bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydraulically Actuated Patient Transfer Device With Passivity Based Control
Authors: Humphreys Heather C. , Book Wayne J. , Huggins James D.
Published: February 2014

This paper describes the development of a hydraulically actuated patient transfer device, utilizing a force amplifying passivity based control strategy. The patient transfer device is intended for moving mobility limited patients, for example, from a bed to a chair, from a wheelchair into a car, or from the floor into a wheelchair. Our needs assessment has indicated that a more powerful, more easily maneuverable device is needed which is operable by a single caregiver with one hand. For this purpose, we are proposing a coordinated force amplifying control strategy. The caregiver input to the device is measured from a force sensor mounted on the device near the patient. The output is the force applied by the device actuators in the same direction as the input; this force may be amplified to assist the caregiver. Passivity-based control provides a way to implement this force amplifying control to aid in stability, which is critical for a device that interacts directly with humans. This paper describes the implementation of this force amplifying passivity-based control on a simpler pre-prototype two DOF patient transfer device.
SOC Detection of Diesel Engines Based on Online Estimation of Motored Pressure
Authors: Gao Guojing , Yang Fuyuan , Ouyang Minggao , Fang Cheng
Published: February 2014

In this paper, a diesel SOC (Start of Combustion) online detection method is developed in a diesel engine equipped with serial produced in-cylinder pressure signal sensors. Motored pressure trace is estimated in real time and the difference between the measured actual cylinder pressure and the estimated motored pressure is calculated. SOC is defined as the separation point of the two different pressure traces. In order to realize accurate motored pressure estimation, a thermodynamic analysis of the motored process of engines is done and a new concept “equivalent adiabatic exponent” is proposed. The pressure difference 0.2 MPa is taken as the criteria of combustion start. The SOC detection algorithm is executed in a MCU based electronic control unit. Engine tests are done in steady states as well as dynamic states.
Validation and Results of a Pseudo-Multi-Zone Combustion Trajectory Prediction Model for Capturing Soot and NOx Formation on a Medium Duty Diesel Engine
Authors: Bittle Joshua A. , Gao Zhiming , Jacobs Timothy J.
Published: February 2014

A pseudo-multi-zone phenomenological model has been created with the ultimate goal of supporting efforts to enable broader commercialization of low temperature combustion modes in diesel engines. The benefits of low temperature combustion are the simultaneous reduction in soot and nitric oxide emissions and increased engine efficiency if combustion is properly controlled. Determining what qualifies as low temperature combustion for any given engine can be difficult without expensive emissions analysis equipment. This determination can be made off-line using computer models or through factory calibration procedures. This process could potentially be simplified if a real-time prediction model could be implemented to run for any engine platform — this is the motivation for this study.

The major benefit of this model is the ability for it to predict the combustion trajectory, i.e. local temperature and equivalence ratio in the burning zones. The model successfully captures all the expected trends based on the experimental data and even highlights an opportunity for simply using the average reaction temperature and equivalence ratio as an indicator of emissions levels alone — without solving formation sub-models.

This general type of modeling effort is not new, but a major effort was made to minimize the calculation duration to enable implementation as an input to real-time next-cycle engine controller Instead of simply using the predicted engine out soot and NOx levels, control decisions could be made based on the trajectory. This has the potential to save large amounts of calibration time because with minor tuning (the model has only one automatically determined constant) it is hoped that the control algorithm would be generally applicable.
Analysis and Resolution of Piston Pin Joint Tick Noise
Authors: Hall Chris , Chen Yu , Mian Omar
Published: February 2014

A new measurement system and methodology has been developed which allows for direct measurement of the piston pin behavior of an internal combustion engine, particularly as it relates to pin joint ticking noise contributing to Noise Vibration and Harshness (NVH). Based on the measured dynamic of the piston pin during engine operation, the root cause of the pin joint ticking noise in this application was defined to be sticking of the pin at the end of the exhaust stroke which prevented pin lift. In order to better understand and mitigate this phenomenon, numerical simulation was conducted by means of Elasto Hydrodynamic Lubrication (EHL).

The output of this simulation showed that modifying the shape of the connecting rod pin bore by ovality has a significant effect on the pin motion and pin acceleration which could eliminate the pin joint tick noise. This improved pin bore shape was tested in the engine and confirmed to eliminate the pin joint ticking noise by manipulating the pin motion and disallowing piston pin sticking. Finally, an analysis of the newly developed methodology to root cause and solve pin joint ticking is compared to the prior methodology.
A New Physics-Based Misfire Detection Technique for a SI Engine
Authors: Boudaghi Kh. N. M. , Shahbakhti M. , Jazayeri S. A.
Published: February 2014

Control and detection of misfire is an essential part of on-board diagnosis of modern SI engines. This study proposes a novel model-based technique for misfire detection of a multi-cylinder SI engine. The new technique uses a dynamic engine model to determine mean output power, which is then used to calculate a new parameter for misfire detection. The new parameter directly relates to combustion period and is sensitive to the engine speed fluctuations caused by misfire. The new technique only requires measured engine speed data and it is computationally viable for use in a typical ECU.

The new technique is evaluated experimentally on a 4-cylinder 1.6-liter SI engine. Three types of misfires are studied including single, continues, and multiple events. The steady-state and transient experiments were done for a wide range of engine speeds and engine loads, using a vehicle chassis dynamometer and on-road vehicle testing. The validation results show the new technique is capable to detect all the three types of misfire with up to 97 percent accuracy during steady-state conditions. The new technique is augmented with a compensation factor to improve the accuracy of the technique for transient operations. The resulting technique is shown to be capable of detecting misfire during both transient and steady-state engine conditions.
Diesel-Ignited Propane Dual Fuel Low Temperature Combustion in a Heavy-Duty Diesel Engine
Authors: Polk A. C. , Carpenter C. D. , Guerry E. S. , Dwivedi U. , Srinivasan K. K. , Krishnan S. R. , Rowland Z.
Published: February 2014

This paper presents an experimental analysis of diesel-ignited propane dual fuel low temperature combustion (LTC) based on performance, emissions, and in-cylinder combustion data from a modern, heavy-duty diesel engine. The engine used for these experiments was a 12.9-liter, six-cylinder, direct injection heavy-duty diesel engine with electronic unit diesel injection pumps, a variable geometry turbocharger, and cooled exhaust gas recirculation (EGR). The experiments were performed with gaseous propane (the primary fuel) fumigated upstream of the turbocharger and diesel (the pilot fuel) injected directly into the cylinders. Results are presented for a range of diesel injection timings (SOIs) from 10° BTDC to 50° BTDC at a brake mean effective pressure (BMEP) of 5 bar and a constant engine speed of 1500 RPM. The effects of SOI, percent energy substitution (PES) of propane (i.e., replacement of diesel fuel energy with propane), intake boost pressure, and cooled EGR on the dual fuel LTC process were investigated. The approach was to determine the effects of SOI while maximizing the PES of propane. Dual fuel LTC was achieved with very early SOIs (e.g., 50° BTDC) coupled with high propane PES (> 84%), which yielded near-zero NOx (< 0.02 g/kW-hr) and very low smoke emissions (< 0.1 FSN). Increasing the propane PES beyond 84% at the SOI of 50° BTDC yielded a high COV of IMEP due to retarded combustion phasing (CA50). Intake boost pressures were increased and EGR rates were decreased to minimize the COV, allowing higher propane PES (∼ 93%); however, lower fuel conversion efficiencies (FCE) and higher HC and CO emissions were observed.
Combustion Characteristics of Diesel Spray Under Low O2 Concentration Condition
Authors: Azetsu Akihiko , Nagashima Youhei , Yamamoto Kei
Published: February 2014

The spray combustion of diesel fuel under conditions of very low ambient O2 concentrations was examined in this study. The detailed combustion characteristics were evaluated using two different sets of experimental apparatuses. A high-temperature, high-pressure combustion vessel with dual observation windows was employed to visualize the spray flame. The sequential images were obtained by using a high-speed color video camera and were analyzed using the two color method to quantify the temporal variation of the two dimensional distribution of soot temperature and KL factor. Both the ambient O2 concentration and the CO2 mixing ratio were varied as experimental parameters. A second constant volume vessel with a smaller internal volume was also employed as an experimental apparatus to conduct analyses of heat release rates based on temporal variations of pressure.

Based on a series of systematic experiments, we confirmed that O2 concentration is the primary factor affecting both the ignition delay and combustion period, while the level of CO2 mixing has little effect. Decreasing O2 concentrations were associated with delays in the appearance of the luminous flame following the onset of light emission from OH radicals. The heat release rate study showed the possibility of the existence of endothermic reactions during this period. The flame temperature was observed to decrease as the O2 concentration decreased and as the CO2 ratio increased, resulting in reduced NOx emissions. The amount of soot inside the flame initially increased with decreasing O2 concentrations, but then decreased starting at an O2 concentration of approximately 11%, such that minimal amounts of soot were generated at very low O2 levels. Both visual observations and emissions measurements confirmed that the simultaneous reduction of NOx, soot and CO can be successfully achieved under very low O2 concentrations.
Study of Particle Size Distribution Emitted From a Diesel Engine by Diesel and Biodiesel-Diesel Blends Fuels
Authors: Cheng Xiaobei , Chen Liang , Yan Fangqin , Chen Guohua
Published: February 2014

The effect of diesel and biodiesel blends on particle size and number concentration distributions were studied in diesel engine under different operating conditions, including speeds, loads, and injection timing. The results showed that the engine load was more influential on particle size distribution than the engine speed. At the high load, diesel fuels produced mainly accumulation-mode particles, and at medium or lower load, diesel fuel produced more nuclei-mode particles. The injection timing had obviously influence on particle size distribution and number concentration. Advanced injection timing induced higher number concentrations of nuclei-mode particles for the low load and more accumulation mode particles for high load. Compared to the neat diesel fuel, the combustion process was improved when fueled with diesel-biodiesel blends. The oxygen contained in the biodiesel fuel may improve combustion. The number and mass concentration of PM was greatly decreased with the increase in biodiesel blend ratio. Biodiesel blends had an early start of injection, and particle size distributions tended to be ultra-fine particles with the increase in the ratio of biodiesel blend. The average mid-diameter range of particles was significantly affected by the change in fuel injection timing.
NS 999 Electric Switcher Update
Authors: Barbee Gibson , Westreich Philippe
Published: February 2014

Norfolk Southern Railway Company (NS) is developing an all-electric switching locomotive, the NS 999, to provide a zero point source emission electric locomotive option for rail switching service. The original NS 999, unveiled in September 2009, suffered from poor battery management and challenging battery packaging. The rebuilt NS 999, anticipated in the 4th quarter 2013, will be powered by Axion Power’s PbC® batteries. The Axion PbC® batteries provide increased charge/discharge cycle life and charge acceptance compared to conventional Valve Regulated Lead–Acid (VRLA) batteries, as well as increased usable energy when configured in series as ‘long strings.’

NS and Axion will review the challenges of the initial NS 999 battery management system, improvements to the battery management system, and test results from the Norfolk Southern Hybrid Locomotive Simulator using Axion’s PbC® lead–carbon hybrid battery/supercapacitor. Axion will present test data showing the low variation in strings of PbC® batteries compared to VRLA while simulating locomotive switching. PbC® batteries have a unique charging curve, known as “concave down, increasing,” which allows the batteries to self-equalize in strings. This characteristic of PbC® batteries provides for simpler battery management and reduced maintenance charging, while increasing the usable energy available within the string.

The rebuilt experimental locomotive NS 999 will use Axion’s PbC® lead–carbon batteries for the energy storage system to power locomotive switching and recover braking energy. If this research is successful, a zero point source emission electric locomotive could provide an option to reduce emissions in urban non-attainment areas and reduce dependence on petroleum. The NS 999 electric switcher is the first step to the ultimate goal of recovering braking energy from high power conventional diesel locomotives.
Design of a Multi-Use, Highly Efficient Intermodal Container System
Authors: Gorbunov Maksym
Published: February 2014

This paper details the design of a shipping container concept with a purpose of being not only highly efficient in transport but also after arrival. In order to reduce mass while also increasing the ability to carry heavier loads, Lightweight structures and materials are employed instead of simple steels or cast iron used in current designs. The second goal of the design was to create a weld free structure that can be easily assembled and disassembled without the need for special labor and skills saving time, space and resources when shipping empty container or storing containers that are not in use. Shipping containers often clutter construction sites and temporary establishments like concerts and flea markets. By being able to break down and efficiently store containers businesses in charge of these temporary establishments can save valuable real estate and run much more efficiently.

Another design feature is creating an entirely modular system. Each container is made from completely interchangeable parts that can be swapped in and out for ones that have different function like container variations that provides insulation or active temperature or humidity control for temperature sensitive products or high security configurations for hazardous materials or expensive goods. In order to provide such interchangeability, the frame is designed to be strong and rigid enough to be able to handle the required loads without relying on wall plates. The combination of these design points leads to a transportation system that can not only be deployed using existing intermodal infrastructure but can serve a secondary purpose once it arrives at its destination. Because the containers are modular and highly versatile, they can be assembled into large floor space, multistory structures. Containers and trailers normally used as office space at construction sites are cramped, uncomfortable and very unsightly. Using this system, large two story office space of several thousand square feet can be erected using no more than a dozen containers. The modular walls can be used to swap in ceiling or wall panels that let in natural light, harness solar power or allow plumbing systems, electrical wiring, thermal insulation or ventilation. Because of the weld-free design and ultra-lightweight components, structure assembly and disassembly is simple with unskilled labor and common tools. This is especially important because the most impactful application of this system could be in disaster relief. Single containers can be used as substitutes for single family homes and large container assemblies can be used to create anything kind of community use structure from shower clusters to temporary schools to dining halls to administrative buildings creating a sustainable temporary community.
Development of Railroad Wheel Rim Axial Residual Stress in Heavy Axle Load Service
Authors: Lonsdale Cameron , Oliver John , Maram Rama Krishna , Cummings Scott
Published: February 2014

Vertical split rim (VSR) failures remain a failure mode for wheels in North America, and are of concern to wheel manufacturers and railroads alike. Both forged and cast wheels have suffered VSRs in service. Extensive testing during the last several years, using x-ray diffraction techniques, has shown the axial residual stress pattern within the railroad wheel rim is significantly different for new AAR Class C wheels vs. AAR Class C wheels that have failed due to a VSR, and non-failed AAR Class C wheels that have been operating in service. VSRs almost always begin at areas of tread damage, resulting from shelling or spalling, and cracking propagates into the rim section under load. At the rim locations tested, the as-manufactured wheels have a relatively “flat” axial residual stress profile, compressive but near neutral, caused by the rim quenching operation, while wheels that have been in service have a layer of high axial compressive stress at the tread surface, and a balancing zone of axial tensile stress underneath. The magnitude and direction of this axial tensile stress is consistent with the crack propagation of a VSR failure. When cracks from tread surface damage propagate into this subsurface axial tensile zone, a VSR can occur under sufficient additional service loading, such as loads caused by in-service wheel/rail impacts from tread damage. Further, softer Class U (untreated) wheels, removed from service and tested, were found to have a balancing axial tensile stress layer deeper below the tread surface than that found in used Class C wheels.

This paper describes recent x-ray diffraction testing to measure the axial residual stress profile in wheel rims operated in the Facility for Accelerated Service Testing (FAST) train at the Transportation Technology Center (TTC), in Pueblo, CO. The goal of the testing was to determine the development rate and magnitude of wheel rim axial residual stress, as a function of known load and service mileage. Four new Class C wheelsets and four new Class U wheelsets were placed in service under the FAST train, and these wheelsets were subsequently removed at various mileage levels for evaluation. Two radial rim slices were cut from each wheel at each mileage level, and x-ray diffraction was used to measure the axial residual stress within the wheel rim section. The last two Class C wheelsets and last two Class U wheelsets were also exposed to an extended drag braking event at FAST, where wheel treads were heated by tread braking. The authors describe the testing and discuss the axial residual stress results in detail, with emphasis on implications for service.
Systematic procedure to optimize chamber seasoning conditions with optical emission spectroscopy in plasma etching
Authors: Hyun Baek Kye , Wook Park Sang , Jung Seong Geum , Jin Min Gyung , Choi Gilhyeun , Kang Ho-Kyu , Seung Jung Eun , Han Chonghun , Edgar Thomas F.
Published: February 2014

As chamber conditions gradually change with wafer processing, periodic wet cleaning is an inevitable event in semiconductor manufacturing. Since the chamber conditions are initialized during the wet cleaning, a chamber conditioning process called chamber seasoning follows the wet cleaning step. In this paper, a systematic procedure to optimize chamber seasoning for plasma etching is proposed, and the effectiveness is demonstrated in a semiconductor manufacturing environment. In order to quantitatively analyze plasma conditions for chamber seasoning and to achieve the optimum conditions objectively, a normalization technique for optical emission spectroscopy called a self-background normalization technique and a computational optimization process is suggested. By applying the optimized chamber seasoning conditions, a plasma reactor which is suffering from a serious etch rate drift after wet cleaning returns to a production ready status. Also, the etch rate of Si, which is an index for production readiness, is perfectly matched to 37.8 A/s for production. Hopefully, the proposed methodology in this paper will be disseminated to semiconductor manufacturers who experience similar issues after wet cleaning.
Monitor unit calculations for external photon and electron beams: Report of the AAPM Therapy Physics Committee Task Group No. 71
Authors: Gibbons John P. , Antolak John A. , Followill David S. , Huq M. Saiful , Klein Eric E. , Lam Kwok L. , Palta Jatinder R. , Roback Donald M. , Reid Mark , Khan Faiz M.
Published: February 2014

A protocol is presented for the calculation of monitor units (MU) for photon and electron beams, delivered with and without beam modifiers, for constant source‐surface distance (SSD) and source‐axis distance (SAD) setups. This protocol was written by Task Group 71 of the Therapy Physics Committee of the American Association of Physicists in Medicine (AAPM) and has been formally approved by the AAPM for clinical use. The protocol defines the nomenclature for the dosimetric quantities used in these calculations, along with instructions for their determination and measurement. Calculations are made using the dose per MU under normalization conditions, , that is determined for each userˈs photon and electron beams. For electron beams, the depth of normalization is taken to be the depth of maximum dose along the central axis for the same field incident on a water phantom at the same SSD, where = 1 cGy/MU. For photon beams, this task group recommends that a normalization depth of 10 cm be selected, where an energy‐dependent ≤ 1 cGy/MU is required. This recommendation differs from the more common approach of a normalization depth of dm, with = 1 cGy/MU, although both systems are acceptable within the current protocol. For photon beams, the formalism includes the use of blocked fields, physical or dynamic wedges, and (static) multileaf collimation. No formalism is provided for intensity modulated radiation therapy calculations, although some general considerations and a review of current calculation techniques are included. For electron beams, the formalism provides for calculations at the standard and extended SSDs using either an effective SSD or an air‐gap correction factor. Example tables and problems are included to illustrate the basic concepts within the presented formalism.
Evaluation of image guided motion management methods in lung cancer radiotherapy
Authors: Zhuang Ling , Yan Di , Liang Jian , Ionascu Dan , Mangona Victor , Yang Kai , Zhou Jun
Published: February 2014

Purpose:

To evaluate the accuracy and reliability of three target localization methods for image guided motion management in lung cancer radiotherapy.

Methods:

Three online image localization methods, including (1) 2D method based on 2D cone beam (CB) projection images, (2) 3D method using 3D cone beam CT (CBCT) imaging, and (3) 4D method using 4D CBCT imaging, have been evaluated using a moving phantom controlled by (a) 1D theoretical breathing motion curves and (b) 3D target motion patterns obtained from daily treatment of 3 lung cancer patients. While all methods are able to provide target mean position (MP), the 2D and 4D methods can also provide target motion standard deviation (SD) and excursion (EX). For each method, the detected MP/SD/EX values are compared to the analytically calculated actual values to calculate the errors. The MP errors are compared among three methods and the SD/EX errors are compared between the 2D and 4D methods. In the theoretical motion study (a), the dependency of MP/SD/EX error on EX is investigated with EX varying from 2.0 cm to 3.0 cm with an increment step of 0.2 cm. In the patient motion study (b), the dependency of MP error on target sizes (2.0 cm and 3.0 cm), motion patterns (four motions per patient) and EX variations is investigated using multivariant linear regression analysis.

Results:

In the theoretical motion study (a), the MP detection errors are −0.2 ± 0.2, −1.5 ± 1.1, and −0.2 ± 0.2 mm for 2D, 3D, and 4D methods, respectively. Both the 2D and 4D methods could accurately detect motion pattern EX (error < 1.2 mm) and SD (error < 1.0 mm). In the patient motion study (b), MP detection error vector (mm) with the 2D method (0.7 ± 0.4) is found to be significantly less than with the 3D method (1.7 ± 0.8,p < 0.001) and the 4D method (1.4 ± 1.0, p < 0.001) using paired t‐test. However, no significant difference is found between the 4D method and the 3D method. Based on multivariant linear regression analysis, the variances of MP error in SI direction explained by target sizes, motion patterns, and EX variations are 9% with the 2D method, 74.4% with the 3D method, and 27% with the 4D method. The EX/SD detection errors are both < 1.0 mm for the 2D method and < 2.0 mm for the 4D method.

Conclusions:

The 2D method provides the most accurate MP detection regardless of the motion pattern variations, while its performance is limited by the accuracy of target identification in the projection images. The 3D method causes the largest error in MP determination, and its accuracy significantly depends on target sizes, motion patterns, and EX variations. The 4D method provides moderate MP detection results, while its accuracy relies on a regular motion pattern. In addition, the 2D and 4D methods both provide accurate measurement of the motion SD/EX, providing extra information for motion management.
Assessment and management of interfractional variations in daily diagnostic‐quality‐CT guided prostate‐bed irradiation after prostatectomy
Authors: Liu Feng , Ahunbay Ergun , Lawton Colleen , Allen Li X.
Published: February 2014

Purpose:

To quantify interfractional anatomic variations and limitations of the current practice of image‐guided radiation therapy (IGRT) for prostate‐bed patients and to study dosimetric benefits of an online adaptive replanning scheme that addresses the interfractional variations.

Methods:

Contours for the targets and organs at risk (OARs) from daily diagnostic‐quality CTs acquired with in‐room CT (CTVision, Siemens) were generated by populating the planning contours using an autosegmentation tool based on deformable registration (ABAS, Elekta) with manual editing for ten prostate‐bed patients treated with postoperative daily CT‐guided IMRT. Dice similarity coefficient (DSC) obtained by maximizing the overlap of contours for a structure between the daily and plan contours was used to quantify the organ deformation between the plan and daily CTs. Three interfractional‐variation‐correction schemes, the current standard practice of IGRT repositioning, a previously developed online adaptive RT (ART), and the full reoptimization, were applied to these daily CTs and a number of dose‐volume quantities for the targets and organs at risk were compared for their effectiveness to account for the interfractional variations.

Results:

Large interfractional organ deformations in prostate‐bed irradiation were seen. The mean DSCs for CTV, rectum, and bladder were 86.6 ± 5.1% (range from 61% to 97%), 77.3% ± 7.4% (range from 55% to 90%), and 75.4% ± 11.2% (range from 46% to 96%), respectively. The fractional and cumulative dose‐volume quantities for CTV and PTV: V100 (volume received at least 100% prescription dose), and rectum and bladder: V45Gy and V60Gy (volume received at least 45 or 60 Gy), were compared for the repositioning, adaptive, reoptimization, and original plans. The fractional and cumulative dosimetric results were nearly the same. The average cumulative CTV V100 were 88.0%, 98.4%, 99.2%, and 99.3% for the IGRT, ART, reoptimization, and original plans, respectively. The corresponding rectal V45Gy (V60Gy) were 58.7% (27.3%), 48.1% (20.7%), 43.8% (16.1%), and 44.9% (16.8%). The results for bladder were comparable among three schemes. Paired two‐tailed Wilcoxon signed‐rank tests were performed and it was found that ART and reoptimization provide better target coverage and better OAR sparing, especially rectum sparing.

Conclusions:

The interfractional organ motions and deformations during prostate‐bed irradiation are significant. The online adaptive replanning scheme is capable of effectively addressing the large organ deformation, resulting in cumulative doses equivalent to those originally planned.
The torque on a dipole in uniform motion
Authors: Griffiths David J. , Hnizdo V.
Published: February 2014

We calculate the torque on an ideal (point) dipole moving with constant velocity through uniform electric and magnetic fields.
Assessing the flexibility of research-based instructional strategies: Implementing tutorials in introductory physics in the lecture environment
Authors: Kryjevskaia Mila , Boudreaux Andrew , Heins Dustin
Published: February 2014

Materials from Tutorials in Introductory Physics, originally designed and implemented by the Physics Education Group at the University of Washington, were used in modified form as interactive lectures under conditions significantly different from those suggested by the curriculum developers. Student learning was assessed using tasks drawn from the physics education research literature. Use of tutorials in the interactive lecture format yielded gains in student understanding comparable to those obtained through the canonical tutorial implementation at the University of Washington, suggesting that student engagement with the intellectual steps laid out in the tutorials, rather than the specific strategies used in facilitating such engagement, plays the central role in promoting student learning. We describe the implementation details and assessment of student learning for two different tutorials: one focused on mechanical waves, used at North Dakota State University, and one on Galilean relativity, used at Western Washington University. Also discussed are factors that may limit the generalizability of the results.
Subconscious (Un)Attachment to a Sponsor: An Irrational Effect of Facility Naming Rights
Authors: Delia Elizabeth B.
Published: February 2014

As global sponsorship spending increases, so too do efforts to gauge effects of sponsorship. However, much of the sponsorship literature to date has emphasized the influence of sponsorship from a business perspective, thus neglecting to address the social and psychological influence of sponsorship on the consumer. Reasoning that such deep levels of consumer inquiry cannot be accomplished through (post)positivist inquiry, I pursue an interpretive ethnographic mode of inquiry, using Syracuse University fandom as a case study. In doing so, I engage in reflexive autobiography as a method of critical inquiry to interrogate my own (personal, professional, and academic) experience with sponsorship (specifically, facility naming rights) as a Syracuse fan. Through this introspection, I discover my perception of and connection to the sponsor are inherently complex, as I possess a subconscious yet meaningful attachment to the sponsor that contributes to my overall well-being.
Cell Surface ABP1-TMK Auxin-Sensing Complex Activates ROP GTPase Signaling
Authors: Xu Tongda , Dai Ning , Chen Jisheng , Nagawa Shingo , Cao Min , Li Hongjiang , Zhou Zimin , Chen Xu , De Rycke Riet , Rakusová Hana , Wang Wuyi , Jones Alan M. , Friml Jiří , Patterson Sara E. , Bleecker Anthony B. , Yang Zhenbiao
Published: February 2014

A Different Route

The plant hormone auxin regulates a variety of developmental processes and responses to environmental inputs, often via changes in gene transcription.

Xu
et al.

(p.
1025
) analyzed a signaling pathway involving ABP1 (auxin-binding protein 1) that affects the cytoskeleton and endocytosis in
Arabidopsis
without changing gene transcription. Instead, ABP1 functions at the cell surface to bind auxin and a family of membrane kinases, thereby activating intracellular guanosine triphosphatases to initiate important developmental changes in cell shape.
Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome
Authors: Colak Dilek , Zaninovic Nikica , Cohen Michael S. , Rosenwaks Zev , Yang Wang-Yong , Gerhardt Jeannine , Disney Matthew D. , Jaffrey Samie R.
Published: February 2014

Repeat Silencing

Fragile X syndrome, a genetic cause of many cases of autism and mental retardation, involves expansion of a trinucleotide repeat in the
fragile X mental retardation 1 (FMR1)
gene. Working with human embryonic stem cells,

Colak
et al.

(p.
1002
) found that the expanded repeat region was transcribed into the untranslated region of
FMR1
messenger RNA, which then bound to the DNA repeat region in the
FMR1
gene, inactivating the gene. The findings explain how the trinucleotide repeat expansion causes RNA-directed gene silencing during development in fragile X syndrome.
Detection of a Recurrent
DNAJB1-PRKACA
Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma
Authors: Honeyman Joshua N. , Simon Elana P. , Robine Nicolas , Chiaroni-Clarke Rachel , Darcy David G. , Lim Irene Isabel P. , Gleason Caroline E. , Murphy Jennifer M. , Rosenberg Brad R. , Teegan Lydia , Takacs Constantin N. , Botero Sergio , Belote Rachel , Germer Soren , Emde Anne-Katrin , Vacic Vladimir , Bhanot Umesh , LaQuaglia Michael P. , Simon Sanford M.
Published: February 2014

Oncogenic Suspect Exposed

It can be difficult logistically to study the genomics of rare variants of common cancers. Nevertheless,

Honeyman
et al.

(p.
1010
) studied fibrolamellar hepatocellular carcinoma (FL-HCC), a rare and poorly understood liver tumor that affects adolescents and young adults and for which there is no effective treatment. FL-HCCs from 15 patients all expressed a chimeric RNA transcript and protein containing sequences from a molecular chaperone fused in frame with sequences from the catalytic domain of protein kinase A. The chimeric protein retained kinase activity in vitro. Such recurrent gene fusions in cancer may signal a role in pathogenesis and provide an opportunity for therapeutic intervention.
The Neural Code That Makes Us Human
Authors: Grodzinsky Yosef , Nelken Israel
Published: February 2014

How does a certain pattern of vibration in the air reliably represent a meaningful speech sound?

[Also see Report by

Mesgarani
et al.

]
New Review Slams Fusion Project's Management
Authors: Clery Daniel
Published: February 2014

ITER, the international fusion reactor project in France, is reeling from an assessment that found serious problems with the project's leadership, management, and governance.
Twitter Offers Entire Data Pool, but Some Wary of Diving In
Authors: Bohannon John
Published: February 2014

Twitter offers academics full access to its vast data, but the legal strings attached to the data worry some researchers.
E.U. Privacy Protection Bill Would Hamper Research, Scientists Warn
Authors: Rabesandratana Tania
Published: February 2014

Proposed new rules would make it more difficult to use patients' data without their consent.
Can Down Syndrome Be Treated?
Authors: Underwood Emily
Published: February 2014

People with Down syndrome are signing up for trials of several drugs aimed at helping their cognitive impairment, even as researchers explore more radical ideas to "cure" the genetic disorder.
Chimeric Plantibody Passively Protects Mice against Aerosolized Ricin Challenge
Authors: Sully Erin K. , Whaley Kevin J. , Bohorova Natasha , Bohorov Ognian , Goodman Charles , Kim Do H. , Pauly Michael H. , Velasco Jesus , Hiatt Ernie , Morton Josh , Swope Kelsi , Roy Chad J. , Zeitlin Larry , Mantis Nicholas J.
Published: February 2014

Recent incidents in the United States and abroad have heightened concerns about the use of ricin toxin as a bioterrorism agent. In this study, we produced, using a robust plant-based platform, four chimeric toxin-neutralizing monoclonal antibodies that were then evaluated for the ability to passively protect mice from a lethal-dose ricin challenge. The most effective antibody, c-PB10, was further evaluated in mice as a therapeutic following ricin exposure by injection and inhalation.
Demonstration of Plasmid-Mediated Drug Resistance in Mycobacterium abscessus
Authors: Matsumoto Cristianne Kayoko , Bispo Paulo José Martins , Santin Katiane , Nogueira Christiane Lourenço , Leão Sylvia Cardoso
Published: February 2014

Plasmid-mediated kanamycin resistance was detected in a strain of
Mycobacterium abscessus
subsp.
bolletii
responsible for a nationwide epidemic of surgical infections in Brazil. The plasmid did not influence susceptibility to tobramycin, streptomycin, trimethoprim-sulfamethoxazole, clarithromycin, or ciprofloxacin. Plasmid-mediated drug resistance has not been described so far in mycobacteria.
Interlaboratory Reproducibility and Proficiency Testing within the Human Papillomavirus Cervical Cancer Screening Program in Catalonia, Spain
Authors: Ibáñez R. , Félez-Sánchez M. , Godínez J. M. , Guardià C. , Caballero E. , Juve R. , Combalia N. , Bellosillo B. , Cuevas D. , Moreno-Crespi J. , Pons L. , Autonell J. , Gutierrez C. , Ordi J. , de Sanjosé S. , Bravo I. G.
Published: February 2014

In Catalonia, a screening protocol for cervical cancer, including human papillomavirus (HPV) DNA testing using the Digene Hybrid Capture 2 (HC2) assay, was implemented in 2006. In order to monitor interlaboratory reproducibility, a proficiency testing (PT) survey of the HPV samples was launched in 2008. The aim of this study was to explore the repeatability of the HC2 assay's performance. Participating laboratories provided 20 samples annually, 5 randomly chosen samples from each of the following relative light unit (RLU) intervals: <0.5, 0.5 to 0.99, 1 to 9.99, and ≥10. Kappa statistics were used to determine the agreement levels between the original and the PT readings. The nature and origin of the discrepant results were calculated by bootstrapping. A total of 946 specimens were retested. The kappa values were 0.91 for positive/negative categorical classification and 0.79 for the four RLU intervals studied. Sample retesting yielded systematically lower RLU values than the original test (
P
< 0.005), independently of the time elapsed between the two determinations (median, 53 days), possibly due to freeze-thaw cycles. The probability for a sample to show clinically discrepant results upon retesting was a function of the RLU value; samples with RLU values in the 0.5 to 5 interval showed 10.80% probability to yield discrepant results (95% confidence interval [CI], 7.86 to 14.33) compared to 0.85% probability for samples outside this interval (95% CI, 0.17 to 1.69). Globally, the HC2 assay shows high interlaboratory concordance. We have identified differential confidence thresholds and suggested the guidelines for interlaboratory PT in the future, as analytical quality assessment of HPV DNA detection remains a central component of the screening program for cervical cancer prevention.
Benchmarking of Methods for Genomic Taxonomy
Authors: Larsen Mette V. , Cosentino Salvatore , Lukjancenko Oksana , Saputra Dhany , Rasmussen Simon , Hasman Henrik , Sicheritz-Pontén Thomas , Aarestrup Frank M. , Ussery David W. , Lund Ole
Published: February 2014

One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is—that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the
gyrB
gene (for the
Enterobacteraceae
family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring
k
-mers (substrings of
k
nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
Coinfection of Fusobacterium nucleatum and Actinomyces israelii in Mastoiditis Diagnosed by Next-Generation DNA Sequencing
Authors: Salipante Stephen J. , Hoogestraat Daniel R. , Abbott April N. , SenGupta Dhruba J. , Cummings Lisa A. , Butler-Wu Susan M. , Stephens Karen , Cookson Brad T. , Hoffman Noah G.
Published: February 2014

Some bacterial infections involve potentially complex mixtures of species that can now be distinguished using next-generation DNA sequencing. We present a case of mastoiditis where Gram stain, culture, and molecular diagnosis were nondiagnostic or discrepant. Next-generation sequencing implicated coinfection of
Fusobacterium nucleatum
and
Actinomyces israelii
, resolving these diagnostic discrepancies.
Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Malaria Infections in an Area of Endemicity in Thailand
Authors: Sattabongkot Jetsumon , Tsuboi Takafumi , Han Eun-Taek , Bantuchai Sirasate , Buates Sureemas
Published: February 2014

The loop-mediated isothermal amplification (LAMP) method, developed by our group for diagnosis of four human malaria parasites, was evaluated on a large scale at a remote clinic in Thailand where malaria is endemic. A total of 899 febrile patients were analyzed in this study. LAMP was first evaluated in 219 patients, and the result was compared to those of two histidine-rich protein (HRP)-2 rapid diagnostic tests (RDTs) and microscopy as a gold standard. LAMP DNA extraction was conducted by a simple boiling method, and the test results were assessed visually. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 95.7%, 100%, 100%, and 98%, respectively, for LAMP and 98.6%, 98%, 95.8%, and 99.3%, respectively, for RDTs. Since RDT-positive results were based on one out of two RDTs, the sensitivity of RDTs was slightly higher than that of LAMP. However, LAMP tended to be more specific than RDTs. LAMP next was evaluated in 680 patients, and the result was compared to that of microscopy as a gold standard. Sensitivity, specificity, PPV, NPV, and diagnostic accuracy of LAMP were 88.9%, 96.9%, 92.2%, 95.5%, and 94.6%, respectively. Nested PCR was used to confirm the discrepant results. Malaria LAMP in a remote clinic in Thailand achieved an acceptable result, indicating that LAMP malaria diagnosis is feasible in a field setting with limited technical resources. Additionally, the rapid boiling method for extracting DNA from dried blood spots proved to be simple, fast, and suitable for use in the field.
Clinical Implications of Evolutionary Patterns of Homologous, Full-Length Hepatitis B Virus Quasispecies in Different Hosts after Perinatal Infection
Authors: Liu Feng , Yu De-Min , Huang Su-Yuan , Yu Jia-Lun , Zhang Dong-Hua , Gong Qi-Ming , Zhang Xin-Xin
Published: February 2014

Chronic hepatitis B virus (HBV) infection via perinatal transmission is common in the Asia-Pacific region, but related quasispecies (QS) characteristics are not yet defined. To investigate the homologous, full-length HBV QS after perinatal infection and their clinical implications, five pairs of mother-daughter patients with chronic HBV infection (one patient with liver cirrhosis, one with immune tolerance, and eight with chronic hepatitis) were included. Full-length HBV were amplified by PCR from serum samples before antiviral treatment and cloned; an average of 17 clones per sample were sequenced, and the QS complexities, diversities, and evolution patterns were analyzed. Full-length HBV sequence similarities within mother-daughter pairs were 91.3 to 98.3%. The QS complexities of full-length HBV were similar between mothers and daughters (median of 0.9734 compared to 0.9688,P> 0.05), as were the diversities (median of 3.396 × 10−3compared to 4.617 × 10−3substitutions/site,P> 0.05). However, the distribution patterns of QS complexities and diversities within specific genes were different, and QS genetic distances of the mothers were higher than those of daughters, both more evident in pairs with different antiviral responses and different immune phases or stages. The nucleotide substitution rate of full-length HBV was 14.388 × 10−5substitutions/site/year, whereas the preC/C gene rate was the highest. Mutations and indels were more common in clones from the mothers, which decreased the affinity of epitopes by 6- to 89-fold. The various genes from homologous HBV genomes evolved in different patterns despite numerically comparable full-length QS complexities and diversities. The different patterns may correlate with the immune stages of chronic HBV infection, which warrants further study.