bluuebunny/crossref_metadata_2025 huggingface dataset:
Turbulent Flows Over a Backward Facing Step Simulated Using a Modified Partially Averaged Navier–Stokes Model
Authors: Huang Renfang , Luo Xianwu , Ji Bin , Ji Qingfeng
Published: November 2016

A modified partially averaged Navier–Stokes model (MPANS) is proposed by treating the standard k–ε model as the parent model and formulating the unresolved-to-total kinetic energy ratio fk as a function of the local grid size and turbulence length scale. Flows over a backward facing step are used to evaluate the performance of MPANS mode. Computations of the standard k–ε model, the constant fk partially averaged Navier–Stokes (PANS) models (fk = 0.6, 0.7), and the two-stage PANS model are carried out for comparisons. Based on the detailed analyses of calculated results and experimental data, the MPANS model performs better to predict the reattachment length together with the corner vortex and provides overall improved statistics of skin frictions, pressures, velocity profiles, and Reynolds stresses, demonstrating its promising applications in industrial turbomachines that often encounter with flow separations.
Hydrogen Production via Catalytic Autothermal Reforming of Desulfurized Jet-A Fuel
Authors: Zhang Shuyang , Wang Xiaoxin , Li Peiwen
Published: November 2016

On-board hydrogen production via catalytic autothermal reforming is beneficial to vehicles using fuel cells because it eliminates the challenges of hydrogen storage. As the primary fuel for both civilian and military air flight application, Jet-A fuel (after desulfurization) was reformed for making hydrogen-rich fuels in this study using an in-house-made Rh/NiO/K-La-Ce-Al-OX ATR catalyst under various operating conditions. Based on the preliminary thermodynamic analysis of reaction equilibrium, important parameters such as ratios of H2O/C and O2/C were selected, in the range of 1.1–2.5 and 0.5–1.0, respectively. The optimal operating conditions were experimentally obtained at the reactor’s temperature of 696.2 °C, which gave H2O/C = 2.5 and O2/C = 0.5, and the obtained fuel conversion percentage, hydrogen yield (can be large than 1 from definition), and energy efficiency were 88.66%, 143.84%, and 64.74%, respectively. In addition, a discussion of the concentration variation of CO and CO2 at different H2O/C, as well as the analysis of fuel conversion profile, leads to the finding of effective approaches for suppression of coke formation.
Quantitative Assessment of Advanced Energy Efficiency Retrofitting for Hospitals in India
Authors: Pedamallu Lakshman Ravi Teja , Singh Vivek Kumar , Gomes Alvaro Peixoto Filipe
Published: November 2016

Achieving energy efficiency in buildings is an important factor in developed and as well in developing countries in order to meet its energy demand. Over the past few years, a number of reports have been emerged stating that the buildings sectors are responsible for approximately 31% of global final energy demand. Buildings account for 35% of total final energy consumption in India and building energy consumption is growing about 8% per years. Final energy demand in Indian building sector will grow up-to five times by the end of this century, driven by rapid income and population growth. Hospitals are institutions for the care of people with health problems and are usually functional 24hrs a day, all year around, which demands a lot of energy. Health sector is one of the largest and fastest growing sectors in India. By 2020, it is expected to become a $ 280 billion industry. In India hospitals contribute 23% of total energy consumption and the hospital building growth rate 12–15% in last decade. The World Health Organization estimated that India need 80,000 additional hospital beds every year to meet the demands of India’s population. The aim of this study is to assess the energy demand, energy savings & reduced greenhouse gas emissions by increasing the energy efficiency using advanced retrofitting. Bottom-Up Energy Analysis System (BUENAS) is an end use energy demand projection model for Hospital buildings in India, to normalize the assessment of energy-saving models also going to fill the gap in energy demand reduction by energy system modeling and decomposition analysis. Energy efficiency retrofitting of existing buildings plays a major role in developing country like India in order improve its energy security and minimizing the greenhouse gases. The positive effects of retrofitting of energy efficiency and need the policies and target base proposal for government intention to achieve the potential for energy efficiency are discussed.
Lubricant Free Foil Bearings Pave Way to Highly Efficient and Reliable Flywheel Energy Storage System
Authors: Heshmat Hooshang , Walton James F.
Published: November 2016

Advanced compliant foil bearings capable of operating in low ambient pressures associated with soft vacuum are now paving the way to a new type of flywheel energy storage system. Many conventional flywheel energy storage system design approaches use active magnetic bearings with backup bearing technologies to meet the need for high speed operation in a low ambient pressure environment. Low ambient pressures are needed to overcome the power loss limitations associated with windage at high surface speeds. However, bearing technologies that rely on active control tend to be large, are dynamically soft which necessitates backup bearings and require a power supply which consumes some of the stored power to maintain rotor levitation.

In this paper the authors will demonstrate both theoretically and experimentally the ability of advanced 5th generation compliant foil bearings to support large flywheel rotors weighing in excess of 900 N and which can operate to speeds in excess of 40,000 rpm. Testing conducted at pressures as low as 7 kPa demonstrates the ability of foil bearings to operate in low ambient pressures consistent with flywheel energy storage system needs for low windage loss. The authors will also present a hypothesis and the mechanisms involved in a hydrodynamic phenomenon that allows a foil bearing to operate successfully when the mean free path of the air molecules is exceedingly large due to low ambient pressures.
Design and Performance Improvement of Mirror Augmented Photovoltaic Systems
Authors: Bodhanker Prathusha , Bradish Ann , Kissock John Kelly
Published: November 2016

Augmenting photo-voltaic (PV) system performance using fixed flat mirrors boosts PV power output. Previous literature reports that fixed flat mirrors create non-uniform irradiance on the PV panels, which limits the current and decreases panel efficiency. Triplex panels have a modified cell string architecture that splits the panel into three separate sections to address this problem. This paper describes an experimental setup consisting of a pyranometer to measure total solar irradiation, an air temperature sensor, a standard PV panel with and without mirrors, and a triplex panel with and without mirrors. The sensor and PV panels are connected to Daystar Multi-tracer logger to collect the instantaneous data. The experiment is simulated using TracePro® to determine the distribution of radiation reflected onto the PV panels. Both simulated and measured results indicate the bottom part of the mirror augmented panels receive the most solar irradiance followed by middle portion, followed by top portion. The results document the difference in performance between standard and Triplex panels with fixed flat mirrors and suggest configurations that maximize performance.
Calorimetric Evaluation of Novel Concentrating Solar Receiver Geometries With Enhanced Effective Solar Absorptance
Authors: Ortega Jesus D. , Yellowhair Julius E. , Ho Clifford K. , Christian Joshua M. , Andraka Charles E.
Published: November 2016

Direct solar power receivers consist of tubular arrays, or panels, which are typically tubes arranged side by side and connected to an inlet and outlet manifold. The tubes absorb the heat incident on the surface and transfer it to the fluid contained inside them. To increase the solar absorptance, high temperature black paint or a solar selective coating is applied to the surface of the tubes. However, current solar selective coatings degrade over the lifetime of the receiver and must be reapplied, which reduces the receiver thermal efficiency and increases the maintenance costs. This work presents an evaluation of several novel receiver shapes which have been denominated as fractal like geometries (FLGs). The FLGs are geometries that create a light-trapping effect, thus, increasing the effective solar absorptance and potentially increasing the thermal efficiency of the receiver. Five FLG prototypes were fabricated out of Inconel 718 and tested in Sandia’s solar furnace at two irradiance levels of ∼15 and 30 W/cm2 and two fluid flow rates. Photographic methods were used to capture the irradiance distribution on the receiver surfaces and compared to results from ray-tracing models. This methods provided the irradiance distribution and the thermal input on the FLGs. Air at nearly atmospheric pressure was used as heat transfer fluid. The air inlet and outlet temperatures were recorded, using a data acquisition system, until steady state was achieved. Computational fluid dynamics (CFD) models, using the Discrete Ordinates (DO) radiation and the k-ω Shear Stress Transport (SST) equations, were developed and calibrated, using the test data, to predict the performance of the five FLGs at different air flow rates and irradiance levels. The results showed that relative to a flat plate (base case), the new FLGs exhibited an increase in the effective solar absorptance from 0.86 to 0.92 for an intrinsic material absorptance of 0.86. Peak surface temperatures of ∼1000°C and maximum air temperature increases of ∼200°C were observed. Compared to the base case, the new FLGs showed a clear air outlet temperature increase. Thermal efficiency increases of ∼15%, with respect to the base case, were observed. Several tests, in different days, were performed to assess the repeatability of the results. The results obtained, so far, are very encouraging and display a very strong potential for incorporation in future solar power receivers.
Design Optimization of Electrical Hubs Using Hybrid Evolutionary Algorithm
Authors: Perera A. T. D. , Nik Vahid M. , Mauree D. , Scartezzini J.-L.
Published: November 2016

Integration of non-dispatchable renewable energy sources such as wind and solar into the grid is challenging due to the stochastic nature of energy sources. Hence, electrical hubs (EH) and virtual power plants that combine non-dispatchable energy sources, energy storage and dispatchable energy sources such as internal combustion generators and micro gas turbines are getting popular. However, designing such energy systems considering the electricity demand of a neighborhood, curtailments for grid interactions and real time pricing (RTP) of the main utility grid (MUG) is a difficult exercise. Seasonal and hourly variation of electricity demand, potential for each non-dispatchable energy source and RTP of MUG needs to be considered when designing the energy system. Representation of dispatch strategy plays a major role in this process where simultaneous optimization of system design and dispatch strategy is required. This study presents a bi-level dispatch strategy based on reinforced learning for simultaneous optimization of system design and operation strategy of an EH. Artificial Neural Network (ANN) was combined with a finite state controller to obtain the operating state of the system. Pareto optimization is conducted considering, lifecycle cost and system autonomy to obtain optimum system design using evolutionary algorithm.
Investigation of Grain Harvesting and Drying Strategies to Improve Energy Efficiency and Profitability
Authors: Almberg Evan R. , Twedt Michael P. , Gent Stephen P.
Published: November 2016

The objective of this study was to determine the effects of harvest time and drying techniques on the energy requirements and profitability of grain production, particularly corn (Zea mays). In most grain production scenarios, supplemental drying is required post-harvest to allow long-term storage of the crop. Traditional high-temperature, high airflow drying systems have been known to be an energy intensive and high cost process of grain production. However, advanced continuous flow drying systems have shown to be 30% or more energy efficient than systems produced in recent decades. In this study, harvesting times (early fall, mid-fall, late fall) were compared to quantify the effects of field losses as the fall progresses with the potentially reduced drying requirement as the crop undergoes natural drying in the field. A model was developed to investigate the energy and economics of drying, based on harvest period, dryer efficiency, field drydown, and field losses. A sensitivity analysis was completed that focused on the energy consumption of artificial drying based upon harvesting conditions, as well as economic factors of field drying and fuel cost. Preliminary results of the study have shown that the use of higher efficiency drying systems combined with moderately prompt harvest times generally provide the most profitable scenario, while delayed harvest times increase the likelihood of field loss, which are not typically offset by the reduced drying requirements.
Dynamic Analysis and Characterization of Conventional Hydraulic Power Supply Units
Authors: Schmidt Lasse , Liedhegener Michael , Bech Michael M. , Andersen Torben O.
Published: November 2016

Hydraulic power units operated as constant supply pressure systems remain to be widely used in the industry, to supply valve controlled hydraulic drives etc., where the hydraulic power units are constituted by variable pumps with mechanical outlet pressure control, driven by induction motors. In the analysis of supplied drives, both linear and rotary, emphasis is commonly placed on the drives themselves and the related loads, and the supply system dynamics is often given only little attention, and usually neglected or taken into account in a simplified fashion. The simplified supply system dynamics used in such analyzes is often justified by short supply lines and/or the utilization of accumulators near valve inlets, accounting for the majority of possible supply pressure variations. Such considerations are reasonable in many test benches, where the supply pressure variations are small enough such that limited impact on the drive dynamics is observed. Such ideal properties however, are not necessarily present in industrial hydraulic applications for various reasons, with the most common being large volumes of supply lines. Long supply lines, hence large supply line volumes, between the supply system and drives will reduce the flow-to-pressure gain of the supply system, and hence increase the time constant of the supply pressure dynamics. A consequence of this may be large variations in the supply pressure, hence large variations in the pump shaft torque, and thereby the induction motor load torque, with possible excitation of the induction motor dynamics as a result. In such cases, the coupled dynamics of the pressure controlled pump and induction motor may influence the supply pressure significantly, possibly affecting the dynamics of the supplied drives, especially in cases where pilot operated valves with internal pilot supply are used. This paper is concerned with the analysis and characterization of the coupled pump-induction motor dynamics, confined to hydraulic power units constituted by an axial piston pump with mechanical outlet pressure control, driven by an induction motor operated at grid conditions. Furthermore, a simplified general model representation of the coupled dynamics is established, accounting for the entire dominating dynamics of the supply unit. Results demonstrate the accuracy of the simplified model representation.
Fluid Stiction With Mechanical Contact: A Theoretical Model
Authors: Scheidl Rudolf , Zhidong Hu
Published: November 2016

Published theoretical work about fluid stiction between two separating plates was so far limited to a finite initial gap. It was shown that pressure and force evolution are well described by fluid film lubrication equations if cavitation is taken into account. The practically important case that plate separation starts from a mechanical contact condition was only studied by experiments. They showed that quite substantial negative pressures can occur in the gap for a very short time and that the peak forces are varying strongly even between consecutive experiments with equal test conditions. In this paper two models are presented which complement the Reynolds equations with dynamical bubble evolution equations. Initial gap height, bubble number density, and initial bubble radius are the three unknown parameters of these models. Initial gap height accounts for surface roughness, the two other parameters refer to the bubble nucleation of the fluid in the small roughness indentations of the gap. A first model employs the Rayleigh-Plesset bubble dynamic model. It requires that the bubbles stay small compared to the gap. Results show that its stiction force dynamics is two orders of magnitude faster than experimentally observed and that the bubble size condition is violated. The second model assumes that bubbles span over the whole gap height and that the flow of the liquid between the bubbles is guided by the Reynolds equation. This model can be brought into reasonable agreement with the experiments. Force variation from experiment to experiment can at least in part be reproduced by a random variation of the initial bubble sizes. The model exhibits a kind of boundary layer behavior close to the outer boundary. This layer represents the interaction zone between bubble growth dynamics, pressure distribution due to viscous flow, and the pressure boundary condition.
Soft Switching in Switched Inertance Hydraulic Circuits
Authors: Yudell Alexander C. , Van de Ven James D.
Published: November 2016

Switched Inertance Hydraulic Systems (SIHS) use inductive, capacitive, and switching elements to boost or buck a pressure from a source to a load in an ideally lossless manner. Real SIHS circuits suffer a variety of energy losses, with throttling of flow during transitions of the high-speed valve resulting in 44% of overall losses. These throttling energy losses can be mitigated by applying the analog of zero-voltage-switching, a soft switching strategy, adopted from power electronics. In the soft switching circuit, the flow that would otherwise be throttled across the transitioning valve is stored in a capacitive element and bypassed through check valves in parallel with the switching valves. To evaluate the effectiveness of soft switching in a boost converter SIHS, a lumped parameter model was constructed. The model demonstrates that soft switching can improve the efficiency of the circuit up to 42% and extend the power delivery capabilities of the circuit by 76%.
Experimental Investigation on Effective Bulk Modulus and Effective Volume in an External Gear Pump
Authors: Nakagawa Shuichi , Ichiyanagi Takayoshi , Nishiumi Takao
Published: November 2016

Pressure ripples generated by a positive displacement pump in a hydraulic system can lead to severe noise and vibration problems. The source impedance of a positive displacement pump has a considerable impact on the generation of pressure ripples. It is, therefore, important to be able to predict the source impedance in order to design quiet hydraulic systems.

The source impedance of a positive displacement pump depends, amongst other things, on bulk modulus and volume. However, it is known that the mathematical model that takes into account the bulk modulus of hydraulic oil and the volume of a discharge room in the pump results in an estimated value of the source impedance that is greater than the measured value.

In this study, the factors which affect the source impedance of an external gear pump for an agricultural tractor have been investigated. In particular, the effect of the following factors has been investigated experimentally: the effective bulk modulus as determined by the components of the pump: leakage in the pump: the specific volume ratio of entrained air to hydraulic oil: and the volume of the tooth space of the pump. In addition, the effect of volumetric change of the discharge room by pumping action has been investigated using CFD with moving mesh technique.
Load-Force-Adaptive Outlet Throttling: An Easily Commissionable Independent Metering Control Strategy
Authors: Lübbert Jan , Sitte André , Beck Benjamin , Weber Jürgen
Published: November 2016

This paper deals with a novel independent metering valve system which is intended to be used in medium sized mobile machines. The system uses a mechanical pressure compensator to enable a very simple SISO control algorithm which does not need any feedback parameters to be adjusted. The algorithm is capable of handling resistive and pulling loads at a certain desired velocity and inlet chamber pressure level. The paper gives a brief summary of the systematic approach to deriving the valves structure and compares different control approaches for the complete hydraulic system comprising several actuators. Special emphasis is given to the preferred solution, which is verified on a laboratory test rig consisting of reasonably priced mobile machine components. Furthermore a linear model of system and control structure is constructed to give detailed information regarding the dynamic characteristics of the controlled drive. The energetic benefits of the novel system architecture in comparison to a standard coupled metering flow sharing system are investigated by means of a levelling movement performed on the test rig and a simulated synthetic high power digging cycle.
Dielectric barrier characteristics of Si-rich silicon nitride films deposited by plasma enhanced atomic layer deposition
Authors: Kim Hwanwoo , Song Hyoseok , Shin Changhee , Kim Kangsoo , Jang Woochool , Kim Hyunjung , Shin Seokyoon , Jeon Hyeongtag
Published: November 2016

This work proposes a new method toward improving dielectric barrier characteristics through low dielectric permittivity (k) amorphous silicon nitride films (SiNx) deposited by plasma enhanced atomic layer deposition (PEALD). The dielectric constants of the atomic layer deposition (ALD) SiNx films were in the range of 4.25–4.71 and were relatively lower than that of SiNx deposited by plasma enhanced chemical vapor deposition (PECVD). The dielectric constants of the PEALD SiNx films were nearly identical to the values for PECVD silicon carbon nitride films (SiCN). Although the ALD SiNx films were low-k, they exhibited similar levels of film stress as PECVD SiNx, and the density of ALD SiNx film was higher than that of PECVD SiCN films. The ability to suppress copper (Cu) diffusion through 10-nm thick SiNx dielectric barriers in silicon dioxide/barrier/Cu/tantalum nitride structures on Si substrates was evaluated via Auger electron spectroscopy analysis. Although PEALD SiNx films possessed low dielectric constants (<5), their barrier property to Cu diffusion was nearly equivalent to that of PECVD SiNx. The PECVD SiCN films also exhibited low dielectric constants but showed weak barrier property. Therefore, the low-k ALD SiNx reported herein could be used as a thin film thickness dielectric barrier layer in future advanced technologies.
Similarity measurement of lung masses for medical image retrieval using kernel based semisupervised distance metric
Authors: Wei Guohui , Ma He , Qian Wei , Qiu Min
Published: November 2016

Purpose:

To develop a new algorithm to measure the similarity between the query lung mass and reference lung mass data set for content‐based medical image retrieval (CBMIR).

Methods:

A lung mass data set including 746 mass regions of interest (ROIs) was assembled. Among them, 375 ROIs depicted malignant lesions and 371 depicted benign lesions. Each mass ROI is represented by a vector of 26 texture features. A kernel function was employed to map the original data in input space to a feature space. In this space, a semisupervised distance metric was learned, which used differential scatter discriminant criterion to represent the semantic relevance, and the regularization term to represent the visual similarity. The learned distance metric can measure the similarity of the query mass and reference mass data set. The clustering accuracy is used to configure the parameters. The retrieval accuracy and classification accuracy are used as the performance assessment index.

Results:

After configuring the parameters, a mean clustering accuracy of 0.87 can be achieved. For retrieval accuracy, our algorithm achieves better performance than other state‐of‐the‐art retrieval algorithms when applying a leave‐one‐out validation method to the testing data set. For classification accuracy, the area under the ROC curve of our algorithm can be achieved as 0.941 ± 0.006. The running times of 346 query images with the proposed algorithm are 5.399 and 6.0 s, respectively.

Conclusions:

The study results demonstrated the proposed algorithm outperforms the compared algorithms, when taking the semantic relevant and visual similarity into account in kernel space. The algorithm can be used in a CBMIR system for a query mass to retrieve similarity masses, which can help doctors make better decisions.
Type IV Acromioclavicular Joint Separation in a Collegiate Basketball Player
Authors: Ronchetti Gail M. , Welch Christopher A. , Smith Brent I. , Blair Danielle E.
Published: November 2016

A 19-year-old female basketball athlete sustained a right shoulder injury during collegiate competition resulting from a collision causing severe pain and discomfort. The patient was diagnosed with a unique type IV acromioclavicular (AC) separation. Surgical stabilization of the AC joint and slow progression in rehabilitation with immobilization assisted in protecting the reconstruction. Accurate diagnosis and appropriate intervention helped to lead to the successful recovery and return to play for this patient. There are few cases of type IV acromioclavicular separation reported in the literature and none related to basketball. This case presents the challenges related to the diagnosis and rehabilitation following surgical reconstruction of a type IV acromioclavicular separation.
Exploring Career Longevity in Athletic Training: Factors Influencing Persistence in the NCAA Division I Setting
Authors: Mazerolle Stephanie M. , Eason Christianne M. , Lazar Rhyan A. , Mensch James M.
Published: November 2016

We examined factors that have contributed to career longevity in the profession of athletic training in the NCAA Division I setting. Longevity is an important topic for athletic trainers, as many depart the setting for various reasons, and viability of a lifelong career is often questioned. Fourteen (11 males and 3 females) athletic trainers who have worked in NCAA Division I athletics for 15 years or more volunteered to participate in this study and completed one-on-one phone interviews. An inductive analysis was completed. Data saturation was reached with our sample, and we completed member checks and multiple analyst triangulation. Our results showed having a passion for the role and job, having an acceptance of the athletics lifestyle, having a support network, and having family and work integration were the major reasons our participants have been able to persist as an athletic trainer within the NCAA Division I setting.
Universal space-time scaling symmetry in the dynamics of bosons across a quantum phase transition
Authors: Clark Logan W. , Feng Lei , Chin Cheng
Published: November 2016

Shaking the lattice uncovers universality

Most of our knowledge of quantum phase transitions (QPTs)—which occur as a result of quantum, rather than thermal, fluctuations—comes from experiments performed in equilibrium conditions. Less is known about the dynamics of a system going through a QPT, which have been hypothesized to depend on a single time and length scale. Clark
et al.
confirmed this hypothesis in a gas of cesium atoms in an optical lattice, which was shaken progressively faster to drive the gas through a QPT.

Science
, this issue p.
606
Exploring genetic suppression interactions on a global scale
Authors: van Leeuwen Jolanda , Pons Carles , Mellor Joseph C. , Yamaguchi Takafumi N. , Friesen Helena , Koschwanez John , Ušaj Mojca Mattiazzi , Pechlaner Maria , Takar Mehmet , Ušaj Matej , VanderSluis Benjamin , Andrusiak Kerry , Bansal Pritpal , Baryshnikova Anastasia , Boone Claire E. , Cao Jessica , Cote Atina , Gebbia Marinella , Horecka Gene , Horecka Ira , Kuzmin Elena , Legro Nicole , Liang Wendy , van Lieshout Natascha , McNee Margaret , San Luis Bryan-Joseph , Shaeri Fatemeh , Shuteriqi Ermira , Sun Song , Yang Lu , Youn Ji-Young , Yuen Michael , Costanzo Michael , Gingras Anne-Claude , Aloy Patrick , Oostenbrink Chris , Murray Andrew , Graham Todd R. , Myers Chad L. , Andrews Brenda J. , Roth Frederick P. , Boone Charles
Published: November 2016

A global genetic suppression network

The genetic background of an organism can influence the overall effects of new genetic variants. Some mutations can amplify a deleterious phenotype, whereas others can suppress it. Starting with a literature survey and expanding into a genomewide assay, van Leeuwen
et al.
generated a large-scale suppression network in yeast. The data set reveals a set of general properties that can be used to predict suppression interactions. Furthermore, the study provides a template for extending suppression studies to other genes or to more complex organisms.

Science
, this issue p.
599
A transcription factor hierarchy defines an environmental stress response network
Authors: Song Liang , Huang Shao-shan Carol , Wise Aaron , Castanon Rosa , Nery Joseph R. , Chen Huaming , Watanabe Marina , Thomas Jerushah , Bar-Joseph Ziv , Ecker Joseph R.
Published: November 2016

Complex transcription factor interactions

To respond to environmental changes, such as drought, plants must regulate numerous cellular processes. Working in the model plant
Arabidopsis
, Song
et al.
profiled the binding of 21 transcription factors to chromatin and mapped the complex gene regulatory networks involved in the response to the plant hormone abscisic acid. The work provides a framework for understanding and modulating plant responses to stress.

Science
, this issue p.
598
A radical approach to posttranslational mutagenesis
Authors: Hofmann Raphael , Bode Jeffrey W.
Published: November 2016

Introducing diverse protein side chains via carbon-carbon bond-forming reactions
Priceless
Virtual Competition The Promise and Perils of the Algorithm-Driven Economy
Ariel Ezrachi and Maurice E. Stucke
Harvard University Press, 2016. 364 pp.
Authors: Nalebuff Barry
Published: November 2016

A cautionary tome probes the cost of black box algorithms
How tobacco smoke changes the (epi)genome
Authors: Pfeifer Gerd P.
Published: November 2016

Distinct mutation types are found in diverse cancers associated with smoking
fii, a bacterial locus required for filamentous phage infection and its relation to colicin-tolerant tolA and tolB
Authors: Sun T P , Webster R E
Published: November 2016

We describe mutations in a new bacterial locus, designated fii, which do not allow the filamentous bacteriophage f1 to infect bacteria harboring the F plasmid. Mutations at this locus do not affect the ability of F plasmid-containing bacteria to undergo conjugation or be infected by the F plasmid-specific RNA phage f2. The filamentous phage can still adsorb to the F sex pilus, but the DNA is unable to enter the bacteria. All fii mutants become tolerant to colicins E1, E2, and E3. Strains with amber mutations in fii also are unable to plaque P1, even though they can be infected with this phage. Mutations in fii also prevent infection of bacteria harboring the N plasmid by the filamentous bacteriophage IKe. The fii locus maps adjacent to tolA, mutants of which demonstrate tolerance to high levels of the E and K colicins. The three genes tolA, tolB, and fii are shown to reside on a 4.3-kilobase fragment of the Escherichia coli chromosome. Each gene has been cloned into a chimeric plasmid and shown to complement, in trans, mutations at the corresponding chromosomal locus. Studies in maxicells show that the product of fii appears to be a 24-kilodalton protein which copurifies with the cell envelope. The product of tolA has been identified tentatively as a 51-kilodalton protein. Data from cloning, Tn5 mutagenesis, and P1 transduction studies are consistent with the gene order sucA-fii-tolA-tolB-aroG near 17 min on the E. coli map.
Isolation of genes preferentially expressed during Bacillis subtilis spore outgrowth
Authors: Gianni M , Galizzi A
Published: November 2016

From the Charon 4A library of Ferrari et al (J. Bacteriol. 146:430-432, 1981) we isolated three genes involved in Bacillus subtilis spore outgrowth by screening the library by hybridization with labeled RNA from outgrowing spores in the presence of an excess of unlabeled vegetative RNA. Hybridization competition experiments with purified clones showed that the clones contained sequences that were transcribed only during spore outgrowth or preferentially during spore outgrowth. Fragments of the cloned DNAs were subcloned in plasmid pJH101, and by using plasmid integration and PBS1 transduction the chromosomal loci were mapped. The three loci which we mapped are outG and outH, which are located between polC and dnaA, and outI, which is located near pycA. Using the cloned DNAs and derived plasmids in dot hybridization experiments with RNA extracted from cells at different developmental stages, we defined for two clones a region that is transcribed only during the outgrowth phase.
Isolation of recombination-defective and UV-sensitive mutants of Bacillus megaterium
Authors: English J D , Vary P S
Published: November 2016

Mutants of Bacillus megaterium QMB1551 sensitive to mitomycin C or methyl methanesulfonate were isolated and characterized phenotypically. Cell survival after UV-light and gamma-ray exposure was determined, as was transductional recombination. Of the mutants tested, three were sensitive to UV but remained recombination proficient. The UV-sensitive mutants were also reduced in host cell reactivation. At least three mutants had undetectable transduction frequencies, i.e., less than 0.3 to 1.3% of the parental strain frequencies, and so appear to be recombination deficient. Sensitivities of these mutant strains to UV light and gamma radiation were compared with those of parental B. megaterium as well as parental, recE4, recA1, uvrA19, and uvrB109 strains of Bacillus subtilis. In each case, the strains of B. megaterium, including the parental strains, showed a higher percentage of cell survival than B. subtilis.
Specific location of penicillin-binding proteins within the cell envelope of Escherichia coli
Authors: Barbas J A , Díaz J , Rodríguez-Tébar A , Vázquez D
Published: November 2016

This communication deals with the location of penicillin-binding proteins in the cell envelope of Escherichia coli. For this purpose, bacterial cells have been broken by various procedures and their envelopes have been fractioned. To do so, inner (cytoplasmic) and outer membranes were separated by isopycnic centrifugation in sucrose gradients. Some separation methods (Osborn et al., J. Biol. Chem. 247:3962-3972, 1972; J. Smit, Y. Kamio, and H. Nikaido, J. Bacteriol. 124:942-958, 1975) revealed that penicillin-binding proteins are not exclusively located in the inner membrane. They are also found in the outer membrane (A. Rodríguez-Tébar, J. A. Barbas, and D. Vásquez, J. Bacteriol. 161:243-248, 1985). Under the milder conditions for cell rupture used in this work, an intermembrane fraction, sedimenting between the inner and outer membrane, can be recovered from the gradients. This fraction has a high content of both penicillin-binding proteins and phospholipase B activity and may correspond to the intermembrane adhesion sites (M. H. Bayer, G. P. Costello, and M. E. Bayer, J. Bacteriol. 149:758-769, 1982). We postulate that this intermembrane fraction is a labile structure that contains a high amount of all penicillin-binding proteins which are usually found in both the inner and outer membranes when the adhesion sites are destroyed by the cell breakage and fractionation procedures.
Transfer of chromosomal mutations to plasmids via Hfr-mediated conduction
Authors: Park C , Hazelbauer G L
Published: November 2016

Nonconjugative plasmids can be transferred from an Hfr donor to a recipient by Hfr-mediated conduction. We found that this phenomenon can be employed to obtain a plasmid in which a mutation in a chromosomal gene has been transferred to the copy of that gene contained in the hybrid plasmid.
Adaptation of the acetogen Clostridium thermoautotrophicum to minimal medium
Authors: Savage M D , Drake H L
Published: November 2016

Clostridium thermoautotrophicum was adapted to minimal medium and cultivated at the expense of glucose, methanol, or H2-CO2. No supplemental amino acids were required for growth of the adapted strain, and nicotinic acid was the sole essential vitamin. Neither N2 nor nitrate could replace ammonium as the nitrogen source, and biotin was preferentially stimulatory for glucose cell lines. Growth in minimal medium yielded substantially higher acetate concentrations per unit of biomass formed than did growth in undefined medium.
Conjugative transfer of the naturally occurring plasmids of Acetobacter xylinum by IncP-plasmid-mediated mobilization
Authors: Valla S , Coucheron D H , Kjosbakken J
Published: November 2016

Broad-host-range plasmids and cloning vectors were conjugatively transferred to Acetobacter xylinum. One of the plasmids, RP4::Mu cts61, was used for the insertion of Tn1 into the 16-, 44-, and 64-kilobase-pair plasmids of A. xylinum. The Tn1-labeled plasmids could be mobilized by a helper plasmid. Many of the Tn1 insertions affected the copy number of the plasmids.
Mutations in tar suppress defects in maltose chemotaxis caused by specific malE mutations
Authors: Manson M D , Kossmann M
Published: November 2016

Maltose-binding protein (MBP), which is encoded by the malE gene, is the maltose chemoreceptor of Escherichia coli, as well as an essential component of the maltose uptake system. Maltose-loaded MBP is thought to initiate a chemotactic response by binding to the tar gene product, the signal transducer Tar, which is also the aspartate chemoreceptor. To study the interaction of MBP with Tar, we selected 14 malE mutants which had specific defects in maltose taxis. Three of these mutants were fully active in maltose transport and produced MBP in normal amounts. The isoelectric points of the MBPs from these three mutants were identical to (malE461 and malE469) or only 0.1 pH unit more basic than (malE454) the isoelectric point of the wild-type protein (pH 5.0). Six of the mutations, including malE454, malE461, and malE469, were mapped in detail; they were located in two regions within malE. We also isolated second-site suppressor mutations in the tar gene that restored maltose taxis in combination with the closely linked malE454 and malE461 mutations but not with the malE469 mutation, which maps in a different part of the gene. This allele-specific suppression confirmed that MBP and Tar interact directly.
Cloning of genes that encode a new heat-labile enterotoxin of Escherichia coli
Authors: Pickett C L , Twiddy E M , Belisle B W , Holmes R K
Published: November 2016

The genes for a new enterotoxin were cloned from Escherichia coli SA53. The new toxin was heat labile and activated adenylate cyclase but was not neutralized by antisera against cholera toxin or E. coli heat-labile enterotoxin. Subcloning and minicell experiments indicated that the toxin is composed of two polypeptide subunits that are encoded by two genes. The two toxin subunits exhibited mobilities on polyacrylamide gels that are similar to those of cholera toxin and E. coli heat-labile enterotoxin subunits. A 0.8-kilobase DNA probe for the new enterotoxin failed to hybridize with the cloned structural genes for E. coli heat-labile enterotoxin.
Influence of growth rate and iron limitation on the expression of outer membrane proteins and enterobactin by Klebsiella pneumoniae grown in continuous culture
Authors: Lodge J M , Williams P , Brown M R
Published: November 2016

The influence of the growth rate on outer membrane protein composition and enterobactin production was studied with Klebsiella pneumoniae grown under conditions of iron limitation in chemostats. More enterobactin was produced at fast (D = 0.4 h-1) and slow (D = 0.1 h-1) growth rates in continuous cultures than in either logarithmic- or stationary-phase batch cultures. When the growth rate was controlled under conditions of carbon limitation and the iron level was reduced to 0.5 microM, the iron-regulated outer membrane proteins and enterobactin were induced at the fast growth rate. At the slow growth rate, although the iron-regulated outer membrane proteins were barely visible, a significant level of enterobactin was still produced. These results suggest that under conditions of either carbon or iron limitation, the growth rate can influence the induction of the high-affinity iron uptake system of K. pneumoniae. Other outer membrane proteins, including a 39-kilodalton peptidoglycan-associated protein, were found to vary with the growth rate and nutrient limitation.
Cloning and expression of the pilin gene of Pseudomonas aeruginosa PAK in Escherichia coli
Authors: Strom M S , Lory S
Published: November 2016

Many strains of Pseudomonas aeruginosa possess pili which have been implicated in the pathogenesis of the organism. This report presents the cloning and expression in Escherichia coli of the gene encoding the structural subunit of the pili of P. aeruginosa PAK. Total DNA from this strain was partially digested with Sau3A and inserted into the cloning vector pUC18. Recombinant E. coli clones were screened with oligonucleotide probes prepared from the constant region of the previously published amino acid sequence of the mature pilin subunit. Several positive clones were identified, and restriction maps were generated. Each clone contained an identical 1.1-kilobase HindIII fragment which hybridized to the oligonucleotide probes. Western blot analysis showed that all of the clones expressed small amounts of the P. aeruginosa pilin subunit, which has a molecular mass of ca. 18,000. This expression occurred independently of the orientation of the inserted DNA fragments in the cloning vector, indicating that synthesis was directed from an internal promoter. However, subclones containing the 1.1-kilobase HindIII fragment in a specific orientation produced an order of magnitude more of the pilin subunit. While the expressed pilin antigen was located in both the cytoplasmic and outer membrane fractions of E. coli, none appeared to be polymerized into a pilus structure.
Synthesis of disulfide-bonded outer membrane proteins during the developmental cycle of Chlamydia psittaci and Chlamydia trachomatis
Authors: Hatch T P , Miceli M , Sublett J E
Published: November 2016

The disulfide bond cross-linked major outer membrane protein (MOMP) of the extracellular elementary bodies (EBs) of Chlamydia psittaci was reduced to its monomeric form within 1 h of entry of EBs into host cells by a process which was inhibited by chloramphenicol, while monomeric forms of three cross-linked cysteine-rich proteins could not be detected in Sarkosyl outer membrane complexes at any time in either extracellular or intracellular forms of C. psittaci. Synthesis and incorporation of the MOMP into outer membrane complexes were detected early in the infection cycle (12 h postinfection), while synthesis and incorporation of the cysteine-rich proteins were not observed until reticulate bodies had begun to reorganize into EBs at 20 to 22 h postinfection. By 46 h postinfection, the intracellular population of C. psittaci consisted mainly of EBs, the outer membrane complexes of which were replete with monomeric MOMP and cross-linked cysteine-rich proteins. Upon lysis of infected cells at 46 h, the MOMP was rapidly cross-linked, and infectious EBs were released. The status of the MOMP of intracellular Chlamydia trachomatis was similar to the status of the MOMP of C. psittaci in that the MOMP was largely uncross-linked at 24 and 48 h postinfection, but formed interpeptide disulfide bonds when it was exposed to an extracellular environment late in the developmental cycle. In contrast to C. psittaci, only a fraction of the cross-linked MOMP of infecting EBs of C. trachomatis was reduced by 4 h postinfection, and reduction of the MOMP was not inhibited by chloramphenicol. Exposure of extracellular EBs of C. trachomatis and C. psittaci to dithiothreitol reduced the MOMP but failed to stimulate metabolic activities normally associated with reticulate bodies.
Stage-specific DNA methylation in a fungal plant pathogen
Authors: Jupe E R , Magill J M , Magill C W
Published: November 2016

Significantly more 5-methylcytosine residues were found in the DNA from the dormant sclerotia of Phymatotrichum omnivorum than in the DNA from the metabolically active mycelia of the fungus, as shown by high-pressure liquid chromatography of acid-hydrolyzed DNA digests and by restriction of the DNA with the isoschizomers MspI and HpaII. N6-Methyladenine was not detected in GATC sequences in the DNA isolated from either stage.
Luciferase-dependent oxygen consumption by bioluminescent vibrios
Authors: Makemson J C
Published: November 2016

Oxygen uptake due to luciferase in two luminous Vibrio species was estimated in vivo by utilizing inhibitors having specificities for luciferase (decanol) and cytochromes (cyanide). Cyanide titration of respiration revealed a component of oxygen uptake less sensitive to cyanide which was completely inhibitable by low concentrations of decanol. From this it was estimated that in vivo luciferase is responsible for less than 12% (Vibrio harveyi) or 20% (Vibrio fischeri) of the total respiration. From these data in vivo bioluminescent quantum yields are estimated to be not lower than 1.7 and 2.6%, respectively.
Partial purification and characterization of pyruvate, orthophosphate dikinase from Rhodospirillum rubrum
Authors: Ernst S M , Budde R J , Chollet R
Published: November 2016

We confirmed an earlier report (B. B. Buchanan, J. Bacteriol. 119:1066-1068, 1974) that the nonsulfur purple photosynthetic bacterium Rhodospirillum rubrum contains pyruvate, orthophosphate dikinase (EC 2.7.9.1) activity that is absolutely dependent upon all three substrates by performing enzyme assays in both the forward (phosphoenolpyruvate formation) and reverse (ATP formation) directions. Of the various carbon sources tested, photoheterotrophic growth on DL-lactate plus bicarbonate proved to be best for the production of dikinase activity units. A four-step protocol, which included batch DEAE-cellulose processing, ammonium sulfate fractionation, and chromatography on hydroxylapatite and Blue A Dyematrex gels, was devised for partially purifying the enzyme from such cells. The protein was purified about 80-fold to an apparent electrophoretic purity of about 60% and a final specific activity of 3.6 U/mg of protein, with about a 35% overall recovery of activity units. Estimations of native and monomeric relative molecular weights by sucrose density gradient centrifugation, high-pressure liquid chromatography-based size exclusion chromatography, denaturing electrophoresis, and immunoblotting suggested that the holoenzyme was most likely a homodimer of 92.7-kilodalton subunits. The results are compared with related previous data on the nonphotosynthetic bacterial dikinase and the C4 mesophyll chloroplast enzyme.