scholarly journals Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale

2021 ◽  
Author(s):  
Rachel E. Szabo ◽  
Sammy Pontrelli ◽  
Jacopo Grilli ◽  
Julia A. Schwartzman ◽  
Shaul Pollak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Natural Populations ◽  
Natural Environments ◽  
Biological Interactions ◽  
Ecological Processes ◽  
Shotgun Metagenomics ◽  
Wide Range ◽  
Resource Patches ◽  
The Impact

In many natural environments, microorganisms self-assemble around heterogeneously distributed resource patches. The growth and collapse of populations on resource patches can unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of biological interactions and nutrient fluxes. Despite the potential importance of patch-level dynamics for the large-scale evolution and function of microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we addressed this challenge in the context of microbially-mediated degradation of particulate organic matter by characterizing the natural marine communities that assembled on over one thousand individual microscale chitin particles. Through shotgun metagenomics, we found significant variation in microscale community composition despite the similarity in initial species pools across replicates. Strikingly, a subset of particles was highly populated by rare chitin-degrading strains; we hypothesized that their conditional success reflected the impact of stochastic colonization and growth on community assembly. In contrast to the conserved functional structures that emerge in ecosystems at larger scales, this taxonomic variability translated to a wide range of predicted chitinolytic abilities and growth returns at the level of individual particles. We found that predation by temperate bacteriophages, especially of degrader strains, was a significant contributor to the variability in the bacterial compositions and yields observed across communities. Our study suggests that initial stochasticity in assembly states at the microscale, amplified through biotic interactions, may have significant consequences for the diversity and functionality of microbial communities at larger scales.

scholarly journals Stability of microbiota in vineyard soils across consecutive years.

2021 ◽  
Author(s):  
Alessandro Cestaro ◽  
emanuela coller ◽  
Davide Albanese ◽  
erika stefani ◽  
Massimo Pindo ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Geographic Origin ◽  
Soil Microbial Communities ◽  
Geographical Location ◽  
Taxonomic Structure ◽  
Ecological Processes ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
The Impact

Agricultural soils harbor rich and diverse microbial communities that have a deep influence on soil properties and productivity. Large scale studies have shown the impact of environmental parameters like climate or chemical composition on the distribution of bacterial and fungal species. Comparatively, little data exists documenting how soil microbial communities change between different years. Quantifying the temporal stability of soil microbial communities will allow us to better understand the relevance of the differences between environments and their impact on ecological processes on the global and local scale. We characterized the bacterial and fungal components of the soil microbiota in ten vineyards in two consecutive years. Despite differences of species richness and diversity between the two years, we found a general stability of the taxonomic structure of the soil microbiota. Temporal differences were smaller than differences due to geographical location, vineyard land management or differences between sampling sites within the same vineyard. Using machine learning, we demonstrated that each site was characterized by a distinctive microbiota, and we identified a reduced set of indicator species that could classify samples according to their geographic origin across different years with high accuracy.

scholarly journals Introduction. Antarctic ecology from genes to ecosystems: the impact of climate change and the importance of scale

2006 ◽  
Vol 362 (1477) ◽  
pp. 5-9 ◽  
Author(s):  
Andrew Clarke ◽  
Nadine M Johnston ◽  
Eugene J Murphy ◽  
Alex D Rogers
Keyword(s):  
Large Scale ◽  
Extreme Environment ◽  
Molecular Techniques ◽  
Remotely Sensed Data ◽  
Evolutionary Processes ◽  
Glacial Cycles ◽  
Ecological Processes ◽  
Wide Range ◽  
Genes To Ecosystems ◽  
The Impact

Antarctica offers a unique natural laboratory for undertaking fundamental research on the relationship between climate, evolutionary processes and molecular adaptation. The fragmentation of Gondwana and the development of wide-scale glaciation have resulted in major episodes of extinction and vicariance, as well as driving adaptation to an extreme environment. On shorter time-scales, glacial cycles have resulted in shifts in distribution, range fragmentation and allopatric speciation, and the Antarctic Peninsula is currently experiencing among the most rapid climatic warming on the planet. The recent revolution in molecular techniques has provided a suite of innovative and powerful tools to explore the consequences of these changes, and these are now providing novel insights into evolutionary and ecological processes in Antarctica. In addition, the increasing use of remotely sensed data is providing a large-scale view of the system that allows these processes to be set in a wider spatial context. In these two volumes, we collect a wide range of papers exploring these themes, concentrating on recent advances and emphasizing the importance of spatial and temporal scale in understanding ecological and evolutionary processes in Antarctica.

scholarly journals OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data

2021 ◽  
Author(s):  
Theresa A Harbig ◽  
Sabrina Nusrat ◽  
Tali Mazor ◽  
Qianwen Wang ◽  
Alexander Thomson ◽  
...  
Keyword(s):  
Longitudinal Data ◽  
Large Scale ◽  
Cancer Genomics ◽  
Temporal Patterns ◽  
Molecular Data ◽  
Liquid Biopsies ◽  
Sequencing Technologies ◽  
Molecular Features ◽  
Wide Range ◽  
The Impact

Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, e.g. emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. OncoThreads is freely available at http://oncothreads.gehlenborglab.org and implemented in Javascript using the cBioPortal web API as a backend.

Ivan Kavaleridze`s dramaturgy on the Sumy stage

2021 ◽  
Author(s):  
D.V. Budianskyi
Keyword(s):  
Large Scale ◽  
Musical Comedy ◽  
Historical Figures ◽  
Wide Range ◽  
Socialist Realist ◽  
History Of ◽  
Characteristic Features ◽  
Old Men ◽  
The Impact ◽  
First Time

The characteristic features of I. Kavaleridze’s drama is considered in the article. It is noted that there are signs of the artist’s individuality, attraction to expressionist forms, artistic techniques characteristic for the art of sculpture: symbolism, monumentality, hyperbole. I. Kavaleridze was well versed in the drama laws, understood the specifics of the stage events construction, had a large arsenal of literary means, thanks to which the characters’ monologues and dialogues were extremely expressive and colorful. In his work, he implemented original solutions that were ahead of time. Therefore, many of the artist’s ideas and achievements received due recognition only after his death. I. Kavaleridze’s creative heritage covers a wide range of both purely artistic and general philosophical problems. Among them the formation of the era of modernism and its features in the Ukrainian art of the early XX century, the impact of revolutionary ideas on the work of the 1920s, the role of spiritual leaders of the Ukrainian people T. Shevchenko and G. Skovoroda in the formation of national consciousness, political and ideological pressure on figurative art language and the formation of a socialist-realist canon, etc. The analysis of the productions of I. Kavalerizde’s plays “The First Furrow” and “Gregory and Paraskeva” on the stage of the Mykhailo Shchepkin Sumy Theater of Drama and Musical Comedy in 1970-1972. The article notes that these plays were staged in Sumy for the first time in the history of Ukrainian theater. The premiere of “The First Furrow” (the play was called “Old Men”) took place on March 19, 1970. The figure of the national genius Hryhoriy Skov oroda was als o embodied for the first time on t he stage in Sumy in th e play “Hryhoriy and Paraskeva”. It premiered on October 21, 1972. I. Rybchynsky, Honored Artist of the USSR, performed the production. Creating generalized historical outlines of people’s life, features of life at that time, depicting psychological portraits of people in various, sometimes-dramatic collisions, in the productions of I. Kavaleridze’s plays on the Sumy stage the emphasis was on universal values such as virtue, love. The main character was the Ukrainian people, who nurtured such large-scale historical figures, gave them strength and wisdom for great achievements. Based on publications in periodicals of that time, memoirs of Ukrainian directors, the peculiarities of the director’s interpretation, stenographic and musical design of these plays on the Sumy stage are considered. Considerable attention is paid to the analysis of acting works in I. Kavaleridze’s plays. In particular, the peculiarities of the actor’s embodiment of the image of the national genius Hryhoriy Skovoroda on the stage are presented. It is noted that I. Kavaleridze’s plays, created in a difficult political, social and ideological context, are rightly considered to be highly artistic works of Ukrainian drama. Their staging was carried out on various theatrical stages, including Mykhailo Shchepkin Sumy Theater of Drama and Musical Comedy is an important page of national theatrical art.

scholarly journals Economics of the disintegration of the Greenland ice sheet

2019 ◽  
Vol 116 (25) ◽  
pp. 12261-12269 ◽  
Author(s):  
William Nordhaus
Keyword(s):  
Climate Change ◽  
Large Scale ◽  
Social Cost ◽  
Climate Models ◽  
Ice Sheet ◽  
Greenland Ice Sheet ◽  
Reduced Form ◽  
Small Contribution ◽  
Wide Range ◽  
The Impact

Concerns about the impact on large-scale earth systems have taken center stage in the scientific and economic analysis of climate change. The present study analyzes the economic impact of a potential disintegration of the Greenland ice sheet (GIS). The study introduces an approach that combines long-run economic growth models, climate models, and reduced-form GIS models. The study demonstrates that social cost–benefit analysis and damage-limiting strategies can be usefully extended to illuminate issues with major long-term consequences, as well as concerns such as potential tipping points, irreversibility, and hysteresis. A key finding is that, under a wide range of assumptions, the risk of GIS disintegration makes a small contribution to the optimal stringency of current policy or to the overall social cost of climate change. It finds that the cost of GIS disintegration adds less than 5% to the social cost of carbon (SCC) under alternative discount rates and estimates of the GIS dynamics.

scholarly journals InSAR Greece with Parallelized Persistent Scatterer Interferometry: A National Ground Motion Service for Big Copernicus Sentinel-1 Data

2020 ◽  
Vol 12 (19) ◽  
pp. 3207
Author(s):  
Ioannis Papoutsis ◽  
Charalampos Kontoes ◽  
Stavroula Alatza ◽  
Alexis Apostolakis ◽  
Constantinos Loupasakis
Keyword(s):  
Time Series ◽  
Ground Motion ◽  
Large Scale ◽  
Persistent Scatterer Interferometry ◽  
Persistent Scatterers ◽  
Processing Chain ◽  
Persistent Scatterer ◽  
Basin Scale ◽  
Wide Range ◽  
The Impact

Advances in synthetic aperture radar (SAR) interferometry have enabled the seamless monitoring of the Earth’s crust deformation. The dense archive of the Sentinel-1 Copernicus mission provides unprecedented spatial and temporal coverage; however, time-series analysis of such big data volumes requires high computational efficiency. We present a parallelized-PSI (P-PSI), a novel, parallelized, and end-to-end processing chain for the fully automated assessment of line-of-sight ground velocities through persistent scatterer interferometry (PSI), tailored to scale to the vast multitemporal archive of Sentinel-1 data. P-PSI is designed to transparently access different and complementary Sentinel-1 repositories, and download the appropriate datasets for PSI. To make it efficient for large-scale applications, we re-engineered and parallelized interferogram creation and multitemporal interferometric processing, and introduced distributed implementations to best use computing cores and provide resourceful storage management. We propose a new algorithm to further enhance the processing efficiency, which establishes a non-uniform patch grid considering land use, based on the expected number of persistent scatterers. P-PSI achieves an overall speed-up by a factor of five for a full Sentinel-1 frame for processing in a 20-core server. The processing chain is tested on a large-scale project to calculate and monitor deformation patterns over the entire extent of the Greek territory—our own Interferometric SAR (InSAR) Greece project. Time-series InSAR analysis was performed on volumes of about 12 TB input data corresponding to more than 760 Single Look Complex Sentinel-1A and B images mostly covering mainland Greece in the period of 2015–2019. InSAR Greece provides detailed ground motion information on more than 12 million distinct locations, providing completely new insights into the impact of geophysical and anthropogenic activities at this geographic scale. This new information is critical to enhancing our understanding of the underlying mechanisms, providing valuable input into risk assessment models. We showcase this through the identification of various characteristic geohazard locations in Greece and discuss their criticality. The selected geohazard locations, among a thousand, cover a wide range of catastrophic events including landslides, land subsidence, and structural failures of various scales, ranging from a few hundredths of square meters up to the basin scale. The study enriches the large catalog of geophysical related phenomena maintained by the GeObservatory portal of the Center of Earth Observation Research and Satellite Remote Sensing BEYOND of the National Observatory of Athens for the opening of new knowledge to the wider scientific community.

scholarly journals Activity-dependent myelination: A glial mechanism of oscillatory self-organization in large-scale brain networks

2020 ◽  
Vol 117 (24) ◽  
pp. 13227-13237 ◽  
Author(s):  
Rabiya Noori ◽  
Daniel Park ◽  
John D. Griffiths ◽  
Sonya Bells ◽  
Paul W. Frankland ◽  
...  
Keyword(s):  
White Matter ◽  
Large Scale ◽  
Phase Synchronization ◽  
Brain Networks ◽  
Self Organization ◽  
Conduction Delay ◽  
Neural Communication ◽  
Wide Range ◽  
The Impact ◽  
Activity Dependent

Communication and oscillatory synchrony between distributed neural populations are believed to play a key role in multiple cognitive and neural functions. These interactions are mediated by long-range myelinated axonal fiber bundles, collectively termed as white matter. While traditionally considered to be static after development, white matter properties have been shown to change in an activity-dependent way through learning and behavior—a phenomenon known as white matter plasticity. In the central nervous system, this plasticity stems from oligodendroglia, which form myelin sheaths to regulate the conduction of nerve impulses across the brain, hence critically impacting neural communication. We here shift the focus from neural to glial contribution to brain synchronization and examine the impact of adaptive, activity-dependent changes in conduction velocity on the large-scale phase synchronization of neural oscillators. Using a network model based on primate large-scale white matter neuroanatomy, our computational and mathematical results show that such plasticity endows white matter with self-organizing properties, where conduction delay statistics are autonomously adjusted to ensure efficient neural communication. Our analysis shows that this mechanism stabilizes oscillatory neural activity across a wide range of connectivity gain and frequency bands, making phase-locked states more resilient to damage as reflected by diffuse decreases in connectivity. Critically, our work suggests that adaptive myelination may be a mechanism that enables brain networks with a means of temporal self-organization, resilience, and homeostasis.

Motion Simulation Experiments for Driver Behavior and Road Vehicle Dynamics

2011 ◽  
Vol 11 (4) ◽  
Author(s):  
Kemper Lewis ◽  
Kevin Hulme ◽  
Edward Kasprzak ◽  
Deborah Moore-Russo ◽  
Gregory Fabiano
Keyword(s):  
Vehicle Dynamics ◽  
Large Scale ◽  
Driving Simulation ◽  
Vehicle Design ◽  
Simulation Environment ◽  
Learning Mechanisms ◽  
Road Vehicle ◽  
Wide Range ◽  
Traffic Systems ◽  
The Impact

This paper discusses the design and development of a motion-based driving simulation and its integration into driving simulation research. The integration of the simulation environment into a road vehicle dynamics curriculum is also presented. The simulation environment provides an immersive experience to conduct a wide range of research on driving behavior, vehicle design and intelligent traffic systems. From an education perspective, the environment is designed to promote hands-on student participation in real-world engineering experiences that enhance conventional learning mechanisms for road vehicle dynamics and engineering systems analysis. The paper assesses the impact of the environment on student learning objectives in an upper level vehicle dynamics course and presents results from research involving teenage drivers. The paper presents an integrated framework for the use of real-time simulation and large-scale visualization to both study driving behaviors and to discover the impact that design decisions have on vehicle design using a realistic simulated driving interface.

Interactions between human behaviour and the built environment in terms of facility management

Facilities ◽  
2018 ◽  
Vol 36 (1/2) ◽  
pp. 2-12 ◽  
Author(s):  
Darja Kobal Grum
Keyword(s):  
Built Environment ◽  
Low Income ◽  
Well Being ◽  
Human Behaviour ◽  
Natural Environments ◽  
Psychological Well Being ◽  
Content Type ◽  
Sustainable Solutions ◽  
Wide Range ◽  
The Impact

Purpose In comparison with the relations between the human and natural environments that have been the central focus of environmental psychology for many years, the interactions between the psychological processes underlying human behaviour and the built environment have only recently regained the interest of researchers. In this paper, the author first discusses the reasons for the slower development of human – built environment relations. Afterwards, the author systematically examines the impact that the research of environmental stress, namely, poor housing and poor neighbourhood quality, had on the contemporary understanding of human – built environment relations. Design/methodology/approach The author focuses on social, biophilic and evidence-based design. The author proposes deeper psychological engagement in correlation with human behaviour, psychological well-being and society. The author highlights the inclusion of psychologists in interdisciplinary research teams addressing the development of sustainable solutions to the issues of residential environments. Findings It has been shown that substandard house quality, high noise, lack of natural light in houses, poorer physical quality of urban neighbourhoods, living in a low-income neighbourhood, etc. are linked to elevated physiological and psychological stress. Despite this evidence, there is still a gap between building designers and building users in modern industrialised societies, which could deepen tenants’ dissatisfaction due to specific behavioural needs and consequently lower their psychological well-being and health risk behaviour. Research limitations/implications These are potential risks of error arising from the use of assumptions, limited samples size and data from the secondary resources. Originality/value The major contributions of this paper are as follows. If the environment is understood as a dynamic, constantly changing and complex system of a wide range of players, the author can discern in this environment a dynamic that is otherwise characteristic of emotional dynamics. Expressed participants’ high satisfaction with residential status does not necessarily generate high expectations regarding real estate factors.

Approximate weighted matching on emerging manycore and multithreaded architectures

2012 ◽  
Vol 26 (4) ◽  
pp. 413-430 ◽  
Author(s):  
Mahantesh Halappanavar ◽  
John Feo ◽  
Oreste Villa ◽  
Antonino Tumeo ◽  
Alex Pothen
Keyword(s):  
Approximation Algorithms ◽  
Large Scale ◽  
Scientific Computing ◽  
Graph Matching ◽  
Combinatorial Problem ◽  
Fine Tuning ◽  
Matching Problem ◽  
Weighted Matching ◽  
Wide Range ◽  
The Impact

Graph matching is a prototypical combinatorial problem with many applications in high-performance scientific computing. Optimal algorithms for computing matchings are challenging to parallelize. Approximation algorithms are amenable to parallelization and are therefore important to compute matchings for large-scale problems. Approximation algorithms also generate nearly optimal solutions that are sufficient for many applications. In this paper we present multithreaded algorithms for computing half-approximate weighted matching on state-of-the-art multicore (Intel Nehalem and AMD Magny-Cours), manycore (Nvidia Tesla and Nvidia Fermi), and massively multithreaded (Cray XMT) platforms. We provide two implementations: the first uses shared work queues and is suited for all platforms; and the second implementation, based on dataflow principles, exploits special features available on the Cray XMT. Using a carefully chosen dataset that exhibits characteristics from a wide range of applications, we show scalable performance across different platforms. In particular, for one instance of the input, an R-MAT graph (RMAT-G), we show speedups of about [Formula: see text] on [Formula: see text] cores of an AMD Magny-Cours, [Formula: see text] on [Formula: see text] cores of Intel Nehalem, [Formula: see text] on Nvidia Tesla and [Formula: see text] on Nvidia Fermi relative to one core of Intel Nehalem, and [Formula: see text] on [Formula: see text] processors of Cray XMT. We demonstrate strong as well as weak scaling for graphs with up to a billion edges using up to 12,800 threads. We avoid excessive fine-tuning for each platform and retain the basic structure of the algorithm uniformly across platforms. An exception is the dataflow algorithm designed specifically for the Cray XMT. To the best of the authors' knowledge, this is the first such large-scale study of the half-approximate weighted matching problem on multithreaded platforms. Driven by the critical enabling role of combinatorial algorithms such as matching in scientific computing and the emergence of informatics applications, there is a growing demand to support irregular computations on current and future computing platforms. In this context, we evaluate the capability of emerging multithreaded platforms to tolerate latency induced by irregular memory access patterns, and to support fine-grained parallelism via light-weight synchronization mechanisms. By contrasting the architectural features of these platforms against the Cray XMT, which is specifically designed to support irregular memory-intensive applications, we delineate the impact of these choices on performance.

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