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            "title": "The algorithmic origins of life",
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                    "firstName": "Sara Imari",
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            "abstractNote": "Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation—where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies—may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.",
            "publicationTitle": "Journal of The Royal Society Interface",
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            "date": "02/06/2013",
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            "title": "Systems biology: The reincarnation of systems theory applied in biology?",
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            "abstractNote": "With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.",
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            "title": "The mechanism of the inhibition of iron absorption by tea",
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                    "firstName": "R W",
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            "abstractNote": "Previous human studies have shown that drinking tea during meals significantly inhibits the absorption of both food iron and medicinal iron. This study provides evidence from experiments with rats that the tannins in the tea are responsible for the inhibition, probably by forming non-absorbable complexes with the iron within the intestinal lumen. The molar ratio of tannin: iron is dependent on the pH, being 1:1 at pH 2,0 2:1 at pH 5,5 and 3:1 at pH 8,0. Since tannins are present in many vegetable foods the formation of such complexes may be a factor in the poor availability for absorption of much food iron.",
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            "libraryCatalog": "NCBI PubMed",
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                    "tag": "Chemical Phenomena",
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                    "tag": "Depression, Chemical",
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                {
                    "tag": "Hydrogen-Ion Concentration",
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                {
                    "tag": "Intestinal Absorption",
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                },
                {
                    "tag": "Iron",
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                },
                {
                    "tag": "Molecular Weight",
                    "type": 1
                },
                {
                    "tag": "Tannins",
                    "type": 1
                },
                {
                    "tag": "Tea",
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            ],
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            "dateAdded": "2014-12-11T20:02:13Z",
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            "title": "The Eurasian Heartland: A continental perspective on Y-chromosome diversity",
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                    "creatorType": "author",
                    "firstName": "R. Spencer",
                    "lastName": "Wells"
                },
                {
                    "creatorType": "author",
                    "firstName": "Nadira",
                    "lastName": "Yuldasheva"
                },
                {
                    "creatorType": "author",
                    "firstName": "Ruslan",
                    "lastName": "Ruzibakiev"
                },
                {
                    "creatorType": "author",
                    "firstName": "Peter A.",
                    "lastName": "Underhill"
                },
                {
                    "creatorType": "author",
                    "firstName": "Irina",
                    "lastName": "Evseeva"
                },
                {
                    "creatorType": "author",
                    "firstName": "Jason",
                    "lastName": "Blue-Smith"
                },
                {
                    "creatorType": "author",
                    "firstName": "Li",
                    "lastName": "Jin"
                },
                {
                    "creatorType": "author",
                    "firstName": "Bing",
                    "lastName": "Su"
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                {
                    "creatorType": "author",
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                {
                    "creatorType": "author",
                    "firstName": "Karuppiah",
                    "lastName": "Balakrishnan"
                },
                {
                    "creatorType": "author",
                    "firstName": "Mark",
                    "lastName": "Read"
                },
                {
                    "creatorType": "author",
                    "firstName": "Nathaniel M.",
                    "lastName": "Pearson"
                },
                {
                    "creatorType": "author",
                    "firstName": "Tatiana",
                    "lastName": "Zerjal"
                },
                {
                    "creatorType": "author",
                    "firstName": "Matthew T.",
                    "lastName": "Webster"
                },
                {
                    "creatorType": "author",
                    "firstName": "Irakli",
                    "lastName": "Zholoshvili"
                },
                {
                    "creatorType": "author",
                    "firstName": "Elena",
                    "lastName": "Jamarjashvili"
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                    "firstName": "Spartak",
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                    "firstName": "Behrouz",
                    "lastName": "Nikbin"
                },
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                    "creatorType": "author",
                    "firstName": "Ashur",
                    "lastName": "Dostiev"
                },
                {
                    "creatorType": "author",
                    "firstName": "Ogonazar",
                    "lastName": "Aknazarov"
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                {
                    "creatorType": "author",
                    "firstName": "Pierre",
                    "lastName": "Zalloua"
                },
                {
                    "creatorType": "author",
                    "firstName": "Igor",
                    "lastName": "Tsoy"
                },
                {
                    "creatorType": "author",
                    "firstName": "Mikhail",
                    "lastName": "Kitaev"
                },
                {
                    "creatorType": "author",
                    "firstName": "Mirsaid",
                    "lastName": "Mirrakhimov"
                },
                {
                    "creatorType": "author",
                    "firstName": "Ashir",
                    "lastName": "Chariev"
                },
                {
                    "creatorType": "author",
                    "firstName": "Walter F.",
                    "lastName": "Bodmer"
                }
            ],
            "abstractNote": "The nonrecombining portion of the human Y chromosome has proven to be a valuable tool for the study of population history. The maintenance of extended haplotypes characteristic of particular geographic regions, despite extensive admixture, allows complex demographic events to be deconstructed. In this study we report the frequencies of 23 Y-chromosome biallelic polymorphism haplotypes in 1,935 men from 49 Eurasian populations, with a particular focus on Central Asia. These haplotypes reveal traces of historical migrations, and provide an insight into the earliest patterns of settlement of anatomically modern humans on the Eurasian continent. Central Asia is revealed to be an important reservoir of genetic diversity, and the source of at least three major waves of migration leading into Europe, the Americas, and India. The genetic results are interpreted in the context of Eurasian linguistic patterns.\n\ngets 3000-1000BC for entry to india, but not seen in Iran -- small migration?\n\nassumes 3000 for dom of horse - means of migration",
            "publicationTitle": "Proceedings of the National Academy of Sciences of the United States of America",
            "publisher": "",
            "place": "",
            "date": "2001-8-28",
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            "journalAbbreviation": "Proc Natl Acad Sci U S A",
            "DOI": "10.1073/pnas.171305098",
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            "shortTitle": "The Eurasian Heartland",
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            "creatorSummary": "Kates et al.",
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            "title": "Sustainability Science",
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                    "creatorType": "author",
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                    "creatorType": "author",
                    "firstName": "Robert",
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                    "creatorType": "author",
                    "firstName": "J. Michael",
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                {
                    "creatorType": "author",
                    "firstName": "Carlo C.",
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                    "firstName": "Ian",
                    "lastName": "Lowe"
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                {
                    "creatorType": "author",
                    "firstName": "James J.",
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                    "firstName": "Hans Joachim",
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                {
                    "creatorType": "author",
                    "firstName": "Bert",
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                {
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                    "firstName": "Nancy M.",
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                    "firstName": "Gilberto C.",
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            "abstractNote": "A high and sustainable quality of life is a central goal for humanity. Our current socio-ecological regime and its set of interconnected worldviews, institutions, and technologies all support the goal of unlimited growth of material production and consumption as a proxy for quality of life. However, abundant evidence shows that, beyond a certain threshold, further material growth no longer significantly contributes to improvement in quality of life. Not only does further material growth not meet humanity's central goal, there is mounting evidence that it creates significant roadblocks to sustainability through increasing resource constraints (i.e., peak oil, water limitations) and sink constraints (i.e., climate disruption). Overcoming these roadblocks and creating a sustainable and desirable future will require an integrated, systems level redesign of our socio-ecological regime focused explicitly and directly on the goal of sustainable quality of life rather than the proxy of unlimited material growth. This transition, like all cultural transitions, will occur through an evolutionary process, but one that we, to a certain extent, can control and direct. We suggest an integrated set of worldviews, institutions, and technologies to stimulate and seed this evolutionary redesign of the current socio-ecological regime to achieve global sustainability.",
            "publicationTitle": "Proceedings of the National Academy of Sciences",
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            "pages": "2483-2489",
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            "DOI": "10.1073/pnas.0812570106",
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            "PMID": "19240221",
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            "shortTitle": "Overcoming systemic roadblocks to sustainability",
            "language": "en",
            "libraryCatalog": "www.pnas.org",
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            "tags": [
                {
                    "tag": "Ecology",
                    "type": 1
                },
                {
                    "tag": "cultural adaptation",
                    "type": 1
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                {
                    "tag": "societal decline",
                    "type": 1
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            "creatorSummary": "Harris and Markl",
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            "title": "Keyhole limpet hemocyanin: molecular structure of a potent marine immunoactivator. A review",
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                    "firstName": "J R",
                    "lastName": "Harris"
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                {
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                    "firstName": "J",
                    "lastName": "Markl"
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            ],
            "abstractNote": "OBJECTIVES\n\nIn this short review we present a survey of the available biochemical and electron microscopic data on keyhole limpet hemocyanin (KLH).\n\n\nRESULTS\n\nThe biosynthesis of KLH and its biological role are discussed and the purification of the two isoforms of KLH (KLH1 and KLH2) presented in some detail. The determination of the molecular mass of KLH, its functional unit structure, carbohydrate content, immunological analysis and aspects of the molecular biology of KLH are all dealt with. Transmission electron microscopy (TEM) and crossed immunoelectrophoresis have played a significant part in the understanding of KLH structure. We present a summary of TEM studies on the native oligomers of KLH, the experimental manipulation of the different oligomeric states, immunological analysis and subunit reassociation.\n\n\nCONCLUSION\n\nThis fundamental structural information provides the scientific background upon which the understanding of the in vivo immunostimulatory function of KLH can be based.",
            "publicationTitle": "European urology",
            "publisher": "",
            "place": "",
            "date": "2000",
            "volume": "37 Suppl 3",
            "issue": "",
            "section": "",
            "partNumber": "",
            "partTitle": "",
            "pages": "24-33",
            "series": "",
            "seriesTitle": "",
            "seriesText": "",
            "journalAbbreviation": "Eur. Urol.",
            "DOI": "52389",
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            "url": "",
            "accessDate": "",
            "PMID": "10828684",
            "PMCID": "",
            "ISSN": "",
            "archive": "",
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            "shortTitle": "Keyhole limpet hemocyanin",
            "language": "",
            "libraryCatalog": "NCBI PubMed",
            "callNumber": "",
            "rights": "",
            "extra": "",
            "tags": [
                {
                    "tag": "Adjuvants, Immunologic",
                    "type": 1
                },
                {
                    "tag": "Animals",
                    "type": 1
                },
                {
                    "tag": "Carbohydrates",
                    "type": 1
                },
                {
                    "tag": "Hemocyanin",
                    "type": 1
                },
                {
                    "tag": "Microscopy, Electron",
                    "type": 1
                },
                {
                    "tag": "Models, Chemical",
                    "type": 1
                },
                {
                    "tag": "Molecular Biology",
                    "type": 1
                },
                {
                    "tag": "Molecular Weight",
                    "type": 1
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                {
                    "tag": "Mollusca",
                    "type": 1
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                {
                    "tag": "Protein Structure, Quaternary",
                    "type": 1
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            "creatorSummary": "Harris et al.",
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        "data": {
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            "version": 6,
            "itemType": "journalArticle",
            "title": "Keyhole limpet hemocyanin (KLH), I: Reassociation from Immucothel followed by separation of KLH1 and KLH2",
            "creators": [
                {
                    "creatorType": "author",
                    "firstName": "J R",
                    "lastName": "Harris"
                },
                {
                    "creatorType": "author",
                    "firstName": "W",
                    "lastName": "Gebauer"
                },
                {
                    "creatorType": "author",
                    "firstName": "F U",
                    "lastName": "Guderian"
                },
                {
                    "creatorType": "author",
                    "firstName": "J",
                    "lastName": "Markl"
                }
            ],
            "abstractNote": "Studies of keyhole limpet hemocyanin (KLH) normally require purification of functional complexes directly from living animals. An alternative procedure is described wherein a commercial preparation of KLH which is fully dissociated into its subunits (Immucothel, biosyn Arzneimittel GmbH) is reassociated in the presence of a high concentration of calcium and magnesium. The reassociation products, when observed by electron microscopy, consist of didecamers, multidecamers and flexible tubules of varying length. The two forms of KLH described previously and designated KLH1 and KLH2, are present in the reassociated mixture as homo-oligomers/polymers and can be separated by selective dissociation of the KLH2 by treatment with 1% ammonium molybdate-0.2% PEG at pH 5.7, followed by gel filtration chromatography in this solution. In addition to discrete elution peaks containing didecameric KLH1 and dissociated subunits of KLH2, a leading peak contains a tubular/polymeric form of KLH1, not previously described. Under negative staining in conditions designed specifically for the creation of 2-dimensional crystals on mica (the negative staining-carbon film procedure), this tubular form of KLH1 can be transformed into a larger diameter multidecameric form, again not previously described for KLH1. The purified KLH2 peak is indistinguishable from subunit material prepared from living animals. This, Immucothel appears to provide a standardized source of subunits suitable for biochemical and structural studies on the two types of KLH.",
            "publicationTitle": "Micron (Oxford, England: 1993)",
            "publisher": "",
            "place": "",
            "date": "Feb 1997",
            "volume": "28",
            "issue": "1",
            "section": "",
            "partNumber": "",
            "partTitle": "",
            "pages": "31-41",
            "series": "",
            "seriesTitle": "",
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            "journalAbbreviation": "Micron",
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            "accessDate": "",
            "PMID": "9232834",
            "PMCID": "",
            "ISSN": "0968-4328",
            "archive": "",
            "archiveLocation": "",
            "shortTitle": "Keyhole limpet hemocyanin (KLH), I",
            "language": "",
            "libraryCatalog": "NCBI PubMed",
            "callNumber": "",
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            "tags": [
                {
                    "tag": "Animals",
                    "type": 1
                },
                {
                    "tag": "Chromatography, Gel",
                    "type": 1
                },
                {
                    "tag": "Crystallization",
                    "type": 1
                },
                {
                    "tag": "Hemocyanin",
                    "type": 1
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                {
                    "tag": "Indicators and Reagents",
                    "type": 1
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                {
                    "tag": "Macromolecular Substances",
                    "type": 1
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                {
                    "tag": "Microscopy, Electron",
                    "type": 1
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                    "tag": "Mollusca",
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        "data": {
            "key": "GX9V7Z3H",
            "version": 6,
            "itemType": "journalArticle",
            "title": "Keyhole limpet hemocyanin (KLH), II: Characteristic reassociation properties of purified KLH1 and KLH2",
            "creators": [
                {
                    "creatorType": "author",
                    "firstName": "J R",
                    "lastName": "Harris"
                },
                {
                    "creatorType": "author",
                    "firstName": "W",
                    "lastName": "Gebauer"
                },
                {
                    "creatorType": "author",
                    "firstName": "S M",
                    "lastName": "Söhngen"
                },
                {
                    "creatorType": "author",
                    "firstName": "M V",
                    "lastName": "Nermut"
                },
                {
                    "creatorType": "author",
                    "firstName": "J",
                    "lastName": "Markl"
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            ],
            "abstractNote": "Subunits of the two types of keyhole limpet hemocyanin (KLH1 and KLH2), purified by gel filtration chromatography and preparative polyacrylamide gel electrophoresis from Immucothel, have been used for macromolecular reassociation studies. In-vitro reassociation has been achieved with a standardized system using a Tris-saline stabilizing buffer at pH 7.4 containing 100 mM calcium and magnesium chloride at 4 degrees C. The relatively slow progress of reassociation has been monitored and the varying oligomeric forms of KLH1 and KLH2 produced have been studied by transmission electron microscopy, using specimens negatively stained with 5% ammonium molybdate containing 1% trehalose. Specimens have also been prepared by platinum-carbon shadowing, following freeze-cleavage. The two hemocyanins reassociate to produce characteristic oligomeric and polymeric forms. Subunits of purified KLH1 reassociate to produce a small number of didecamers, short multidecamers (ca 33 nm diameter) and much larger quantity of a ca 25 nm diameter flexible/undulatory tubular form of varying length. These tubules exhibit characteristic oblique features, indicative of an 'open' helical structure which appears to be a loosly or incompletely annealed twisted ribbon of subunits. After a period of days the tubules aggregate in parallel to produce large paracrystalline bundles, which do not have a tendency to associate end-to-end. Following transfer of this reassociated KLH1 to low calcium magnesium stabilizing buffer, the tubular bundles are unstable; they slowly break down into shorter lengths, fragments, subunit groups and individual subunits, which subsequently regenerate decamers, didecamers, and some multidecamers. Subunits of purified KLH2 reassociate to produce ca 25 nm diameter 'closed' tubules, which do not exhibit the oblique 'open' features shown by the KLH1 tubules; however, the ends of the these 'closed' tubules are often oblique. In addition to the tubular form, KLH2 reassociation also generates a somewhat small proportion of ca 33 nm diameter multidecamers, often containing many decamers and more than one 'nucleating' didecamer. On transfer to low calcium magnesium stabilizing buffer the KLH2 tubules are remarkably stable, but the number of multidecamers slowly increases with time. There is a significant structural difference between the short KLH1 multidecamers (only detected following in-vitro reassociation) and those of KLH2 quite apart from their length. Study of the metal shadowed specimens confirmed the difference between the KLH1 and KLH2 tubular forms, with relatively smooth helical surface ridges and a rougher internal surface, indicating internalization of subunit domains that are not required for the construction of the tubular wall, in accord with current understanding of the subunit organization within the native molecules.",
            "publicationTitle": "Micron (Oxford, England: 1993)",
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            "date": "Feb 1997",
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            "shortTitle": "Keyhole limpet hemocyanin (KLH), II",
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            "tags": [
                {
                    "tag": "Calcium Chloride",
                    "type": 1
                },
                {
                    "tag": "Crystallization",
                    "type": 1
                },
                {
                    "tag": "Electrophoresis, Polyacrylamide Gel",
                    "type": 1
                },
                {
                    "tag": "Freezing",
                    "type": 1
                },
                {
                    "tag": "Hemocyanin",
                    "type": 1
                },
                {
                    "tag": "Indicators and Reagents",
                    "type": 1
                },
                {
                    "tag": "Macromolecular Substances",
                    "type": 1
                },
                {
                    "tag": "Magnesium Chloride",
                    "type": 1
                },
                {
                    "tag": "Molybdenum",
                    "type": 1
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                    "firstName": "T.",
                    "lastName": "Sitalaximi"
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                    "firstName": "Sonali",
                    "lastName": "Gaikwad"
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                    "firstName": "R.",
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                    "firstName": "Phillip",
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                    "firstName": "Toomas",
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                    "firstName": "Richard",
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                    "firstName": "V. K.",
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                    "lastName": "Keller"
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            "abstractNote": "In order to investigate capillary physiology, a glass micropipette system was developed that allowed in situ perfusion of microvessels as well as rapid changes of perfusion solutions. Theta tube (WPI, Inc.; 1.5-mm o.d. glass stock capillary tubing which is divided into two hemicylindrical sides by a central glass septum) was pulled to a smaller diameter of approx 300-600 microns and inserted into the shank of a sharpened cannulating micropipette tip constructed from large-bore glass stock (1.6 mm i.d.). The resulting dead volume between the end of the Theta supply tube and the tip of the outer cannulating tip was approximately 90 nl. The perfusate was driven in a circuit from a pressurized feed reservoir down one side of the Theta supply tube pipette and back through the second side into a reservoir maintained at a lower pressure. The pressure gradient between the two reservoirs established a high-volume flow rate and subsequently a short perfusate transit time from the feed to the collection reservoir. The average pressure in the two reservoirs determined the pressure which drove the perfusate from the cannulating tip. At normal pressures and flows, the time required to change perfusion fluid composition at the pipette tip was less than 1 min, and discharge hematocrit of a red blood cell suspension was indistinguishable from the hematocrit measured in the feed reservoir.(ABSTRACT TRUNCATED AT 250 WORDS)",
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            "date": "Mar 1993",
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                }
            ],
            "abstractNote": "Ecological memory (EM) is defined as the capability of the past states or experiences of a community to influence the present or future ecological responses of the community. As a relatively new concept, EM has received considerable attention in the study of ecosystem structure and function, such as community succession, ecological restoration, biological invasion, and natural resource management. This review summarized the definition, components, and categories of EM, and discussed the possible mechanisms and affecting factors of EM. Also, the potential applications of EM were proposed, in order to further understand the mechanisms of community succession and to guide ecological restoration.",
            "publicationTitle": "Ying yong sheng tai xue bao = The journal of applied ecology / Zhongguo sheng tai xue xue hui, Zhongguo ke xue yuan Shenyang ying yong sheng tai yan jiu suo zhu ban",
            "publisher": "",
            "place": "",
            "date": "Mar 2011",
            "volume": "22",
            "issue": "3",
            "section": "",
            "partNumber": "",
            "partTitle": "",
            "pages": "549-555",
            "series": "",
            "seriesTitle": "",
            "seriesText": "",
            "journalAbbreviation": "Ying Yong Sheng Tai Xue Bao",
            "DOI": "",
            "citationKey": "",
            "url": "",
            "accessDate": "",
            "PMID": "21657006",
            "PMCID": "",
            "ISSN": "1001-9332",
            "archive": "",
            "archiveLocation": "",
            "shortTitle": "[Ecological memory and its potential applications in ecology",
            "language": "",
            "libraryCatalog": "NCBI PubMed",
            "callNumber": "",
            "rights": "",
            "extra": "",
            "tags": [
                {
                    "tag": "1"
                },
                {
                    "tag": "Conservation of Natural Resources",
                    "type": 1
                },
                {
                    "tag": "Ecology",
                    "type": 1
                },
                {
                    "tag": "Ecosystem",
                    "type": 1
                },
                {
                    "tag": "Geography",
                    "type": 1
                }
            ],
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            "relations": {},
            "dateAdded": "2014-12-11T20:02:13Z",
            "dateModified": "2014-12-11T20:02:13Z"
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