bluuebunny/crossref_metadata_2025 huggingface dataset:
Parallel signatures of selection in temporally isolated lineages of pink salmon
Authors: Seeb L. W. , Waples R. K. , Limborg M. T. , Warheit K. I. , Pascal C. E. , Seeb J. E.
Published: April 2014

Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly abundant and widely ranging salmonid, provide a naturally occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two‐year semelparous life history. The species is composed of two reproductively isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction‐site‐associated DNA (RAD) sequencing to discover and genotype approximately 8000 SNP loci in three population pairs of even‐ and odd‐year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd‐year than within the even‐year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation‐based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.
Business in Fragile Environments: Capabilities for Conflict Prevention
Authors: Ganson Brian
Published: April 2014

While normative frameworks proscribing and prescribing company action in conflict‐prone environments grow in number, both the practice‐oriented and more theoretical literature have been relatively silent on the question of whether and how a company's distinctive organizational capabilities contribute to conflict risk mitigation or conflict resolution in fragile contexts. This article links the practical experience of company managers with conflict management theory to posit that organizational capabilities are a crucial explanatory variable for the gap between desired and observed company performance in fragile contexts. It models a management system for conflict prevention with empirical and theoretical referents. The model provides practitioners with useful diagnostic entry points as they work to improve company operations. At the same time, it brings together diverse conflict management perspectives on company operations in fragile environments so that future case data may be ordered and compared and further theoretical propositions developed and tested.
Mediators' Cognitive Role Schema
Authors: Zarankin Adi , Wall James A. , Zarankin Tal G.
Published: April 2014

This study identifies the cognitive role schema of 189 practicing mediators. An initial analysis of the mediators' questionnaire responses revealed 13 facets in the mediators' schema, and a second analysis condensed this to four goals: agreement, improvement of the parties' relationship, benefit the parties as well as society, and improve the mediation process. Not only do these facets indicate how the mediators think, but they also provide predictions about the mediators' behavior (e.g., they will strive primarily for agreement).
Lead Extraction Experience with High Frequency Excimer Laser
Authors: TANAWUTTIWAT TANYANAN , GALLEGO DANIEL , CARRILLO ROGER G.
Published: April 2014

Background

A higher frequency Excimer laser sheath using an 80‐Hz pulse repetitive rate was approved by the Food and Drug Administration in April 2012. We reported our initial clinical experience with a high‐frequency Excimer laser sheath and compared it with lower‐frequency laser sheaths which have been previously used.

Methods

In this single center, retrospective cohort study, we evaluated patients who underwent lead extraction from December 2008 to May 2013. Those who underwent lead removal without using a laser sheath or with approaches other than subclavian were excluded. Primary endpoints included total laser time, number of pulses, and complications. Data on clinical characteristics, lead type, indications, and outcomes were prospectively collected and analyzed.

Results

A total of 427 patients were included in the study (72.6% male; age 67.9 ± 15.23 years). Lower frequency and higher frequency laser sheaths were used in 315 and 112 patients, respectively. A total of 821 leads were removed with 765 leads (93.2%) extracted using the Excimer laser sheath. Lead age was 5.71 ± 4.96 years. Complete extraction was seen in all patients. A higher‐frequency laser sheath was associated with a lower laser time and a lower total number of laser pulses even after adjustments for the number of leads, type of leads, and lead age. In the higher frequency group, mortality rate was 0.9% and minor complication rate was 3.6%.

Conclusions

When compared with the lower‐frequency laser sheath, the higher‐frequency laser sheath requires less laser times and more efficient amount of pulses for lead extraction with comparable success rate. Due to the rarity of major and minor complications, no statistical significance was found between the two groups.
Touch attitudes in cross‐sex friendships: We're just friends
Authors: MILLER MICHAEL J. , DENES AMANDA , DIAZ BRIANNA , RANJIT YERINA
Published: April 2014

Results from this survey indicated that within heterosexual cross‐sex friendships, perceptions of friendship intimacy for females were more strongly tied to their positive attitudes toward: enacting and receiving more touch, enacting and receiving more safe haven (e.g., caretaking) touch, and perceiving touch as more sexually arousing, when compared to males. Females were more motivated not to touch their cross‐sex friends in public regardless of intimacy perceptions and did not positively perceive safe haven touch if they did not have a romantic partner. It is argued that males' and females' attitudes toward touch in cross‐sex friendships diverge due to evolved differences related to parental investment and the manner in which they are socialized to perceive their roles in cross‐sex friendships.
Pay‐Back‐Revenue‐Sharing Contract in Coordinating Supply Chains with Random Yield
Authors: Tang Sammi Y. , Kouvelis Panos
Published: April 2014

We consider coordination issues in supply chains where supplier's production process is subject to random yield losses. For a simple supply chain with a single supplier and retailer facing deterministic demand, a pay back contract which has the retailer paying a discount price for the supplier's excess units can provide the right incentive for the supplier to increase his production size and achieve coordination. Building upon this result, we consider coordination issues for two other supply chains: one with competing retailers, the other with stochastic demand. When retailers compete for both demand and supply, they tend to over‐order. We show that a combination of a pay back and revenue sharing mechanism can coordinate the supply chain, with the pay back mechanism correcting the supplier's under‐producing problem and the revenue sharing mechanism correcting the retailers' over‐ordering problem. When demand is stochastic, we consider a modified pay‐back‐revenue‐sharing contract under which the retailer agrees to not only purchase the supplier's excess output (beyond the retailer's order), but also share with the supplier a portion of the revenue made from the sales of the excess output. We show that this contract, by giving the supplier additional incentives in the form of revenue share, can achieve coordination.
Can Organic Amendments Be Useful in Transforming a Mediterranean Shrubland into a Dehesa?
Authors: Tarrasón David , Ojeda Gerardo , Ortiz Oriol , Alcañiz Josep M.
Published: April 2014

Transforming a shrubland into a dehesa system may be useful for recovering certain productive and regulatory functions of ecosystems such as grazing potential, soil erosion control, and also for reducing the risk of wildfire. However, the productivity of the herbaceous cover and tree development in the transformed system may be limited by soil fertility, especially after wildfire events. Previous studies have shown that adequate doses of sewage sludge may improve soil fertility and facilitate plant recovery, but few studies have focused on plant biodiversity assessment. Here, we compare the effects of sewage sludge that has undergone different post‐treatments (dewatering, composting, or thermal drying) as a soil amendment used to transform a fire‐affected shrubland into a dehesa, on tree growth and pasture composition (vegetation cover, species richness, and diversity). In the short term, sewage sludge causes changes in both pasture cover and tree growth. Although no major differences in vegetation species richness and composition have been detected, fertilization using sewage sludge was shown to modify the functional diversity of the vegetation community. Rapid replacement of shrubs by herbaceous cover and ruderal plants (e.g. Bromus hordeaceus and Leontodon taraxacoides) and of the three grass species sown (Festuca arundinacea, Lolium perenne, and Dactylis glomerata) was observed, whereas N‐fixing species (leguminous) tended to be more abundant in nonfertilized soils and soils amended with composted sludge. These results indicate that sewage sludge modifies the functionality of vegetation when applied to soils, and that the response varies according to the treatment that the sludge has undergone.
Why Pine Barrens Restoration Should Favor Barrens Over Pine
Authors: Bried Jason T. , Patterson William A. , Gifford Neil A.
Published: April 2014

Pine barrens include an assortment of pyrogenic plant communities occurring on glacial outwash or rocky outcrops scattered along the Atlantic coastal plain from New Jersey to Maine, and inward across New England, New York, Pennsylvania, and the northern Great Lakes region. At least historically, pine barrens provided some of the highest quality terrestrial shrublands and young forests in the eastern North American sub‐boreal and northern temperate region. However, the mosaic open‐canopy, sparse‐shrub, and grassland early successional state is generally lacking in contemporary pine barrens. Many sites in the northeastern United States have converted to overgrown scrub oak (Quercus ilicifolia, Quercus prinoides) thickets and closed canopied pitch pine (Pinus rigida)‐dominated forests. Thinning pitch pine is a contentious issue for the imperiled pitch pine‐scrub oak barrens community type (G2 Global Rarity Rank, 6–20 occurrences). Here we provide a historical, ecological, and resource management rationale for thinning pitch pine forest to restore savanna‐like open barrens with a mosaic of scrub oaks, heath shrubs, and prairie‐like vegetation. We postulate that the contemporary dominance of pitch pine forest is largely of recent anthropogenic origin, limits habitat opportunities for at‐risk shrubland fauna, and poses a serious wildfire hazard. We suggest maintaining pitch pine‐scrub oak barrens at 10–30% average pitch pine cover to simultaneously promote shrubland biodiversity and minimize fire danger.
Exploring the Uncertainties in Cancer Risk Assessment Using the Integrated Probabilistic Risk Assessment (IPRA) Approach
Authors: Slob Wout , Bakker Martine I. , Biesebeek Jan Dirk te , Bokkers Bas G. H.
Published: April 2014

Current methods for cancer risk assessment result in single values, without any quantitative information on the uncertainties in these values. Therefore, single risk values could easily be overinterpreted. In this study, we discuss a full probabilistic cancer risk assessment approach in which all the generally recognized uncertainties in both exposure and hazard assessment are quantitatively characterized and probabilistically evaluated, resulting in a confidence interval for the final risk estimate. The methodology is applied to three example chemicals (aflatoxin, N‐nitrosodimethylamine, and methyleugenol). These examples illustrate that the uncertainty in a cancer risk estimate may be huge, making single value estimates of cancer risk meaningless. Further, a risk based on linear extrapolation tends to be lower than the upper 95% confidence limit of a probabilistic risk estimate, and in that sense it is not conservative. Our conceptual analysis showed that there are two possible basic approaches for cancer risk assessment, depending on the interpretation of the dose‐incidence data measured in animals. However, it remains unclear which of the two interpretations is the more adequate one, adding an additional uncertainty to the already huge confidence intervals for cancer risk estimates.
Trade Liberalisation: The Effects of Free Trade Agreements on the Competitiveness of the Dairy Sector
Authors: Couillard Catherine , Turkina Ekaterina
Published: April 2014

In recent years, preferential trade agreements (PTAs), free trade agreements (FTAs) in particular, have proliferated while WTO negotiations have stagnated. This paper contributes to the literature on trade liberalisation and the agricultural sector by analysing the effects of FTAs on the competitiveness of the dairy sector across 76 countries and over a 20‐year period from 1990 to 2009. With a longitudinal econometric model, the results demonstrate that when a country has a revealed comparative advantage in the dairy sector, FTAs positively influence several indicators of competitiveness in the dairy sector, such as production, market share and trade balance. The results also indicate that multilateral FTAs are more beneficial than bilateral FTAs. There is strong empirical evidence that FTAs are more beneficial to developed countries than to developing countries. There is no statistical evidence to support the hypothesis about a relationship between FTAs and farm‐gate price.
Deterministic polynomial factoring and association schemes
Authors: Arora Manuel , Ivanyos Gábor , Karpinski Marek , Saxena Nitin
Published: April 2014

The problem of finding a nontrivial factor of a polynomial$f(x)$over a finite field${\mathbb{F}}_q$has many known efficient, but randomized, algorithms. The deterministic complexity of this problem is a famous open question even assuming the generalized Riemann hypothesis (GRH). In this work we improve the state of the art by focusing on prime degree polynomials; let$n$be the degree. If$(n-1)$has a ‘large’$r$-smooth divisor$s$, then we find a nontrivial factor of$f(x)$in deterministic$\mbox{poly}(n^r,\log q)$time, assuming GRH and that$s=\Omega (\sqrt{n/2^r})$. Thus, for$r=O(1)$our algorithm is polynomial time. Further, for$r=\Omega (\log \log n)$there are infinitely many prime degrees$n$for which our algorithm is applicable and better than the best known, assuming GRH. Our methods build on the algebraic-combinatorial framework of$m$-schemes initiated by Ivanyos, Karpinski and Saxena (ISSAC 2009). We show that the$m$-scheme on$n$points, implicitly appearing in our factoring algorithm, has an exceptional structure, leading us to the improved time complexity. Our structure theorem proves the existence of small intersection numbers in any association scheme that has many relations, and roughly equal valencies and indistinguishing numbers.
Methodology for Global Optimization of Computationally Expensive Design Problems
Authors: Koullias Stefanos , Mavris Dimitri N.
Published: April 2014

The design of unconventional systems requires early use of high-fidelity physics-based tools to search the design space for improved and potentially optimum designs. Current methods for incorporating these computationally expensive tools into early design for the purpose of reducing uncertainty are inadequate due to the limited computational resources that are available in early design. Furthermore, the lack of finite difference derivatives, unknown design space properties, and the possibility of code failures motivates the need for a robust and efficient global optimization (EGO) algorithm. A novel surrogate model-based global optimization algorithm capable of efficiently searching challenging design spaces for improved designs is presented. The algorithm, called fBcEGO for fully Bayesian constrained EGO, constructs a fully Bayesian Gaussian process (GP) model through a set of observations and then uses the model to make new observations in promising areas where improvements are likely to occur. This model remedies the inadequacies of likelihood-based approaches, which may provide an incomplete inference of the underlying function when function evaluations are expensive and therefore scarce. A challenge in the construction of the fully Bayesian GP model is the selection of the prior distribution placed on the model hyperparameters. Previous work employs static priors, which may not capture a sufficient number of interpretations of the data to make any useful inferences about the underlying function. An iterative method that dynamically assigns hyperparameter priors by exploiting the mechanics of Bayesian penalization is presented. fBcEGO is incorporated into a methodology that generates relatively few infeasible designs and provides large reductions in the objective function values of design problems. This new algorithm, upon implementation, was found to solve more nonlinearly constrained algebraic test problems to higher accuracies relative to the global minimum than other popular surrogate model-based global optimization algorithms and obtained the largest reduction in the takeoff gross weight objective function for the case study of a notional 70-passenger regional jet when compared with competing design methods.
Loading and Design Parameter Uncertainty in the Dynamics and Performance of High-Speed-Parallel-Helical-Stage of a Wind Turbine Gearbox1
Authors: Alemayehu Fisseha M. , Ekwaro-Osire Stephen
Published: April 2014

In operation, wind turbine gearboxes (WTGs) are subjected to variable torsional and nontorsional loads. In addition, the manufacturing and assembly process of these devices results in uncertainty in the design parameters of the system. WTGs are reported to fail in their early life of operation within 3–7 years as opposed to the expected 20 years of operation. Their downtime and maintenance process is the most costly of the failures of any subassembly of wind turbines (WTs). The objective of this work is to perform a probabilistic multibody dynamic analysis (PMBDA) of the high-speed-parallel-helical-stage (HSPHS) of a WTG that considers the uncertainties of generator-side torque-loading and input-shaft speed as well as assembly and design parameter uncertainties. Component reliability (Rc) or probability of failure (Pf) and probabilistic sensitivities of all the input variables toward five performance functions have been measured and conclusions have been drawn. As opposed to the traditional deterministic approach, PMBDA has demonstrated a new aspect of design and installation of WTGs. In addition to revealing Rc or system reliability or underperformance through Pf, the method will also help designers to critically consider certain variables through the probabilistic sensitivity results.
Innovative Active Vehicle Safety Using Integrated Stabilizer Pendulum and Direct Yaw Moment Control
Authors: Goodarzi Avesta , Diba Fereydoon , Esmailzadeh Ebrahim
Published: April 2014

Basically, there are two main techniques to control the vehicle yaw moment. First method is the indirect yaw moment control, which works on the basis of active steering control (ASC). The second one being the direct yaw moment control (DYC), which is based on either the differential braking or the torque vectoring. An innovative idea for the direct yaw moment control is introduced by using an active controller system to supervise the lateral dynamics of vehicle and perform as an active yaw moment control system, denoted as the stabilizer pendulum system (SPS). This idea has further been developed, analyzed, and implemented in a standalone direct yaw moment control system, as well as, in an integrated vehicle dynamic control system with a differential braking yaw moment controller. The effectiveness of SPS has been evaluated by model simulation, which illustrates its superior performance especially on low friction roads.
Modeling and Dynamical Feedback Control of a Vehicle Diesel Engine Speed and Air-Path
Authors: Wang Haoping , Tian Yang , Bosche Jérôme , El Hajjaji Ahmed
Published: April 2014

This paper presents a modeling and dynamical feedback stabilization control of a diesel engine which is equipped with a variable geometry turbocharger (VGT) and exhaust gas recirculation (EGR) valve. A fourth-order dimensional nonlinear model which takes into account the engine crankshaft speed dynamics and the air-path dynamics is proposed for the considered diesel engine. The difficulties for the control design are that the referred system is nonlinear, nonminimum phase unstable and coupled system. The fuel flow rate Wf which is considered as input for the engine crankshaft subsystem and acts as an external perturbation for the three-order dimensional nonminimum phase air-path subsystem. The global control objectives are to track desired values of engine speed, intake manifold pressure and compressor flow mass rate which can be suitably chosen according to low emission criterions. For the considered objectives, a dynamical feedback stabilization control with a two-loop structure of inner outer loop is proposed. The inner loop considers a control based on a Lyapunov function which realizes the desired engine speed trajectory tracking. The outer loop which is developed from a particular extended nonlinear air-path subsystem with its modified outputs concerns the coordinated EGR and VGT control and ensures both the desired intake manifold pressure and the desired compressor mass flow rate trajectory tracking. Meanwhile, this outer loop dynamical feedback stabilization control provides also the external fuel mass flow rate perturbation rejection. From the corresponding numerical simulation results, the proposed method efficiency is validated.
Conceptual Design and Composition Principles Analysis of a Novel Collaborative Rectification Structure Pump
Authors: Li Yang , Jiao Zongxia , Yan Liang , Dong Wenhao
Published: April 2014

In order to provide a solution of active rectification for linear pumps in pump control system, a novel collaborative rectification structure is conceptually designed in this paper. The fundamental subsystem is the direct drive pump cell (DDPC). A DDPC consists of a cylinder and a valve, and the piston rod and the valve spool are integrated together. The DDPC could be driven by a linear oscillating motor directly. The DDPC working process is logically modeled as a state machine. Certain theorems are given and proved to illustrate the composition principles of a pump system with collaborative rectification. The kinematic flow rate of the collaborative rectification pump is studied. According to the comparison to the existing linear pumps, the novel pump has more structure compactness and control flexibility.
Novel Adaptive Recurrent Legendre Neural Network Control for PMSM Servo-Drive Electric Scooter
Authors: Lin Chih-Hong
Published: April 2014

Because an electric scooter driven by permanent magnet synchronous motor (PMSM) servo system has the unknown nonlinearity and the time-varying characteristics, its accurate dynamic model is difficult to establish for the design of the linear controller in whole system. In order to conquer this difficulty and raise robustness, a novel adaptive recurrent Legendre neural network (NN) control system, which has fast convergence and provide high accuracy, is proposed to control for PMSM servo-drive electric scooter under external torque disturbance in this study. The novel adaptive recurrent Legendre NN control system consists of a recurrent Legendre NN control with adaptation law and a remunerated control with estimation law. In addition, the online parameter tuning methodology of the recurrent Legendre NN control and the estimation law of the remunerated control can be derived by using the Lyapunov stability theorem. Finally, comparative studies are demonstrated by experimental results in order to show the effectiveness of the proposed control scheme.
Reliability-Based Vehicle Safety Assessment and Design Optimization of Roadway Radius and Speed Limit in Windy Environments
Authors: Shin Jaekwan , Lee Ikjin
Published: April 2014

This paper presents a reliability-based analysis of road vehicle accidents and the optimization of roadway radius and speed limit design based on vehicle dynamics, mainly focusing on windy environments. The performance functions are formulated as failure modes of vehicle rollover and sideslip and are defined on a finite set of basic variables with probabilistic characteristics, so-called random variables. The random variables are vehicle speed, steer angle, tire–road friction coefficient, road bank angle, and wind speed. The probability of accident was evaluated using the first-order reliability method (FORM) and numerical studies were conducted using a single-unit truck model. The analysis demonstrates that wind is a significant factor when assessing vehicle safety on roads, and probabilistic studies such as reliability-based design optimization (RBDO) are necessarily required to enhance vehicle safety in windy environments. Accordingly, design optimization of roadway radius and speed limit was conducted, and new designs were proposed satisfying the target reliability. This study suggests that probabilistic mechanics and theory can be of value for analysis and design of wind-related vehicle safety.
Design of Nonlinear Rotational Stiffness Using a Noncircular Pulley-Spring Mechanism
Authors: Kim Bongsu , Deshpande Ashish D.
Published: April 2014

We present a new methodology for designing a nonlinear rotational spring with a desired passive torque profile by using a noncircular pulley-spring mechanism. A synthesis procedure for the shape of the noncircular pulley is presented. The method is based on an infinitesimal calculus approach that leads to an analytical solution, and the method is extended to address practical design issues related to the cable routing. Based on the synthesis method, an antagonistic spring configuration is designed for bilateral torque generation and is designed such that there is no slack in the routing cables. Two design examples are presented, namely, double exponential torque generation and gravity compensation for an inverted pendulum. Experiments with a mechanism for gravity compensation of an inverted pendulum validate our approach. We extend our approach to generate nonlinear torques at two joints by introducing the concept of torque decomposition. Experiments with a two-link robotic arm show that the gravitational forces from the masses on each link are accurately compensated for with our noncircular pulley-spring mechanisms.
Investigation of Clamping Effect on the Welding Residual Stress and Deformation of Monel Plates by Using the Ultrasonic Stress Measurement and Finite Element Method
Authors: Javadi Yashar
Published: April 2014

Welding of nickel-based alloys is increasingly used in the industry to manufacture many important components of the marine industries, chemical processing, etc. In this study, a 3D thermomechanical finite element (FE) analysis is employed to evaluate residual stresses and deformations caused by the tungsten inert gas (TIG) welding of Monel 400 (Nickel-Copper alloy) plates. The FE results related to the residual stresses and deformations have been verified by using the hole-drilling stress measurement and common dimensional measurement tools, respectively. Residual stresses analyzed by the FE simulation are then compared with those obtained from ultrasonic stress measurement. The ultrasonic stress measurement is based on acoustoelasticity law, which presents the relation between the acoustic waves and the stress of material. The ultrasonic stress measurement is carried out by using longitudinal critically refracted (LCR) waves which are longitudinal ultrasonic waves propagated parallel to the surface inside the tested material. Two welded plates are experimentally prepared (with and without using clamp) to investigate the clamping effect on the welding residual stress and deformations. By utilizing the FE analysis along with the LCR method, the distribution of longitudinal residual stress could be achieved. It has been concluded that the applied methodologies are enough accurate to distinguish the clamping effect on the welding residual stresses and deformations of Monel plates.
Vacuum compatibility of 3D-printed materials
Authors: Povilus Alexander P. , Wurden Caroline J. , Vendeiro Zak , Baquero-Ruiz Marcelo , Fajans Joel
Published: April 2014

The fabrication fidelity and vacuum properties are tested for currently available 3D-printed materials including polyamide, glass, acrylic, and sterling silver. The silver was the only material found to be suitable to ultrahigh vacuum environments due to outgassing and sublimation observed in other materials.
Errata: "Beam Damage of Poly(vinyl chloride) [PVC] Film as Observed by X-ray Photoelectron Spectroscopy" [Surf. Sci. Spectra 10, 57 (2003)]
Authors: Engelhard M. H. , Krishna A. , Kulkarni P. , Lee C. Y. , Baer D. R.
Published: April 2014

A figure was omitted inadvertently from the article beginning on page 57 of SSS Volume 10. Below is the entire introduction plus referenced figures for this article. The entire corrected article may be retrieved from SSS Online.
Lipid membranes and single ion channel recording for the advanced physics laboratory
Authors: Klapper Yvonne , Nienhaus Karin , Röcker Carlheinz , Ulrich Nienhaus G.
Published: April 2014

We present an easy-to-handle, low-cost, and reliable setup to study various physical phenomena on a nanometer-thin lipid bilayer using the so-called black lipid membrane technique. The apparatus allows us to precisely measure optical and electrical properties of free-standing lipid membranes, to study the formation of single ion channels, and to gain detailed information on the ion conduction properties of these channels using statistical physics and autocorrelation analysis. The experiments are well suited as part of an advanced physics or biophysics laboratory course; they interconnect physics, chemistry, and biology and will be appealing to students of the natural sciences who are interested in quantitative experimentation.
Bioelectrical impedance analysis as a laboratory activity: At the interface of physics and the body
Authors: Mylott Elliot , Kutschera Ellynne , Widenhorn Ralf
Published: April 2014

We present a novel laboratory activity on RC circuits aimed at introductory physics students in life-science majors. The activity teaches principles of RC circuits by connecting ac-circuit concepts to bioelectrical impedance analysis (BIA) using a custom-designed educational BIA device. The activity shows how a BIA device works and how current, voltage, and impedance measurements relate to bioelectrical characteristics of the human body. From this, useful observations can be made including body water, fat-free mass, and body fat percentage. The laboratory is engaging to pre-health and life-science students, as well as engineering students who are given the opportunity to observe electrical components and construction of a commonly used biomedical device. Electrical concepts investigated include alternating current, electrical potential, resistance, capacitance, impedance, frequency, phase shift, device design, and the use of such topics in biomedical analysis.
Biologic: Gene circuits and feedback in an introductory physics sequence for biology and premedical students
Authors: Cahn S. B. , Mochrie S. G. J.
Published: April 2014

We describe an educational module on feedback and gene circuits that constitute the final topic in a new year-long introductory physics sequence aimed at biology and premedical students at Yale University. The overall goals of this sequence are threefold. First to demonstrate the application of physics and mathematics in the life sciences. Second to introduce biological science majors to mathematical and physical tools, principles, and experiences. Third to seed an enduring appreciation of quantitative approaches in biology and medicine. Here, we present a module on feedback and gene circuits that focuses on a genetic toggle switch and a repressilator. The genetic toggle switch consists of two genes, each of whose protein products represses the other's expression, while the repressilator consists of three genes, each of whose protein products represses the next gene's expression. Analytic, numerical, and electronic treatments of the genetic toggle switch show bistability. A similar treatment of the repressilator reveals sustained oscillations.
Biophysics software for interdisciplinary education and research
Authors: Deutsch J. M.
Published: April 2014

Biophysics encompasses many disciplines, and so transcends the knowledge and skills of the individual student; its instruction therefore provides formidable challenges. This paper describes educational materials that were developed by the author and have been used successfully in an interdisciplinary course on biophysics, taken by undergraduates from a variety of disciplines. Projects were devised on topics that ranged from x-ray diffraction to the Hodgkin–Huxley equations. They are team-based and strongly encourage collaboration. Extensive use is made of software, written in Python/SciPy, which was modified by students to explore a large range of phenomena. This software can also be used in lectures, in the teaching of more traditional biophysics courses, and in research.
Chemical energy in an introductory physics course for the life sciences
Authors: Dreyfus Benjamin W. , Gouvea Julia , Geller Benjamin D. , Sawtelle Vashti , Turpen Chandra , Redish Edward F.
Published: April 2014

Energy is a complex idea that cuts across scientific disciplines. An approach to energy that incorporates chemical bonds and chemical reactions is better equipped to meet the needs of life sciences students than a traditional introductory physics approach that focuses primarily on mechanical energy. We present a curricular sequence, or thread, designed to build up students' understanding of chemical energy in an introductory physics course for the life sciences. This thread is designed to connect ideas about energy from physics, biology, and chemistry. We describe the kinds of connections among energy concepts that we develop to build interdisciplinary coherence and present some examples of curricular materials and student data that illustrate our approach.
Women among physics faculty
Authors: White Susan C.
Published: April 2014

Women among physics faculty
Angular velocity and centripetal acceleration relationship
Authors: Monteiro Martín , Cabeza Cecilia , Marti Arturo C. , Vogt Patrik , Kuhn Jochen
Published: April 2014

During the last few years, the growing boom of smartphones has given rise to a considerable number of applications exploiting the functionality of the sensors incorporated in these devices. A sector that has unexpectedly taken advantage of the power of these tools is physics teaching, as reflected in several recent papers.1–10 In effect, the use of smartphones has been proposed in several physics experiments spanning mechanics, electromagnetism, optics, oscillations, and waves, among other subjects. Although mechanical experiments have received considerable attention, most of them are based on the use of the accelerometer.1–8 An aspect that has received less attention is the use of rotation sensors or gyroscopes.9,10 An additional advance in the use of these devices is given by the possibility of obtaining data using the accelerometer and the gyroscope simultaneously. The aim of this paper is to consider the relation between the centripetal acceleration and the angular velocity. Instead of using a formal laboratory setup, in this experiment a smartphone is attached to the floor of a merry-go-round, found in many playgrounds. Several experiments were performed with the roundabout rotating in both directions and with the smart-phone at different distances from the center. The coherence of the measurements is shown.
Pitch Perception of Pulse Pairs with Random Repetition Rate
Authors: McClellan Max E. , Small Arnold M.
Published: April 2014

Time-separation pitch (TSP) is a pitch effect that arises from temporally separated, highly correlated waveforms and is related to the reciprocal of time delay between the leading edges of such waveforms. On the assumption that spectral cues are responsible for TSP perception, it was suggested that random triggering of dc pulse pairs with fixed time delay would render the spectrum unspecifiable in an exact sense, thereby degrading the performance of subjects matching pure tones in pitch to TSP. On the assumption that a time-analyzing mechanism is responsible for TSP perception, it was predicted that the presentation of single, nonrepetitive dc pulse pairs would make TSP difficult to perceive since minimum information on which to base a pitch judgment would be available per unit time. The results were not as predicted, i.e., the distributions of pitch matches were essentially the same for conditions of random triggering and single pulse pairs and were highly similar to those generated with regularly triggered dc pulse pairs. These results suggest that the amount of “information” available per unit time is not particularly important to TSP perception and, further, that the assumption concerning a spectral mechanism does not hold.
Some Computations of Circumferential Wave Velocities
Authors: Goodman R. R. , Bunney R. E.
Published: April 2014

The theory of circumferential waves has been extended for large cylinders (ka≫1) in the manner developed by Grace and Goodman [J. Acoust. Soc. Am. 39, 173–174 (1966)]. Numerical evaluations of the secular determinant have been made. The results can be checked easily with the limit ka→∞. Certain difficulties arise in the asymptotic expansions of Bessel functions, which depend on whether the ratio of circumferential velocity to shear velocity is greater than or less than unity. Values of the circumferential wave velocity and attenuation have been computed for steel and aluminum for values of ka pertinent to the experimental data, which will be discussed in the following paper.
Determination of Structural-System Transfer Functions by Time Correlation
Authors: Champ Stanley G.
Published: April 2014

This paper proposes a method for determining transfer functions for structural systems exposed to random vibration. The technique used depends heavily upon certain properties of the time-correlation functions for its utility. It is shown that the usual errors, which are introduced into the transfer function by noise in the data, system internal noise, and data cutoff transients, can be eliminated. It is also shown that the method proposed is applicable to both open-loop and closed-loop systems, and that the use of large amounts of normal-system operating data in condensed form combine to effect economies in time and accuracies in the transfer function (impulse functions or sinusoids are usually used). A brief recount of the theory is given with 3 suggestions for laboratory technique. Laboratory results are presented.
Scattering of sound from concentric cylindrical shells
Authors: Akay Adnan
Published: April 2014

Scattered sound field from three concentric shells ensonified by a plane wave is treated. Formulation of the problem is carried out using impedance expressions for the shells and the acoustic media interior and exterior to the shells. Results of exact equations of elasticity have been used to obtain the shell impedances, making the results applicable to arbitrary thicknesses. The results show that in a target made up of multiple shells and layers, the first elastic continuum that the incoming waves interact, which most closely resembles an impenetrable target dominates scattering. For example, a very thick shell or a very light-density fluid layer effectively insulates scattering from the layers or shells in its interior. When locally resistive compliant coatings are placed on the surfaces of the shell, they alter the scattering response. A very compliant layer on the exterior of the target changes it to a pressure-release type of boundary. © 1991 Acoustical Society of America.
The Transcription Factor Gata6 Links Tissue Macrophage Phenotype and Proliferative Renewal
Authors: Rosas Marcela , Davies Luke C. , Giles Peter J. , Liao Chia-Te , Kharfan Bashar , Stone Timothy C. , O’Donnell Valerie B. , Fraser Donald J. , Jones Simon A. , Taylor Philip R.
Published: April 2014

Gata6 Controls Peritoneal Macs

Macrophages seed tissues throughout the body and are shaped both phenotypically and functionally by the microenvironment they inhabit. Despite such heterogeneity, most tissue macrophages self-renew by local proliferation. How this is regulated, however, is unclear.Rosaset al.(p.645, published online 24 April) used gene expression analysis to show that the transcription factor Gata6 is specifically expressed in peritoneal macrophages. Gata6 was critical for maintaining the transcriptional signature of peritoneal macrophages and for their proliferative renewal during homeostasis and under inflammatory conditions.
Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
Authors: Skoglund Pontus , Malmström Helena , Omrak Ayça , Raghavan Maanasa , Valdiosera Cristina , Günther Torsten , Hall Per , Tambets Kristiina , Parik Jüri , Sjögren Karl-Göran , Apel Jan , Willerslev Eske , Storå Jan , Götherström Anders , Jakobsson Mattias
Published: April 2014

Hunters and Farmers

The Neolithic period in Europe saw the transition from a hunter-gatherer lifestyle to farming. Previous genetic analyses have suggested that hunter-gatherers were replaced by immigrant farmers.

Skoglund
et al.

(p.
747
, published online 24 April) sequenced one Mesolithic and nine Neolithic Swedish individuals to examine the transition from hunter-gatherers to farmers. Substantial genetic differentiation was observed between hunter-gatherers and farmers: There was lower genetic diversity within the hunter-gatherers and gene flow from the hunter-gatherers into the farmers but not vice versa.
Causal Relationship between Microbial Ecology Dynamics and Proteolysis during Manufacture and Ripening of Protected Designation of Origin (PDO) Cheese Canestrato Pugliese
Authors: De Pasquale Ilaria , Calasso Maria , Mancini Leonardo , Ercolini Danilo , La Storia Antonietta , De Angelis Maria , Di Cagno Raffaella , Gobbetti Marco
Published: April 2014

Pyrosequencing of the 16S rRNA gene, community-level physiological profiles determined by the use of Biolog EcoPlates, and proteolysis analyses were used to characterize Canestrato Pugliese Protected Designation of Origin (PDO) cheese. The number of presumptive mesophilic lactococci in raw ewes' milk was higher than that of presumptive mesophilic lactobacilli. The numbers of these microbial groups increased during ripening, showing temporal and numerical differences. Urea-PAGE showed limited primary proteolysis, whereas the analysis of the pH 4.6-soluble fraction of the cheese revealed that secondary proteolysis increased mainly from 45 to 75 days of ripening. This agreed with the concentration of free amino acids. Raw ewes' milk was contaminated by several bacterial phyla:
Proteobacteria
(68%; mainly
Pseudomonas
),
Firmicutes
(30%; mainly
Carnobacterium
and
Lactococcus
),
Bacteroidetes
(0.05%), and
Actinobacteria
(0.02%). Almost the same microbial composition persisted in the curd after molding. From day 1 of ripening onwards, the phylum
Firmicutes
dominated.
Lactococcus
dominated throughout ripening, and most of the
Lactobacillus
species appeared only at 7 or 15 days. At 90 days,
Lactococcus
(87.2%),
Lactobacillus
(4.8%; mainly
Lactobacillus plantarum
and
Lactobacillus sakei
), and
Leuconostoc
(3.9%) dominated. The relative utilization of carbon sources by the bacterial community reflected the succession. This study identified strategic phases that characterized the manufacture and ripening of Canestrato Pugliese cheese and established a causal relationship between mesophilic lactobacilli and proteolysis.
Mechanism of Algal Aggregation by Bacillus sp. Strain RP1137
Authors: Powell Ryan J. , Hill Russell T.
Published: April 2014

Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified
Bacillus
sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting.
Bacterial Targets as Potential Indicators of Diesel Fuel Toxicity in Subantarctic Soils
Authors: van Dorst Josie , Siciliano Steven D. , Winsley Tristrom , Snape Ian , Ferrari Belinda C.
Published: April 2014

Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic diversity, with the resulting community heavily dominated by a few species, principally
Pseudomonas
. The decline in richness and phylogenetic diversity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial
amoA
gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC
20
) of 155 mg kg
−1
, which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community.