducting dipole causes significant changes in the measured diamagnetic flux and what appears to be an isotropic plasma pressure profile (p˜p||). This poster describes the reconstruction of plasma current and plasma pressure profiles from external measurements of the equilibrium magnetic field, which vary substantially as a function of time depending upon variations in neutral pressure and multifrequency ECRH power levels. Previous free-boundary reconstructions of plasma equilibrium showed the plasma to be anisotropic and highly peaked at the location of the cyclotron resonance of the microwave heating sources. Reconstructions of the peaked plasma pressures confined by a levitated dipole incorporate the small axial motion of the dipole (±5 mm), time varying levitation coil currents, eddy currents flowing in the vacuum vessel, constant magnetic flux linking the superconductor, and new flux loops located near the hot plasma in order to closely couple to plasma current and dipole current variations. I. Karim, et al., J. Fusion Energy, 26 (2007) 99.

Evolutionary innovation and diversification of carotenoid-based pigmentation in finches.

PubMed

Ligon, Russell A; Simpson, Richard K; Mason, Nicholas A; Hill, Geoffrey E; McGraw, Kevin J

2016-12-01

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary "innovation" that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes-where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved-supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus

PubMed Central

Smith, Oliver; Clapham, Alan; Rose, Pam; Liu, Yuan; Wang, Jun; Allaby, Robin G.

2014-01-01

The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes. PMID:24499968

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili

PubMed Central

Rudall, Paula J.; Bateman, Richard M.

2010-01-01

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean ‘flower’ are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression. PMID:20047867

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili.

PubMed

Rudall, Paula J; Bateman, Richard M

2010-02-12

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean 'flower' are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression.

Geomorphological evolution of landslides near an active normal fault in northern Taiwan, as revealed by lidar and unmanned aircraft system data

NASA Astrophysics Data System (ADS)

Chang, Kuo-Jen; Chan, Yu-Chang; Chen, Rou-Fei; Hsieh, Yu-Chung

2018-03-01

Several remote sensing techniques, namely traditional aerial photographs, an unmanned aircraft system (UAS), and airborne lidar, were used in this study to decipher the morphological features of obscure landslides in volcanic regions and how the observed features may be used for understanding landslide occurrence and potential hazard. A morphological reconstruction method was proposed to assess landslide morphology based on the dome-shaped topography of the volcanic edifice and the nature of its morphological evolution. Two large-scale landslides in the Tatun volcano group in northern Taiwan were targeted to more accurately characterize the landslide morphology through airborne lidar and UAS-derived digital terrain models and images. With the proposed reconstruction method, the depleted volume of the two landslides was estimated to be at least 820 ± 20 × 106 m3. Normal faulting in the region likely played a role in triggering the two landslides, because there are extensive geological and historical records of an active normal fault in this region. The subsequent geomorphological evolution of the two landslides is thus inferred to account for the observed morphological and tectonic features that are indicative of resulting in large and life-threatening landslides, as characterized using the recent remote sensing techniques.

Patterns of host-plant choice in bees of the genus Chelostoma: the constraint hypothesis of host-range evolution in bees.

PubMed

Sedivy, Claudio; Praz, Christophe J; Müller, Andreas; Widmer, Alex; Dorn, Silvia

2008-10-01

To trace the evolution of host-plant choice in bees of the genus Chelostoma (Megachilidae), we assessed the host plants of 35 Palearctic, North American and Indomalayan species by microscopically analyzing the pollen loads of 634 females and reconstructed their phylogenetic history based on four genes and a morphological dataset, applying both parsimony and Bayesian methods. All species except two were found to be strict pollen specialists at the level of plant family or genus. These oligolectic species together exploit the flowers of eight different plant orders that are distributed among all major angiosperm lineages. Based on ancestral state reconstruction, we found that oligolecty is the ancestral state in Chelostoma and that the two pollen generalists evolved from oligolectic ancestors. The distinct pattern of host broadening in these two polylectic species, the highly conserved floral specializations within the different clades, the exploitation of unrelated hosts with a striking floral similarity as well as a recent report on larval performance on nonhost pollen in two Chelostoma species clearly suggest that floral host choice is physiologically or neurologically constrained in bees of the genus Chelostoma. Based on this finding, we propose a new hypothesis on the evolution of host range in bees.

Pangea with a twist of paleomagnetism. Easy as ABC?

NASA Astrophysics Data System (ADS)

Pastor-Galan, D.

2017-12-01

Most tectonic reconstructions assume supercontinents to be single and stable super-plates, for example the majority of the reconstructions show Pangea as a quasi-stable superplate from 320 to 180 Ma. Although we know to a first order the pre-break-up configuration of Pangea, its configuration during amalgamation (Pangea A, B, C… hypotheses) and therefore its tectonic evolution during the Late Carboniferous and Permian are largely unknown and controversial. As a consequence, we do not know how and why Pangea became a supercontinent nor the processes responsible for its break-up. Paleomagnetic evidence seems contradictory supporting differnt configurations and large-scale vertical axis rotations in the core of Pangea implying >>1500km of shortening/extension, not easily explained by the preserved geologic record or by the reconstructions derived from it. Synchronously and maybe related, two major and enigmatic events occurred within the Pangean supercontinent: (1) extensive magmatism whose link to crustal and/or mantle dynamics is unclear and (2) widespread development of extensional basins containing the bulk of the Earth oil/gas reserves. The geodynamic consequences of these processes happening in the core of Pangea involve processes such as intra-continental subduction, delamination, rifting, megashear motion and development of major basins. Finally, Pangea did not break along the sutures of the Iapetus/Rheic oceans whose consumption in the Late Paleozoic gave rise to the supercontinent. Intraplate deformation has never considered in tectonic models for the supercontinent cycle and however may be key to understand the large vertical axis rotations, the role of lithospheric weaknesses leading to supercontinent break-up, and the formation of intraplate basins. Together with plate non rigidity, crustal loss and growth are crucial geological problems that are generally ignored in plate reconstructions. The assumptions of plate rigidity and conservation of continental lithosphere introduce errors that we are propagating into the past, making our reconstructions less precise in Paleozoic and pre-Cambrian times. A newer reconstruction of the late Palaeozoic tectonic evolution of Pangea including all those parameters will solve the Pangea A, B or C conundrum.

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

Zou, Lianfeng; Li, Jonathan; Zakharov, Dmitri

Using in situ transmission electron microscopy that spatially and temporally resolves the evolution of the atomic structure in the surface and subsurface regions, we Find that the surface segregation of Au atoms in a Cu(Au) solid solution results in the nucleation and growth of a (2 × 1) missing-row reconstructed, half-unit-cell thick L1 2 Cu 3Au(110) surface alloy. Our in situ electron microscopy observations and atomistic simulations demonstrate that the (2 × 1) reconstruction of the Cu 3Au(110) surface alloy remains as a stable surface structure as a result of the favored Cu-Au diatom configuration.

The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes

PubMed Central

2010-01-01

Background The family Polypteridae, commonly known as "bichirs", is a lineage that diverged early in the evolutionary history of Actinopterygii (ray-finned fish), but has been the subject of far less evolutionary study than other members of that clade. Uncovering patterns of morphological change within Polypteridae provides an important opportunity to evaluate if the mechanisms underlying morphological evolution are shared among actinoptyerygians, and in fact, perhaps the entire osteichthyan (bony fish and tetrapods) tree of life. However, the greatest impediment to elucidating these patterns is the lack of a well-resolved, highly-supported phylogenetic tree of Polypteridae. In fact, the interrelationships of polypterid species have never been subject to molecular phylogenetic analysis. Here, we infer the first molecular phylogeny of bichirs, including all 12 recognized species and multiple subspecies using Bayesian analyses of 16S and cyt-b mtDNA. We use this mitochondrial phylogeny, ancestral state reconstruction, and geometric morphometrics to test whether patterns of morphological evolution, including the evolution of body elongation, pelvic fin reduction, and craniofacial morphology, are shared throughout the osteichthyan tree of life. Results Our molecular phylogeny reveals 1) a basal divergence between Erpetoichthys and Polypterus, 2) polyphyly of P. endlicheri and P. palmas, and thus 3) the current taxonomy of Polypteridae masks its underlying genetic diversity. Ancestral state reconstructions suggest that pelvic fins were lost independently in Erpetoichthys, and unambiguously estimate multiple independent derivations of body elongation and shortening. Our mitochondrial phylogeny suggested species that have lower jaw protrusion and up-righted orbit are closely related to each other, indicating a single transformation of craniofacial morphology. Conclusion The mitochondrial phylogeny of polypterid fish provides a strongly-supported phylogenetic framework for future comparative evolutionary, physiological, ecological, and genetic analyses. Indeed, ancestral reconstruction and geometric morphometric analyses revealed that the patterns of morphological evolution in Polypteridae are similar to those seen in other osteichthyans, thus implying the underlying genetic and developmental mechanisms responsible for those patterns were established early in the evolutionary history of Osteichthyes. We propose developmental and genetic mechanisms to be tested under the light of this new phylogenetic framework. PMID:20100320

Active Visual SLAM with Exploration for Autonomous Underwater Navigation

DTIC Science & Technology

2012-01-01

tourism. Reconstruction of Notre Dame de Paris (Snavely et al., 2006). (c) Web-scale landmark recognition engine (Zheng et al., 2009). eters for an...structures, such as Notre Dame Cathedral in Paris and the Great Wall of China (Figure 1.3(b)), using photographs compiled from the Internet. Given the...representation. Originally developed for text-based applications, expansion of this approach to images were found in Leung and Malik (2001), Sivic and Zisserman

A mixed-order nonlinear diffusion compressed sensing MR image reconstruction.

PubMed

Joy, Ajin; Paul, Joseph Suresh

2018-03-07

Avoid formation of staircase artifacts in nonlinear diffusion-based MR image reconstruction without compromising computational speed. Whereas second-order diffusion encourages the evolution of pixel neighborhood with uniform intensities, fourth-order diffusion considers smooth region to be not necessarily a uniform intensity region but also a planar region. Therefore, a controlled application of fourth-order diffusivity function is used to encourage second-order diffusion to reconstruct the smooth regions of the image as a plane rather than a group of blocks, while not being strong enough to introduce the undesirable speckle effect. Proposed method is compared with second- and fourth-order nonlinear diffusion reconstruction, total variation (TV), total generalized variation, and higher degree TV using in vivo data sets for different undersampling levels with application to dictionary learning-based reconstruction. It is observed that the proposed technique preserves sharp boundaries in the image while preventing the formation of staircase artifacts in the regions of smoothly varying pixel intensities. It also shows reduced error measures compared with second-order nonlinear diffusion reconstruction or TV and converges faster than TV-based methods. Because nonlinear diffusion is known to be an effective alternative to TV for edge-preserving reconstruction, the crucial aspect of staircase artifact removal is addressed. Reconstruction is found to be stable for the experimentally determined range of fourth-order regularization parameter, and therefore not does not introduce a parameter search. Hence, the computational simplicity of second-order diffusion is retained. © 2018 International Society for Magnetic Resonance in Medicine.

Reminiscing about 15 years of interoperability efforts

DOE PAGES

Van de Sompel, Herbert; Nelson, Michael L.

2015-11-01

Over the past fifteen years, our perspective on tackling information interoperability problems for web-based scholarship has evolved significantly. In this opinion piece, we look back at three efforts that we have been involved in that aptly illustrate this evolution: OAI-PMH, OAI-ORE, and Memento. Understanding that no interoperability specification is neutral, we attempt to characterize the perspectives and technical toolkits that provided the basis for these endeavors. With that regard, we consider repository-centric and web-centric interoperability perspectives, and the use of a Linked Data or a REST/HATEAOS technology stack, respectively. In addition, we lament the lack of interoperability across nodes thatmore » play a role in web-based scholarship, but end on a constructive note with some ideas regarding a possible path forward.« less

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

Online Tools for Astronomy and Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, B. S.

2005-01-01

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.

Web-Based Education Prior to Outpatient Orthopaedic Surgery Enhances Early Patient Satisfaction Scores: A Prospective Randomized Controlled Study.

PubMed

van Eck, Carola F; Toor, Aneet; Banffy, Michael B; Gambardella, Ralph A

2018-01-01

A good patient-surgeon relationship relies on adequate preoperative education and counseling. Several multimedia resources, such as web-based education tools, have become available to enhance aspects of perioperative care. The purpose of this study was to evaluate the effect of an interactive web-based education tool on perioperative patient satisfaction scores after outpatient orthopaedic surgery. It was hypothesized that web-based education prior to outpatient orthopaedic surgery enhances patient satisfaction scores. Randomized controlled trial; Level of evidence, 1. All patients undergoing knee arthroscopy with meniscectomy, chondroplasty, or anterior cruciate ligament reconstruction or shoulder arthroscopy with rotator cuff repair were eligible for inclusion and were randomized to the study or control group. The control group received routine education by the surgeon, whereas the study group received additional web-based education. At the first postoperative visit, all patients completed the OAS CAHPS (Outpatient and Ambulatory Surgery Consumer Assessment of Healthcare Providers and Systems) survey. Differences in patient satisfaction scores between the study and control groups were determined with an independent t test. A total of 177 patients were included (104 [59%] males; mean age, 42 ± 14 years); 87 (49%) patients were randomized to receive additional web-based education. Total patient satisfaction score was significantly higher in the study group (97 ± 5) as compared with the control group (94 ± 8; P = .019), specifically for the OAS CAHPS core measure "recovery" (92 ± 13 vs 82 ± 23; P = .001). Age, sex, race, workers' compensation status, education level, overall health, emotional health, procedure type and complexity, and addition of a video did not influence patient satisfaction scores. Supplemental web-based patient education prior to outpatient orthopaedic surgery enhances patient satisfaction scores.

E-Government Goes Semantic Web: How Administrations Can Transform Their Information Processes

NASA Astrophysics Data System (ADS)

Klischewski, Ralf; Ukena, Stefan

E-government applications and services are built mainly on access to, retrieval of, integration of, and delivery of relevant information to citizens, businesses, and administrative users. In order to perform such information processing automatically through the Semantic Web,1 machine-readable2 enhancements of web resources are needed, based on the understanding of the content and context of the information in focus. While these enhancements are far from trivial to produce, administrations in their role of information and service providers so far find little guidance on how to migrate their web resources and enable a new quality of information processing; even research is still seeking best practices. Therefore, the underlying research question of this chapter is: what are the appropriate approaches which guide administrations in transforming their information processes toward the Semantic Web? In search for answers, this chapter analyzes the challenges and possible solutions from the perspective of administrations: (a) the reconstruction of the information processing in the e-government in terms of how semantic technologies must be employed to support information provision and consumption through the Semantic Web; (b) the required contribution to the transformation is compared to the capabilities and expectations of administrations; and (c) available experience with the steps of transformation are reviewed and discussed as to what extent they can be expected to successfully drive the e-government to the Semantic Web. This research builds on studying the case of Schleswig-Holstein, Germany, where semantic technologies have been used within the frame of the Access-eGov3 project in order to semantically enhance electronic service interfaces with the aim of providing a new way of accessing and combining e-government services.

Fast ancestral gene order reconstruction of genomes with unequal gene content.

PubMed

Feijão, Pedro; Araujo, Eloi

2016-11-11

During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree. Since this problem is NP-hard for most rearrangement models, exact solutions are practical only for small instances, and heuristics have to be used for larger datasets. This type of approach can be called event-based. Another common approach is based on finding conserved structures between the input genomes, such as adjacencies between genes, possibly also assigning weights that indicate a measure of confidence or probability that this particular structure is present on each ancestral genome, and then finding a set of non conflicting adjacencies that optimize some given function, usually trying to maximize total weight and minimizing character changes in the tree. We call this type of methods homology-based. In previous work, we proposed an ancestral reconstruction method that combines homology- and event-based ideas, using the concept of intermediate genomes, that arise in DCJ rearrangement scenarios. This method showed better rate of correctly reconstructed adjacencies than other methods, while also being faster, since the use of intermediate genomes greatly reduces the search space. Here, we generalize the intermediate genome concept to genomes with unequal gene content, extending our method to account for gene insertions and deletions of any length. In many of the simulated datasets, our proposed method had better results than MLGO and MGRA, two state-of-the-art algorithms for ancestral reconstruction with unequal gene content, while running much faster, making it more scalable to larger datasets. Studing ancestral reconstruction problems under a new light, using the concept of intermediate genomes, allows the design of very fast algorithms by greatly reducing the solution search space, while also giving very good results. The algorithms introduced in this paper were implemented in an open-source software called RINGO (ancestral Reconstruction with INtermediate GenOmes), available at https://github.com/pedrofeijao/RINGO .

DPTEdb, an integrative database of transposable elements in dioecious plants.

PubMed

Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

2016-01-01

Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php. © The Author(s) 2016. Published by Oxford University Press.

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

Szöllősi, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

2013-01-01

Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree–species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

Human Migration Patterns in Yemen and Implications for Reconstructing Prehistoric Population Movements

PubMed Central

Miró-Herrans, Aida T.; Al-Meeri, Ali; Mulligan, Connie J.

2014-01-01

Population migration has played an important role in human evolutionary history and in the patterning of human genetic variation. A deeper and empirically-based understanding of human migration dynamics is needed in order to interpret genetic and archaeological evidence and to accurately reconstruct the prehistoric processes that comprise human evolutionary history. Current empirical estimates of migration include either short time frames (i.e. within one generation) or partial knowledge about migration, such as proportion of migrants or distance of migration. An analysis of migration that includes both proportion of migrants and distance, and direction over multiple generations would better inform prehistoric reconstructions. To evaluate human migration, we use GPS coordinates from the place of residence of the Yemeni individuals sampled in our study, their birthplaces and their parents' and grandparents' birthplaces to calculate the proportion of migrants, as well as the distance and direction of migration events between each generation. We test for differences in these values between the generations and identify factors that influence the probability of migration. Our results show that the proportion and distance of migration between females and males is similar within generations. In contrast, the proportion and distance of migration is significantly lower in the grandparents' generation, most likely reflecting the decreasing effect of technology. Based on our results, we calculate the proportion of migration events (0.102) and mean and median distances of migration (96 km and 26 km) for the grandparent's generation to represent early times in human evolution. These estimates can serve to set parameter values of demographic models in model-based methods of prehistoric reconstruction, such as approximate Bayesian computation. Our study provides the first empirically-based estimates of human migration over multiple generations in a developing country and these estimates are intended to enable more precise reconstruction of the demographic processes that characterized human evolution. PMID:24759992

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes

PubMed Central

Nakatani, Yoichiro; McLysaght, Aoife

2017-01-01

Abstract Motivation: It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Results: Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. Conclusions: We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. Availability and implementation: The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request. Contact: yoichiro.nakatani@tcd.ie or aoife.mclysaght@tcd.ie Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881993

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.

PubMed

Nakatani, Yoichiro; McLysaght, Aoife

2017-07-15

It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip , and the software written in Java is available upon request. yoichiro.nakatani@tcd.ie or aoife.mclysaght@tcd.ie. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Indocyanine green-based fluorescent angiography in breast reconstruction

PubMed Central

Chae, Michael P.; Rozen, Warren Matthew

2016-01-01

Background Fluorescent angiography (FA) has been useful for assessing blood flow and assessing tissue perfusion in ophthalmology and other surgical disciplines for decades. In plastic surgery, indocyanine green (ICG) dye-based FA is a relatively novel imaging technology with high potential in various applications. We review the various FA detector systems currently available and critically appraise its utility in breast reconstruction. Methods A review of the published English literature dating from 1950 to 2015 using databases, such as PubMed, Medline, Web of Science, and EMBASE was undertaken. Results In comparison to the old fluorescein dye, ICG has a superior side effect profile and can be accurately detected by various commercial devices, such as SPY Elite (Novadaq, Canada), FLARE (Curadel LLC, USA), PDE-Neo (Hamamatsu Photonics, Japan), Fluobeam 800 (Fluoptics, France), and IC-View (Pulsion Medical Systems AG, Germany). In breast reconstruction, ICG has established as a safer, more accurate tracer agent, in lieu of the traditional blue dyes, for detection of sentinel lymph nodes with radioactive isotopes (99m-Technetium). In prosthesis-based breast reconstruction, intraoperative assessment of the mastectomy skin flap to guide excision of hypoperfused areas translates to improved clinical outcomes. Similarly, in autologous breast reconstructions, FA can be utilized to detect poorly perfused areas of the free flap, evaluate microvascular anastomosis for patency, and assess SIEA vascular territory for use as an alternative free flap with minimal donor site morbidity. Conclusions ICG-based FA is a novel, useful tool for various applications in breast reconstruction. More studies with higher level of evidence are currently lacking to validate this technology. PMID:27047782

Late-Pleistocene evolution of the East Mediterranean shallow continental shelf of north-central Israel

NASA Astrophysics Data System (ADS)

Shtienberg, Gilad; Dix, Justin; Waldmann, Nicolas; Makovsky, Yizhaq; Bookman, Revital; Roskin, Joel; Bialik, Or; Golan, Arik; Sivan, Dorit

2016-04-01

Sea-level fluctuations are a dominant and dynamic mechanism that control coastal environmental through time. This is especially the case for the successive regressions and transgressions over the last interglacial cycle, which have shaped the deposition, preservation and erosion patterns of unconsolidated sediments currently submerged on continental shelves. The current study focuses on an integrated high-resolution marine and terrestrial litho-stratigraphic and geophysical framework of the north-central Mediterranean coastal zone of Israel. The interpretation enabled the reconstruction of the coastal evolution over the last ˜130 ka. A multi-disciplinary approach was applied by compiling existing elevation raster grids, bathymetric charts, detailed lithological borehole data-sets, a dense 110 km long sub-bottom geophysical survey and seven continuous boreholes sediment records. Based on seismic stratigraphic analysis, observed geometries, and reflective appearances, six bounding surfaces and seven seismic units were identified and characterized. Meanwhile, the chronostratigraphy of the terrestrial side was constructed through integration of magnetic susceptibility, sedimentological and geochemical analysis with 17 new OSL ages. The seismic units were correlated with the available terrestrial borehole data and then associated to the retrieved terrestrial chronostratigraphy to produce a 4D reconstruction model of the paleo-landscape. The entire unconsolidated sequence overlies a calcareous aeolianite (locally named Kurkar unit) dated from ˜131 - ˜104 ka, which represents the top of the last interglacial cycle dune sediments. The lower unconsolidated unit consists of a red silty loam dated to ˜71 ka. This Red-Paleosol unit is overlaid by a dark brown clayey silty loam This Brown-Paleosol unit dates to ˜58 - ˜36 ka and is overlaid by a dark silty clay wetland deposit dated to ˜21 - ˜10 ka. The wetland unit is topped by a quartz sand dated to ˜6.6 - 0.1 ka. This approach allowed us to investigate the relationship between the lithological units and sea-level change and thus enable the reconstruction of the coastal evolution over the last ˜130 ka. This reconstruction suggests that the stratigraphy is dominated by a sea level lowstand during which aeolian, fluvial and paleosol sediments were deposited in a terrestrial environment. The coastal-terrestrial landscape was flooded by the early to middle Holocene transgression. The results of this study provide a valuable framework for future national strategic shallow-water infrastructure construction and also for the possible locations of past human settlements in relation to coastal evolution through time.

New Perspectives: Wave Mechanical Interpretations of Dark Matter, Baryon and Dark Energy

NASA Astrophysics Data System (ADS)

Russell, Esra

We model the cosmic components: dark matter, dark energy and baryon distributions in the Cosmic Web by means of highly nonlinear Schrodinger type and reaction diffusion type wave mechanical descriptions. The construction of these wave mechanical models of the structure formation is achieved by introducing the Fisher information measure and its comparison with highly nonlinear term which has dynamical analogy to infamous quantum potential in the wave equations. Strikingly, the comparison of this nonlinear term and the Fisher information measure provides a dynamical distinction between lack of self-organization and self-organization in the dynamical evolution of the cosmic components. Mathematically equivalent to the standard cosmic fluid equations, these approaches make it possible to follow the evolution of the matter distribution even into the highly nonlinear regime by circumventing singularities. Also, numerical realizations of the emerging web-like patterns are presented from the nonlinear dynamics of the baryon component while dark energy component shows Gaussian type dynamics corresponding to soliton-like solutions.

Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae.

PubMed

Nagler, Christina; Haug, Joachim T

2016-01-01

Parasites significantly influence food webs and ecosystems and occur all over the world in almost every animal group. Within crustaceans there are numerous examples of ectoparasites; for example, representatives of the isopod group Cymothoidae. These obligatory parasitic isopods are relatively poorly studied regarding their functional morphology. Here we present new details of the morphological adaptations to parasitism of the cymothoiid ingroup Nerocila with up-to-date imaging methods (macro photography, stereo imaging, fluorescence photography, micro CT, and histology). Central aspects of the study were (1) the morphology of the mouthparts and (2) the attachment on the host, hence the morphology of the thoracopods. The mouthparts (labrum, mandibles, paragnaths, maxillulae, maxillae, maxillipeds) form a distinct mouth cone and are most likely used for true sucking. The mouthparts are tightly "folded" around each other and provide functional rails for the only two moving mouthparts, mandible and maxillula. Both are not moving in an ancestral-type median-lateral movement, but are strongly tilted to move more in a proximal-distal axis. New details concerning the attachment demonstrate that the angular arrangement of the thoracopods is differentiated to impede removal by the host. The increased understanding of morphological adaptation to parasitism of modern forms will be useful in identifying disarticulated (not attached to the host) fossil parasites.

Preliminary publications book 2 from project on mineral resources, metallogenesis, and tectonics of northeast Asia

USGS Publications Warehouse

Nokleberg, Warren J.; Miller, Robert J.; Naumova, Vera V.; Khanchuk, Alexander I.; Parfenov, Leonid M.; Kuzmin, Mikhail I.; Bounaeva, Tatiana M.; Obolenskiy, Alexander A.; Rodionov, Sergey M.; Seminskiy, Zhan V.; Diggles, Michael F.

2003-01-01

This is the Web version of a CD-ROM publication. This report consists of summary major compilations and syntheses accomplished in the six-year project through April 2003 for the study on the Mineral Resources, Metallogenesis, and Tectonics of Northeast Asia (Eastern and Southern Siberia, Mongolia, Northeastern China, South Korea, and Japan). The major scientific goals and benefits of the project are to: (1) provide a comprehensive international data base on the mineral resources of the region that is the first, extensive knowledge available in English; (2) provide major new interpretations of the origin and crustal evolution of mineralizing systems and their host rocks, thereby enabling enhanced, broad-scale tectonic reconstructions and interpretations; and (3) promote trade and scientific and technical exchanges between the North America and Northeast Asia. Data from the project are providing sound scientific data and interpretations for commercial firms, governmental agencies, universities, and individuals that are developing new ventures and studies in the project area, and for land-use planning studies that deal with both mineral potential issues. Northeast Asia has vast potential for known and undiscovered mineral deposits; however, little information existed in English in the West until publication of products from this project. Consequently, data and interpretations from the project are providing basic knowledge for major scientific, commercial, national, and international endeavors by other interested individuals and groups.

Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae

PubMed Central

Haug, Joachim T.

2016-01-01

Parasites significantly influence food webs and ecosystems and occur all over the world in almost every animal group. Within crustaceans there are numerous examples of ectoparasites; for example, representatives of the isopod group Cymothoidae. These obligatory parasitic isopods are relatively poorly studied regarding their functional morphology. Here we present new details of the morphological adaptations to parasitism of the cymothoiid ingroup Nerocila with up-to-date imaging methods (macro photography, stereo imaging, fluorescence photography, micro CT, and histology). Central aspects of the study were (1) the morphology of the mouthparts and (2) the attachment on the host, hence the morphology of the thoracopods. The mouthparts (labrum, mandibles, paragnaths, maxillulae, maxillae, maxillipeds) form a distinct mouth cone and are most likely used for true sucking. The mouthparts are tightly “folded” around each other and provide functional rails for the only two moving mouthparts, mandible and maxillula. Both are not moving in an ancestral-type median-lateral movement, but are strongly tilted to move more in a proximal-distal axis. New details concerning the attachment demonstrate that the angular arrangement of the thoracopods is differentiated to impede removal by the host. The increased understanding of morphological adaptation to parasitism of modern forms will be useful in identifying disarticulated (not attached to the host) fossil parasites. PMID:27441121

Geography and Similarity of Regional Cuisines in China

PubMed Central

Zhu, Yu-Xiao; Huang, Junming; Zhang, Zi-Ke; Zhang, Qian-Ming; Zhou, Tao; Ahn, Yong-Yeol

2013-01-01

Food occupies a central position in every culture and it is therefore of great interest to understand the evolution of food culture. The advent of the World Wide Web and online recipe repositories have begun to provide unprecedented opportunities for data-driven, quantitative study of food culture. Here we harness an online database documenting recipes from various Chinese regional cuisines and investigate the similarity of regional cuisines in terms of geography and climate. We find that geographical proximity, rather than climate proximity, is a crucial factor that determines the similarity of regional cuisines. We develop a model of regional cuisine evolution that provides helpful clues for understanding the evolution of cuisines and cultures. PMID:24260166

Geography and similarity of regional cuisines in China.

PubMed

Zhu, Yu-Xiao; Huang, Junming; Zhang, Zi-Ke; Zhang, Qian-Ming; Zhou, Tao; Ahn, Yong-Yeol

2013-01-01

Food occupies a central position in every culture and it is therefore of great interest to understand the evolution of food culture. The advent of the World Wide Web and online recipe repositories have begun to provide unprecedented opportunities for data-driven, quantitative study of food culture. Here we harness an online database documenting recipes from various Chinese regional cuisines and investigate the similarity of regional cuisines in terms of geography and climate. We find that geographical proximity, rather than climate proximity, is a crucial factor that determines the similarity of regional cuisines. We develop a model of regional cuisine evolution that provides helpful clues for understanding the evolution of cuisines and cultures.

Reconstructing human evolution: Achievements, challenges, and opportunities

PubMed Central

Wood, Bernard

2010-01-01

This contribution reviews the evidence that has resolved the branching structure of the higher primate part of the tree of life and the substantial body of fossil evidence for human evolution. It considers some of the problems faced by those who try to interpret the taxonomy and systematics of the human fossil record. How do you to tell an early human taxon from one in a closely related clade? How do you determine the number of taxa represented in the human clade? How can homoplasy be recognized and factored into attempts to recover phylogeny? PMID:20445105

Mobile Web-Based Follow-up for Postoperative ACL Reconstruction: A Single-Center Experience.

PubMed

Higgins, James; Semple, John; Murnaghan, Lucas; Sharpe, Sarah; Theodoropoulos, John

2017-12-01

The initial 6 weeks after surgery has been identified as an area for improvement in patient care. During this period, the persistence of symptoms that go unchecked can lead to unscheduled emergency room and clinic visits, calls to surgeons' offices, and readmissions. To analyze postoperative data from a previous study examining postoperative outcomes in 2 patient populations following breast reconstruction and anterior cruciate ligament (ACL) reconstruction with use of a patient-centered mobile application. Here, the authors establish whether this method of follow-up can provide useful insight specific to the orthopaedic patient population, and they determine whether the mobile platform has the potential to modify their postoperative treatment. In addition, the authors examine its utility for orthopaedic physicians and patients. Case series; Level of evidence, 4. Eligible patients undergoing ACL reconstruction from 2 surgeons were consecutively recruited to use a mobile smartphone application that allowed physicians to monitor their recovery at home. Data from 32 patients were collected via the application and analyzed to evaluate recovery trends during the first 6 postoperative weeks. Following completion of the study, patients and physicians were interviewed on their experience. Data collected from each question in the mobile application provided insightful trends on daily real-time indicators of postoperative recovery. The application identified 1 patient who required in-person reassessment to rule out a possible infection, following surgeon review of an uploaded image. It was estimated that the majority of patients could have avoided follow-up at 2 and 6 weeks, owing to the application's efficacy. Participants described their satisfaction with the device as excellent (43%), good (40%), fair (10%), and poor (7%), and 94% (n = 30) of patients reported that they would respond to questions using a similar application in the future. Both physicians rated their experience as positive and identified useful traits in the web portal. This system can accurately assess patient recovery; it has the potential to change how postoperative orthopaedic patients are followed, and it is well received by patients and physicians. Recognition of the study's limitations and employment of user feedback to improve the current application are essential before a formal randomized controlled trial is conducted.

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

PubMed Central

Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C.; Bell, Thomas

2015-01-01

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. PMID:25833854

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities.

PubMed

Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C; Bell, Thomas

2015-05-07

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

G. H. Mead in the history of sociological ideas.

PubMed

da Silva, Filipe Carreira

2006-01-01

My aim is to discuss the history of the reception of George Herbert Mead's ideas in sociology. After discussing the methodological debate between presentism and historicism, I address the interpretations of those responsible for Mead's inclusion in the sociological canon: Herbert Blumer, Jürgen Habermas, and Hans Joas. In the concluding section, I assess these reconstructions of Mead's thought and suggest an alternative more consistent with my initial methodological remarks. In particular, I advocate a reconstruction of Mead's ideas that apprehends simultaneously its evolution over time and its thematic breadth. Such a historically minded reconstruction can be not only a useful corrective to possible anachronisms incurred by contemporary social theorists, but also a fruitful resource for their theory-building endeavors. Only then can meaningful and enriching dialogue with Mead begin. Copyright 2006 Wiley Periodicals, Inc.

Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

PubMed Central

Preston, Jill C.; Kellogg, Elizabeth A.

2006-01-01

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

Selection and paucity of phylogenetic signal challenge the utility of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans (Protista, Ciliophora).

PubMed

Rajter, Ľubomír; Vďačný, Peter

2018-05-12

The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans. We identified several mutually interconnected problems associated with the ciliate alpha-tubulin gene: the paucity of phylogenetic signal, molecular homoplasies and non-neutral evolution. Positive selection may generate molecular homoplasies (parallel evolution), while negative selection may cause a small number of changes and hence little phylogenetic informativness. Both problems were encountered in nucleotide and amino acid alpha-tubulin alignments, indicating an action of various selective pressures. Taking into account the involvement of alpha-tubulin in many essential biological processes, this protein could be so strongly affected by purifying selection that it even might have become an inappropriate molecular marker for reconstruction of phylogenetic relationships. Therefore, a great caution should be paid when tubulin genes are included in phylogenetic and/or phylogenomic analyses. Copyright © 2018 Elsevier Inc. All rights reserved.

SIFTER search: a web server for accurate phylogeny-based protein function prediction

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

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

SIFTER search: a web server for accurate phylogeny-based protein function prediction

DOE PAGES

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

2015-05-15

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

A web based Radiation Oncology Dose Manager with a rich User Interface developed using AJAX, ruby, dynamic XHTML and the new Yahoo/EXT User Interface Library.

PubMed

Vali, Faisal; Hong, Robert

2007-10-11

With the evolution of AJAX, ruby on rails, advanced dynamic XHTML technologies and the advent of powerful user interface libraries for javascript (EXT, Yahoo User Interface Library), developers now have the ability to provide truly rich interfaces within web browsers, with reasonable effort and without third-party plugins. We designed and developed an example of such a solution. The User Interface allows radiation oncology practices to intuitively manage different dose fractionation schemes by helping estimate total dose to irradiated organs.

Conservation of globin genes in the "living fossil" Latimeria chalumnae and reconstruction of the evolution of the vertebrate globin family.

PubMed

Schwarze, Kim; Burmester, Thorsten

2013-09-01

The (hemo-)globins are among the best-investigated proteins in biomedical sciences. These small heme-proteins play an important role in oxygen supply, but may also have other functions. In addition to well known hemoglobin and myoglobin, six other vertebrate globin types have been identified in recent years: neuroglobin, cytoglobin, globin E, globin X, globin Y, and androglobin. Analyses of the genome of the "living fossil" Latimeria chalumnae show that the coelacanth is the only known vertebrate that includes all eight globin types. Thus, Latimeria can also be considered as a "globin fossil". Analyses of gene synteny and phylogenetic reconstructions allow us to trace the evolution and the functional changes of the vertebrate globin family. Neuroglobin and globin X diverged from the other globin types before the separation of Protostomia and Deuterostomia. The cytoglobins, which are unlikely to be involved in O2 supply, form the earliest globin branch within the jawed vertebrates (Gnathostomata), but do not group with the agnathan hemoglobins, as it has been proposed before. There is strong evidence from phylogenetic reconstructions and gene synteny that the eye-specific globin E and muscle-specific myoglobin constitute a common clade, suggesting a similar role in intracellular O2 supply. Latimeria possesses two α- and two β-hemoglobin chains, of which one α-chain emerged prior to the divergence of Actinopterygii and Sarcopterygii, but has been retained only in the coelacanth. Notably, the embryonic hemoglobin α-chains of Gnathostomata derive from a common ancestor, while the embryonic β-chains - with the exception of a more complex pattern in the coelacanth and amphibians - display a clade-specific evolution. Globin Y is associated with the hemoglobin gene cluster, but its phylogenetic position is not resolved. Our data show an early divergence of distinct globin types in the vertebrate evolution before the emergence of tetrapods. The subsequent loss of globins in certain taxa may be associated with changes in the oxygen-dependent metabolism. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. Copyright © 2013 Elsevier B.V. All rights reserved.