bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Roughness on a High-Pressure Steam Turbine Stage: An Experimental and Numerical Study
Authors: Bellucci Juri , Rubechini Filippo , Marconcini Michele , Arnone Andrea , Arcangeli Lorenzo , Maceli Nicola , Dossena Vincenzo
Published: August 2014

This work deals with the influence of roughness on high-pressure steam turbine stages. It is divided in three parts. In the first one, an experimental campaign on a linear cascade is described, in which blade losses are measured for different values of surface roughness and in a range of Reynolds numbers of practical interest. The second part is devoted to the basic aspects of the numerical approach and consists of a detailed discussion of the roughness models used for computations. The fidelity of such models is then tested against measurements, thus allowing their fine-tuning and proving their reliability. Finally, comprehensive computational fluid dynamics (CFD) analysis is carried out on a high-pressure stage, in order to investigate the influence of roughness on the losses over the entire stage operating envelope. Unsteady effects that may affect the influence of the roughness, such as the upcoming wakes on the rotor blade, are taken into account, and the impact of transition-related aspects on the losses is discussed.
Robust Optimal Operation of a Gas Turbine Cogeneration Plant Under Uncertain Energy Demands
Authors: Yokoyama Ryohei , Ohkura Masashi , Wakui Tetsuya
Published: August 2014

Some optimal operation methods based on the mixed-integer linear programming (MILP) have been proposed to operate energy supply plants properly from the viewpoints of economics, energy saving, and CO2 emission reduction. However, most of the methods are effective only under certain energy demands. In operating an energy supply plant actually, it is necessary to determine the operational strategy properly based on predicted energy demands. In this case, realized energy demands may differ from the predicted ones. Therefore, it is necessary to determine the operational strategy so that it is robust against the uncertainty in energy demands. In this paper, an optimization method based on the MILP is proposed to conduct the robust optimal operation of energy supply plants under uncertain energy demands. The uncertainty in energy demands is expressed by their intervals. The operational strategy is determined to minimize the maximum regret in the operational cost under the uncertainty. In addition, a hierarchical relationship among operation modes and on/off states of equipment, energy demands, and energy flow rates of equipment is taken into account. First, a general formulation of a robust optimal operation problem is presented, which is followed by a general solution procedure. Then, in a numerical study, the proposed method is applied to a gas turbine cogeneration plant for district energy supply. Through the study, some features of the robust optimal operation are clarified, and the validity and effectiveness of the proposed method are ascertained.
A Three-Dimensional Computational Study of Pulsating Flow Inside a Double Entry Turbine
Authors: Newton Peter , Martinez-Botas Ricardo , Seiler Martin
Published: August 2014

The double entry turbine contains two different gas entries, each feeding 180 deg of a single rotor wheel. This geometry can be beneficial for use in turbocharging and is uniquely found in this application. The nature of the turbocharging process means that the double entry turbine will be fed by a highly pulsating flow from the exhaust of an internal combustion engine, most often with out-of-phase pulsations in each of the two entries. Until now research on the double entry turbine under pulsating flow conditions has been limited to experimental work. Although this is of great value in showing how pulsating flow will affect the performance of the double entry turbine, the level of detail with which this can be studied is limited. This paper is the first to use a three-dimensional computational analysis to study the flow structures within a double entry turbine under conditions of pulsating flow. The analysis looks at one condition of pulsating flow with out-of-phase pulsations. The computational results are validated against experimental data taken from the turbocharger test facility at Imperial College and a good agreement is found. The analysis first looks at the degree of mass flow storage within different components of the turbine and discusses the effect on the performance of the turbine. Each of the volute limbs is found to be subject to a large degree of mass storage throughout a pulse cycle demonstrating a definite impact of the unsteady flow. The rotor wheel shows a much smaller degree of mass flow storage overall due to the pulsating flow; however, each rotor passage is subject to a much larger degree of mass flow storage due to the instantaneous flow inequality between the two volute inlets. This is a direct consequence of the double entry geometry. The following part of the analysis studies the loss profile within the turbine under pulsating flow using the concept of entropy generation rate. A significant change in the loss profile of the turbine is found throughout the period of a pulse cycle showing a highly changing flow regime. The major areas of loss are found to be due to tip leakage flow and mixing within the blade passage.
The Matching of a Vaned Diffuser With a Radial Compressor Impeller and Its Effect on the Stage Performance
Authors: Casey Michael , Rusch Daniel
Published: August 2014

The matching of a vaned diffuser with a centrifugal impeller is examined with a one-dimensional (1D) analysis combined with extensive experimental data. A matching equation is derived to define the required throat area of the diffuser relative to the throat area of the impeller at different design speeds and validated by comparison with a wide range of compressor designs. The matching equation is then used to give design guidelines for the throat area of vaned diffusers operating with impellers at different tip-speed Mach numbers. An analysis of test data for a range of high pressure ratio turbocharger compressor stages is presented in which different matching between the diffuser and the impeller has been experimentally examined. The test data includes different impellers with different diffuser throat areas over a wide range of speeds. It is shown that the changes in performance with speed and diffuser throat area can be explained on the basis of the tip-speed Mach number which causes both the diffuser and impeller to choke at the same mass flow. Based on this understanding, a radial compressor map prediction method is extended to include this parameter, so that more accurate maps for matched and mismatched vaned diffusers can be predicted.
Bending Instability of a General Cross Section Thin-Wall Tube for Minimal Radius of Curvature Passage
Authors: Ziso Hadas , Shoham Moshe
Published: August 2014

This paper describes an analytical tool for the design of thin-wall tubes for passage through minimal radius of curvature trajectory. The design is based on a model of thin-wall tube buckling under pure bending. An extended analytical solution for general initial cross section is found based on Brazier method by energy theory of elastic stability. The model predicts the critical moment, curvature, flattening, and stress and allows choosing the most suitable cross section shape for a specific purpose. For example, tubes with ocular and rounded-ocular cross sections were found suitable for semiflexible applications such as endoscopy, where they elastically cross a sharp corner.
Hierarchical Optimization-Based Approach for Two-Dimensional Rectangular Layout Design Problems
Authors: Fujita Kikuo , Yamasaki Shintaro , Kawamoto Masayuki
Published: August 2014

In this study, we propose a hierarchical optimization-based approach for two-dimensional rectangular layout design problems. Decomposition-based optimization has been a key approach for complicated design problems in multidisciplinary design optimization (MDO), but the main focus has been design problems where the design variables are continuous. On the other hand, various approaches have been developed for layout design based on evolutionary algorithms, e.g., simulated annealing (SA) and genetic algorithms (GAs) which can handle its combinatorial nature in an effective manner. In the present study, we aim to introduce a new paradigm by combining decomposition-based optimization and evolutionary algorithms for solving complicated layout design problems. In this approach, the original layout problem is decomposed into the top-level layout problem and a set of sublevel layout problems, where the layouts obtained from the sublevel problems are used as components of the top-level problem. Since the preferable shapes of these components are unclear when the sublevel problems are solved, a set of Pareto optima are provided in the sublevel problems and these solutions are used as candidate components in the top-level problem. A computational design algorithm is developed based on this approach, which represents the layout topology with sequence pair and the shape of each subsystem or component with the aspect ratio, and they are optimized using GAs. The Pareto optimality of the sublevels is handled by multi-objective GAs, and a set of Pareto optima is generated simultaneously. The top-level and sublevel layout problems are coordinated via the exchange of preferable ranges for the shapes and layout. This approach was implemented and applied to an example problem to demonstrate its performance and capability.
Tribological Behavior of Carbon Nanotubes as an Additive on Lithium Grease
Authors: Mohamed Alaa , Osman T. A. , Khattab A. , Zaki M.
Published: August 2014

Carbon nanotubes (CNTs) with 10 nm average diameter and 5 μm in length were synthesized by electric arc discharge. The morphology and structure of CNTs were characterized by high resolution transmission electron microscopy (HRTEM) and X-ray powder diffraction. The tribological properties of CNTs as an additive on lithium grease were evaluated with a four ball tester. The results show that the grease with CNTs exhibit good performance in antiwear (AW) and decrease the wear scare diameter (WSD) about 63%, decrease friction reduction about 81.5%, and increase the extreme pressure (EP) properties and load carrying capacity about 52% with only 1% wt. of CNTs added to lithium grease. The action mechanism was estimated through analysis of the worn surface with a scanning electron microscope (SEM) and energy dispersive X-ray (EDX). The results indicate that a boundary film mainly composed of CNTs, Cr, iron oxide, and other organic compounds was formed on the worn surface during the friction process.
Self-Powered Eddy Current Damper for Rotordynamic Applications
Authors: Silvagni Mario , Tonoli Andrea , Bonfitto Angelo
Published: August 2014

The vibration control of rotors is often performed using elastomeric or fluid dampers together with rolling element or hydrodynamic type bearings. Electromagnetic dampers seem a valid alternative to conventional solutions and also to active magnetic bearings (AMBs) because their simpler architecture, size and, if of transformer type, also for the absence of power electronics, position sensors, and any fast feedback loop. However, transformer eddy current dampers require a constant voltage power supply than can be provided by an embedded generator to reduce cost and improve the reliability. The present paper proposes a self-powered damper to fulfill these requirements. A three-phase permanent magnet electric generator (connected to the rotating shaft) generates the required power for the damping device. The generator is connected to the damping circuit by means of tuned impedance and a three-phase rectifier.
A bank of beamformers implementing a constant-amplitude panning law
Authors: Hur Yoomi , Abel Jonathan S. , Park Young-cheol , Youn Dae Hee
Published: August 2014

This paper describes a technique for designing a collection of beamformers, a “beamformer bank,” that approximately produces a constant-amplitude panning law. Useful in multichannel audio recording scenarios, a point source will appear with energy above a specified sidelobe level in at most two adjacent beams, and the sum of all beam signals will approximate the source signal. A design method is described in which a specified sidelobe level determines beamwidth as a function of arrival direction and frequency, leading directly to the number and placement of beams at each frequency. Simulation results are presented verifying the proposed technique's performance.
Counting Steps in Institutionalized Older Adults During Daily Life Activities: The Validation of Two Motion Sensors
Authors: Martien Sofie , Delecluse Christophe , Seghers Jan , Boen Filip
Published: August 2014

The primary purpose of this study was to assess the validity of two motion sensors in measuring steps in institutionalized older adults during daily life activities. Sixty-eight nursing home residents (85.8 ± 5.6 years) were equipped with a hip-worn and ankle-worn piezoelectric pedometer (New Lifestyles 2000) and with an arm-mounted multisensor (SenseWear Mini). An investigator with a hand counter tallied the actual steps. The results revealed that the multisensor and hip- and ankle-worn pedometer significantly underestimated step counts (89.6 ± 17.2%, 72.9 ± 25.8%, and 20.8 ± 24.6%, respectively). Walking speed accounted for 41.6% of the variance in percent error of the ankle-worn pedometer. The threshold value for accurate step counting was set at 2.35 km/hr, providing percent error scores within ± 5%. The ankle-worn piezoelectric pedometer can be useful for accurate quantification of walking steps in the old and old-old (> 85 years) walking faster than 2.35 km/hr.
Effect of ActiGraph GT3X+ Position and Algorithm Choice on Step Count Accuracy in Older Adults
Authors: Korpan Sheila M. , Schafer Jenessa L. , Wilson Kaylie C.S. , Webber Sandra C.
Published: August 2014

Accelerometer step count accuracy may be affected by gait speed, device positioning, and analysis algorithm selection. We assessed ActiGraph GT3X+ step count accuracy related to device placement and analysis algorithm in older adults with walking aids (n = 13) and without walking aids (n = 22). Participants (81.5 ± 5.0 years of age) completed a timed 100-m walk wearing five GT3X+ monitors (hips, ankles, lumbar spine). Individuals with walking aids had slower gait speeds (0.8 ± 0.20 m/s versus 1.2 ± 0.20 m/s without walking aids, p < .001). Intraclass correlation coefficient values for observed versus monitored steps were highest when ankle placement and the low frequency extension (LFE) algorithm were used (left ankle ICC = .989, right ankle ICC = .998). Using the GT3X+ ankle placement and analyzing data with the LFE algorithm resulted in the most accurate step counts in older adults.
Is the Provision of Physical Education to Senior-Years Students Associated With Greater Physical Activity Levels? Insight Into a Province-Wide Policy
Authors: Comte Melisa , Hobin Erin , Manske Steve , Casey Catherine , Griffith Jane , Leggett Carly , Veugelers Paul , Murnaghan Donna , McGavock Jonathan
Published: August 2014

Objectives:

The purpose of this study was to determine if participation in physical education (PE) was associated with increased moderate-to-vigorous physical activity (MVPA) levels in adolescents.

Methods:

This was a cross sectional study comparing MVPA levels in senior-years students—grade 11 and 12—enrolled in high school PE during the semester data were collected compared with those not enrolled in PE in that same semester. The primary outcome measure was daily MVPA measured by accelerometry. The primary exposure was participation in PE.

Results:

Among the 508 adolescents (16.9 ± 0.8 yrs, 49% female, n = 338 exposed to PE) studied, no differences in MVPA (47.0 ± 25.8 vs. 43.9 ± 25.0 mins/day, P = .25) or sedentary time (540.2 ± 94.7 vs. 550.2 ± 79.4 mins/day, P = .79) were noted between students enrolled in PE compared with students not enrolled in PE. Participation in PE was associated with a greater odds of achieving >60 minutes of MVPA daily (OR: 1.69; 95% CI: 1.04−2.75). This association was stronger among boys (OR: 2.4; 95% CI: 1.2−4.8) than girls (OR: 1.17; 95% CI: 5−2.7).

Conclusion:

Enrollment in PE in grade 11 or 12 is associated with modestly higher levels of MVPA and an increased likelihood of meeting PA guidelines among students in grades 11 and 12, particularly among boys.
Contextual Influences on Weight Status Among Impoverished Adolescents: Neighborhood Amenities for Physical Activity and State Laws for Physical Education Time Requirements
Authors: Oh April Y. , Hennessy Erin , McSpadden Kate E. , Perna Frank M.
Published: August 2014

Purpose:

This study examines the relationship between state laws for physical education and neighborhood amenities for physical activity on weight status in adolescents of low socioeconomic status.

Methods:

Data from 2 national data sources: Classification of Laws Associated with School Students (CLASS) and the National Survey of Children’s Health (NSCH) were combined and analyzed.

Results:

Multinomial regression models found that adolescents in states with strong PE law were associated with a lower odds of being obese [OR = 0.63 (0.41, 0.97)]; however, when PE law and neighborhood amenities were included, only neighborhood amenities were associated with lower odds of obesity, but also greater odds of overweight status.

Conclusion:

This study emphasizes the potential significance of state laws on low SES groups to combat obesity; as well as the potential differential effects of local level factors, and alignment with policy goals for healthy weight.
Measuring the Ability to Tolerate Activity-Related Discomfort: Initial Validation of the Physical Activity Acceptance Questionnaire (PAAQ)
Authors: Butryn Meghan L. , Arigo Danielle , Raggio Greer A. , Kaufman Alison Infield , Kerrigan Stephanie G. , Forman Evan M.
Published: August 2014

Background:

Physical activity (PA) is essential for health, but many adults find PA adherence challenging. Acceptance of discomfort related to PA may influence an individual’s ability to begin and sustain a program of exercise. The aim of this study was to evaluate the psychometric properties of the Physical Activity Acceptance Questionnaire (PAAQ).

Methods:

The PAAQ was administered to 3 distinct samples (N = 418). Each sample completed additional self-report measures; 1 sample also wore accelerometers for 7 days (at baseline and 6 months later).

Results:

The PAAQ demonstrated high internal validity for its total score (α = .89) and 2 subscales (Cognitive Acceptance α = .86, Behavioral Commitment α = .85). The PAAQ also showed convergent validity with measures of mindfulness, self-reported physical activity levels, and accelerometer-verified levels of moderate-to-vigorous PA (MVPA; P-values < .05). The Cognitive Acceptance subscale showed predictive validity for objectively-verified PA levels among individuals attempting to increase PA over 6 months (P = .05). Test-retest reliability for a subset of participants (n = 46) demonstrated high consistency over 1 week (P < .0001).

Conclusions:

The PAAQ demonstrates sound psychometric properties, and shows promise for improving the current understanding of PA facilitators and barriers among adults.
Total Activity Counts and Bouted Minutes of Moderate-To-Vigorous Physical Activity: Relationships With Cardiometabolic Biomarkers Using 2003–2006 NHANES
Authors: Wolff-Hughes Dana L. , Fitzhugh Eugene C. , Bassett David R. , Churilla James R.
Published: August 2014

Purpose:

To contrast associations of accelerometer-measured moderate-to-vigorous physical activity (MVPA) accumulated in bouts and total activity counts (TAC) with cardiometabolic biomarkers in U.S. adults.

Methods:

Using 2003–2006 National Health and Nutrition Examination Survey (NHANES) data, the sample was comprised of adults ≥ 20 years, not pregnant or lactating, with self-reported PA and at least 4 days of ≥ 10 hours accelerometer wear time (N = 5668). Bouted MVPA represented the minutes/day with ≥ 2020 counts/minute in bouts of 10 minutes or longer and TAC represented the total activity counts per day. Biomarkers included: cholesterol, triglyceride, glycohemoglobin, plasma glucose, C-peptide, insulin, C-reactive protein, homocysteine, blood pressure, body mass index (BMI), waist circumference, and skinfolds. Nested regression models were conducted which regressed each biomarker on bouted MVPA and TAC simultaneously, while adjusting for relevant covariates.

Results:

Results indicated TAC was more strongly associated with 11 biomarkers: HDL-C, triglyceride, plasma glucose, C-peptide, insulin, C-reactive protein, homocysteine, systolic blood pressure, waist circumference, triceps skinfold, and subscapular skinfold. Bouted MVPA, however, only displayed stronger associations with BMI.

Conclusions:

The total volume of physical activity, represented by TAC, appears to have stronger associations with cardiometabolic biomarkers than MVPA accumulated in bouts.
Physical and Sedentary Activity Levels Among Preschoolers in Home-Based Childcare: A Systematic Review
Authors: Vanderloo Leigh M. , Martyniuk Olivia J. M. , Tucker Patricia
Published: August 2014

Background:

Although preschoolers’ physical activity in center-based childcare has received considerable attention, less is known regarding this group’s activity levels within home-based childcare. This review aimed to explore and synthesize the literature on preschoolers’ physical and sedentary activity levels in home-based childcare. Outdoor playtime was also examined to contribute to the understanding of preschoolers’ activity levels within this particular setting.

Methods:

Nine online databases were searched for peer-reviewed, English-language, primary studies that quantitatively measured physical and sedentary activity levels of preschoolers attending home-based childcare. Studies were excluded if they were nonprimary research, if they lacked a preschool-aged sample, if they did not quantitatively measure physical or sedentary activity, or if they took place in an ineligible environment.

Results:

Seven articles were included in this review; 3 had objective measures of activity levels, and 4 relied on nonobjective measures. Accelerometry data suggest that preschoolers’ average sedentary, moderate-to-vigorous, and total physical activity levels in home-based childcare ranged from 39.5 to 49.6, 1.8 to 9.7, and 10.4 to 33.8 min/hr, respectively. Outdoor playtime appears to be inconsistent in home-based childcare.

Conclusion:

Physical activity among preschoolers attending home-based childcare appears to be relatively low and widely varied. Sedentary time has received less attention in home-based childcare settings. Future research examining activity levels in this unique environment is warranted.
Reliability and Validity of 2 Self-Report Measures to Assess Sedentary Behavior in Older Adults
Authors: Gennuso Keith P. , Matthews Charles E. , Colbert Lisa H.
Published: August 2014

Background:

The purpose of this study was to examine the reliability and validity of 2 currently available physical activity surveys for assessing time spent in sedentary behavior (SB) in older adults.

Methods:

Fifty-eight adults (≥65 years) completed the Yale Physical Activity Survey for Older Adults (YPAS) and Community Health Activities Model Program for Seniors (CHAMPS) before and after a 10-day period during which they wore an ActiGraph accelerometer (ACC). Intraclass correlation coefficients (ICC) examined test-retest reliability. Overall percent agreement and a kappa statistic examined YPAS validity. Lin’s concordance correlation, Pearson correlation, and Bland-Altman analysis examined CHAMPS validity.

Results:

Both surveys had moderate test-retest reliability (ICC: YPAS = 0.59 (P < .001), CHAMPS = 0.64 (P < .001)) and significantly underestimated SB time. Agreement between YPAS and ACC was low (κ = −0.0003); however, there was a linear increase (P < .01) in ACC-derived SB time across YPAS response categories. There was poor agreement between ACC-derived SB and CHAMPS (Lin’s r = .005; 95% CI, −0.010 to 0.020), and no linear trend across CHAMPS quartiles (P = .53).

Conclusions:

Neither of the surveys should be used as the sole measure of SB in a study; though the YPAS has the ability to rank individuals, providing it with some merit for use in correlational SB research.
SMN2
splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy
Authors: Naryshkin Nikolai A. , Weetall Marla , Dakka Amal , Narasimhan Jana , Zhao Xin , Feng Zhihua , Ling Karen K. Y. , Karp Gary M. , Qi Hongyan , Woll Matthew G. , Chen Guangming , Zhang Nanjing , Gabbeta Vijayalakshmi , Vazirani Priya , Bhattacharyya Anuradha , Furia Bansri , Risher Nicole , Sheedy Josephine , Kong Ronald , Ma Jiyuan , Turpoff Anthony , Lee Chang-Sun , Zhang Xiaoyan , Moon Young-Choon , Trifillis Panayiota , Welch Ellen M. , Colacino Joseph M. , Babiak John , Almstead Neil G. , Peltz Stuart W. , Eng Loren A. , Chen Karen S. , Mull Jesse L. , Lynes Maureen S. , Rubin Lee L. , Fontoura Paulo , Santarelli Luca , Haehnke Daniel , McCarthy Kathleen D. , Schmucki Roland , Ebeling Martin , Sivaramakrishnan Manaswini , Ko Chien-Ping , Paushkin Sergey V. , Ratni Hasane , Gerlach Irene , Ghosh Anirvan , Metzger Friedrich
Published: August 2014

Drugs that provide the splice of life

Motor neurons relay signals from the nervous system to muscle fibers. In patients with spinal muscular atrophy, a protein required for the survival of these neurons is deficient or missing altogether, so the neurons gradually die and the patients' muscles waste away. The disease is currently untreatable. Naryshkin
et al.
discovered small-molecule drugs that cause cells to produce the missing protein by altering how a specific mRNA is put together, or “spliced” (see the Perspective by Vigevani and Valcárcel). When the researchers used the drugs to treat diseased mice, the mice showed marked improvement in muscle mass, motor function, and survival.

Science
, this issue p.
688
; see also p.
624
Water droplets in oil are microhabitats for microbial life
Authors: Meckenstock Rainer U. , von Netzer Frederick , Stumpp Christine , Lueders Tillmann , Himmelberg Anne M. , Hertkorn Norbert , Schmitt-Kopplin Philipp , Harir Mourad , Hosein Riad , Haque Shirin , Schulze-Makuch Dirk
Published: August 2014

Microbial life thrives in an oily bubble

Microorganisms can break down hydrocarbons in oil reservoirs. Microbes grow primarily at the interface between oil and water, where they can find nutrients and dispose of metabolites. Meckenstocket al.now show that tiny water droplets can also provide a suitable home for hydrocarbon-degrading microorganisms. The authors examined oil from Pitch Lake, Trinidad and Tobago, and found that diverse microorganisms thrived in these tiny isolated microhabitats.

Science, this issue p.673
Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome
Authors: Gagnon Matthieu G. , Lin Jinzhong , Bulkley David , Steitz Thomas A.
Published: August 2014

Better blood thinner, without bleeding

Blood thinners prevent heart attacks and strokes by making it harder for blood to clot, but these drugs can put patients at risk of dangerous bleeding. Now Moeckle
et al.
describe an enzyme that can prevent clots without this perilous side effect. They engineered the enzyme apyrase to remove the pro-clotting molecule ADP from the blood quickly. In dogs and mice with heart attacks, apyrase stopped blood cells from aggregating, the first step in forming a clot. At the highest dose, the animals suffered less heart damage and did not bleed excessively. In comparison, clopidogrel, a blood thinner used currently in patients, protected the heart less well and did cause excessive bleeding.

Science
, this issue p.
684
The environmental controls that govern the end product of bacterial nitrate respiration
Authors: Kraft Beate , Tegetmeyer Halina E. , Sharma Ritin , Klotz Martin G. , Ferdelman Timothy G. , Hettich Robert L. , Geelhoed Jeanine S. , Strous Marc
Published: August 2014

How microbes compete for nitrate

Much of the ammonia fertilizer we use ends up in surface or coastal waters as nitrate. This runoff lowers water quality and damages ecosystems. Although microbial nitrogen respiration influences the fate of nitrate, it is unclear which environmental factors exert the most control. Kraft
et al.
performed multiple long-term incubation studies of microbial communities from marine sediments. The relative supply of nitrate and nitrite, as well as total carbon and nitrogen, provided selective pressures that drove communities toward denitrification or ammonification. The average generation time of the community also strongly influenced which respiration pathway dominated.

Science
, this issue p.
676
Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mole accuracy
Authors: Yang Jun , Hu Weifeng , Usvyat Denis , Matthews Devin , Schütz Martin , Chan Garnet Kin-Lic
Published: August 2014

Working out how to pack benzene in silico

Many organic compounds crystallize in several different energetically similar packing arrangements, or polymorphs. This complicates processes such as drug formulation that rely on reproducible crystallization. Yang
et al.
have now achieved the long-standing goal of calculating a crystal packing arrangement from first principles to an accuracy that can distinguish polymorphs (see the Perspective by Price). They used benzene as a prototypical test case and applied quantum chemical methods that improve estimates of multibody interactions. The results bode well for future applications of theory to optimization of crystallization protocols.

Science
, this issue p.
640
; see also p.
619
Integration of growth and patterning during vascular tissue formation in
Arabidopsis
Authors: De Rybel Bert , Adibi Milad , Breda Alice S. , Wendrich Jos R. , Smit Margot E. , Novák Ondřej , Yamaguchi Nobutoshi , Yoshida Saiko , Van Isterdael Gert , Palovaara Joakim , Nijsse Bart , Boekschoten Mark V. , Hooiveld Guido , Beeckman Tom , Wagner Doris , Ljung Karin , Fleck Christian , Weijers Dolf
Published: August 2014

How to plumb the root is the problem

The vascular system of the plant root is generated from four seemingly similar cells. At some point, though, these cells' decendents need to follow different fates. Combining computational modeling with manipulation of hormone signaling in Arabidopsis, De Rybel
et al.
discovered the importance of a small bridge connecting two of the four cells (see the Perspective by Mellor and Bishopp). This feature locked in asymmetry in hormone signaling, so that those cells closest to the xylem delivered the maximal response. Two feedback loops in the model function distinctly, with one generating a domain rich in auxin and the other establishing a sharp boundary between domains.

Science
, this issue p.
10.1126/science.1255215
; see also p.
622
Probing the solar system's prenatal history
Authors: Bizzarro Martin
Published: August 2014

Radiometric studies can probe the pre-birth conditions of the solar system

[Also see Report by

Lugaro
et al.

]
Inflammation debate reignites
Authors: Leslie Mitch
Published: August 2014

Reanalyzing same data, paper challenges controversial study casting doubt on use of mouse models.
Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6
Authors: Yang Ruifeng , Cong Xu , Du Shaocai , Fei Ran , Rao Huiying , Wei Lai
Published: August 2014

The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5′ untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1.
Rapid Detection of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae from Urine Samples by Use of the ESBL NDP Test
Authors: Dortet Laurent , Poirel Laurent , Nordmann Patrice
Published: August 2014

From June to September 2012, 500 urine samples were recovered from patients with urinary tract infections (UTI) due to Gram-negative bacilli (≥10
4
leukocytes/ml and ≥10
5
Gram-negative isolates/ml) who visited the University hospital Bicêtre (France). They were challenged with extended-spectrum-β-lactamase (ESBL)-producing
Enterobacteriaceae
(ESBL-E) using the rapid diagnostic ESBL NDP test. Results of the ESBL NDP test were compared to the results of the double-disc susceptibility test (DDST) performed on solid-agar plates and molecular identification of the β-lactamase genes. Among the 450 nonduplicate urine samples, 11.3% were positive for ESBL-E by using the DDST, the ESBL determinants being mostly of the CTX-M type (CTX-M-15) according to molecular testing. Results of the ESBL NDP test were obtained within 15 min. The sensitivity and specificity of the ESBL NDP test were 98% and 99.8%, respectively, whereas the positive and negative predictive values of this test were 98% and 99.8%, respectively. A perfect correlation between cefotaxime resistance and positivity of the ESBL NDP test was observed. Therefore, the ESBL NDP test offers a powerful tool for a rapid identification of ESBL-E and associated resistance to expanded-spectrum cephalosporins. It may be useful in particular for guiding first-line antibiotic therapy.
Exploring the Potential of Next-Generation Sequencing in Detection of Respiratory Viruses
Authors: Prachayangprecha Slinporn , Schapendonk Claudia M. E. , Koopmans Marion P. , Osterhaus Albert D. M. E. , Schürch Anita C. , Pas Suzan D. , van der Eijk Annemiek A. , Poovorawan Yong , Haagmans Bart L. , Smits Saskia L.
Published: August 2014

Efficient detection of human respiratory viral pathogens is crucial in the management of patients with acute respiratory tract infection. Sequence-independent amplification of nucleic acids combined with next-generation sequencing technology and bioinformatics analyses is a promising strategy for identifying pathogens in clinical and public health settings. It allows the characterization of hundreds of different known pathogens simultaneously and of novel pathogens that elude conventional testing. However, major hurdles for its routine use exist, including cost, turnaround time, and especially sensitivity of the assay, as the detection limit is dependent on viral load, host genetic material, and sequencing depth. To obtain insights into these aspects, we analyzed nasopharyngeal aspirates from a cohort of 81 Thai children with respiratory disease for the presence of respiratory viruses using a sequence-independent next-generation sequencing approach and routinely used diagnostic real-time reverse transcriptase PCR (real-time RT-PCR) assays. With respect to the detection of rhinovirus and human metapneumovirus, the next-generation sequencing approach was at least as sensitive as diagnostic real-time RT-PCR in this small cohort, whereas for bocavirus and enterovirus, next-generation sequencing was less sensitive than real-time RT-PCR. The advantage of the sequencing approach over real-time RT-PCR was the immediate availability of virus-typing information. Considering the development of platforms capable of generating more output data at declining costs, next-generation sequencing remains of interest for future virus diagnosis in clinical and public health settings and certainly as an additional tool when screening results from real-time RT-PCR are negative.
Integrating Forecast Probabilities in Antibiograms: a Way To Guide Antimicrobial Prescriptions More Reliably?
Authors: Maurer Florian P. , Courvalin Patrice , Böttger Erik C. , Hombach Michael
Published: August 2014

Antimicrobial susceptibility testing (AST) assigns pathogens to “susceptible” or “resistant” clinical categories based on clinical breakpoints (CBPs) derived from MICs or inhibition zone diameters and indicates the likelihood for therapeutic success. AST reports do not provide quantitative measures for the reliability of such categorization. Thus, it is currently impossible for clinicians to estimate the technical forecast uncertainty of an AST result regarding clinical categorization. AST error rates depend on the localization of pathogen populations in relation to CBPs. Bacterial species are, however, not homogeneous, and subpopulations behave differently with respect to AST results. We addressed how AST reporting errors differ between isolates with and without acquired drug resistance determinants. Using as an example the beta-lactams and their most important resistance mechanisms, we analyzed different pathogen populations for their individual reporting error probabilities. Categorization error rates were significantly higher for bacterial populations harboring resistance mechanisms than for the wild-type population. Reporting errors for amoxicillin-clavulanic acid and piperacillin-tazobactam in
Escherichia coli
infection cases were almost exclusively due to the presence of broad-spectrum- and extended-spectrum-beta-lactamase (ESBL)-producing microorganisms (79% and 20% of all errors, respectively). Clinicians should be aware of the significantly increased risk of erroneous AST reports for isolates producing beta-lactamases, particularly ESBL and AmpC. Including probability indicators for interpretation would improve AST reports.
Isolation of Dengue Virus-Specific Memory B Cells with Live Virus Antigen from Human Subjects following Natural Infection Reveals the Presence of Diverse Novel Functional Groups of Antibody Clones
Authors: Smith Scott A. , de Alwis A. Ruklanthi , Kose Nurgun , Jadi Ramesh S. , de Silva Aravinda M. , Crowe James E.
Published: August 2014

Natural dengue virus (DENV) infection in humans induces antibodies (Abs) that neutralize the serotype of infection in a potent and type-specific manner; however, most Abs generated in response to infection are serotype cross-reactive and poorly neutralizing. Such cross-reactive Abs may enhance disease during subsequent infection with a virus of a different DENV serotype. Previous screening assays for DENV-specific human B cells and antibodies, using viral and recombinant antigens, mainly led to the isolation of dominant nonneutralizing B cell clones. To improve upon our ability to recover and study rare but durable and potently neutralizing DENV-specific Abs, we isolated human DENV-specific B cells by using a primary screen of binding to live virus, followed by a secondary screen with a high-throughput, flow cytometry-based neutralization assay to identify DENV-specific B cell lines prior to generation of hybridomas. Using this strategy, we identified several new classes of serotype-specific and serotype-cross-neutralizing anti-DENV monoclonal Abs (MAbs), including ultrapotent inhibitory antibodies with neutralizing activity concentrations of <10 ng/ml. We isolated serotype-specific neutralizing Abs that target diverse regions of the E protein, including epitopes present only on the intact, fully assembled viral particle. We also isolated a number of serotype-cross-neutralizing MAbs, most of which recognized a region in E protein domain I/II containing the fusion loop. These data provide insights into targets of the protective Ab-mediated immune response to natural DENV infection, which will prove valuable in the design and testing of new experimental DENV vaccines.

IMPORTANCE
Dengue virus infection is one of the most common mosquito-borne diseases and occurs in most countries of the world. Infection of humans with dengue virus induces a small number of antibodies that inhibit the infecting strain but also induces a large number of antibodies that can bind but do not inhibit dengue virus strains of other serotypes. We used a focused screening strategy to discover a large number of rare potently inhibiting antibodies, and we mapped the regions on the virus that were recognized by such antibodies. Our studies revealed that humans have the potential to generate very potent antibodies directed to diverse regions of the dengue virus surface protein. These studies provide important new information about protection from dengue virus infection that will be useful in the design and testing of new experimental dengue vaccines for humans.
Inhibition of Enterovirus 71 by Adenosine Analog NITD008
Authors: Deng Cheng-Lin , Yeo Huimin , Ye Han-Qing , Liu Si-Qing , Shang Bao-Di , Gong Peng , Alonso Sylvie , Shi Pei-Yong , Zhang Bo
Published: August 2014

Enterovirus 71 (EV71) is a major viral pathogen in China and Southeast Asia. There is no clinically approved vaccine or antiviral therapy for EV71 infection. NITD008, an adenosine analog, is an inhibitor of flavivirus that blocks viral RNA synthesis. Here we report that NITD008 has potent antiviral activity against EV71. In cell culture, the compound inhibits EV71 at a 50% effective concentration of 0.67 μM and a 50% cytotoxic concentration of 119.97 μM. When administered at 5 mg/kg in an EV71 mouse model, the compound reduced viral loads in various organs and completely prevented clinical symptoms and death. To study the antiviral mechanism and drug resistance, we selected escape mutant viruses by culturing EV71 with increasing concentrations of NITD008. Resistance mutations were reproducibly mapped to the viral 3A and 3D polymerase regions. Resistance analysis with recombinant viruses demonstrated that either a 3A or a 3D mutation alone could lead to resistance to NITD008. A combination of both 3A and 3D mutations conferred higher resistance, suggesting a collaborative interplay between the 3A and 3D proteins during viral replication. The resistance results underline the importance of combination therapy required for EV71 treatment.

IMPORTANCE
Human enterovirus 71 (EV71) has emerged as a major cause of viral encephalitis in children worldwide, especially in the Asia-Pacific region. Vaccines and antivirals are urgently needed to prevent and treat EV71 infections. In this study, we report the
in vitro
and
in vivo
efficacy of NITD008 (an adenosine analog) as an inhibitor of EV71. The efficacy results validated the potential of nucleoside analogs as antiviral drugs for EV71 infections. Mechanistically, we showed that mutations in the viral 3A and 3D polymerases alone or in combination could confer resistance to NITD008. The resistance results suggest an intrinsic interaction between viral proteins 3A and 3D during replication, as well as the importance of combination therapy for the treatment of EV71 infections.
The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers
Authors: Gao Feng , Kasprzak Wojciech K. , Szarko Christine , Shapiro Bruce A. , Simon Anne E.
Published: August 2014

Many plant viruses without 5′caps or 3′ poly(A) tails contain 3′ proximal, cap-independent translation enhancers (3′CITEs) that bind to ribosomal subunits or translation factors thought to assist in ribosome recruitment. Most 3′CITEs participate in a long-distance kissing-loop interaction with a 5′ proximal hairpin to deliver ribosomal subunits to the 5′ end for translation initiation.
Pea Enation Mosaic Virus
(PEMV) contains two adjacent 3′CITEs in the center of its 703-nucleotide 3′ untranslated region (3′UTR), the ribosome-binding, kissing-loop T-shaped structure (kl-TSS) and eukaryotic translation initiation factor 4E-binding Panicum mosaic virus-like translation enhance (PTE). We now report that PEMV contains a third, independent 3′CITE located near the 3′ terminus. This 3′CITE is composed of three hairpins and two pseudoknots, similar to the TSS 3′CITE of the carmovirus
Turnip crinkle virus
(TCV). As with the TCV TSS, the PEMV 3′TSS is predicted to fold into a T-shaped structure that binds to 80S ribosomes and 60S ribosomal subunits. A small hairpin (kl-H) upstream of the 3′TSS contains an apical loop capable of forming a kissing-loop interaction with a 5′ proximal hairpin and is critical for the accumulation of full-length PEMV in protoplasts. Although the kl-H and 3′TSS are dispensable for the translation of a reporter construct containing the complete PEMV 3′UTR
in vitro
, deleting the normally required kl-TSS and PTE 3′CITEs and placing the kl-H and 3′TSS proximal to the reporter termination codon restores translation to near wild-type levels. This suggests that PEMV requires three 3′CITEs for proper translation and that additional translation enhancers may have been missed if reporter constructs were used in 3′CITE identification.

IMPORTANCE
The rapid life cycle of viruses requires efficient translation of viral-encoded proteins. Many plant RNA viruses contain 3′ cap-independent translation enhancers (3′CITEs) to effectively compete with ongoing host translation. Since only single 3′CITEs have been identified for the vast majority of individual viruses, it is widely accepted that this is sufficient for a virus's translational needs.
Pea Enation Mosaic Virus
possesses a ribosome-binding 3′CITE that can connect to the 5′ end through an RNA-RNA interaction and an adjacent eukaryotic translation initiation factor 4E-binding 3′CITE. We report the identification of a third 3′CITE that binds weakly to ribosomes and requires an upstream hairpin to form a bridge between the 3′ and 5′ ends. Although both ribosome-binding 3′CITEs are critical for virus accumulation
in vivo
, only the CITE closest to the termination codon of a reporter open reading frame is active, suggesting that artificial constructs used for 3′CITE identification may underestimate the number of CITEs that participate in translation.