Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSIC

Corporate governance compliance and disclosure in the banking sector: using data from Japan

Using regression model this study investigates which characteristics of a bank is associated with the extent of corporate governance disclosure in Japan. The findings suggest that on average 8 banks out of a sample of 46 disclose optimal corporate governance information. The regression model results reveal in general that non-executive directors, cross-ownership, capital adequacy ratio and type of auditors are associated with the extent of corporate governance disclosure. Of these four variables, non-executive directors have a more significant impact on the extent of disclosure contrary to total assets and audit firms of banks in the context of Japan. The findings of this paper are relevant for corporate regulators, professional associations and developers of corporate governance code when designing or updating corporate governance code

Liquidity measures and cost of trading in an illiquid market

We provide the first in-depth study of trading on the Ukrainian stock exchange, using trade-by-trade data. Although Ukraine has some large listed companies, the market is quite illiquid. We study the efficiency of five liquidity measures in the market. The proportion of no-trading days is the most reliable of the five, while turnover, which is widely used in the literature, is a poor measure. On trading cost, trades in all size categories are executed within the quoted spread, as in other dealership markets, with medium-sized trades being the cheapest. The cost of sales is higher than the cost of purchases under all market conditions

Man-machines and embodiment: From cartesian physiology to Claude Bernard’s “living machine”

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time (1748) entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience

Preface to the special issue on man-made seismicity in Italy

Until a few years ago, Italy suffered from a deep lack of publicly shared knowledge about induced seismicity, compared to many other countries. No public data were available to perform scientific studies of the phenomenon, and the few papers published from 1964 to 2004 came from in-house operations of private companies (Mucciarelli, 2013)

Lithium and beryllium in the Gaia-Enceladus galaxy

Data from Gaia DR2 and The Apache Point Observatory Galactic Evolution Experiment surveys revealed a relatively new component in the inner Galactic halo, which is likely the dynamical remnant of a disrupted dwarf galaxy named Gaia-Enceladus that collided with the Milky Way about 10 Gyr ago. This merging event offers an extraordinary opportunity to study chemical abundances of elements in a dwarf galaxy, since they are generally hampered in external galaxies. Here, we focus on 7Li and 9Be in dwarf stars that are out of reach even in Local Group galaxies. Searching in GALAH, Gaia-ESO survey and in literature, we found several existing 7Li abundance determinations of stars belonging to the Gaia-Enceladus galaxy. The 7Li abundances of stars at the low metallicity end overlap with those of the Galactic halo. These are effective extragalactic 7Li measurements, which suggest that the 7Li Spite plateau is universal, as is the cosmological 7Li problem. We found a 7Li-rich giant out of 101 stars, which suggests a small percentage similar to that of the Milky Way. We also collect 9Be abundance for a subsample of 25 Gaia-Enceladus stars from literature. Their abundances share the Galactic [Be/H] values at the low metallicity end but grow slower with [Fe/H] and show a reduced dispersion. This suggests that the scatter observed in the Milky Way could reflect the different 9Be evolution patterns of different stellar components that are mixed-up in the Galactic halo

Man-machines and embodiment: From cartesian physiology to Claude Bernard’s “living machine”

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time (1748) entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience.A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn't a famous book of the time (1748) entitled L'Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience

CCS from industrial sources

The literature concerning the application of CCS to industry is reviewed. Costs are presented for different sectors including ``high purity'' (processes which inherently produce a high concentration of CO2), cement, iron and steel, refinery and biomass. The application of CCS to industry is a field which has had much less attention than its application to the electricity production sector. Costs range from less than $2011 10/tCO 2 up to above$ 2011 100/tCO 2 . In the words of a synthesis report from the United Nations Industrial Development Organisation (UNIDO) ``This area has so far not been the focus of discussions and therefore much attention needs to be paid to the application of CCS to industrial sources if the full potential of CCS is to be unlocked''

Determinants of environmental management in the red sea hotels: Personal and organizational values and contextual variables

What motivates firms to adopt environmental management practices is one of the most significant aspects in the contemporary academic debate in which the review of the existing literature yields, with an obvious contextual bias toward developed world, contested theories and inconclusive findings. Providing a unique model that brings together the individual and organizational levels of analysis on firms' adoption of environmental management practices, this study aims to provide a new insight from the context of developing world. Data from 158 Red Sea hotels reveal two identifiable dimensions of environmental management-planning and organization, and operations-that can be explained as originating from different values. Whereas organizational altruism is a powerful predictor of both dimensions, managers' personal values and organizational competitive orientation are only relevant to environmental operations. The evidence also indicates that contextual variables such as chain affiliation, hotel star rating, and size are important to explain hotels' environmental management behaviors. © 2012 ICHRIE