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Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state
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Does an ‘iron gate’ carbon preservation mechanism exist in organic–rich wetlands?
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Investigation of the Ligand–Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry
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Preserving correlations between trajectories for efficient path sampling
Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective on Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this “noise guidance” synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.
Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in B acillus subtilis biofilms: Defective cells and preserve symmetry in Bacillus subtilis biofilms
Toxin-antitoxin modules are gene pairs encoding a toxin and its antitoxin, and are found on the chromosomes of many bacteria, including pathogens. This paper characterizes the specific contribution of the TxpA and YqcG toxins in elimination of defective cells from developing Bacillus subtilis biofilms. On nutrient limitation, defective cells accumulated in the biofilm breaking its symmetry. Deletion of the toxins resulted in accumulation of morphologically abnormal cells, and interfered with the proper development of the multicellular community. Dual physiological responses are of significance for TxpA and YqcG activation: nitrogen deprivation enhances the transcription of both TxpA and YqcG toxins, and simultaneously sensitizes the biofilm cells to their activity. Furthermore, we demonstrate that while both toxins when overexpressed affect the morphology of the developing biofilm, the toxin TxpA can act to lyse and dissolve pre-established B. subtilis biofilms.
Amendment to Programmatic Agreement among the U.S. Department of Energy, National Nuclear Security Administration, Los Alamos Field Office, the New Mexico State Historic Preservation Office and the Advisory Council on History Preservation Concerning Management of the Historic Properties of Los Alamos National Laboratory, Los Alamos, New Mexico (AGREEMENT)
The Field Office has a cultural resources program manager. The LANL Management and Operating Contractor has a staff of cultural resource specialists who meet the qualifications set forth in the Secretary of the Interior's Standards and Guidelines for Professional Qualifications (36 CFR Part 61), or work under the supervision of individuals who meet these qualifications. Any future Management and Operating Contractor will have a staff of Secretary of the Interior-qualified cultural resource specialists.
Towards Resilient Design of Leader-following Consensus with Attack Identification and Privacy Preservation Capabilities
This paper considers a leader-following consensus in the presence of unknown but bounded cyber-attacks. Specifically, we consider the following cyber-attack scenarios: (i) an attacker aims to destabilize the consensus dynamics by injecting exogenous signals to both the actuators of the followers and/or the communication network, (ii) an eavesdropper adversary aims to obtain information on the physical state of the agents. To this end, a novel resilient leader-following consensus algorithm based on a competitive interaction method is proposed. In addition, it is demonstrated that by appropriately choosing the information exchanged between the agents, the proposed control framework also enables the cooperative system to either distributively identify the compromised communication links in real-time or to protect the privacy of the physical state of the agents from the eavesdropper. Here, a numerical example is provided to illustrate the proposed resilient control algorithms.
Preservation of rat hearts in subfreezing temperature isochoric conditions to – 8 °C and 78 MPa
Highlights: • A novel method of low-temperature organ preservation is tested using rat hearts. • Isochoric systems allow ice-free preservation at temperatures well below freezing. • Conventional heart preservation employs on-ice storage in atmospheric conditions. • Histological quality is improved in hearts preserved in a −4 °C isochoric system. Isochoric (constant volume) preservation at subfreezing temperatures is being investigated as a novel method for preserving cells and organs. This study is a first initial effort to evaluate the efficacy of this method for heart preservation, and to provide a preliminary outline of appropriate preservation parameters. To establish a baseline for further studies, rat hearts were preserved in a University of Wisconsin (UW) intracellular solution for one hour under isochoric conditions at: 0 °C (atmospheric pressure - 0.1 MPa), - 4 °C (41 MPa), - 6 °C (60 MPa) and – 8 °C (78 MPa). The viability of the heart was evaluated using Langendorff perfusion and histological examination. The physiological performance of hearts preserved at – 4 °C (41 MPa) was comparable to that of a heart preserved on ice at atmospheric pressure, with no statistically significant difference in histological injury score. However, hearts preserved at −4 °C displayed substantially reduced interstitial edema compared to hearts preserved by conventional hypothermic preservation in UW on ice at atmospheric pressure, suggesting significant protection from increased vascular permeability following preservation. Hearts preserved at – 6 °C (60 MPa) suffered injury from cellular swelling and extensive edema, and at – 8 °C (78 MPa) hearts experienced significant morphological disruption. To the best of our knowledge, this is the first publication showing that a mammalian organ can survive low subfreezing temperatures without the use of a cryoprotective additive. Lowering the preservation temperature reduces metabolism and improves preservation quality, and these results suggest that improvements in preservation are possible at subzero temperatures with low to moderate pressures observed at −4 °C. Notably, tissue damage was observed at lower temperatures (−6 °C or below) accompanying further elevation of pressure associated with isochoric preservation that may prove detrimental. Therefore, subfreezing temperature isochoric preservation protocols should optimize, a combination of temperature and pressure that will minimize the negative effects of elevated pressure while retaining the beneficial effect of lower temperatures and reduced metabolism.
Preserving NASA Historic and Current Mission Data and Adding Value to These for Future Researchers
The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has been actively involved in many aspects of ensuring the long-term preservation of NASA earth science data and knowledge. This involves both the recovery and preservation of early NASA meteorological and other earth observation data, as well as preserving the more recent Earth Observation System (EOS) mission data sets which continue or have reached their end of lifetime. The GES DISC adds value to these preserved data by adding metadata and making the data available online to future researchers. The early NASA meteorological and earth observation data sets from the 1960s and 70s were originally archived on magnetic tapes, and visualizations of these data were preserved on 70-mm film. As these media have aged, their contents have been at risk of permanent loss. NASA has given the task of preserving these early data sets to the GES DISC and making these data sets easily available to the public. The data from these early missions are potentially useful to climate researchers as these are some of the only global measurements made at their time. These old data on magnetic tapes and film strips do not contain easily readable metadata, and so to add value the GES DISC has added digital metadata to them so that the data are searchable and findable. The GES DISC is also involved in preserving the data and knowledge from the EOS era missions. The GES DISC follows the guidelines developed for the preservation of data as specified in the NASA EOS Data and Information System (EOSDIS) Earth Science Data Preservation Content Specification (423-SPEC-001) document. To date, the GES DISC has consulted with the data science teams from the following missions: UARS, Earth Probe TOMS, Aura HIRDLS, and SORCE, in order to properly preserve their data and accompanying documentation. The GES DISC is also currently working with the EOS science teams from TRMM, AIRS, MLS, OMI and additional missions to ensure that the relevant documents and data sets are properly archived for future researchers. A standardized procedure for mission data preservation following 423-SPEC-001 makes preservation among the many NASA EOSDIS data centers uniform, so that these could be transitioned easily to a common EOSDIS preservation repository. This presentation will give an overview of the preservation and recovery of the old NASA historical data sets archived at the GES DISC, as well as the data and documentation preservation efforts of the EOS era missions.
Factors influencing organic carbon preservation in marine sediments
The organic matter that escapes decomposition is buried and preserved in marine sediments, with much debate as to whether the amount depends on bottom-water O2 concentration. One group argues that decomposition is more efficient with O2, and hence, organic carbon will be preferentially oxidized in its presence, and preserved in its absence. Another group argues that the kinetics of organic matter decomposition are similar in the presence and absence of O2, and there should be no influence of O2 on preservation. A compilation of carbon preservation shows that both groups are right, depending on the circumstances of deposition. At high rates of deposition, such as near continental margins, little difference in preservation is found with varying bottom-water O2. It is important that most carbon in these sediments decomposes by anaerobic pathways regardless of bottom-water O2. Hence, little influence of bottom-water O2 on preservation would, in fact, be expected. As sedimentation rate drops, sediments deposited under oxygenated bottom water become progressively more aerobic, while euxinic sediments remain anaerobic. Under these circumstances, the relative efficiencies of aerobic and anaerobic decomposition could affect preservation. Indeed, enhanced preservation is observed in low-O2 and euxinic environments. To explore in detail the factors contributing to this enhanced carbon preservation, aspects of the biochemistries of the aerobic and anaerobic process are reviewed. Other potential influences on preservation are also explored. Finally, a new model for organic carbon decomposition, the "pseudo-G" model, is developed. This model couples the degradation of refractory organic matter to the overall metabolic activity of the sediment, and has consequences for carbon preservation due to the mixing together of labile and refractory organic matter by bioturbation.
Towards a Standard for Provenance and Context for Preservation of Data for Earth System Science
Long-term data sets with data from many missions are needed to study trends and validate model results that are typical in Earth System Science research. Data and derived products originate from multiple missions (spaceborne, airborne and/or in situ) and from multiple organizations. During the missions as well as well past their termination, it is essential to preserve the data and products to support future studies. Key aspects of preservation are: preserving bits and ensuring data are uncorrupted, preserving understandability with appropriate documentation, and preserving reproducibility of science with appropriate documentation and other artifacts. Computer technology provides adequate standards to ensure that, with proper engineering, bits are preserved as hardware evolves. However, to ensure understandability and reproducibility, it is essential to plan ahead to preserve all the relevant data and information. There are currently no standards to identify the content that needs to be preserved, leading to non-uniformity in content and users not being sure of whether preserved content is comprehensive. Each project, program or agency can specify the items to be preserved as a part of its data management requirements. However, broader community consensus that cuts across organizational or national boundaries would be needed to ensure comprehensiveness, uniformity and long-term utility of archived data. The Federation of Earth Science Information Partners (ESIP), a diverse network of scientists, data stewards and technology developers, has a forum for ESIP members to collaborate on data preservation issues. During early 2011, members discussed the importance of developing a Provenance and Context Content Standard (PCCS) and developed an initial list of content items. This list is based on the outcome of a NASA and NOAA meeting held in 1998 under the auspices of the USGCRP, documentation requirements from NOAA and our experience with some of the NASA Earth science missions. The items are categorized into the following 8 high level categories: Preflight/Pre-Operations, Products (Data), Product Documentation, Mission Calibration, Product Software, Algorithm Input, Validation, Software Tools.
Towards a Preservation Content Standard for Earth Observation Data
Information from Earth observing missions (remote sensing with airborne and spaceborne instruments, and in situ measurements such as those from field campaigns) is proliferating in the world. Many agencies across the globe are generating important datasets by collecting measurements from instruments on board aircraft and spacecraft, globally and constantly. The data resulting from such measurements are a valuable resource that needs to be preserved for the benefit of future generations. These observations are the primary record of the Earths environment and therefore are the key to understanding how conditions in the future will compare to conditions today. Earth science observational data, derived products and models are used to answer key questions of global significance. In the near-term, as long as the missions data are being used actively for scientific research, it continues to be important to provide easy access to the data and services commensurate with current information technology. For the longer term, when the focus of the research community shifts toward new missions and observations, it is essential to preserve the previous mission data and associated information. This will enable a new user in the future to understand how the data were used for deriving information, knowledge and policy recommendations and to repeat the experiment to ascertain the validity and possible limitations of conclusions reached in the past and to provide confidence in long term trends that depended on data from multiple missions. Organizations that collect, process, and utilize Earth observation data today have a responsibility to ensure that the data and associated content continue to be preserved by them or are gathered and handed off to other organizations for preservation for the benefit of future generations. In order to ensure preservation of complete content necessary for understanding and reusing the data and derived digital products from todays missions, it is necessary to develop a specification of such preservation content. While there are existing standards that address archival and preservation in general, there are no existing international standards or specifications today to address what content should be preserved. The purpose of this paper is to outline briefly the existing standards that apply to preservation, describe a recent effort in getting an international standard in place for specifying preservation content for Earth observation data and derived digital data products and the remaining work needed to arrive at a standard.
A review of preservational variation of fossil inclusions in amber of different chemical groups
Fossils in amber are a particularly important and unique palaeobiological resource. Amber is best known for preserving exceptionally life-like fossils, including microscopic anatomical details, but this fidelity of preservation is an end-member of a wide spectrum of preservation quality. Many amber sites only preserve cuticle or hollow moulds, and most amber sites have no fossils at all. The taphonomic processes that control this range in preservation are essentially unknown. Here, we review the relationship between amber groups and fossil preservation, based on published data, to determine whether there is a correlation between resin type and aspects of preservation quality. We found that ambers of different chemistry demonstrated statistically significant differences in the preservational quality and the propensity of a site to contain fossils. This indicates that resin chemistry does influence preservational variation; however, there is also evidence that resin chemistry alone cannot explain all the variation. To effectively assess the impact of this (and other) variables on fossilisation in amber, and therefore biases in the amber fossil record, a more comprehensive sampling of bioinclusions in amber, coupled with rigorous taphonomic experimentation, is required.
Fossil preservation and the stratigraphic ranges of taxa
The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.
Developing a Standard for Earth Observation Data Preservation Content - A Path to Future Usability
For datasets to be usable, many pieces of information in addition to the data themselves are essential. During the active parts of the lifecycle of dataset generating projects, the needed information is usually accessible through individuals familiar with the various aspects of the projects. However, the utility of datasets tends to outlive the lives of projects, by several decades in many cases. Thus it is essential to capture all the relevant information about the datasets, data, metadata and associate knowledge that is sufficient to read, understand, interpret and reuse the datasets, while the projects are still active. The capture and preservation should be such that the data are usable when no consultation is available from the original project participants. Identification of specific categories of content through an international standard is beneficial to the user communities of the future, so that projects involving Earth observations and generating data products can consistently plan for preservation and future usability of the project outcomes. While there are existing standards that address archival and preservation in general, there are no existing international standards or specifications today to address what content should be preserved. The standard, ISO 19165-1, titled "Geographic Information - Preservation of digital data and metadata Part 1: Fundamentals" considers geographic information preservation in general. It acknowledges that "specific content items needed to preserve the full provenance and context of the data and associated metadata depend on the needs of the designated community and types of datasets (e.g., maps, remotely sensed data from satellites and airborne instruments, physical samples). Follow-up parts to this standard may be developed detailing content items appropriate to individual disciplines." NASA proposed an extension to this standard, titled "Geographic information -- Preservation of digital data and metadata -- Part 2: Content specifications for Earth observation data and derived digital products." The development of this extension is in progress with participation by an international team representing nine countries. The purpose of this paper is to introduce this standard and report on its status.
Second phase of the OECD NEA international initiative on the preservation of records, knowledge and memory across generations - 15616
The OECD/NEA initiative on the Preservation of Records, Knowledge and Memory across Generations (RK and M) constitutes an activity within the area of transfer of information about radioactive waste disposal projects for the benefit of future generations. Launched in 2011, the initiative has now entered Phase-II, which will run through to 2017. Building on results of Phase-I, which was dedicated to exploring issues of strategic relevance for the preservation of RK and M, Phase-II of the initiative will focus on developing an understanding of the interactions between the identified issues, while continuing to examine hitherto little aspects of the same issues. This corresponds to a systemic approach to RK and M preservation consisting in employing different means and methods to preserve RK and M, which are in a complementary but also redundant relationship to each other, and in situating and analysing activities in a wider context than radioactive waste management. The strategic issues for RK and M preservation are the use of archives, cultural heritage, the so-called Key Information File, transfer of responsibilities after closure, regulations governing RK and M preservation, markers and international mechanisms that could be adapted to foster RK and M preservation. The issues were discussed extensively at 'Constructing Memory - An International Conference and Debate', which was organised by the OECD/NEA with the support of Andra (French Radioactive Waste Management Organisation) and took place in September 2014 in Verdun, France. (authors)