Profiling of the Microbiome Associated With Nitrogen Removal During Vermifiltration of Wastewater From a Commercial Dairy.

Vermifiltration is a biological treatment process during which earthworms (e.g., Eisenia fetida) and microorganisms reduce the organic load of wastewater. To infer microbial pathways responsible for nutrient conversion, past studies characterized the microbiota in vermifilters and suggested that nitrifying and denitrifying bacteria play a significant role during this wastewater treatment process. In contrast to previous studies, which were limited by low-resolution sequencing methods, the work presented here utilized next generation sequencing to survey in greater detail the microbiota of wastewater from a commercial dairy during various stages of vermifiltration. To complement sequence analysis, nitrogenous compounds in and gaseous emissions from the wastewater were measured. Analysis of 16S rRNA gene profiles from untreated wastewater, vermifilter influent, and vermifilter effluent suggested that members of Comamonadaceae, a family of the Betaproteobacteria involved in denitrification, increased in abundance during the vermifiltration process. Subsequent functional gene analysis indicated an increased abundance of nitrification genes in the effluent and suggested that the nitrogen removal during vermifiltration is due to the microbial conversion of ammonia, a finding that was also supported by the water chemistry and emission data. This study demonstrates that microbial communities are the main drivers behind reducing the nitrogen load of dairy wastewater during vermifiltration, providing a valuable knowledge framework for more sustainable and economical wastewater management strategies for commercial dairies

Enhancing Domain Word Embedding via Latent Semantic Imputation

We present a novel method named Latent Semantic Imputation (LSI) to transfer external knowledge into semantic space for enhancing word embedding. The method integrates graph theory to extract the latent manifold structure of the entities in the affinity space and leverages non-negative least squares with standard simplex constraints and power iteration method to derive spectral embeddings. It provides an effective and efficient approach to combining entity representations defined in different Euclidean spaces. Specifically, our approach generates and imputes reliable embedding vectors for low-frequency words in the semantic space and benefits downstream language tasks that depend on word embedding. We conduct comprehensive experiments on a carefully designed classification problem and language modeling and demonstrate the superiority of the enhanced embedding via LSI over several well-known benchmark embeddings. We also confirm the consistency of the results under different parameter settings of our method.Comment: ACM SIGKDD 201

Proteomic Techniques in the Physiological Proteomics Core Facility

poster abstractA new software package, IdentiQuantXL, has been developed in the Physiological Proteomics Core Facility to provide large-scale protein identification and label-free quantification using either low or high resolution LC-MS/MS data. Though many software packages have been developed to perform label-free quantification of proteins in complex biological samples using peptide intensities generated by liquid chromatography - tandem mass spectrometry (LC-MS/MS), two important issues hinder the use of peptide intensity measurements: (i) It is difficult to accurately determine the retention time of each peptide peak, especially for low resolution data, and (ii) many peptides cannot be used for protein quantification. To address these two key issues, we have developed a new method to enable accurate peptide peak retention time determination and multiple filters to eliminate unqualified peptides for protein quantification. Repeatability and linearity have been tested using ion trap-derived low resolution data from six very different samples, i.e., standard peptides, kidney tissue lysates, HT29-MTX cell lysates, depleted human serum, human serum albumin-bound proteins, and standard proteins spiked in kidney tissue lysates. In all these unique experiments, at least 90.8% of proteins (up to 1,390) had CVs ≤ 3 0% across 10 technique replicates, and at least 92.1% of proteins (up to 2,013) had R2 ≥ 0.9500 across 7 concentrations. The performance of our strategy was verified using identical amounts of standard protein (lysozyme) spiked in complex biological samples (cell culture media containing secreted proteins) with a CV of 8.6% across eight injections. The excellent performance was further confirmed by comparing label-free mass spectrometry to Western blot detection of prolactin, which was decreased 17.1fold in dwarfed mice compared to wild-type using the label-free quantification strategy and very low or undetectable using Western blot. The results indicate that our new platform, named IdentiQuantXL, accurately quantifies thousands of peptides and proteins in complex samples. It has been applied in the aqueous humor proteome in patients with Fuchs endothelial corneal dystrophy. While many software packages focus only on high resolution data, our strategy is designed for both high and low resolution data. Consequently, it is very useful for data generated by low resolution mass spectrometers such as the LTQ, especially when the dynamic exclusion of ions in data acquisition is enabled to obtain more MS/MS fragments of low-abundance peptides to maximally identify proteins in a complex biological sample. Supported by NIEHS RC2ES018810 and NIGMS R01GM08521

Octet baryon magnetic moments from QCD sum rules

A comprehensive study is made for the magnetic moments of octet baryons in the method of QCD sum rules. A complete set of QCD sum rules is derived using the external field method and generalized interpolating fields. For each member, three sum rules are constructed from three independent tensor structures. They are analyzed in conjunction with the corresponding mass sum rules. The performance of each of the sum rules is examined using the criteria of OPE convergence and ground-state dominance, along with the role of the transitions in intermediate states. Individual contributions from the u, d and s quarks are isolated and their implications in the underlying dynamics are explored. Valid sum rules are identified and their predictions are obtained. The results are compared with experiment and previous calculations.Comment: 21 pages, 11 figures, 6 figures; added a reference, minor change in tex

XMM-Newton observations of XTE J1817-330 and XTE J1856+053

The black hole candidate XTE J1817-330 was discovered in outburst on 26 January 2006 with RXTE/ASM. One year later, on 28 February 2007, another X-ray transient discovered in 1996, XTE J1856+053, was detected by RXTE during a new outburst. We report on the spectra obtained by XMM-Newton of these two black hole candidates.Comment: Replaced with corrected versio

N to Δ\Delta transition amplitudes from QCD sum rules

We present a calculation of the N to $\Delta$ electromagnetic transition amplitudes using the method of QCD sum rules. A complete set of QCD sum rules are derived for the entire family of transitions from the baryon octet to decuplet. They are analyzed in conjunction with the corresponding mass sum rules using a Monte-Carlo-based analysis procedure. The performance of each of the sum rules is examined using the criteria of OPE convergence and ground-state dominance, along with the role of the transitions in intermediate states. Individual contributions from the u, d and s quarks are isolated and their implications in the underlying dynamics are explored. Valid sum rules are identified and their predictions are obtained. The results are compared with experiment and other calculations.Comment: 18 pages, 8 figures, 7 tables. Updated references and Fig. 7 and Fig.

Eta-nucleon coupling constant in QCD with SU(3) symmetry breaking

We study the $\eta$NN coupling constant using the method of QCD sum rules starting from the vacuum-to-eta correlation function of the interpolating fields of two nucleons. The matrix element of this correlation has been taken with respect to nucleon spinors to avoid unwanted pole contribution. The SU(3)-flavor symmetry breaking effects have been accounted for via the $\eta$-mass, s-quark mass and eta decay constant to leading order. Out of the four sum rules obtained by taking the ratios of the two sum rules in conjunction with the two sum rules in nucleon mass, three are found to give mutually consistent results. We find the SU(3) breaking effects significant, as large as 50% of the SU(3) symmetric part.Comment: 13 pages, 12 figure

Fully-Automated Driving: The Road to Future Vehicles

The study investigated the impact of fully-automated vehicle control on driver behaviour, physiology and the uptake of secondary tasks in varying traffic conditions. Previous studies have indicated the potential ironies of such automation on fatigue, stress and situational awareness, but have also suggested potential benefits through enhanced safety, more efficient traffic flows and reduced driver workload. The research was undertaken in a high-fidelity driving simulator that allowed drivers to see, feel and hear the impact of the automated control. Independent factors of Drive Type (manual control, fully-automated) and Traffic Density (light, heavy) were manipulated in a repeated-measures experimental design. 49 drivers participated. Drivers experiencing full vehicle automation tended to refrain from behaviours, such as overtaking, that required them to temporarily retake manual control, accepting the resulting increase in journey time. Automation improved safety margins in car following, but this benefit was restricted only to conditions of light surrounding traffic. Automation also reduced heart rate and increased driver fatigue, the latter being mitigated somewhat by high traffic density. Furthermore, drivers became more heavily involved with in-vehicle entertainment than they were in manual driving, affording less visual attention to the road ahead. Drivers do appear happy to forgo their supervisory responsibilities in preference of a more entertaining automated drive. However, these responsibilities are taken more seriously as supervisory demand increases

Lowest-energy structures of 13-atom binary clusters: Do icosahedral clusters exist in binary liquid alloys?

Although the existence of 13-atom icosahedral clusters in one-component close-packed undercooled liquids was predicted more than half a century ago by Frank, the existence of such icosahedral clusters is less clear in liquid alloys. We study the lowest-energy structures of 13-atom AxB13-x Lennard-Jones binary clusters using the modified space-fixed genetic algorithm and the artificial Lennard-Jones potential designed by Kob and Andersen. Curiously, the lowest-energy structures are non-icosahedral for almost all compositions. The role played by the icosahedral cluster in a binary glass is questionable.Comment: 10 pages, 3 figure (conference paper of LAM12) to be published in J. Non-Crystalline Solid