Sequence clustering strategies improve remote homology recognitions while reducing search times

Sequence databases are rapidly growing, thereby increasing thecoverage of protein sequence space, but this coverage is unevenbecause most sequencing efforts have concentrated on a smallnumber of organisms. The resulting granularity of sequence spacecreates many problems for profile-based sequence comparisonprograms. In this paper, we suggest several strategies thataddress these problems, and at the same time speed up the searchesfor homologous proteins and improve the ability of profile methodsto recognize distant homologies. One of our strategies combinesdatabase clustering, which removes highly redundant sequence,and a two-step PSI-BLAST (PDB-BLAST), which separates sequencespaces of profile composition and space of homology searching.The combination of these strategies improves distant homologyrecognitions by more than 100%, while using only 10% of theCPU time of the standard PSI-BLAST search. Another method, intermediateprofile searches, allows for the exploration of additional searchdirections that are normally dominated by large protein sub-familieswithin very diverse families. All methods are evaluated witha large fold-recognition benchmark.     

Na+ and/or Cl− Toxicities Determine Salt Sensitivity in Soybean (Glycine max (L.) Merr.), Mungbean (Vigna radiata (L.) R. Wilczek), Cowpea (Vigna unguiculata (L.) Walp.), and Common Bean (Phaseolus vulgaris L.)

Grain legumes are important crops, but they are salt sensitive. This research dissected the responses of four (sub)tropical grain legumes to ionic components (Na⁺ and/or Cl⁻) of salt stress. Soybean, mungbean, cowpea, and common bean were subjected to NaCl, Na⁺ salts (without Cl⁻), Cl⁻ salts (without Na⁺), and a “high cation” negative control for 57 days. Growth, leaf gas exchange, and tissue ion concentrations were assessed at different growing stages. For soybean, NaCl and Na⁺ salts impaired seed dry mass (30% of control), more so than Cl⁻ salts (60% of control). All treatments impaired mungbean growth, with NaCl and Cl⁻ salt treatments affecting seed dry mass the most (2% of control). For cowpea, NaCl had the greatest adverse impact on seed dry mass (20% of control), while Na⁺ salts and Cl⁻ salts had similar intermediate effects (~45% of control). For common bean, NaCl had the greatest adverse effect on seed dry mass (4% of control), while Na⁺ salts and Cl⁻ salts impaired seed dry mass to a lesser extent (~45% of control). NaCl and Na⁺ salts (without Cl⁻) affected the photosynthesis (P_n) of soybean more than Cl⁻ salts (without Na⁺) (50% of control), while the reverse was true for mungbean. Na⁺ salts (without Cl⁻), Cl⁻ salts (without Na⁺), and NaCl had similar adverse effects on P_n of cowpea and common bean (~70% of control). In conclusion, salt sensitivity is predominantly determined by Na⁺ toxicity in soybean, Cl⁻ toxicity in mungbean, and both Na⁺ and Cl⁻ toxicity in cowpea and common bean.     

Mobility of trace elements from selected Australian fly ashes and its potential impact on aquatic ecosystems

Batch leaching tests have been performed on fly ashes collected from four Australian power stations fuelled by chemically different coals. Two acidic and two alkaline fly ashes were subjected to long-term (144 h) leaching tests, and the behaviour of As, B, Mo and Se was investigated to obtain data on their potential for mobilisation during fly ash-water interactions. All four elements are mobile under different conditions and over different leaching times. The concentrations of these elements released in leaching solutions with initial pH values of 4, 7 and 10 were used to assess the influence of pH conditions on element mobility from the acidic and alkaline fly ashes. The most mobile of the four elements leached were Mo from alkaline fly ashes and B from acidic fly ashes. Arsenic concentration increased with time in leachate solutions from acidic and alkaline fly ashes; however, in solutions in contact with alkaline fly ashes the As concentration, after reaching a maximum, later decreased with time. Selenium mobility shows a similar pattern to that of As, with similar leaching concentrations. Boron has the highest relative mobility of all four elements. A process possibly responsible for the decrease in concentration of B, As and Se in alkaline leaching solutions is the formation of ettringite. Equilibrium between the solid phase (ash) and the leaching solution was not reached in any of the leaching experiments. The pH of the leaching solution is the key factor affecting the mobility of these trace elements in these fly ashes.     

Synthesis and properties of some 9,10-dihydro-7H-imidazo[1,2-b]benz[d,e]isoquinolin-7-one derivatives

The various routes of synthesis of some methoxy- and acetylamino-9,10-dihydro-7H-imidazo[1,2-b]benz[d,e]isoquinolin-7-one derivatives are described. The mixtures of geometric isomers obtained were separated and the chemical constitution of individual isomers was confirmed by the u.v., i.r., n.m.r. and mass spectroscopy. The fluorescence properties of individual isomers were also determined.     

Grain Size Variation in Coatings

An increase in grain size during deposition occurs in physical vapor deposition. Columnar grain structures result as the coating thickens beyond the point of constant grain size (>25 μm). As the deposition is taking place, the grain size of the Ti coating increases from that on the order of 0.01 (Jim to that greater than 1.0 μm. At a certain critical thickness during deposition, t_c, the grain size stabilizes. This study examines the minimum coating thickness required to produce the ultimate grain size. Then this investigation relates the critical thickness to the texture of the coating.     

Toward Better Understanding of Task Difficulty during Physicians’ Interaction with Electronic Health Record System (EHRs)

ABSTRACT

The goal of this study was to assess the relationship of task difficulty and mental effort with performance during physicians’ interaction with electronic health records (EHRs). A total of 38 physicians were asked to identify abnormal results and take follow-up action to “close the loop” on care delivery. Task difficulty was quantified via task-flow strategies and computer mouse-click patterns. Mental effort was quantified using eye movements based on changes in pupillary dilations (task evoked pupillary response or TEPR) and blink rate. Performance was quantified based on commission errors (error vs. no-error). Results indicated that physicians had different task-flow strategies; however, with improved awareness of the patient status, they exhibited an optimal task-flow strategy. Overall, performance was related to task-flow strategies, computer mouse-click patterns, and blink rate, indicating that physicians had lower task-difficulty and experienced lower mental effort with improved awareness of patient follow-up status. This is an important finding demonstrating that task-flows are a dominant predictor of physician performance when comparing between EHR designs. On the contrary, mouse-click patterns and blink rate are both useful predictors of physician performance when assessment was done within an EHR.     

Hydrophilic polycarbonate chips for generation of oil-in-water (O/W) and water-in-oil-in-water (W/O/W) emulsions

Modification of the surfaces of polycarbonate (PC) with the use of a solution of tin (II) chloride renders them hydrophilic. The surface draping is stable against exposure to water and to alcohols. Exposure to alkanes reduces but does not diminish the effect. The method is compatible—in using the same solvent and temperature—with the hydrophobic modification of PC (Jankowski et al. in Lab Chip 11:1151–1156, 2011). The combination of these methods makes it possible to generate single and multiple monodisperse emulsions with the use of flow-focusing junctions in systems made in PC—a material that is suitable for fabrication of multilayer, high-throughput microfluidic devices.     

Hydrophilic polycarbonate chips for generation of oil-in-water (O/W) and water-in-oil-in-water (W/O/W) emulsions

Modification of the surfaces of polycarbonate (PC) with the use of a solution of tin (II) chloride renders them hydrophilic. The surface draping is stable against exposure to water and to alcohols. Exposure to alkanes reduces but does not diminish the effect. The method is compatible—in using the same solvent and temperature—with the hydrophobic modification of PC Jankowski et al. ( Lab Chip 11:748–752, 2011). The combination of these methods makes it possible to generate single and multiple monodisperse emulsions with the use of flow-focusing junctions in systems made in PC—material that is suitable for fabrication of multilayer, high throughput microfluidic devices.     

Structural damage identification by adding virtual masses

This paper presents a method for damage identification by adding virtual masses to the structure in order to increase its sensitivity to local damages. The main concept is based on the Virtual Distortion Method (VDM), which is a fast structural reanalysis method that employs virtual distortions or pseudo loads to simulate structural modifications. In this paper, the structure with an added virtual mass is called the virtual structure. First, the acceleration frequency response of the virtual structure is constructed numerically by the VDM using local dynamic data measured only by a single excitation sensor and a single acceleration sensor. Second, the value of the additional mass is determined via sensitivity analysis of the constructed frequency responses of the virtual structure with respect to damage parameters; only the natural frequencies with high sensitivity are selected. This process is repeated for all the considered placements of the virtual mass. At last, the selected natural frequencies of all the virtual structures are used together for damage identification of the real structure. A finite element (FE) model of a plane frame is used to introduce and verify the proposed method. The damage can be identified precisely and effectively even under simulated 5 % Gaussian noise pollution.     

Identification of coexistent load and damage

Load reconstruction and damage identification are crucial problems in structural health monitoring. However, it seems there is not much investigation on identification of coexistent load and damage, although in practice they usually exist together. This paper presents a methodology to solve this problem based on the Virtual Distortion Method. A damaged structure is modeled by an equivalent intact structure subjected to the same loads and to virtual distortions which model the damages. The measured structural response is used to identify the loads, the distortions and to recover the stress-strain relationship of the damaged elements. This way both the damage type and extent are identified. The approach can be used off-line and online by repetitive applications in a moving time window. A numerical experiment of a truss with 5% measurement error validates that the two tested damage types (constant stiffness reduction and breathing crack) can be identified along with the loads.