1,066 research outputs found
Discourse or gimmick? Digital marginalia in online scholarship
Marginalia has been studied as discourse, as historical documentation and as evidence of reader response. As many academic texts are now available electronically, it seems a natural step to incorporate the interactive, social functions of the Web 2.0. Digital marginalia in an academic publishing context has been a largely unsuccessful venture to this date, yet there are several promising developments. Tools have emerged that enable readers annotate online texts in an approximation of paper-based marginalia, with the additional affordances of two- (or many-) way discourse, digital archiving, and the ability to hide the annotations. This article reviews the contemporary practices of digital marginalia, narrowing in to focus on digital marginalia as a form of academic discourse and peer review. I analyse several case studies of digital marginalia and discourse within this context, including Nature’s trial of open peer review, Wellcome Open Research, PLOS ONE and PubPeer’s systems, as well as my own experience using open peer review with Hypothes.is in a special ‘disrupted’ issue of the Journal of Media Practice. The article examines the relative success of these initiatives, attitudes toward open peer review and concludes with some promising developments for the future of digital marginalia and discourse in academic publishing
Prebiotic Homochirality as a Critical Phenomenon
The development of prebiotic homochirality on early-Earth or another
planetary platform may be viewed as a critical phenomenon. It is shown, in the
context of spatio-temporal polymerization reaction networks, that environmental
effects -- be them temperature surges or other external disruptions -- may
destroy any net chirality previously produced. In order to understand the
emergence of prebiotic homochirality it is important to model the coupling of
polymerization reaction networks to different planetary environments.Comment: 6 Pages, 1 Figure, In Press: Origins of Life and Evolution of
Biosphere
The origin of large molecules in primordial autocatalytic reaction networks
Large molecules such as proteins and nucleic acids are crucial for life, yet
their primordial origin remains a major puzzle. The production of large
molecules, as we know it today, requires good catalysts, and the only good
catalysts we know that can accomplish this task consist of large molecules.
Thus the origin of large molecules is a chicken and egg problem in chemistry.
Here we present a mechanism, based on autocatalytic sets (ACSs), that is a
possible solution to this problem. We discuss a mathematical model describing
the population dynamics of molecules in a stylized but prebiotically plausible
chemistry. Large molecules can be produced in this chemistry by the coalescing
of smaller ones, with the smallest molecules, the `food set', being buffered.
Some of the reactions can be catalyzed by molecules within the chemistry with
varying catalytic strengths. Normally the concentrations of large molecules in
such a scenario are very small, diminishing exponentially with their size.
ACSs, if present in the catalytic network, can focus the resources of the
system into a sparse set of molecules. ACSs can produce a bistability in the
population dynamics and, in particular, steady states wherein the ACS molecules
dominate the population. However to reach these steady states from initial
conditions that contain only the food set typically requires very large
catalytic strengths, growing exponentially with the size of the catalyst
molecule. We present a solution to this problem by studying `nested ACSs', a
structure in which a small ACS is connected to a larger one and reinforces it.
We show that when the network contains a cascade of nested ACSs with the
catalytic strengths of molecules increasing gradually with their size (e.g., as
a power law), a sparse subset of molecules including some very large molecules
can come to dominate the system.Comment: 49 pages, 17 figures including supporting informatio
One-Center Charge Transfer Transitions in Manganites
In frames of a rather conventional cluster approach, which combines the
crystal field and the ligand field models we have considered different charge
transfer (CT) states and O 2p-Mn 3d CT transitions in MnO octahedra.
The many-electron dipole transition matrix elements were calculated using the
Racah algebra for the cubic point group. Simple "local" approximation allowed
to calculate the relative intensity for all dipole-allowed and
CT transitions. We present a self-consistent description of
the CT bands in insulating stoichiometric LaMnO compound with the
only Mn valent state and idealized octahedral MnO centers
which allows to substantially correct the current interpretation of the optical
spectra. Our analysis shows the multi-band structure of the CT optical response
with the weak low-energy edge at 1.7 eV, associated with forbidden
transition and a series of the weak and strong
dipole-allowed high-energy transitions starting from 2.5 and 4.5 eV,
respectively, and extending up to nearly 11 eV. The most intensive features are
associated with two strong composite bands near eV and
eV, respectively, resulting from the superposition of the dipole-allowed
and CT transitions. These predictions are in good
agreement with experimental spectra. The experimental data point to a strong
overscreening of the crystal field parameter in the CT states of
MnO centers.Comment: 10 pages, 3 figure
Non-Enzymatic Decomposition of Collagen Fibers by a Biglycan Antibody and a Plausible Mechanism for Rheumatoid Arthritis
Rheumatoid arthritis (RA) is a systemic autoimmune inflammatory and destructive joint disorder that affects tens of millions of people worldwide. Normal healthy joints maintain a balance between the synthesis of extracellular matrix (ECM) molecules and the proteolytic degradation of damaged ones. In the case of RA, this balance is shifted toward matrix destruction due to increased production of cleavage enzymes and the presence of (autoimmune) immunoglobulins resulting from an inflammation induced immune response. Herein we demonstrate that a polyclonal antibody against the proteoglycan biglycan (BG) causes tissue destruction that may be analogous to that of RA affected tissues. The effect of the antibody is more potent than harsh chemical and/or enzymatic treatments designed to mimic arthritis-like fibril de-polymerization. In RA cases, the immune response to inflammation causes synovial fibroblasts, monocytes and macrophages to produce cytokines and secrete matrix remodeling enzymes, whereas B cells are stimulated to produce immunoglobulins. The specific antigen that causes the RA immune response has not yet been identified, although possible candidates have been proposed, including collagen types I and II, and proteoglycans (PG's) such as biglycan. We speculate that the initiation of RA associated tissue destruction in vivo may involve a similar non-enzymatic decomposition of collagen fibrils via the immunoglobulins themselves that we observe here ex vivo
Origin of magnetoelectric behavior in BiFeO
The magnetoelectric behavior of BiFeO has been explored on the basis of
accurate density functional calculations. The structural, electronic, magnetic,
and ferroelectric properties of BiFeO are predicted correctly without
including strong correlation effect in the calculation. Moreover, the
experimentally-observed elongation of cubic perovskite-like lattice along the
[111] direction is correctly reproduced. At high pressure we predicted a
pressure-induced structural transition and the total energy calculations at
expanded lattice show two lower energy ferroelectric phases, closer in energy
to the ground state phase. Band-structure calculations show that BiFeO will
be an insulator in A- and G-type antiferromagnetic phases and a metal in other
magnetic configurations. Chemical bonding in BiFeO has been analyzed using
various tools and electron localization function analysis shows that
stereochemically active lone-pair electrons at the Bi sites are responsible for
displacements of the Bi atoms from the centro-symmetric to the
noncentrosymmetric structure and hence the ferroelectricity. A large
ferroelectric polarization (88.7 C/cm) is predicted in accordance
with recent experimental findings. The net polarization is found to mainly (
98%) originate from Bi atoms. Moreover the large scatter in experimentally
reported polarization values is due to the large anisotropy in the spontaneous
polarization.Comment: 19 pages, 12 figures, 4 table
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The biomechanics of amnion rupture: an X-ray diffraction study
Pre-term birth is the leading cause of perinatal and neonatal mortality, 40% of which are attributed to the pre-term premature rupture of amnion. Rupture of amnion is thought to be associated with a corresponding decrease in the extracellular collagen content and/or increase in collagenase activity. However, there is very little information concerning the detailed organisation of fibrillar collagen in amnion and how this might influence rupture. Here we identify a loss of lattice like arrangement in collagen organisation from areas near to the rupture site, and present a 9% increase in fibril spacing and a 50% decrease in fibrillar organisation using quantitative measurements gained by transmission electron microscopy and the novel application of synchrotron X-ray diffraction. These data provide an accurate insight into the biomechanical process of amnion rupture and highlight X-ray diffraction as a new and powerful tool in our understanding of this process
Homochiral growth through enantiomeric cross-inhibition
The stability and conservation properties of a recently proposed
polymerization model are studied. The achiral (racemic) solution is linearly
unstable once the relevant control parameter (here the fidelity of the
catalyst) exceeds a critical value. The growth rate is calculated for different
fidelity parameters and cross-inhibition rates. A chirality parameter is
defined and shown to be conserved by the nonlinear terms of the model. Finally,
a truncated version of the model is used to derive a set of two ordinary
differential equations and it is argued that these equations are more realistic
than those used in earlier models of that form.Comment: 20 pages, 6 figures, Orig. Life Evol. Biosph. (accepted
Magnetism, FeS colloids, and Origins of Life
A number of features of living systems: reversible interactions and weak
bonds underlying motor-dynamics; gel-sol transitions; cellular connected
fractal organization; asymmetry in interactions and organization; quantum
coherent phenomena; to name some, can have a natural accounting via
interactions, which we therefore seek to incorporate by expanding the horizons
of `chemistry-only' approaches to the origins of life. It is suggested that the
magnetic 'face' of the minerals from the inorganic world, recognized to have
played a pivotal role in initiating Life, may throw light on some of these
issues. A magnetic environment in the form of rocks in the Hadean Ocean could
have enabled the accretion and therefore an ordered confinement of
super-paramagnetic colloids within a structured phase. A moderate H-field can
help magnetic nano-particles to not only overcome thermal fluctuations but also
harness them. Such controlled dynamics brings in the possibility of accessing
quantum effects, which together with frustrations in magnetic ordering and
hysteresis (a natural mechanism for a primitive memory) could throw light on
the birth of biological information which, as Abel argues, requires a
combination of order and complexity. This scenario gains strength from
observations of scale-free framboidal forms of the greigite mineral, with a
magnetic basis of assembly. And greigite's metabolic potential plays a key role
in the mound scenario of Russell and coworkers-an expansion of which is
suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed
Krishnaswami Alladi, Springer 201
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