Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

The development of optimized high performance liquid chromatography systems for the analysis of improvised explosives

Existing instrumental techniques must be adaptable to the analysis of novel explosives if science is to keep up with the practices of terrorists and criminals. The focus of this work has been the development of analytical techniques for the analysis of two types of novel explosives: ascorbic acid-based propellants, and improvised mixtures of concentrated hydrogen peroxide/fuel. In recent years, the use of these explosives in improvised explosive devices (IEDs) has increased. It is therefore important to develop methods which permit the identification of the nature of the original explosive from post-blast residues. Ascorbic acid-based propellants are low explosives which employ an ascorbic acid fuel source with a nitrate/perchlorate oxidizer. A method which utilized ion chromatography with indirect photometric detection was optimized for the analysis of intact propellants. Post-burn and post-blast residues if these propellants were analyzed. It was determined that the ascorbic acid fuel and nitrate oxidizer could be detected in intact propellants, as well as in the post-burn and post-blast residues. Degradation products of the nitrate and perchlorate oxidizers were also detected. With a quadrupole time-of-flight mass spectrometer (QToFMS), exact mass measurements are possible. When an HPLC instrument is coupled to a QToFMS, the combination of retention time with accurate mass measurements, mass spectral fragmentation information, and isotopic abundance patterns allows for the unequivocal identification of a target analyte. An optimized HPLC-ESI-QToFMS method was applied to the analysis of ascorbic acid-based propellants. Exact mass measurements were collected for the fuel and oxidizer anions, and their degradation products. Ascorbic acid was detected in the intact samples and half of the propellants subjected to open burning; the intact fuel molecule was not detected in any of the post-blast residue. Two methods were optimized for the analysis of trace levels of hydrogen peroxide: HPLC with fluorescence detection (HPLC-FD), and HPLC with electrochemical detection (HPLC-ED). Both techniques were extremely selective for hydrogen peroxide. Both methods were applied to the analysis of post-blast debris from improvised mixtures of concentrated hydrogen peroxide/fuel; hydrogen peroxide was detected on variety of substrates. Hydrogen peroxide was detected in the post-blast residues of the improvised explosives TATP and HMTD.

Headspace analysis of smokeless powders: Development of mass calibration methods using microdrop printing for chromatographic and ion mobility spectrometric detection

Smokeless powder additives are usually detected by their extraction from post-blast residues or unburned powder particles followed by analysis using chromatographic techniques. This work presents the first comprehensive study of the detection of the volatile and semi-volatile additives of smokeless powders using solid phase microextraction (SPME) as a sampling and pre-concentration technique. Seventy smokeless powders were studied using laboratory based chromatography techniques and a field deployable ion mobility spectrometer (IMS). The detection of diphenylamine, ethyl and methyl centralite, 2,4-dinitrotoluene, diethyl and dibutyl phthalate by IMS to associate the presence of these compounds to smokeless powders is also reported for the first time. A previously reported SPME-IMS analytical approach facilitates rapid sub-nanogram detection of the vapor phase components of smokeless powders. A mass calibration procedure for the analytical techniques used in this study was developed. Precise and accurate mass delivery of analytes in picoliter volumes was achieved using a drop-on-demand inkjet printing method. Absolute mass detection limits determined using this method for the various analytes of interest ranged between 0.03–0.8 ng for the GC-MS and between 0.03–2 ng for the IMS. Mass response graphs generated for different detection techniques help in the determination of mass extracted from the headspace of each smokeless powder. The analyte mass present in the vapor phase was sufficient for a SPME fiber to extract most analytes at amounts above the detection limits of both chromatographic techniques and the ion mobility spectrometer. Analysis of the large number of smokeless powders revealed that diphenylamine was present in the headspace of 96% of the powders. Ethyl centralite was detected in 47% of the powders and 8% of the powders had methyl centralite available for detection from the headspace sampling of the powders by SPME. Nitroglycerin was the dominant peak present in the headspace of the double-based powders. 2,4-dinitrotoluene which is another important headspace component was detected in 44% of the powders. The powders therefore have more than one headspace component and the detection of a combination of these compounds is achievable by SPME-IMS leading to an association to the presence of smokeless powders.

Identification of genes downstream of endothelin-3 signaling: characterization of WSB1 and SPC12

Signaling of endothelin-3 (Edn3) through its receptor, endothelin receptor B (EdnrB), has been shown to be indispensable for the development of certain neural crest derivatives. Since no research has been directed to investigate what the downstream targets of this signaling pathway are, the purpose of this study was to identify and characterize genes that are transcriptionally regulated by Edn3 signaling. Data from Differential Display RT-PCR of Edn-3 induced cDNA vs. non-induced cDNA obtained from primary neural crest cultures was analyzed. Thirty bands that were differentially expressed were sequenced and submitted for a homology search (BLAST). Among the genes identified were WSB 1 (a member of the SOCS family of negative regulators) and SPC 12 (the smallest subunit, 12kDa, of mammalian signal peptidase). Using whole-mount in-situ hybridization, the expression patterns of EdnrB, WSB 1 and SPC 12 were characterized. WSB 1 and SPC 12 expression patterns were found to overlap with that of EdnrB, suggesting that Edn3 might regulate the transcription of these genes in specific neural crest derived lineages.

The Development of High Performance Liquid Chromatography Systems for the Analysis of Improvised Explosives

Existing instrumental techniques must be adaptable to the analysis of novel explosives if science is to keep up with the practices of terrorists and criminals. The focus of this work has been the development of analytical techniques for the analysis of two types of novel explosives: ascorbic acid-based propellants, and improvised mixtures of concentrated hydrogen peroxide/fuel. In recent years, the use of these explosives in improvised explosive devices (IEDs) has increased. It is therefore important to develop methods which permit the identification of the nature of the original explosive from post-blast residues. Ascorbic acid-based propellants are low explosives which employ an ascorbic acid fuel source with a nitrate/perchlorate oxidizer. A method which utilized ion chromatography with indirect photometric detection was optimized for the analysis of intact propellants. Post-burn and post-blast residues if these propellants were analyzed. It was determined that the ascorbic acid fuel and nitrate oxidizer could be detected in intact propellants, as well as in the post-burn and post-blast residues. Degradation products of the nitrate and perchlorate oxidizers were also detected. With a quadrupole time-of-flight mass spectrometer (QToFMS), exact mass measurements are possible. When an HPLC instrument is coupled to a QToFMS, the combination of retention time with accurate mass measurements, mass spectral fragmentation information, and isotopic abundance patterns allows for the unequivocal identification of a target analyte. An optimized HPLC-ESI-QToFMS method was applied to the analysis of ascorbic acid-based propellants. Exact mass measurements were collected for the fuel and oxidizer anions, and their degradation products. Ascorbic acid was detected in the intact samples and half of the propellants subjected to open burning; the intact fuel molecule was not detected in any of the post-blast residue. Two methods were optimized for the analysis of trace levels of hydrogen peroxide: HPLC with fluorescence detection (HPLC-FD), and HPLC with electrochemical detection (HPLC-ED). Both techniques were extremely selective for hydrogen peroxide. Both methods were applied to the analysis of post-blast debris from improvised mixtures of concentrated hydrogen peroxide/fuel; hydrogen peroxide was detected on variety of substrates. Hydrogen peroxide was detected in the post-blast residues of the improvised explosives TATP and HMTD.

Headspace Analysis of Smokeless Powders: Development of Mass Calibration Methods using Microdrop Printing for Chromatographic and Ion Mobility Spectrometric Detection

Smokeless powder additives are usually detected by their extraction from post-blast residues or unburned powder particles followed by analysis using chromatographic techniques. This work presents the first comprehensive study of the detection of the volatile and semi-volatile additives of smokeless powders using solid phase microextraction (SPME) as a sampling and pre-concentration technique. Seventy smokeless powders were studied using laboratory based chromatography techniques and a field deployable ion mobility spectrometer (IMS). The detection of diphenylamine, ethyl and methyl centralite, 2,4-dinitrotoluene, diethyl and dibutyl phthalate by IMS to associate the presence of these compounds to smokeless powders is also reported for the first time. A previously reported SPME-IMS analytical approach facilitates rapid sub-nanogram detection of the vapor phase components of smokeless powders. A mass calibration procedure for the analytical techniques used in this study was developed. Precise and accurate mass delivery of analytes in picoliter volumes was achieved using a drop-on-demand inkjet printing method. Absolute mass detection limits determined using this method for the various analytes of interest ranged between 0.03 - 0.8 ng for the GC-MS and between 0.03 - 2 ng for the IMS. Mass response graphs generated for different detection techniques help in the determination of mass extracted from the headspace of each smokeless powder. The analyte mass present in the vapor phase was sufficient for a SPME fiber to extract most analytes at amounts above the detection limits of both chromatographic techniques and the ion mobility spectrometer. Analysis of the large number of smokeless powders revealed that diphenylamine was present in the headspace of 96% of the powders. Ethyl centralite was detected in 47% of the powders and 8% of the powders had methyl centralite available for detection from the headspace sampling of the powders by SPME. Nitroglycerin was the dominant peak present in the headspace of the double-based powders. 2,4-dinitrotoluene which is another important headspace component was detected in 44% of the powders. The powders therefore have more than one headspace component and the detection of a combination of these compounds is achievable by SPME-IMS leading to an association to the presence of smokeless powders.

Measuring star formation in high-z massive galaxies: a mid-infrared to submillimetre study of the GOODS NICMOS Survey sample

We present measurements of the mean mid-infrared to submillimetre flux densities of massive (M_*≳ 10^11 M_⊙) galaxies at redshifts 1.7 < z < 2.9, obtained by stacking positions of known objects taken from the GOODS NICMOS Survey (GNS) catalogue on maps at 24 μm (Spitzer/MIPS); 70, 100 and 160 μm (Herschel/PACS); 250, 350 and 500 μm (BLAST); and 870 μm (LABOCA). A modified blackbody spectrum fit to the stacked flux densities indicates a median [interquartile] star formation rate (SFR) of SFR = 63[48, 81] M_⊙ yr^−1. We note that not properly accounting for correlations between bands when fitting stacked data can significantly bias the result. The galaxies are divided into two groups, disc-like and spheroid-like, according to their Sérsic indices, n. We find evidence that most of the star formation is occurring in n≤ 2 (disc-like) galaxies, with median [interquartile] SFR = 122[100, 150] M_⊙ yr^−1, while there are indications that the n > 2 (spheroid-like) population may be forming stars at a median [interquartile] SFR = 14[9, 20] M_⊙ yr^−1, if at all. Finally, we show that star formation is a plausible mechanism for size evolution in this population as a whole, but find only marginal evidence that it is what drives the expansion of the spheroid-like galaxies.

Peridynamic modeling of composite laminates under explosive loading

Peer reviewed

Sustainable solutions for the construction sector: integration of secondary raw materials in the production cycle of concrete

The construction industry is one of the largest consumers of raw materials and energy and one of the highest contributor to green-houses gases emissions. In order to become more sustainable it needs to reduce the use of both raw materials and energy, thus lim-iting its environmental impact. Developing novel technologies to integrate secondary raw materials (i.e. lightweight recycled aggre-gates and alkali activated “cementless” binders - geopolymers) in the production cycle of concrete is an all-inclusive solution to im-prove both sustainability and cost-efficiency of construction industry. SUS-CON “SUStainable, Innovative and Energy-Efficiency CONcrete, based on the integration of all-waste materials” is an European project (duration 2012-2015), which aim was the inte-gration of secondary raw materials in the production cycle of concrete, thus resulting in innovative, sustainable and cost-effective building solutions. This paper presents the main outcomes related to the successful scaling-up of SUS-CON concrete solutions in traditional production plants. Two European industrial concrete producers have been involved, to design and produce both pre-cast components (blocks and panels) and ready-mixed concrete. Recycled polyurethane foams and mixed plastics were used as aggre-gates, PFA (Pulverized Fuel Ash, a by-product of coal fuelled power plants) and GGBS (Ground Granulated Blast furnace Slag, a by-product of iron and steel industries) as binders. Eventually, the installation of SUS-CON concrete solutions on real buildings has been demonstrated, with the construction of three mock-ups located in Europe (Spain, Turkey and Romania)

Multiuser dual-hop relaying over hybrid RF/FSO links

The performance of multiuser dual-hop relaying over mixed radio frequency/free-space optical (RF/FSO) links is investigated. RF links are used for the simultaneous data transmission from m single-antenna sources to the relay, which is equipped with n ≥ m receive antennas and a photo-aperture transmitter. The relay operates under the decode-and-forward protocol and utilizes the popular ordered V-BLAST technique to successively decode each user's transmitted stream. A common norm-based ordering approach is adopted, where the streams are decoded in an ascending order. After the V-BLAST decoding, the relay retransmits the initial information to the destination, which is equipped with a photo-detector, via a point-to-point FSO link in m consecutive timeslots. Analytical expressions for the end-to-end outage probability and average symbol error probability of each user are derived. Some engineering insights are manifested, such as the diversity order, the impact of the pointing error displacement on the FSO link and the severity on the turbulence-induced channel fading.

Resistance of alkali activated slag concretes to chloride environments based on chloride penetration measurements

ABSTRACT

One of the binder systems with low environmental footprint is alkali activated slag concretes (AASC), made by adding alkalis such as sodium hydroxide and sodium silicate to industrial by-products such as ground granulated blast furnace slag (GGBS). Whilst they have the similar behaviour as that of traditional cement systems in terms of strength and structural behaviour, AASC do exhibit superior performance in terms of abrasion and acid resistance and fire protection.
In this article, the authors focus their attention on chloride ingress into different grades of AASC. The mix variables in AASC included water-to-binder, binder to aggregate ratio, percentage of alkali and the SiO2/Na2O ratio (silica modulus, Ms). The first challenge is to get mixes for different range of workability (with slump values from 40mm to 240mm) and reasonable early age and long term compressive strength according to each one. Then the chloride diffusion and migration in those mixes were measured and compared with same normal concretes in the existed literature based on chloride penetration depth. Comparing the chloride ingress between tradition concretes and AASCs is worthwhile to prove the possibility of increasing concrete lifetime in proximity to sea and deciding while such concretes are practical for use. Findings show that compared to the PC concretes, the AAS concretes have lower rate of chloride ingress.

Resistance of alkali activated slag concretes to chloride environments

ABSTRACT: Researchers are focusing their attention on alternative binder systems using 100% supplementary cementitious materials as it allows better control over the microstructure formation and low to moderate environmental footprint. One such system being considered is alkali activated slag concretes (AASC), made by adding alkalis such as sodium hydroxide and sodium silicate to ground granulated blast furnace slag (GGBS). Whilst they have a similar behaviour as that of traditional cement systems in terms of strength and structural behaviour, AASC are reported to exhibit superior performance in terms of abrasion,acid resistance and fire protection.
In this article, the authors investigate chloride ingress into different grades of AASC. The mix variables in AASC included water to binder, and binder to aggregate ratio, percentage of alkali and the SiO2/Na2O ratio (silica modulus, Ms). The first challenge was to develop mixes for different range of workability (with slump values from 40mm to 240mm) and reasonable early age and long term compressive strength. Further chloride ingress into those mixes were assessed and compared with the data from normal concretes based on literature. Findings show that compared to the PC concretes, the AAS concretes have lower rate of chloride ingress.

Alkali-Activated Natural Pozzolan Concrete as New Construction Material

In the near future, geopolymers or alkali-activated cementitious materials will be used as new high-performance construction materials of low environmental impact with a reasonable cost. This material is a good candidate to partially replace ordinary portland cement (OPC) in concrete as a major construction material that plays an outstanding role in the construction industry of different structures. Geopolymer materials are inorganic polymers based on alumina and silica units; they are synthesized from a wide range of dehydroxylated alumina-silicate powders condensed with alkaline silicate in a highly alkaline environment. Geopolymeric materials can be produced from a wide range of alumina-silica, including natural products--such as natural pozzolan and metakaolin--or coproducts--such as fly ash (coal and lignite), oil fuel ash, blast furnace or steel slag, and silica fume--and provide a route toward sustainable development. Using lesser amounts of calcium-based raw materials, lower manufacturing temperature, and lower amounts of fuel result in reduced carbon emissions for geopolymer cement manufacture up to 22 to 72% in comparison with portland cement. A study has been done by the authors to investigate the intrinsic nature of different types of Iranian natural pozzolans to determine the activators and methods that could be used to produce a geopolymer concrete based on alkali-activated natural pozzolan (AANP) and optimize mixture design. The mechanical behavior and durability of these types of geopolymer concrete were investigated and compared with normal OPC concrete mixtures cast by the authors and also reported in the literature. This paper summarizes the main conclusions of the research regarding pozzolanic activity, activator properties, engineering and durability properties, applications and evaluation of carbon footprint, and cost for AANP concrete.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.