Open source software toolchain for automated non‐targeted screening for toxins in alternative foods

Previous published methods for non-targeted screening of toxins in alternative foods such as leaf concentrate, agricultural residues or plastic fed to biological consortia are time consuming and expensive and thus present accessibility, as well as, time-constraint issues for scientists from under resourced settings to identify safe alternative foods. The novel methodology presented here, utilizes a completely free and open source software toolchain for automatically screening unknown alternative foods for toxicity using experimental data from ultra-high-pressure liquid chromatography and mass spectrometry. The process uses three distinct tools (mass spectrometry analysis with MZmine 2, formula assignment with MFAssignR, and data filtering with ToxAssign) enabling it to be modular and easily upgradable in the future. MZmine 2 and MFAssignR have been previously described, while ToxAssign was developed here to match the formulas output by formula assignment to potentially toxic compounds in a local table, then look up toxic data on the Open Food Tox Database for the matched compounds. This process is designed to fill the gap between food safety analysis techniques and developing alternative food production techniques to allow for new methods of food production to be preliminarily tested before animal testing. The methodology was validated against a previous method using proprietary commercial software. The new process identifies all of the toxic elements the previous process identified with more detailed information than the previous process was able to provide automatically. • Efficient analysis to find potentially toxic compounds in alternative foods and resilient foods. • Identification of potentially unsafe products without the use of live animal testing. • Modular free and open source design to allow for upgrading or fitting of user needs

Modelling the hygroscopic growth factors of aerosol material containing a large water-soluble organic fraction, collected at the Storm Peak Laboratory

The compositions of six aggregated aerosol samples from the Storm Peak site have been comprehensively analysed (Hallar et al., 2013), focusing particularly on the large water-extractable organic fraction which consists of both high molecular weight organic compounds and a range of acids and sugar-alcohols. The contribution of the soluble organic fraction of atmospheric aerosols to their hygroscopicity is hard to quantify, largely because of the lack of a detailed knowledge of both composition and the thermodynamic properties of the functionally complex compounds and structures the fraction contains. In this work we: (i) develop a means of predicting the relative solubility of the compounds in the water-extractable organic material from the Storm Peak site, based upon what is known about their chemical composition; (ii) derive the probable soluble organic fraction from comparisons of model predictions with the measured hygroscopicity; (iii) test a model of the water uptake of the total aerosol (inorganic plus total water-extractable organic compounds). Using a novel UNIFAC-based method, different assignments of functional groups to the high molecular weight water soluble organic compounds (WSOC) were explored, together with their effects on calculated hygroscopic growth factors, constrained by the known molecular formulae and the double bond equivalents associated with each molecule. The possible group compositions were compared with the results of ultrahigh resolution mass spectrometry measurements of the organic material, which suggest large numbers of alcohol (–OH) and acid (–COOH) groups. A hygroscopicity index (HI) was developed. The measured hygroscopic growth is found to be consistent with a dissolution of the WSOC material that varies approximately linearly with RH, such that the dissolved fraction is about 0.45–0.85 at 90% relative humidity when ordering by HI, depending on the assumptions made. This relationship, if it also applies to other types of organic aerosol material, provides a simple approach to calculating both water uptake and CCN activity (and the κ parameter for hygroscopic growth). The hygroscopicity of the total aerosol was modelled using a modified Zdanovskii-Stokes-Robinson approach as the sum of that of the three analysed fractions: inorganic ions (predicted), individual organic acids and “sugar alcohols” (predicted), and the high molecular weight WSOC fraction (measured). The calculated growth factors broadly agree with the measurements, and validate the approach taken. The insights into the dissolution of the organic material seem likely to apply to other largely biogenic aerosols from similar remote locations

Sybil tolerance and probabilistic databases to compute web services trust

© Springer International Publishing Switzerland 2015. This paper discusses how Sybil attacks can undermine trust management systems and how to respond to these attacks using advanced techniques such as credibility and probabilistic databases. In such attacks end-users have purposely different identities and hence, can provide inconsistent ratings over the same Web Services. Many existing approaches rely on arbitrary choices to filter out Sybil users and reduce their attack capabilities. However this turns out inefficient. Our approach relies on non-Sybil credible users who provide consistent ratings over Web services and hence, can be trusted. To establish these ratings and debunk Sybil users techniques such as fuzzy-clustering, graph search, and probabilistic databases are adopted. A series of experiments are carried out to demonstrate robustness of our trust approach in presence of Sybil attacks

Perception of clear fricatives by normal-hearing and simulated hearing-impaired listeners

This is the publisher's version, also available electronically from http://scitation.aip.org/content/asa/journal/jasa/123/2/10.1121/1.2821966.Speakers may adapt the phonetic details of their productions when they anticipate perceptual difficulty or comprehension failure on the part of a listener. Previous research suggests that a speaking style known as clear speech is more intelligible overall than casual, conversational speech for a variety of listener populations. However, it is unknown whether clear speech improves the intelligibility of fricative consonants specifically, or how its effects on fricative perception might differ depending on listener population. The primary goal of this study was to determine whether clear speech enhances fricative intelligibility for normal-hearing listeners and listeners with simulated impairment. Two experiments measured babble signal-to-noise ratio thresholds for fricative minimal pair distinctions for 14 normal-hearing listeners and 14 listeners with simulated sloping, recruiting impairment. Results indicated that clear speech helped both groups overall. However, for impaired listeners, reliable clear speech intelligibility advantages were not found for non-sibilant pairs. Correlation analyses comparing acoustic and perceptual data indicated that a shift of energy concentration toward higher frequency regions and greater source strength contributed to the clear speecheffect for normal-hearing listeners. Correlations between acoustic and perceptual data were less consistent for listeners with simulated impairment, and suggested that lower-frequency information may play a role

Molecular and physical characteristics of aerosol at a remote free troposphere site: implications for atmospheric aging

Aerosol properties are transformed by atmospheric processes during long-range transport and play a key role in the Earth's radiative balance. To understand the molecular and physical characteristics of free tropospheric aerosol, we studied samples collected at the Pico Mountain Observatory in the North Atlantic. The observatory is located in the marine free troposphere at 2225&thinsp;m above sea level, on Pico Island in the Azores archipelago. The site is ideal for the study of long-range-transported free tropospheric aerosol with minimal local influence. Three aerosol samples with elevated organic carbon concentrations were selected for detailed analysis. FLEXPART retroplumes indicated that two of the samples were influenced by North American wildfire emissions transported in the free troposphere and one by North American outflow mainly transported within the marine boundary layer. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry was used to determine the detailed molecular composition of the samples. Thousands of molecular formulas were assigned to each of the individual samples. On average  ∼ 60&thinsp;% of the molecular formulas contained only carbon, hydrogen, and oxygen atoms (CHO),  ∼ 30&thinsp;% contained nitrogen (CHNO), and  ∼ 10&thinsp;% contained sulfur (CHOS). The molecular formula compositions of the two wildfire-influenced aerosol samples transported mainly in the free troposphere had relatively low average O∕C ratios (0.48±0.13 and 0.45±0.11) despite the 7–10 days of transport time according to FLEXPART. In contrast, the molecular composition of the North American outflow transported mainly in the boundary layer had a higher average O∕C ratio (0.57±0.17) with 3 days of transport time. To better understand the difference between free tropospheric transport and boundary layer transport, the meteorological conditions along the FLEXPART simulated transport pathways were extracted from the Global Forecast System analysis for the model grids. We used the extracted meteorological conditions and the observed molecular chemistry to predict the relative-humidity-dependent glass transition temperatures (Tg) of the aerosol components. Comparisons of the Tg to the ambient temperature indicated that a majority of the organic aerosol components transported in the free troposphere were more viscous and therefore less susceptible to oxidation than the organic aerosol components transported in the boundary layer. Although the number of observations is limited, the results suggest that biomass burning organic aerosol injected into the free troposphere is more persistent than organic aerosol in the boundary layer having broader implications for aerosol aging.</p

Measurements of branching fraction ratios and CP-asymmetries in suppressed B^- -> D(-> K^+ pi^-)K^- and B^- -> D(-> K^+ pi^-)pi^- decays

We report the first reconstruction in hadron collisions of the suppressed decays B^- -> D(-> K^+ pi^-)K^- and B^- -> D(-> K^+ pi^-)pi^-, sensitive to the CKM phase gamma, using data from 7 fb^-1 of integrated luminosity collected by the CDF II detector at the Tevatron collider. We reconstruct a signal for the B^- -> D(-> K^+ pi^-)K^- suppressed mode with a significance of 3.2 standard deviations, and measure the ratios of the suppressed to favored branching fractions R(K) = [22.0 \pm 8.6(stat)\pm 2.6(syst)]\times 10^-3, R^+(K) = [42.6\pm 13.7(stat)\pm 2.8(syst)]\times 10^-3, R^-(K)= [3.8\pm 10.3(stat)\pm 2.7(syst]\times 10^-3, as well as the direct CP-violating asymmetry A(K) = -0.82\pm 0.44(stat)\pm 0.09(syst) of this mode. Corresponding quantities for B^- -> D(-> K^+ pi^-)pi^- decay are also reported.Comment: 8 pages, 1 figure, accepted by Phys.Rev.D Rapid Communications for Publicatio

Clear speech perception in acoustic and electric hearing

When instructed to speak clearly for people with hearing loss, a talker can effectively enhance the intelligibility of his/her speech by producing "clear" speech. We analyzed global acoustic properties of clear and conversational speech from two talkers and measured their speech intelligibility over a wide range of signal-to-noise ratios in acoustic and electric hearing. Consistent with previous studies, we, found that clear speech had a slower overall rate, higher temporal amplitude modulations, and also produced higher intelligibility than conversational speech. To delineate the role of temporal amplitude modulations in clear speech, we extracted the temporal envelope from a number of frequency bands and replaced speech fine-structure with noise fine-structure to simulate cochlear implants. Although both simulated and actual cochlear-implant listeners required higher signal-to-noise ratios to achieve normal performance, a 3-4 dB difference in speech reception threshold was preserved between clear and conversational speech for all experimental conditions. These results suggest that while temporal fine structure is important for speech recognition in noise in general, the temporal envelope carries acoustic cues that contribute to the clear speech intelligibility advantage. (C) 2004 Acoustical Society of America

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE

Search for anomalous t t-bar production in the highly-boosted all-hadronic final state

A search is presented for a massive particle, generically referred to as a Z', decaying into a t t-bar pair. The search focuses on Z' resonances that are sufficiently massive to produce highly Lorentz-boosted top quarks, which yield collimated decay products that are partially or fully merged into single jets. The analysis uses new methods to analyze jet substructure, providing suppression of the non-top multijet backgrounds. The analysis is based on a data sample of proton-proton collisions at a center-of-mass energy of 7 TeV, corresponding to an integrated luminosity of 5 inverse femtobarns. Upper limits in the range of 1 pb are set on the product of the production cross section and branching fraction for a topcolor Z' modeled for several widths, as well as for a Randall--Sundrum Kaluza--Klein gluon. In addition, the results constrain any enhancement in t t-bar production beyond expectations of the standard model for t t-bar invariant masses larger than 1 TeV.Comment: Submitted to the Journal of High Energy Physics; this version includes a minor typo correction that will be submitted as an erratu

Search for New Physics with Jets and Missing Transverse Momentum in pp collisions at sqrt(s) = 7 TeV

A search for new physics is presented based on an event signature of at least three jets accompanied by large missing transverse momentum, using a data sample corresponding to an integrated luminosity of 36 inverse picobarns collected in proton--proton collisions at sqrt(s)=7 TeV with the CMS detector at the LHC. No excess of events is observed above the expected standard model backgrounds, which are all estimated from the data. Exclusion limits are presented for the constrained minimal supersymmetric extension of the standard model. Cross section limits are also presented using simplified models with new particles decaying to an undetected particle and one or two jets