bluuebunny/crossref_metadata_2025 huggingface dataset:
NASA Broad-Specification Fuels Combustion Technology Program: Status and Description
Authors: Fear J. S.
Published: April 2015

The use of “broad-specification” fuels in aircraft gas turbine engines can be a significant factor in offsetting anticipated shortages of current-specification jet fuel in the latter part of the century. The changes in fuel properties accompanying the use of broad-specification fuels will tend to cause numerous emissions, performance, and durability problems in currently-designed combustion systems. The NASA Broad-Specification Fuels Combustion Technology Program is a contracted effort to evolve and demonstrate the technology required to utilize broad-specification fuels in current and next generation commercial Conventional Takeoff and Landing (CTOL) aircraft engines, and to verify this technology in full-scale engine tests in 1983. The program consists of three phases: Combustor Concept Screening, Combustor Optimization Testing, and Engine Verification Testing.
Development and Operating Experience of Automatic Pulse-Jet Self-Cleaning Air Filters for Combustion Gas Turbines
Authors: Neaman R. G. , Anderson A. W.
Published: April 2015

This paper discusses the development and operating experience of an automatic self-cleaning filter system designed to provide continuous high efficiency air filtration in a desert environment. The need for adequate inlet air treatment for combustion gas turbines has long been recognized. The degree of protection necessary and the ambient conditions under which this has to be achieved vary widely. Of particular interest is the requirement for high efficiency air filtration in the desert regions of the Arabian Peninsula. In the past, conventional gas turbine air filtration systems have proved inadequate to meet this particular need, mainly due to the high ambient dust concentrations experienced.
Development of Offshore Gas Turbine Packages for Power Generation and Mechanical Drive
Authors: Hulme B. G.
Published: April 2015

This paper describes the application of aero-derivative gas turbines for power generation and mechanical drive on fixed offshore oil and gas platforms. Established installation concepts are discussed and a comparison is made between two designs of pre-packaged power plant for installation on North Sea and Arabian Gulf platforms respectively. The structural requirements of such packages are analyzed and the design considerations for a Warren Truss structured machinery module are outlined. Some of the problems associated with installing packaged aero-derivative gas turbine machinery in the extremely aggressive offshore environment are highlighted and preferred solutions are proposed.
Gas Turbine Engine Emissions Measurement Technology: An Overview
Authors: Campbell N. T. , Groth R. H. , Zaccardi V. A.
Published: April 2015

Current technology and practices at Pratt & Whitney Aircraft Group, Commercial Products Division (P& WA) for monitoring gas turbine engine emissions as a function of engine operating parameters, fuels, and environmental factors are discussed from sampling procedures through final data reduction. Mobile laboratories and fixed systems are used to rapidly measure smoke, hydrocarbons, oxygen, oxides of nitrogen, water, carbon monoxide and carbon dioxide content. Calibration gases, traceable to the National Bureau of Standards (NBS), are provided by an in-house calibration laboratory. The data collected are fed into a computer to calculate emission factors, concentration levels, and when requested, gas temperature from the measured emissions. Problem areas, including an overall assessment of measurement accuracy, are discussed.
Radial Pump Impeller Measurements Using a Laser Doppler Velocimeter
Authors: Kannemans H.
Published: April 2015

A shrouded fully transparent radial pump impeller with thin backswept blades has been tested using a laser doppler velocimeter. Two components of the velocity were measured relative to the laboratory reference frame in a plane perpendicular to the axis of rotation. The velocity distribution is presented relative to the blades at different radii and different flow rates over the whole blade passage. The results show that the flow is essentially unsteady and, at low flow rate, highly influenced by viscous effects. A comparison between the experimental data and a potential flow theory shows good agreement at high flow rates.
Near-atomic cryo-EM structure of the helical measles virus nucleocapsid
Authors: Gutsche Irina , Desfosses Ambroise , Effantin Grégory , Ling Wai Li , Haupt Melina , Ruigrok Rob W. H. , Sachse Carsten , Schoehn Guy
Published: April 2015

Measles virus capsid at high resolution

Viruses rely on their capsid proteins to package and protect their genome. For measles virus and other Mononegavirales family members, multiple capsid proteins together form a helical shell around the viral RNA (collectively called the nucleocapsid). Gutsche
et al.
now report a high-resolution cryoelectron microscopy structure of the measles virus nucleocapsid. The structure reveals how the nucleocapsid assembles and how the nucleo-protein and viral RNA interact, both of which may inform drug design

Science
, this issue p.
704
Draft Genome Sequence of Bacillus amyloliquefaciens AP183 with Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus
Authors: Nasrin Shamima , Hossain Mohammad J. , Liles Mark R.
Published: April 2015

Bacillus amyloliquefaciens
AP183 expresses secondary metabolites that inhibit the growth of methicillin-resistant
Staphylococcus aureus
(MRSA). Here, we present a ~3.99-Mbp draft genome sequence of AP183 with the aims of providing insights into the genomic basis of its antibacterial mechanisms and exploring its potential use in preventing MRSA skin colonization.
Complete Genome Sequence of Teviot Paramyxovirus, a Novel Rubulavirus Isolated from Fruit Bats in Australia
Authors: Burroughs Amy L. , Tachedjian Mary , Crameri Gary , Durr Peter A. , Marsh Glenn A. , Wang Lin-Fa
Published: April 2015

The causative agents of a number of emerging zoonotic diseases have been identified as paramyxoviruses originating in bats. We report here the complete genome sequence of two Teviot paramyxoviruses, novel rubulaviruses isolated from urine samples collected from pteropid bats in Australia. The zoonotic potential of Teviot paramyxovirus is undetermined.
Full-Genome Sequences of Severe Fever with Thrombocytopenia Syndrome Virus, Isolated from South Korea in 2014
Authors: Yun Mi-ran , Park Sun-Whan , Kwon TaeSoo , Lee SangHyun , Yoo Won Gi , Choi WooYoung , Lee Won-Ja , Kim Dae-Won
Published: April 2015

Here, we present the full-length genome sequencing of severe fever with thrombocytopenia syndrome (SFTS) virus, isolated from South Korea in 2014. The five Korean strains were compared by phylogenetic analysis with full SFTS genome sequences of two neighboring nations, China and Japan.
Complete Genome Sequence of Paenibacillus polymyxa CF05, a Strain of Plant Growth-Promoting Rhizobacterium with Elicitation of Induced Systemic Resistance
Authors: Lei Mengying , Lu Peng , Jin Liping , Wang Yan , Qin Jialing , Xu Xi , Zhang Liqin , Wang Yongjun
Published: April 2015

Paenibacillus polymyxa
CF05 is a Gram-positive rod-shaped bacterium isolated from the interior of an ancient tree,
Cryptomeria fortunei
, in China. This bacterium displays potent biocontrol effects against certain soil-borne diseases and the elicitation of induced systemic resistance in tomatoes. Here, we report the complete genome sequence of
P. polymyxa
CF05.
Comparative Genomics of the Mucoid and Nonmucoid Strains of Streptococcus pyogenes, Isolated from the Same Patient with Streptococcal Meningitis
Authors: Yoshida Haruno , Ishigaki Yasuhito , Takizawa Asako , Moro Kunihiko , Kishi Yuki , Takahashi Takashi , Matsui Hidenori
Published: April 2015

Mucoid (MTB313) and nonmucoid (MTB314) strains of group A streptococcus
emm
type 1 were simultaneously isolated from a single patient suffering from streptococcal meningitis. Whole-genome sequencing revealed that MTB313 carried a nucleotide substitution within
rocA
, which generated an amber termination codon.
Complete Genome Sequence of the
Alfalfa latent virus
Authors: Nemchinov Lev G. , Shao Jonathan , Postnikova Olga A.
Published: April 2015

The first complete genome sequence of the
Alfalfa latent carlavirus
(ALV) was obtained by primer walking and Illumina RNA sequencing. The virus differs substantially from the Czech ALV isolate and the
Pea streak virus
isolate from Wisconsin. The absence of a clear nucleic acid-binding protein indicates ALV divergence from other carlaviruses.
Draft Genome Sequence of
Dactylonectria macrodidyma
, a Plant-Pathogenic Fungus in the
Nectriaceae
Authors: Malapi-Wight Martha , Salgado-Salazar Catalina , Demers Jill , Veltri Daniel , Crouch Jo Anne
Published: April 2015

Dactylonectria macrodidyma
is part of the
Nectriaceae
, a family containing important plant pathogens. This species possesses the ability to induce disease on grapevine, avocado, and olive. Here, we report the first draft genome of
D. macrodidyma
isolate JAC15-245. The assembled genome was 58 Mbp and contained an estimated 16,454 genes.
Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from
Capsicum annuum
(Bird's Eye Chili) and
Capsicum chinense
(Yellow Lantern Chili), Respectively
Authors: Gan Huan You , Gan Han Ming , Savka Michael A. , Triassi Alexander J. , Wheatley Matthew S. , Naqvi Kubra F. , Foxhall Taylor E. , Anauo Michael J. , Baldwin Mariah L. , Burkhardt Russell N. , O’Bryon Isabelle G. , Dailey Lucas K. , Busairi Nurfatini Idayu , Keith Robert C. , Khair Megat Hazmah Megat Mazhar , Rasul Muhammad Zamir Mohd , Rosdi Nur Aiman Mohd , Mountzouros James R. , Rhoads Aleigha C. , Selochan Melissa A. , Tautanov Timur B. , Polter Steven J. , Marks Kayla D. , Caraballo Alexander A. , Hudson André O.
Published: April 2015

Here, we report the genome sequences of
Bacillus safensis
RIT372 and
Pseudomonas oryzihabitans
RIT370 from
Capsicum
spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (
skfA
) in
Bacillus safensis
RIT372 and turnerbactin and carotenoid in
Pseudomonas oryzihabitans
RIT370.
Draft Genomes of Two Sordariomycete Fungi That Produce Novel Secondary Metabolites
Authors: Stamps Blake W. , Du Lin , Mitchell Carter A. , Cichecwicz Robert H. , Stevenson Bradley S.
Published: April 2015

The genomes of two fungi isolated from soil (MEA-2) and sediment (SUP5-1) were sequenced. Both were members of the order
Hypocreales
, closely related to
Tolypocladium inflatum
, and capable of producing novel secondary metabolites. The draft genomes enabled the characterization of key biosynthetic pathways.
Complete Genome Sequence of Canine Papillomavirus Virus Type 12
Authors: Zhou Dan , Luff Jennifer , Paul Siddhartha , Alkhilaiwi Faris , Usuda Yukari , Wang Naidong , Affolter Verena , Moore Peter , Schlegel Richard , Yuan Hang
Published: April 2015

Papillomaviruses, of the family
Papillomaviridae
, are epitheliotropic, nonenveloped, circular, double-stranded DNA viruses that contribute to benign and malignant tumors in humans and animals. We report here the whole-genome sequence of canine papillomavirus type 12, found at a pigmented plaque located on the skin of a mixed-breed bloodhound.
Draft Genome Sequence of the Biofilm-Forming Stenotrophomonas maltophilia Strain 53
Authors: Akbar Sirwan , Rout Simon P. , Humphreys Paul N.
Published: April 2015

A clinical strain of
Stenotrophomonas maltophilia
(designated strain 53) was obtained, and a whole-genome sequence was generated. The subsequent draft whole-genome sequence demonstrated the presence of a number of genes encoding for proteins involved in resistance to a number of antimicrobial therapies.
Sexual function in women undergoing surgery for deep infiltrating endometriosis: a comparison with healthy women
Authors: Di Donato Nadine , Montanari Giulia , Benfenati Arianna , Monti Giorgia , Leonardi Deborah , Bertoldo Valentina , Facchini Chiara , Raimondo Diego , Villa Gioia , Seracchioli Renato
Published: April 2015

Background

Endometriosis is a chronic and progressive condition of women of reproductive age. It is strongly associated with significant impairment of sexual function.

Aim

To objectively evaluate the impact of laparoscopic excision of endometriosis on sexual function in patients with deep infiltrating endometriosis (DIE) compared to healthy women.

Setting and design

Prospective study, including 250 patients with a diagnosis of DIE scheduled for laparoscopic surgery and 250 healthy women.

Methods

A sexual activity questionnaire, SHOW-Q (Sexual Health Outcomes in Women Questionnaire), was used to collect data pertaining to women's satisfaction, orgasm, desire and pelvic problem interference with sexual function. Women with DIE underwent complete excision of endometriotic lesions. All participants were asked to complete the SHOW-Q questionnaire before and after surgery.

Results

SHOW-Q scores in the endometriosis group before and 6 months after surgery were compared with the healthy group scores. A significant improvement was found between pre- and post-treatment in the scores of the satisfaction scale, desire scale and pelvic problem interference scale of SHOW-Q. The distribution of post-surgery SHOW-Q scores was comparable to healthy women's scores apart from the orgasm scale score, which was unchanged in the post-surgery group.

Conclusions

The surgical approach to treatment has a positive impact not only on organ impairment but also on sexual function in women affected by DIE.
Rifampicin determination in human serum and urine based on a disposable carbon paste microelectrode modified with a hollow manganese oxide@mesoporous silica oxide core-shell nanohybrid
Authors: Gan Tian , Shi Zhaoxia , Wang Kaili , Sun Junyong , Lv Zhen , Liu Yanming
Published: April 2015

This work designed a simple, sensitive, low-cost, and disposable electrochemical platform for the detection of antibiotic rifampicin (RIF) by using a hollow manganese oxide@mesoporous silica oxide (Mn3O4@SiO2) core-shell nanohybrid as sensitive material. The Mn3O4@SiO2 core-shell nanohybrid, prepared by a facile polyacrylic acid soft templating method, was applied to modify a homemade carbon paste microelectrode, which provided a feasible pathway for electron transfer of RIF due to the low density, large surface area, excellent loading capacity, high permeability, and abundant amount of active sites. The electrocatalytic behavior was further used for sensitive detection of RIF by square wave voltammetry. Under optimal conditions, the calibration curve was linear in the range from 30 nmol/L to 3.0 μmol/L. The electrochemical method showed good stability, reproducibility, and selectivity. It could effectively be applied to the determination of RIF in human serum and urine samples.
A comparison of hydrocarbon and alkali metal response in the flame ionization detector used in subcritical water chromatography
Authors: Scott Andrea F. , Thurbide Kevin B. , Quickfall Danica
Published: April 2015

The flame ionization detector (FID) response toward alkali metals and hydrocarbons was compared. Optimal hydrogen flame gas flow rates were found near 40 mL/min for hydrocarbon response and 80 mL/min for alkali response. While each displayed a linear FID response, alkali metals produced several orders of magnitude greater detector sensitivity than hydrocarbons. Of note, KCl, NaCl, LiCl, and ethanol yielded respective FID sensitivity of about 7500, 980, 130, and 1 mV/μg analyte. This was subsequently demonstrated to greatly alter the FID response of organic salts. For example, while formic acid is normally unresponsive in an FID, its potassium salt could be readily detected here at picogram levels. Conversely, this phenomenon also rendered the FID unsuitable for use with buffered mobile phases containing such salts. In particular, FID background and baseline noise levels for formic acid – sodium formate buffers were about 10 times larger than equivalent experiments with methanol–water and up to two orders of magnitude larger than pure water. Overall, the results show that alkali metals respond much stronger in the FID than do hydrocarbons. Accordingly, their presence in organic analytes or mobile phases must therefore be accounted for when using this detector, particularly in areas such as subcritical water chromatography where it is commonly employed.
Minocycline: a bacteriostatic antibiotic with pleiotropic cardioprotective effects
Authors: Brenes-Salazar Jorge A.
Published: April 2015

Minocycline belongs to the family of tetracyclines, which are drugs traditionally approved as antibiotics. Based on preclinical animal cardiac models and clinical neurology trials, this drug has gained special attention as a promising cardiovascular therapeutic agent given its anti-inflammatory, antiapoptotic, antioxidant, and antienzymatic properties. This review focuses on the available evidence for minocycline as a cardioprotective drug, with special attention to mechanisms of action. Ongoing cardiovascular clinical trials are briefly discussed.
Pericardial fluid of cardiac patients elicits arterial constriction: role of endothelin-1
Authors: Nemeth Zoltan , Cziraki Attila , Szabados Sandor , Horvath Ivan , Koller Akos
Published: April 2015

Recently, several vasoactive molecules have been found in pericardial fluid (PF). Thus, we hypothesized that in coronary artery disease due to ischemia or ischemia–reperfusion, the level of vasoconstrictors, mainly endothelin-1 (ET-1), increases in PF, which can increase the vasomotor tone of arteries. Experiments were performed using an isometric myograph. Vasomotor effects of PF from patients undergoing coronary artery bypass graft (PFCABG, n = 14) or valve replacement (PFVR, n = 7) surgery were examined in isolated rat carotid arteries (N = 14; n = 26). Vasomotor responses to KCl (40 or 60 mmol/L) were also tested. The selective endothelin A receptor antagonist BQ123 (10−6mol/L) was used to elucidate the role of ET-1. Both the first and the second additions of KCl elicited increases in the isometric force of the isolated arteries (KCl1, 6.1 ± 0.2 mN; KCl2, 6.5 ± 0.9 mN). PFCABGand PFVRelicited substantial increases in the isometric force of arteries (PFCABG, 3.1 ± 0.7 mN; PFVR, 3.0 ± 0.9 mN; p > 0.05). The presence of the selective endothelin A receptor blocker significantly reduced arterial contractions to PFCABG(before BQ123, 2.6 ± 0.5 mN vs. after BQ123, 0.8 ± 0.1 mN; p < 0.05). This study is the first to demonstrate that PFs of patients elicit substantial arterial constrictions, which is mediated primarily by ET-1. Interfering with the vasoconstrictor action of PF could be a potential therapeutic target to improve coronary blood flow in cardiac patients.
A gradient flow approach to quantization of measures
Authors: Caglioti Emanuele , Golse François , Iacobelli Mikaela
Published: April 2015

In this paper we study a gradient flow approach to the problem of quantization of measures in space dimension one. By embedding our problem in L2, we find a continuous version of this problem corresponding to the limit as the number of atoms in the approximating measure tends to infinity. Under some suitable regularity assumptions on the density, we prove uniform stability and quantitative convergence results for the discrete and continuous dynamics.
Signatures of Majorana dark matter with t-channel mediators
Authors: Garny Mathias , Ibarra Alejandro , Vogl Stefan
Published: April 2015

Three main strategies are being pursued to search for nongravitational dark matter signals: direct detection, indirect detection and collider searches. Interestingly, experiments have reached sensitivities in these three search strategies which may allow detection in the near future. In order to take full benefit of the wealth of experimental data, and in order to confirm a possible dark matter signal, it is necessary to specify the nature of the dark matter particle and of the mediator to the Standard Model. In this paper, we focus on a simplified model where the dark matter particle is a Majorana fermion that couples to a light Standard Model fermion via a Yukawa coupling with a scalar mediator. We review the observational signatures of this model and we discuss the complementarity among the various search strategies, with emphasis in the well motivated scenario where the dark matter particles are produced in the early universe via thermal freeze-out.
MeV particles in a decay chain process from laser-induced processes in ultra-dense deuterium D(0)
Authors: Holmlid Leif
Published: April 2015

The ejection of particles with energy up to 20 MeV u-1 was reported previously from laser-induced processes in ultra-dense deuterium D(0). Studies of the kinetics of particle formation and decay, and of particle penetration through thick plates are now reported. Magnetic deflection is used to remove charged particles like electrons formed at the target. The signals at a collector in the beam at 0.9 m distance and a shadowed loop collector behind a 1.5–4.5 mm thick steel plate at 0.6 m are compared. The signal at the distant collector matches an intermediate particle B in a decay chain A → B → C with formation and decay time constants of 5–15 ns. The signal at the loop collector is delayed relative to the more distant collector, thus showing a delay of the particles penetrating through the steel plate. The signal at this collector is due to pair production with charge cancellation. Compton electrons from gamma radiation are observed at peak current densities of 1 mA cm-2 at the distant collector.
Global limit theorems on the convergence of multidimensional random walks to stable processes
Authors: Agbor A. , Molchanov S. , Vainberg B.
Published: April 2015

Symmetric heavily tailed random walks on Zd, d ≥ 1, are considered. Under appropriate regularity conditions on the tails of the jump distributions, global (i.e. uniform in x, t, ∣x∣ + t → ∞,) asymptotic behavior of the transition probability p(t, 0, x) is obtained. The examples indicate that the regularity conditions are essential.
The Knowledge Management Information Landscape — Awareness, Access, Use and Value of Sources
Authors: Bedford Denise A. D.
Published: April 2015

Information landscape is a critical component of professional and scholarly disciplines. Established disciplines have a managed information foundation covering primary, secondary and tertiary sources, targeted search capabilities, discipline-specific knowledge organisation tools and services, and quality controlled review processes. The information landscapes of emerging disciplines may be more chaotic and unsettled, and present challenges for professionals. This research considers the information landscape of the knowledge management discipline. An open public survey of knowledge professionals provides insights into three factors that affect the landscape including: (1) information awareness; (2) information use and access; and (3) information valuation. Findings highlight key information management challenges, and offer suggestions for solutions.
Enhancing Access to Knowledge Management Literature — A Proposal for Domain-Based Classification Scheme and Thesaurus
Authors: Bedford Denise A. D.
Published: April 2015

Knowledge organisation systems (KOS) include a variety of tools and methods for organising information and knowledge 'things'. When we refer to KOS we generally mean classification schemes, thesauri, semantic networks, and authority control systems. Most academic disciplines are supported by professionally developed and maintained KOS. This is not the case for knowledge management. Knowledge management is insufficiently treated in existing KOS. The research is exploratory in its approach to developing KOS tools for the field. It is engaging in that at every stage of development it leverages the knowledge and input of the larger knowledge management community.
The Role of Power and Jealousy in Cooperation — A Framework for Artificial Agents
Authors: Barachini Franz
Published: April 2015

We are interested in the question of how to motivate people to share valuable information so that group performance can be leveraged. In particular, we investigate the impact of power and jealousy on cooperation. It is an unresolved issue how these two social phenomena influence cooperation. We study the impact of power and jealousy to cooperation models by using dynamic artificial agents and agent populations following combined characteristics. We simulate dynamic multi player goods games and we use the Business Transaction Theory as a basic layer for information valuation. Payoff matrices as they are used in evolutionary game theory are also applied. Our motivation to use artificial agents is manifold. First, we are able to simulate small to huge populations in short time, second we are flexible in changing agent characteristics, and third it is hard to find people who admit being jealous in real life. The technical framework is based on the eclipse development environment. The artificial agents are programmed in Java. Our interdisciplinary approach is new since emotions, in context with collaboration, have never been investigated by artificial agents and game theoretical means. Our findings show that incentives might have a big influence on jealousy and even on egoists.
New secure and robust audio watermarking algorithm based on QR factorization in wavelet domain
Authors: Hemis Mustapha , Boudraa Bachir , Merazi-Meksen Thouraya
Published: April 2015

Digital watermarking consists in embedding imperceptible information into a host signal. It has been proposed to solve problems as varied as the protection of the copyright, content authentication, fingerprinting and broadcast monitoring. This paper presents a new approach for audio watermarking using the QR factorization in wavelet domain. This approach is based on embedding a watermark binary image in the R matrices of low frequency blocks DWT coefficients of audio signal. In this algorithm, the watermark is embedded by applying a Quantization Index Modulation (QIM) process on the determined optimal sample for each matrix R. The watermark can be blindly extracted without the knowledge of the original audio signal. Experimental results show that the proposed audio watermarking scheme maintains high quality of the audio signal. Signal to Noise Ratio (SNR), Log Spectral Distortion (LSD) and Mean Opinion Score (MOS) are about 40 dB, 0.37 dB and 4.84, respectively. Moreover, the scheme is quite robust against common signal processing attacks such as noise addition, filtering and MP3 compression. In addition, this method ensures a secure extraction process by using a private key, making it suitable for secure applications such as copyright protection.
ADPRtool: A novel predicting model for identification of ASP-ADP-Ribosylation sites of human proteins
Authors: Liu Jun , Han Jiuqiang , Lv Hongqiang
Published: April 2015

Post-translational modifications (PTMs) occur in the vast majority of proteins, and they are essential for many protein functions. Computational prediction of the residue location of PTMs enhances the functional characterization of proteins. ADP-Ribosylation is an important type of PTM, because it is implicated in apoptosis, DNA repair, regulation of cell proliferation, and protein synthesis. However, mass spectrometric approaches have difficulties in identifying a vast number of protein ADP-Ribosylation sites. Therefore, a computational method for predicting ADP-Ribosylation sites of human proteins seems useful and necessary. Four types of sequence features and an incremental feature selection technique are utilized to predict protein ADP-Ribosylation sites. The final feature set for ADPR prediction modeling is optimized, based on a minimum redundancy maximum relevance criterion, so as to make more accurate predictions on aspartic acid ADPR modified residues. Our prediction model, ADPRtool, is capable to predict Asp-ADP-Ribosylation sites with a total accuracy of 85.45%, which is as good as most computational PTM site predictors. By using a sequence-based computational method, a new ADP-Ribosylation site prediction model — ADPRtool, is developed, and it has shown great accuracies with total accuracy, Matthew's correlation coefficient and area under receiver operating characteristic curve.
A new model of arcsin-gravity
Authors: Kruglov S. I.
Published: April 2015

The new model of modified F(R)-gravity theory with the function F(R) = R + (a/γ) arcsin (γR) is suggested and investigated. Constant curvature solutions corresponding to the extremum of the effective potential are obtained. We consider both the Jordan and Einstein frames, and the potential and the mass of the scalar degree of freedom are found. It was shown that the de Sitter space-time is unstable but the flat space-time is stable. We calculate the slow-roll parameters ϵ, η, and the e-fold number of the model. Critical points of autonomous equations for the de Sitter phase and the matter dominated epoch are obtained and learned.
Parallel fluorescence and phosphorescence monitoring of singlet oxygen photosensitization in rats
Authors: Dědic Roman , Stíbal Adam , Vyklický Vojtěch , Franěk Miloslav , Svoboda Antonín , Hála Jan
Published: April 2015

The time- and spectral-resolved set-up for measurements of weak infrared luminescence of photosensitizers (PSs) and singlet oxygen using optical lightguides was used on skin of laboratory animals in vivo. Wistar rats with abdominal incisions treated by methylis aminolevulinitis (MAL) were used as a model. A control group of animals with abdominal incisions was also tested. Spectrally resolved fluorescence of the PS was acquired during the treatment from the same spot. The intensity and spectral profile of the fluorescence signal from the skin can be used to guide the detection setup to the investigated spots in the lesion. The rate of bleaching of Protoporphyrin IX band and appearance of a band of its photoproducts during the treatment can be characterized by the exposition ED, under which the latter becomes dominant feature in fluorescence spectrum. ED value differs statistically significantly between the normal skin and the lesion treated by MAL. No direct proportionality was found between the fluorescence signal and singlet oxygen production. Nevertheless, the strong fluorescence signal is necessary but not a sufficient condition for higher singlet oxygen production in vivo. ED value correlates rather well with production of singlet oxygen, but differently in lesion and normal skin. Lifetimes of singlet oxygen differ between spots outside and in the lesion. PS triplet state lifetimes exhibit weak difference between spots treated and untreated by MAL.
Online and semi-online scheduling to minimize makespan on single machine with an availability constraint
Authors: Gao Qiang , Li Ganggang , Lu Xiwen
Published: April 2015

Online and semi-online scheduling problems on a single machine with an availability constraint are considered in this paper. The machine has one unavailable interval in which jobs cannot be processed. Preemption is not allowed. Jobs arrive over time. The objective is to minimize makespan. First we discuss the online version of the problem. After giving its lower bound, we prove that Earliest Release Date (ERD) algorithm is an optimal algorithm. Then we study some semi-online problems in which the largest processing time, the total processing time, the largest release date, or the optimal makespan is known in advance. For these semi-online problems, we give their lower bounds, design semi-online algorithms and prove their competitive ratios, respectively.
A parallel matching algorithm based on order relation for HLA data distribution management
Authors: Liu Yanbing , Sun Hongbo , Fan Wenhui , Xiao Tianyuan
Published: April 2015

In distribution simulation based on High-level architecture (HLA), data distribution management (DDM) is one of HLA services for the purpose of filtering the unnecessary data transferring over the network. DDM admits the sending federates and the receiving federates to express their interest using update regions and subscription regions in a multidimensional routing space. There are several matching algorithms to obtain overlap information between the update regions and subscription regions. When the number of regions increase sharply, the matching process is time consuming. However, the existing algorithms is hard to be parallelized to take advantage of the computing capabilities of multi-core processors. To reduce the computational overhead of region matching, we propose a parallel algorithm based on order relation to accelerate the matching process. The new matching algorithm adopts divide-and-conquer approach to divide the regions into multiple region bound sublists, each of which comprises parts of region bounds. To calculate the intersection inside and amongst the region bound sublists, two matching rules are presented. This approach has good performance since it performs region matching on the sublists parallel and does not require unnecessary comparisons within regions in different sublists. Theoretical analysis has been carried out for the proposed algorithm and experimental result shows that the proposed algorithm has better performance than major existing DDM matching algorithms.
Sedimentological evolution of Sele Formation deep-marine depositional systems of the Central North Sea
Authors: Eldrett James , Tripsanas Efthymios , Davis Christopher , McKie Tom , Vieira Manuel , Osterloff Peter , Sandison Tom
Published: April 2015

The Paleocene–Eocene-aged Sele Formation is developed across the basinal region of the Central North Sea. The section comprises a number of deep-marine fan systems that expanded and contracted across the basin floor in response to relative sea-level changes on the basin margin and fluctuating sediment yield off the Scottish landmass modulated by climate and hinterland uplift. Persistent sediment entry points to the basin resulted in the development of discrete axial and transverse fan fairways with a geometry dictated by an irregular bathymetry sculpted by differential compaction across Mesozoic faults, halokinesis and antecedent fan systems. A high-resolution biostratigraphic framework has allowed the evolution of fan-dispersal systems in response to these effects to be tracked across the basin within four genetic sequences. The proximal parts of the fans comprised channel complexes of low sinuosity, high lateral offset, and low aggradation. The development of these systems in a bathymetrically confined corridor of the Central Graben (
c.
65 km wide), combined with high sediment supply, resulted in the eventual burial of any underlying relief. The behaviour of sand-rich reservoirs in this region is dominated by the permeability contrast between high-quality channel fairways and more heterolithic overbank regions, with the potential for early water breakthrough and aquifer coning in the channel fairways, and unswept volumes in overbank locations. Compartmentalization of compensationally stacked channel bodies occurs locally, with stratigraphic trapping caused by lateral channel pinch-outs, channel-base debrites, mud-rich drapes and abandonment fines. Towards the southern part of Quadrant 22, approximately 150 km down-palaeoflow, the systems became less confined and in this region are dominated by channel–lobe complexes, which continued to interact with an irregular bathymetry controlled by antecedent fans, mass-transport complexes and halokinesis in the form of rising salt diapirs. Reservoirs in this region are inherently stratigraphically compartmentalized by their heterolithic lithology and compensational stacking of lobes, and further complicated by structuration and instability induced by the diapiric or basement structures needed to generate a trapping structure in these settings.
Secure Compilation to Protected Module Architectures
Authors: Patrignani Marco , Agten Pieter , Strackx Raoul , Jacobs Bart , Clarke Dave , Piessens Frank
Published: April 2015

A fully abstract compiler prevents security features of the source language from being bypassed by an attacker operating at the target language level. Unfortunately, developing fully abstract compilers is very complex, and it is even more so when the target language is an untyped assembly language. To provide a fully abstract compiler that targets untyped assembly, it has been suggested to extend the target language with a protected module architecture—an assembly-level isolation mechanism which can be found in next-generation processors. This article provides a fully abstract compilation scheme whose source language is an object-oriented, high-level language and whose target language is such an extended assembly language. The source language enjoys features such as dynamic memory allocation and exceptions. Secure compilation of first-order method references, cross-package inheritance, and inner classes is also presented. Moreover, this article contains the formal proof of full abstraction of the compilation scheme. Measurements of the overhead introduced by the compilation scheme indicate that it is negligible.
Model Continuity in Discrete Event Simulation
Authors: Çetinkaya Deniz , Verbraeck Alexander , Seck Mamadou D.
Published: April 2015

Most of the well-known modeling and simulation (M&S) methodologies state the importance of conceptual modeling in simulation studies, and they suggest the use of conceptual models during the simulation model development process. However, only a limited number of methodologies refers to how to move from a conceptual model to an executable simulation model. Besides, existing M&S methodologies do not typically provide a formal method for model transformations between the models in different stages of the development process. Hence, in the current M&S practice, model continuity is usually not fulfilled. In this article, a model-driven development framework for M&S is presented to bridge the gap between different stages of a simulation study and to obtain model continuity. The applicability of the framework is illustrated with a prototype modeling environment and a case study in the discrete event simulation domain.
TADSim
Authors: Mniszewski Susan M. , Junghans Christoph , Voter Arthur F. , Perez Danny , Eidenbenz Stephan J.
Published: April 2015

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. We present a new class of tools called
application simulators
—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family of molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.
Statistical Debugging for Simulations
Authors: Gore Ross , Reynolds Jr. Paul F. , Kamensky David , Diallo Saikou , Padilla Jose
Published: April 2015

Predictions from simulations have entered the mainstream of public policy and decision-making practices. Unfortunately, methods for gaining insight into faulty simulations outputs have not kept pace. Ideally, an insight gathering method would automatically identify the cause of a faulty output and explain to the simulation developer how to correct it. In the field of software engineering, this challenge has been addressed for general-purpose software through statistical debuggers. We present two research contributions,
elastic predicates
and
many-valued labeling functions
, that enable debuggers designed for general-purpose software to become more effective for simulations employing random variates and continuous numbers. Elastic predicates address deficiencies of existing debuggers related to continuous numbers, whereas many-valued labeling functions support the use of random variates. When used in combinations, these contributions allow a simulation developer tasked with localizing the program statement causing the faulty simulation output to examine 40% fewer statements than the leading alternatives. Our evaluation shows that elastic predicates and many-valued labeling functions maintain their ability to reduce the number of program statements that need to be examined under the imperfect conditions that developers experience in practice.
Physical Modification of Food Starch Functionalities
Authors: BeMiller James N. , Huber Kerry C.
Published: April 2015

Because, in general, native starches do not have properties that make them ideally suited for applications in food products, most starch is modified by dervatization to improve its functionality before use in processed food formulations, and because food processors would prefer not to have to use the modified food starch label designation required when chemically modified starches are used, there is considerable interest in providing starches with desired functionalities that have not been chemically modified. One investigated approach is property modification via physical treatments, that is, modifications of starches imparted by physical treatments that do not result in any chemical modification of the starch. Physical treatments are divided into thermal and nonthermal treatments. Thermal treatments include those that produce pregelatinized and granular cold-water-swelling starches, heat-moisture treatments, annealing, microwave heating, so-called osmotic pressure treatment, and heating of dry starch. Nonthermal treatments include ultrahigh-pressure treatments, instantaneous controlled pressure drop, use of high-pressure homogenizers, dynamic pulsed pressure, pulsed electric field, and freezing and thawing.
Protein-Polysaccharide Interactions to Alter Texture
Authors: van de Velde Fred , de Hoog Els H.A. , Oosterveld Alexander , Tromp R. Hans
Published: April 2015

The sensory perception of texture is an important contributor of our general appreciation of foods. Food texture is mainly described in terms of mouthfeel and afterfeel attributes. The role of oral processing in the perception of texture and the role of microstructure therein have been reviewed regularly over recent years ( Chen & Engelen 2012 , Foegeding et al. 2011 , Stieger & van de Velde 2013 ) and are not, therefore, addressed in this review. The scope of this review relates to the molecules that underlay the texture of foods. Protein, carbohydrate, and fat are the major structuring components in foods. In this review we focus on the physical interactions between proteins and polysaccharides that form the basis for the microstructure and texture of these foods. In general, food products are classified in four categories by their sensory and rheological properties: liquids, semisolids, soft solids, and hard solids ( van Vliet et al. 2009 ). These four categories provide a useful classification framework, although they are not precisely defined by specific rheological properties. The current review focuses on semisolid and soft-solid foods.
Collagen and Gelatin
Authors: Liu Dasong , Nikoo Mehdi , Boran Gökhan , Zhou Peng , Regenstein Joe M.
Published: April 2015

Collagen and gelatin have been widely used in the food, pharmaceutical, and cosmetic industries due to their excellent biocompatibility, easy biodegradability, and weak antigenicity. Fish collagen and gelatin are of renewed interest, owing to the safety and religious concerns of their mammalian counterparts. The structure of collagen has been studied using various modern technologies, and interpretation of the raw data should be done with caution. The structure of collagen may vary with sources and seasons, which may affect its applications and optimal extraction conditions. Numerous studies have investigated the bioactivities and biological effects of collagen, gelatin, and their hydrolysis peptides, using both in vitro and in vivo assay models. In addition to their established nutritional value as a protein source, collagen and collagen-derived products may exert various potential biological activities on cells in the extracellular matrix through the corresponding food-derived peptides after ingestion, and this might justify their applications in dietary supplements and pharmaceutical preparations. Moreover, an increasing number of novel applications have been found for collagen and gelatin. Therefore, this review covers the current understanding of the structure, bioactivities, and biological effects of collagen, gelatin, and gelatin hydrolysates as well as their most recent applications.
High Hydrostatic Pressure Processing: A Promising Nonthermal Technology to Inactivate Viruses in High-Risk Foods
Authors: Lou Fangfei , Neetoo Hudaa , Chen Haiqiang , Li Jianrong
Published: April 2015

Foodborne outbreaks of viral origin have become increasingly a serious public health concern. High-pressure processing (HPP), a nonthermal technology, has come to the forefront for food processing given its minimal effects on food quality. Recent studies have revealed encouraging results for the inactivation of several human viruses by HPP. This review provides comprehensive information on the use of HPP to eliminate viruses in model systems and foods. We address the influences of various parameters, including pressure level, holding time, pH, temperature, and food matrix on the efficacy of pressure inactivation of viruses, as well as insight into the mechanisms for inactivation of enveloped and nonenveloped viruses. HPP is a promising technology for mitigating virus contamination of foods, thus it is essential to identify the optimal parameters for enhancing virus inactivation while ensuring sensory and nutritional quality retention of foods.
Learning Deep Generative Models
Authors: Salakhutdinov Ruslan
Published: April 2015

Building intelligent systems that are capable of extracting high-level representations from high-dimensional sensory data lies at the core of solving many artificial intelligence–related tasks, including object recognition, speech perception, and language understanding. Theoretical and biological arguments strongly suggest that building such systems requires models with deep architectures that involve many layers of nonlinear processing. In this article, we review several popular deep learning models, including deep belief networks and deep Boltzmann machines. We show that (a) these deep generative models, which contain many layers of latent variables and millions of parameters, can be learned efficiently, and (b) the learned high-level feature representations can be successfully applied in many application domains, including visual object recognition, information retrieval, classification, and regression tasks.