37 research outputs found
A protein-dependent side-chain rotamer library
No full textAbstract Background Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. Methods In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Results Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.</p
Phytofiltration of arsenic and cadmium by using an aquatic plant, Micranthemum umbrosum: Phytotoxicity, uptake kinetics, and mechanism
No full textArsenic (As) and cadmium (Cd) are noxious and carcinogenic pollutants that can be removed from water by using emerging, ecofriendly, phytofiltration technology that employs Micranthemum umbrosum. After culturing M. umbrosum for 7 days in a hydroponic experiment, accumulation of 1219±44.11 µg As g−1 and 799.40±30.95 µg Cd g−1 were observed in the leaves, from 1000 µg As L−1 and 1000 µg Cd L−1 of water, respectively. Plant and water samples were analyzed for assessing the As and Cd accumulations, translocations, phytotoxic effects, uptake mechanisms and kinetics, and for evaluating the potential of M. umbrosum in As and Cd phytofiltration. The uptake pattern was leaf>stem>root for both pollutants. The plant showed higher resistance to As than to that to Cd. Uptake of inorganic As species was much greater than that of organic As and was found at above the substrate concentration. However, Cd showed similar uptake pattern to that of inorganic As species, and the data was better fit to a non-linear than a linear model. Low molecular weight substances that have thiol group(s) may be responsible for the binding of As in plants whereas Cd showed a different mechanism to that of As. M. umbrosum showed good As phytofiltration capabilities without any phytotoxic effects, but it was found to be a moderate accumulator of Cd with some phytotoxic effect compare to some other previously studied plant
Phytofiltration of arsenic and cadmium from the water environment using Micranthemum umbrosum(J.F. Gmel) S.F. Blake as a hyperaccumulator
No full textArsenic (As) and cadmium (Cd) pollution in water is an important global issue. Phytofiltration is an eco-friendly technology that helps clean up pollutants using ornamental plants, such as Micranthemum umbrosum (J.F. Gmel) S.F. Blake. After a seven-day hydroponic experiment, M. umbrosum removed 79.3–89.5% As and 60–73.1% Cd from 0 to 1.0 μg As mL–1 and 0.3 to 30.0 μg Cd mL–1 solutions, respectively. For As treatment, root to stem and stem to leaf translocation factors greater than 1.0 indicated that accumulation of As in leaves was large compared to that in stem and roots. However, the accumulation of Cd in roots was higher than that in the leaves and stem. In addition, M. umbrosum completely removed Cd within three days from 0.38 to around 0 μg mL–1Cd in the solution when the plant was exchanged daily. Bio-concentration factors (2350 for As and 3027 for Cd) for M. umbrosum were higher than for other As and Cd phytoremediators. The results show that M. umbrosum can be an effective accumulator of Cd and a hyper-accumulator of As, as it can lower As toxicity to a level close to the limit recommended by the World Health Organization (0.01 μg As mL–1
Arabic nominals in HPSG: A verbal noun perspective
No full textSemitic languages exhibit rich nonconcatenative morphological operations, which can generate a myriad of
derived lexemes. Especially, the feature rich, root-driven morphology in the Arabic language demonstrates the
construction of several verb-derived nominals (verbal nouns) such as gerunds, active participles, passive
participles, locative participles, etc. Although HPSG is a successful syntactic theory, it lacks the
representation of complex nonconcatenative morphology. In this paper, we propose a novel HPSG representation for
Arabic nominals and various verb-derived nouns. We also present the lexical type hierarchy and derivational rules
for generating these verb-derived nominals using the HPSG framework
Potential of Micranthemum umbrosum for phytofiltration of organic arsenic species from oxic water environment
No full textArsenic (As) is a toxic and carcinogenic metalloid that causes various hazards to human health. Phytofiltration is a more eco-friendly and green approach than chemoremediation, or other traditional technologies, for removing As from aquatic environments. Recently, Micranthemum umbrosum was shown as a promising candidate for phytofiltration of inorganic As species. This work examines the potential application of M. umbrosum to phytofiltration of organic As species, such as monomethylarsonic acid (MMAA, CH5AsO3) and dimethylarsinic acid (DMAA, C2H7AsO2), from oxic water environments. M. umbrosum plants were grown in two test concentrations of MMAA and DMAA, or a control, in a hydroponic experiment. After seven days, leaves accumulated 90 +/- 3.2 and 48 +/- 1.6 A mu g As g(-1) (oven dry basis) from 1 A mu g As mL(-1) of water added from MMAA and DMAA, respectively. Bioconcentration factor values and translocation factor values were always greater than 1.0, indicating that M. umbrosum was a good As accumulator and that leaves accumulated significantly higher amounts of As than stems and roots. Analysis of macro- and micronutrient data showed that M. umbrosum had higher resistance to organic As treatments than the control. These results confirm the potential application of M. umbrosum for phytofiltration of organic As from contaminated oxic water environments
Scientometric Analysis of Public Health Literature: A Study based on Scopus Database
No full textPurpose – The main purpose of this study is to evaluate the progress and development of the global literature on public health and review several components of scientometric study including the patterns of growth of literature, authorship, author collaboration, and productivity.
Design/methodology/approach – The current study is exploratory research in nature reviewing secondary literature extracted from a Scopus database and analytical with the application of suitable statistical and scientometric tools to strengthen the empirical validity. Public health literature was assessed quantitatively using scientometric indicators from 2000 to 2015.
Findings – The year 2003 was the most productive and 2015 was the least productive year in Annual Growth Ratio (AGR) of public health published literature across the globe during the period under study. The average Relative Growth Rate (RGR) globally was 0.23 and at this rate, the literature of public health doubles every 4.16 years. Globally, the average Collaborative Coefficient (CC) value for global authors was 0.37 demonstrating that there was no significant magnitude of collaboration among worldwide authors. The average Productivity Per Author (PPA) for global authors is 0.49 which means public health authors produced less than half a publication each year during the study period.
Originality/value – The paper is one of the very few studies which focuses on Scientometric analysis of public health literature using Scopus database. The present research gives a direction to determine the level of collaboration by a Collaborative Coefficient (CC) value which was never been calculated previously
Preparation and characterization of chitosan–caboxymethyl-β-cyclodextrin entrapped nanozero-valent iron composite for Cu (II) and Cr (IV) removal from wastewater
No full textThe entrapment of Fe0 nanoparticles within a chitosan–carboxymethyl β-cyclodextrin complex, a nontoxic and biodegradable stabilizer, yields chitosan–Fe0 nanoparticle–carboxymethyl β-cyclodextrin beads that are 2.5 mm in diameter and contain 50% iron by weight. The complete disappearance of Cr (VI) and Cu (II) may involve both physical adsorption and reduction of Cr (VI) to Cr (III) and Cu (II) to Cu (0) while oxidizing Fe0 to Fe (III). The rate of reduction can be expressed by pseudo-second-order reaction kinetics. The rate constants increased with increasing iron loading and initial concentration at pH 6, while the adsorption of Cr (VI) and Cu (II) was found to be endothermic and exothermic, respectively. The apparent activation energies for Cr (VI) and Cu (II) were found to be 71.99 and 18.38 kJ mol−1, respectively. X-ray photoelectron spectroscopy confirmed the reduction process. The equilibrium data could be well described by both Langmuir and Temkin isotherms for describing monolayer adsorption and chemisorption processes, respectively. Both film diffusion and intraparticle diffusion were found to be the rate-limiting steps from the analysis of an intraparticle diffusion model. Thus, the synthesized chitosan–Fe0-nanoparticle–carboxymethyl β-cyclodextrin beads can be a potential material for in situ remediation of contaminated surface and ground water
