Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server

Near-Infrared Super Resolution Imaging with Metallic Nanoshell Particle Chain Array

We propose a near-infrared super resolution imaging system without a lens or a mirror but with an array of metallic nanoshell particle chain. The imaging array can plasmonically transfer the near-field components of dipole sources in the incoherent and coherent manners and the super resolution images can be reconstructed in the output plane. By tunning the parameters of the metallic nanoshell particle, the plasmon resonance band of the isolate nanoshell particle red-shifts to the near-infrared region. The near-infrared super resolution images are obtained subsequently. We calculate the field intensity distribution at the different planes of imaging process using the finite element method and find that the array has super resolution imaging capability at near-infrared wavelengths. We also show that the image formation highly depends on the coherence of the dipole sources and the image-array distance.Comment: 15 pages, 6 figure

Tracking the Evolution of HIV/AIDS in China from 1989–2009 to Inform Future Prevention and Control Efforts

BACKGROUND: To determine policy implications, this analysis tracks the evolution of HIV/AIDS infection across China to understand current trends and potential risk factors. METHODS AND PRINCIPAL FINDINGS: A retrospective study with spatial analytical model and multilevel spatial models was conducted among 326,157 HIV/AIDS cases reported from 1989-2009. The results indicate that the distribution of HIV/AIDS was clustered at the county level with different directional distributions across China from 2003 to 2009. Compared to 2003, by 2009 there was a 122% increase in HIV cases among rural residents, 294% increase among urban residents, 211% increase among migrants, and 237% increase among permanent residents. The overall proportion of HIV by different routes of transmission showed dramatic changes with a 504% increase in sexual transmission of HIV, 90% decrease in blood/plasma transmission, and 35% decrease in injecting drug user transmission. Sexual transmission was the major transmission route among women (44%) and the elderly (59% in men, 44% in women) as well as among permanent (36%) and urban residents (33%). Among those <65 years old, women increased more than men, but among those ≥ 65 years, men increased more than women. Migrants contributed to the variance of HIV infection between counties but not within counties. The length of highway and urbanization combined with illiteracy were risk factors for HIV/AIDS. CONCLUSIONS/SIGNIFICANCE: Rates of HIV/AIDS among permanent urban residents, particularly women and elderly men, have increased significantly in recent years. To prevent HIV from spreading further among the general population, additional attention should be paid to these populations as well as to migrants

TC-1 observations of flux pileup and dipolarization-associated expansion in the near-Earth magnetotail during substorms

Fifty-three substorms measured by Double Star/TC-1 in the near-Earth magnetotail from July to October, 2004 are studied. The main features of these events are: (a) Magnetic flux pileup characterized by continuous enhancement of B z is observed, which starts almost simultaneously with aurora breakup within 1–3 minutes, indicating that substorm onset is in close relation to flux pileup. (b) Sudden plasma sheet expansion with sharp increases in ion temperature and density is seen in all events, which occurs typically ∼11 minutes after the beginning of pileup. The plasma sheet expansion is shown to be in close relation with the primary substorm dipolarization and, hence, can be referred to as ‘dipolarization-associated expansion’. (c) Evidence indicates that the substorm current wedge first forms earthward of TC-1 position and, hence, inward of the flow braking region, and then propagates tailward with an expansion in the Z-direction. Possible implications of these observations are briefly discussed

Facile Phosphine-Free Synthesis of CdSe/ZnS Core/Shell Nanocrystals Without Precursor Injection

A new simple method for synthesis of core/shell CdSe/ZnS nanocrystals (NCs) is present. By adapting the use of cadmium stearate, oleylamine, and paraffin liquid to a non-injection synthesis and by applying a subsequent ZnS shelling procedure to CdSe NCs cores using Zinc acetate dihydrate and sulfur powder, luminescent CdSe/ZnS NCs with quantum yields of up to 36% (FWHM 42–43 nm) were obtained. A seeding-growth technique was first applied to the controlled synthesis of ZnS shell. This method has several attractive features, such as the usage of low-cost, green, and environmentally friendlier reagents and elimination of the need for air-sensitive, toxic, and expensive phosphines solvent. Furthermore, due to one-pot synthetic route for CdSe/ZnS NCs, the approach presented herein is accessible to a mass production of these NCs

A Policy-Driven Large Scale Ecological Restoration: Quantifying Ecosystem Services Changes in the Loess Plateau of China

As one of the key tools for regulating human-ecosystem relations, environmental conservation policies can promote ecological rehabilitation across a variety of spatiotemporal scales. However, quantifying the ecological effects of such policies at the regional level is difficult. A case study was conducted at the regional level in the ecologically vulnerable region of the Loess Plateau, China, through the use of several methods including the Universal Soil Loss Equation (USLE), hydrological modeling and multivariate analysis. An assessment of the changes over the period of 2000–2008 in four key ecosystem services was undertaken to determine the effects of the Chinese government's ecological rehabilitation initiatives implemented in 1999. These ecosystem services included water regulation, soil conservation, carbon sequestration and grain production. Significant conversions of farmland to woodland and grassland were found to have resulted in enhanced soil conservation and carbon sequestration, but decreased regional water yield under a warming and drying climate trend. The total grain production increased in spite of a significant decline in farmland acreage. These trends have been attributed to the strong socioeconomic incentives embedded in the ecological rehabilitation policy. Although some positive policy results have been achieved over the last decade, large uncertainty remains regarding long-term policy effects on the sustainability of ecological rehabilitation performance and ecosystem service enhancement. To reduce such uncertainty, this study calls for an adaptive management approach to regional ecological rehabilitation policy to be adopted, with a focus on the dynamic interactions between people and their environments in a changing world

Crystalline Gaq3Nanostructures: Preparation, Thermal Property and Spectroscopy Characterization

Crystalline Gaq31-D nanostructures and nanospheres could be fabricated by thermal evaporation under cold trap. The influences of the key process parameters on formation of the nanostructures were also investigated. It has been demonstrated that the morphology and dimension of the nanostructures were mainly controlled by working temperature and working pressure. One-dimensional nanostructures were fabricated at a lower working temperature, whereas nanospheres were formed at a higher working temperature. Larger nanospheres could be obtained when a higher working pressure was applied. The XRD, FTIR, and NMR analyses evidenced that the nanostructures mainly consisted of δ-phase Gaq3. Their DSC trace revealed two small exothermic peaks in addition to the melting endotherm. The one in lower temperature region was ascribed to a transition from δ to β phase, while another in higher temperature region could be identified as a transition from β to δ phase. All the crystalline nanostructures show similar PL spectra due to absence of quantum confinement effect. They also exhibited a spectral blue shift because of a looser interligand spacing and reduced orbital overlap in their δ-phase molecular structures

A Missense Mutation in a Highly Conserved Alternate Exon of Dynamin-1 Causes Epilepsy in Fitful Mice

Dynamin-1 (Dnm1) encodes a large multimeric GTPase necessary for activity-dependent membrane recycling in neurons, including synaptic vesicle endocytosis. Mice heterozygous for a novel spontaneous Dnm1 mutation—fitful—experience recurrent seizures, and homozygotes have more debilitating, often lethal seizures in addition to severe ataxia and neurosensory deficits. Fitful is a missense mutation in an exon that defines the DNM1a isoform, leaving intact the alternatively spliced exon that encodes DNM1b. The expression of the corresponding alternate transcripts is developmentally regulated, with DNM1b expression highest during early neuronal development and DNM1a expression increasing postnatally with synaptic maturation. Mutant DNM1a does not efficiently self-assemble into higher order complexes known to be necessary for proper dynamin function, and it also interferes with endocytic recycling in cell culture. In mice, the mutation results in defective synaptic transmission characterized by a slower recovery from depression after trains of stimulation. The DNM1a and DNM1b isoform pair is highly conserved in vertebrate evolution, whereas invertebrates have only one isoform. We speculate that the emergence of more specialized forms of DNM1 may be important in organisms with complex neuronal function

A discrete firefly algorithm to solve a rich vehicle routing problem modelling a newspaper distribution system with recycling policy

A real-world newspaper distribution problem with recycling policy is tackled in this work. In order to meet all the complex restrictions contained in such a problem, it has been modeled as a rich vehicle routing problem, which can be more specifically considered as an asymmetric and clustered vehicle routing problem with simultaneous pickup and deliveries, variable costs and forbidden paths (AC-VRP-SPDVCFP). This is the first study of such a problem in the literature. For this reason, a benchmark composed by 15 instances has been also proposed. In the design of this benchmark, real geographical positions have been used, located in the province of Bizkaia, Spain. For the proper treatment of this AC-VRP-SPDVCFP, a discrete firefly algorithm (DFA) has been developed. This application is the first application of the firefly algorithm to any rich vehicle routing problem. To prove that the proposed DFA is a promising technique, its performance has been compared with two other well-known techniques: an evolutionary algorithm and an evolutionary simulated annealing. Our results have shown that the DFA has outperformed these two classic meta-heuristics