Correlations between designability and various structural characteristics of protein lattice models

Using six kinds of lattice types (4×4 ,5×5 , and6×6 square lattices;3×3×3 cubic lattice; and2+3+4+3+2 and4+5+6+5+4 triangular lattices), three different size alphabets (HP ,HNUP , and 20 letters), and two energy functions, the designability of proteinstructures is calculated based on random samplings of structures and common biased sampling (CBS) of proteinsequence space. Then three quantities stability (average energy gap),foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the proteintertiary structure.

The contribution of maize cropping in the Midwest USA to global warming: A regional estimate

Agricultural soils emit about 50% of the global flux of N2O attributable to human influence, mostly in response to nitrogen fertilizer use. Recent evidence that the relationship between N2O fluxes and N-fertilizer additions to cereal maize are non-linear provides an opportunity to estimate regional N2O fluxes based on estimates of N application rates rather than as a simple percentage of N inputs as used by the Intergovernmental Panel on Climate Change (IPCC). We combined a simple empirical model of N2O production with the SOCRATES soil carbon dynamics model to estimate N2O and other sources of Global Warming Potential (GWP) from cereal maize across 19,000 cropland polygons in the North Central Region (NCR) of the US over the period 1964–2005. Results indicate that the loading of greenhouse gases to the atmosphere from cereal maize production in the NCR was 1.7 Gt CO2e, with an average 268 t CO2e produced per tonne of grain. From 1970 until 2005, GHG emissions per unit product declined on average by 2.8 t CO2e ha−1 annum−1, coinciding with a stabilisation in N application rate and consistent increases in grain yield from the mid-1970’s. Nitrous oxide production from N fertilizer inputs represented 59% of these emissions, soil C decline (0–30 cm) represented 11% of total emissions, with the remaining 30% (517 Mt) from the combustion of fuel associated with farm operations. Of the 126 Mt of N fertilizer applied to cereal maize from 1964 to 2005, we estimate that 2.2 Mt N was emitted as N2O when using a non-linear response model, equivalent to 1.75% of the applied N.

Fixing the city one photo at a time : mobile logging of maintenance requests

We have designed a mobile application that takes advantage of the built-in features of smart phones such as camera and GPS that allow users to take geo-tagged photos while on the move. Urban residents can take pictures of broken street furniture and public property requiring repair, attach a brief description, and submit the information as a maintenance request to the local government organisation of their city. This paper discusses the design approach that led to the application, highlights a built-in mechanism to elicit user feedback, and evaluates the progress to date with user feedback and log statistics. It concludes with an outlook highlighting user requested features and our own design aspirations for moving from a reporting tool to a civic engagement tool.

Methods used in cross-cultural comparisons of psychological symptoms and their determinants

This paper is the second in a series of reviews of cross-cultural studies of menopausal symptoms. The goal of this review is to compare and contrast methods which have been previously utilized in Cross-Cultural Midlife Women's Health Studies with a view to (1) identifying the challenges in measurement across cultures in psychological symptoms and (2) suggesting a set of unified questions and tools that can be used in future research in this area. This review also aims to examine the determinants of psychological symptoms and how those determinants were measured. The review included eight studies that explicitly compared symptoms in different countries or different ethnic groups in the same country and included: Australian/Japanese Midlife Women's Health Study (AJMWHS), Decisions At Menopause Study (DAMeS), Four Major Ethnic Groups (FMEG), Hilo Women's Health Survey (HWHS), Penn Ovarian Aging Study (POAS), Study of Women's Health Across the Nation (SWAN), Women's Health in Midlife National Study (WHiMNS), and the Women's International Study of Health and Sexuality (WISHeS). This review concludes that mental morbidity does affect vasomotor symptom prevalence across cultures and therefore should be measured. Based on the review of these eight studies it is recommended that the following items be included when measuring psychological symptoms across cultures, feeling tense or nervous, sleeping difficulty, difficulty in concentrating, depressed and irritability along with the CES-D Scale, and the Perceived Stress Scale. The measurement of these symptoms will provide an evidence based approach when forming any future menopause symptom list and allow for comparisons across studies.

Calcium ions promote osteogenic differentiation and mineralization of human dental pulp cells : implication for pulp capping materials

Calcium (Ca) is the main element of most pulp capping materials and plays an essential role in mineralization. Different pulp capping materials can release various concentrations of Ca ions leading to different clinical outcomes. The purpose of this study was to investigate the effects of various concentrations of Ca ions on the growth and osteogenic differentiation of human dental pulp cells (hDPCs). Different concentrations of Ca ions were added to growth culture medium and osteogenic inductive culture medium. A Cell Counting Kit-8 (CCK-8) was used to determine the proliferation of hDPCs in growth culture medium. Osteogenic differentiation and mineralization were measured by alkaline phosphatase (ALP) assay, Alizarin red S/von kossa staining, calcium content quantitative assay. The selected osteogenic differentiation markers were investigated by quantitative real-time polymerase chain reaction (qRT-PCR). Within the range of 1.8–16.2 mM, increased concentrations of Ca ions had no effect on cell proliferation, but led to changes in osteogenic differentiation. It was noted that enhanced mineralized matrix nodule formation was found in higher Ca ions concentrations; however, ALP activity and gene expression were reduced. qRT-PCR results showed a trend towards down-regulated mRNA expression of type I collagen (COL1A2) and Runx2 at elevated concentrations of Ca ions, whereas osteopontin (OPN) and osteocalcin (OCN) mRNA expression was significantly up-regulated. Ca ions content in the culture media can significantly influence the osteogenic properties of hDPCs, indicating the importance of optimizing Ca ions release from dental pulp capping materials in order to achieve desirable clinical outcomes.

Evolutionary relationships and divergence times among the native rats of Australia

Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.

Vibrational spectroscopic study of the minerals cavansite and pentagonite Ca(V4+O)Si4O10.4H2O

The bright blue minerals cavansite and pentagonite, a calcium vanadium silicate Ca(V4+O)Si4O10.4H2O, have been studied by UV–Visible, Raman and infrared spectroscopy. Cavansite shows an open porous structure with very small micron sized holes. Strong UV–Visible absorption bands are observed at around 403, 614 and 789 nm for cavansite and pentagonite. The Raman spectrum of cavansite is dominated by an intense band at 981 cm -1 and pentagonite by a band at 971 cm-1 attributed to the stretching vibrations of (SiO3)n units. Cavansite is characterised by two intense bands at 574 and 672 cm-1 whereas pentagonite by a single band at 651 cm-1. The Raman spectrum of cavansite in the hydroxyl stretching region shows bands at 3504, 3546, 3577, 3604 and 3654 cm-1 whereas pentagonite is a single band at 3532 cm_1. These bands are attributed to water coordinated to calcium and vanadium. XPS studies show that bond energy of oxygen in oxides is 530 eV, and in hydroxides -531.5 eV and for water -533.5 eV. XPS studies show a strong peak at 531.5 eV for cavansite, indicating some OH units in the structure of cavansite.

Evolutionary design of bone scaffolds with reference to material selection

The favourable scaffold for bone tissue engineering should have desired characteristic features, such as adequate mechanical strength and three-dimensional open porosity, which guarantee a suitable environment for tissue regeneration. In fact, the design of such complex structures like bone scaffolds is a challenge for investigators. One of the aims is to achieve the best possible mechanical strength-degradation rate ratio. In this paper we attempt to use numerical modelling to evaluate material properties for designing bone tissue engineering scaffold fabricated via the fused deposition modelling technique. For our studies the standard genetic algorithm was used, which is an efficient method of discrete optimization. For the fused deposition modelling scaffold, each individual strut is scrutinized for its role in the architecture and structural support it provides for the scaffold, and its contribution to the overall scaffold was studied. The goal of the study was to create a numerical tool that could help to acquire the desired behaviour of tissue engineered scaffolds and our results showed that this could be achieved efficiently by using different materials for individual struts. To represent a great number of ways in which scaffold mechanical function loss could proceed, the exemplary set of different desirable scaffold stiffness loss function was chosen. © 2012 John Wiley & Sons, Ltd.