bluuebunny/crossref_metadata_2025 huggingface dataset:
Adapting the minimum variance beamformer to a graphics processing unit for active sonar imaging systems
Authors: Buskenes Jo Inge , Åsen Jon Petter , Nilsen Carl-Inge C. , Austeng Andreas
Published: May 2013

The MVDR beamformer has been shown to improve active sonar image quality compared to conventional methods. Unfortunately, it is also significantly more computationally expensive because a spatial covariance matrix must be estimated and inverted for each image pixel. We target this challenge by altering and mapping the MVDR beamformer to a GPU, and suggest three different solutions depending on the system size. For systems with relatively few channels, we suggest arithmetic optimizations for the estimation step, and show how a GPU can be used to yield image creation rates of more than 1 Mpx/s. For larger systems we show that frequency domain processing is preferable, as this promotes high processing rates at a negligible reduction in image quality. These GPU implementations consistently reduced the runtime by 2–3 orders of magnitude compared to our reference C and Matlab implementations. For even larger systems we suggest employing the LCA beamformer. It does not calculate a weightset, but merely computes the beamformer output for each of a predefined set of weights, and selects the one that best fulfils the MVDR criterion. The LCA creates images with a quality comparable to MVDR, and it is perfectly suited for a GPU.
Some comments about graphic processing unit architectures applied to finite-difference time-domain room acoustics simulation: Present and future trends
Authors: Lopez Jose J. , Navarro Juan M. , Carnicero Diego , Escolano Jose
Published: May 2013

The parallelization of the finite-difference time-domain (FDTD) method for room acoustic simulation using graphic processing units (GPUs) has been subject of study even prior to the introduction of general-purpose computing environments such as the CUDA architecture. Nowadays CUDA offers enough flexibility and processing power to obtain performance gains higher than 200 times compared to single-threaded CPU codes. In this paper, different aspects related to the implementation of FDTD in CUDA are analyzed; first, how the evolution of the different CUDA architectures affects implementations is inquired, paying special attention to the Kepler architecture, the latest available. Also performance increasing by using the different memory subsystems the GPU offers is discussed. Moreover, the performance in the use of the available computing power in the GPU is also analyzed together with the limiting factors such as memory consumption and computing time that prevent the simulation of large rooms at very high frequencies. Finally, some comments and ideas about the possible evolution of the computing power of GPU in the next years are evaluated together with future possibilities that GPU architectures might bring to FDTD applied to room acoustics.
The use of graphical processing unit processing in rough surface scattering
Authors: Abawi Ahmad T. , Hursky Paul
Published: May 2013

The use of graphical processing units (GPU’s) in scientific computation has drawn significant interest in recent years. In this paper we use GPU processing to evaluate the performance of a number of approximate techniques in computing scattering from two-dimensional rough surfaces by comparing their results with those obtained using the boundary element technique, which produces a numerically exact solution of the problem. To compute scattering from a two-dimensional surface, we use a technique that we developed for computing scattering from compact objects, which uses an analytical expression for scattering from a single, flat triangle. In this technique the surface is meshed using triangular patches and the scattering is computed as a coherent sum of scattering from individual triangles. This technique not only provides accurate evaluation of the surface integrals that appear in scattering theory, but it also lends itself easily to the benefits of GPU processing. We apply this technique to the Kirchhoff approximation, the small slope approximation and to a rather less familiar technique based on the work of Dashen et al. [J. Math. Phys.32, 986–996 (1991)].
Reverberation modeling on graphics processing units
Authors: Hursky Paul , Abawi Ahmad T.
Published: May 2013

We will discuss modeling reverberation on GPUs. An accompanying talk will discuss using GPUs to model scattering from rough surfaces. Here we discuss using GPUs to model the two sets of propagation paths, one set from the source to scatterer, the other set from the scatterer to the receiver, and to combine these two sets via a scattering operation and assemble the reverberation waveform at the receiver. We will discuss how we have adapted various aspects of our modeling to a GPU platform. GPUs provide several differentiated memory architectures that an application can exploit. For example, the texture memory provides hardware-assisted interpolation—as a result, we can load a 3D environment into texture memory, sparsely sampled, and then reconstruct interpolated slices as needed the modeling task. GPU architectures have been evolving for many years to meet the demands of computer gaming and rendering, applications most ambitiously served by ray tracing (of light). As a result, NVIDIA provides a ray tracing framework called OptiX, sufficiently general-purpose, that it can be linked with externally provided functions to specialize the mathematics implemented during the ray trace process. We will describe our work on adapting OptiX to underwater acoustic ray tracing.
A cognitive approach for binaural models using a top-down feedback structure
Authors: Braasch Jonas , Parks Anthony , Blauert Jens
Published: May 2013

Current models to explain binaural hearing generally focus on bottom-up processes of the auditory periphery and subcortical brain functions to simulate sound localization and other binaural tasks. While these models have been very successful in explaining a number of psychoacoustic phenomena, their architecture is not suitable to explain experiments that involve cognition. The project presented here seeks to close the gap between functional binaural models and research in applied robotics. A software architecture that was originally designed to simulate the process of music improvisation using a combination of Computational Auditory Scene Analysis, machine learning and logic-based reasoning, the Creative Artificially Intuitive and Reasoning Agent (CAIRA) was extended to simulate a number of basic binaural phenomena including sound localization of multiple-sources, resolving front/back confusions through strategic head movements, and adapting inhibitory parameters to the presented signals to evoke localization dominance. [Work supported by the National Science Foundation, No. 1002851.]
Continuous features of emotion in classical, popular, and game music
Authors: Yamada Masashi
Published: May 2013

In the present study, musical emotion was measured continuously for classical, popular and game music. Eight pieces for each genre were used as stimuli. The following computer system was prepared: The screen showed a cursor on a two-dimensional plane spanned by valence (pleasant-unpleasant) and arousal axes. The position of the cursor was manipulated by a mouse and recorded every 0.5 s. In one session, the system continuously recorded the emotional responses of 20 listeners while listening to each piece. In the other session, the listeners listened to each piece without manipulating the mouse, and then pointed out the overall emotional feature of the piece on the two-dimensional plane. The results showed that the valence did not vary largely for any genre. The arousal varied largely for classical music, but not for game music. For popular music, it varied in between classical and game music. For all genres, the overall emotional values of valence and arousal showed almost equal to the maximum or minimum values in the continuous variation, respectively. This implies that the overall emotional features of a musical piece are almost entirely determined by the part which shows the highest degree of emotion in the piece.
Perceptual outcomes by rapid alternation of the resonant scaling and its relation to the fundamental frequency
Authors: Tsuzaki Minoru , Takeshima Chihiro , Matsui Toshie , Irino Toshio
Published: May 2013

Timbre provided by the resonant characteristics of the vibrating body can be represented as spectral envelope patterns and can contribute as one of the important cues for sound source identification. However, its concept is not strictly established while that of loudness, and of pitch are well known. Recently, the fact that the spectral pattern can be decomposed into two factors, i.e., the shape and size of the resonant body, has been reconsidered. Several psychophysical findings have successfully suggested that a “bottom-up” perceptual mechanism of the decomposition might be implemented. Manipulating the scaling factor of resonance can change the perceptual size of the sound source. By concatenating synthesized vowel segments whose resonant scale (RS) alternates between two values in an “ABA-ABA-” fashion, one can generate series of test stimuli for stream segregation with the galloping rhythm paradigm. The experimental results revealed that the RS factor could provide a reliable cue for streaming. As an extreme variation of this RS alternation, scale alternating wavelet sequences (SAWSs) have been proposed. In the SAWS, the RS alternates at every regular time grid. When the difference between the two RS factors exceeded a certain limit, perceived pitch shifted downwards by an octave.
Quantification of the false vocal-folds effects on the intra-glottal pressures using large eddy simulation
Authors: Mihaescu Mihai , Khosla Sid M. , Gutmark Ephraim J.
Published: May 2013

During the closing phase of the phonation cycle the true vocal-folds (TVF) have a convergent-divergent shape. The negative pressures generated by the flow through the glottal passage are producing closing forces acting on the TVFs towards the center of the larynx. Intra-glottal pressures can affect both vocal-fold vibration and voice production, since they can accelerate the closing phase. This has a positive impact on the voice quality. Large Eddy Simulation approach is used to investigate the intra-glottal forces generated solely by the flow during the closing phase. The influence of the gap between the false vocal-folds (FVFs) and the location of FVFs with respect to the TVFs are analyzed. Based on anatomical measurements, four different gaps between the FVFs and two different distances between the true and false vocal-folds are investigated for the same trans-laryngeal pressure. The TVFs gap is kept constant. All cases exhibit a non-symmetric flow behavior in the mid-frontal plane. As compared with the baseline, significant negative pressures were found acting on the TVFs when the false glottal width is below a certain threshold value. The closing forces are increasing when the FVFs are located at larger distances further downstream from the TVFs.
Non-invasive in vivo measurement of the mechanical properties of human vocal fold tissue
Authors: Kazemirad Siavash , Bakhshaei Hani , Mongeau Luc , Kost Karen
Published: May 2013

The mechanical properties of the vocal fold mucosa have a great effect on the vocal folds oscillations, and voice quality. A non-invasive method was developed and examined to obtain the mechanical properties of human vocal fold tissue in vivo via measurements of the mucosal wave propagation speed during phonation. High speed and MRI images of three subject’s vocal folds were captured while phonating at different pitches. The images obtained from these two techniques were matched and the dimensions of the vocal folds were obtained. The mucosal wave propagation speed was determined for the three subjects at different pitches through an automatic image processing procedure. The shear modulus of the subjects’ vocal fold mucosa was then calculated using a surface (Rayleigh) wave propagation model and the measured wave speeds. This is revealed that the mucosal wave propagation speed and the shear modulus of the vocal fold tissue increased with the pitch. The results were in good agreement with those from other studies obtained via in vitro measurements, thereby supporting the validity of the proposed measurement method. This method offers the potential for in vivo clinical assessments.
Quantification of porcine vocal fold geometry in three dimensions
Authors: Stevens Kimberly A. , Jette Marie E. , Thibeault Susan L. , Thomson Scott L.
Published: May 2013

The geometry of the vocal folds, including the internal spatial distribution of the various tissue types, plays a central role in governing vocal fold flow-induced vibration. Quantifying the tissue geometries is therefore important for voice production research. In this presentation, quantitative measures of porcine vocal fold geometry obtained using three different techniques are reported and compared. MicroCT scans of three fresh porcine larynges were obtained with the folds in abducted and adducted positions. Adducted larynges were frozen, rescanned, cut in the midsagittal plane, and rescanned while frozen. The larynges were then thawed and the vocal folds were dissected. One vocal fold was frozen in optimal cutting temperature medium, serial-sectioned in the coronal plane, and imaged, and the other vocal fold was fixed in 10% formalin and embedded in paraffin before being sectioned and imaged. Geometrical data was obtained and compared between the different sets of histological images and the microCT images. This study provides quantitative measures of porcine vocal fold geometry and characterizes the influence of formalin fixation and histological processing on tissue deformation tissue across the three-dimensional vocal fold, leading the way for similar studies using human vocal folds.
Dynamics of supraglottal flow structures and sound generation in phonation
Authors: Kniesburges Stefan , Hesselmann Christina , Becker Stefan , Döllinger Michael
Published: May 2013

Within the fully coupled multi-physics process of phonation the fluid flow plays an important role in the sound production. Therefore, the study addresses phenomena in the flow downstream of synthetic self-oscillating vocal folds and their influence on the sound production. A test setup consisting of devices for producing and conditioning the flow including a test section was used. The supraglottal channel was developed to prevent acoustic coupling to the vocal folds. Hence, the oscillations were aerodynamically driven. The vocal folds consist of silicone rubber having homogeneous material distribution. The flow was visualized in the immediate supraglottal region using a laser-sheet technique and a highspeed camera. The flow shows asymmetric behavior in cases with channel. The glottal jet is bend to one side depending on the turbulent flow conditions in the channel. In cases without channel, the jet was stabilized by the constant ambient pressure being symmetrical at each instance during an oscillation cycle. Additionally, the acoustic response of the studied supraglottal cases was investigated in an anechoic chamber. The spectral analysis of the data turns out differences in tonal and broadband parts of the acoustic spectrum. The context to the visualized flow structures will be discussed.
Acoustic perturbation equations and Lighthill’s acoustic analogy for the human phonation
Authors: Zoerner Stefan , Šidlof Petr , Hüppe Andreas , Kaltenbacher Manfred
Published: May 2013

In speech, air is driven through the larynx by compression of the lungs. Thereby, air flows through the glottis which forces the vocal folds to oscillate which in turn results in a pulsating air flow. This air flow is the main source of the generated sound—the phonation. The acoustic wave then passes through the vocal tract, which acts as a filter modulating the propagated sound leaving the mouth. We model the fluid-structure-acoustic interaction with a so called hybrid approach. The air flow in the larynx, together with a prescribed vocal fold motion, is simulated with help of the open source solver OpenFOAM. Based on the resulting fluid field, acoustic source terms and the wave propagation is calculated within the finite element solver CFS++. Two methods are available to choose from, Lighthill’s acoustic analogy and an aeroacoustic analogy based on a perturbation ansatz. Additionally, the simulation domain is extended by a realistic but geometrical fixed vocal tract and connected to a propagation region. The different acoustic approaches are compared, by analyzing the acoustic pressure in the glottis (source region) and outside the vocal tract. Moreover, to illustrate the effects of the vocal tract an alternative geometry is used for comparison.
Simultaneously evoked auditory potentials: A novel paradigm for measuring auditory-evoked electroencephalographic activity at successive levels of the auditory neuraxis
Authors: Slugocki Christopher , Bosnyak Dan J. , Trainor Laurel J.
Published: May 2013

Recent electrophysiological work has evinced a capacity for plasticity in subcortical auditory nuclei in adults [Skoe and Kraus (2010)]. Similar plastic effects have been measured in cortically generated auditory potentials [e.g., Bosnyak et al. (2007); Näätänen (2008)], but it is unclear how the two interact. Here we present simultaneously evoked auditory potentials (SEAP), a novel paradigm designed to concurrently elicit electrophysiological brain potentials (EEG) from inferior colliculus (IC), thalamus, and primary and secondary auditory cortices. We use a specially designed stimulus consisting of a carrier frequency (500 Hz), amplitude-modulated at the sum of 37 and 81 Hz (depth 100%). We have shown that it elicits a 500 Hz frequency-following response (FFR; generated in IC), 81 (subcortical), and 37 (primary auditory cortex) Hz steady state responses, and mismatch negativity (when there is an occasional change in carrier frequency; secondary auditory cortex). Furthermore, cortical and subcortical processes are linked as the amplitude of the FFR predicts the amplitudes of the 37 and 81 Hz responses. SEAP offers a new window into the dynamics of encoding along the auditory pathway as well as a new and inexpensive tool with which to measure plasticity at multiple levels of the auditory neuraxis in individuals.
Requirement for Nuclear Calcium Signaling in
Drosophila
Long-Term Memory
Authors: Weislogel Jan-Marek , Bengtson C. Peter , Müller Michaela K. , Hörtzsch Jan N. , Bujard Martina , Schuster Christoph M. , Bading Hilmar
Published: May 2013

Blocking nuclear calcium signaling reversibly inhibits long-term memory formation in flies.
A Network of Substrates of the E3 Ubiquitin Ligases MDM2 and HUWE1 Control Apoptosis Independently of p53
Authors: Kurokawa Manabu , Kim Jiyeon , Geradts Joseph , Matsuura Kenkyo , Liu Liu , Ran Xu , Xia Wenle , Ribar Thomas J. , Henao Ricardo , Dewhirst Mark W. , Kim Wun-Jae , Lucas Joseph E. , Wang Shaomeng , Spector Neil L. , Kornbluth Sally
Published: May 2013

Inhibition of the ubiquitin E3 ligase MDM2 in breast cancer cells could overcome lapatinib resistance.
Promoting Single-Cell Invasion
Authors: Gough Nancy R.
Published: May 2013

EphA2 can promote collective or single-cell invasive phenotypes depending on its cleavage status.
Relationship of
In Vitro
Synergy and Treatment Outcome with Daptomycin plus Rifampin in Patients with Invasive Methicillin-Resistant Staphylococcus aureus Infections
Authors: Rose Warren E. , Berti Andrew D. , Hatch Jacob B. , Maki Dennis G.
Published: May 2013

We report the findings of a study examining the relationship between
in vitro
daptomycin-rifampin synergy and the therapeutic outcome of 12 patients with complex deep methicillin-resistant
Staphylococcus aureus
(MRSA) infections treated for prolonged periods with this combination. Checkerboard synergy was found in nine cases and was 100% predictive of therapeutic success; absence of synergy was found in three cases, two of which were therapeutic failures (
P
= 0.045). No relationship was observed between synergy and outcome by time-kill assessment. Checkerboard synergy may predict clinical response to daptomycin plus rifampin for complex invasive MRSA infections requiring prolonged treatment.
Human Simulated Studies of Aztreonam and Aztreonam-Avibactam To Evaluate Activity against Challenging Gram-Negative Organisms, Including Metallo-β-Lactamase Producers
Authors: Crandon Jared L. , Nicolau David P.
Published: May 2013

Secondary to the stability of aztreonam against metallo-β-lactamases, coupled with avibatam's neutralizing activity against often coproduced extended-spectrum β-lactamases (ESBLs) or AmpC enzymes, the combination of aztreonam and avibactam has been proposed as a principal candidate for the treatment of infections with metallo-β-lactamase-producing Gram-negative organisms. Using the neutropenic-mouse thigh infection model, we evaluated the efficacy of human simulated doses of aztreonam-avibactam and aztreonam against 14
Enterobacteriaceae
and 13
Pseudomonas aeruginosa
isolates, of which 25 produced metallo-β-lactamases. Additionally, six
P. aeruginosa
isolates were also evaluated in immunocompetent animals. A humanized aztreonam dose of 2 g every 6 h (1-h infusion) was evaluated alone and in combination with avibactam at 375 or 600 mg every 6 h (1-h infusion), targeting the percentage of the dosing interval in which free-drug concentrations remained above the MIC (
f
T>MIC). Efficacy was evaluated as the change in bacterial density after 24 h compared with the bacterial density at the initiation of dosing. Aztreonam monotherapy resulted in reductions of two of the
Enterobacteriaceae
bacterial isolates (aztreonam MIC, ≤32 μg/ml;
f
T>MIC, ≥38%) and minimal activity against the remaining isolates (aztreonam MIC, ≥128 μg/ml;
f
T>MIC, 0%). Alternatively, aztreonam-avibactam therapy resulted in the reduction of all 14
Enterobacteriaceae
isolates (aztreonam-avibactam MICs, ≤16 μg/ml;
f
T>MIC, ≥65%) and no difference between the 375- and 600-mg doses of avibactam was noted. Similar pharmacodynamically predictable activity against
P. aeruginosa
was noted in studies with neutropenic and immunocompetent mice, with activity occurring when the MICs were ≤16 μg/ml and variable efficacy noted when the MICs were ≥32 μg/ml. Again, no difference in efficacy between the 375- and 600-mg doses of avibactam was observed. Aztreonam-avibactam represents an attractive treatment option for infections with metallo-β-lactamase-producing Gram-negative pathogens that coproduce ESBLs or AmpC.
Biofilm Formation Avoids Complement Immunity and Phagocytosis of Streptococcus pneumoniae
Authors: Domenech Mirian , Ramos-Sevillano Elisa , García Ernesto , Moscoso Miriam , Yuste Jose
Published: May 2013

Streptococcus pneumoniae
is a frequent member of the microbiota of the human nasopharynx. Colonization of the nasopharyngeal tract is a first and necessary step in the infectious process and often involves the formation of sessile microbial communities by this human pathogen. The ability to grow and persist as biofilms is an advantage for many microorganisms, because biofilm-grown bacteria show reduced susceptibility to antimicrobial agents and hinder recognition by the immune system. The extent of host protection against biofilm-related pneumococcal disease has not been determined yet. Using pneumococcal strains growing as planktonic cultures or as biofilms, we have investigated the recognition of
S. pneumoniae
by the complement system and its interactions with human neutrophils. Deposition of C3b, the key complement component, was impaired on
S. pneumoniae
biofilms. In addition, binding of C-reactive protein and the complement component C1q to the pneumococcal surface was reduced in biofilm bacteria, demonstrating that pneumococcal biofilms avoid the activation of the classical complement pathway. In addition, recruitment of factor H, the downregulator of the alternative pathway, was enhanced by
S. pneumoniae
growing as biofilms. Our results also show that biofilm formation diverts the alternative complement pathway activation by a PspC-mediated mechanism. Furthermore, phagocytosis of pneumococcal biofilms was also impaired. The present study confirms that biofilm formation in
S. pneumoniae
is an efficient means of evading both the classical and the PspC-dependent alternative complement pathways the host immune system.
Selenium Status Alters the Immune Response and Expulsion of Adult Heligmosomoides bakeri Worms in Mice
Authors: Smith Allen D. , Cheung Lumei , Beshah Ethiopia , Shea-Donohue Terez , Urban Joseph F.
Published: May 2013

Heligmosomoides bakeriis a nematode with parasitic development exclusively in the small intestine of infected mice that induces a potent STAT6-dependent Th2 immune response. We previously demonstrated that host protective expulsion of adultH. bakeriworms from a challenge infection was delayed in selenium (Se)-deficient mice. In order to explore mechanisms associated with the delayed expulsion, 3-week-old female BALB/c mice were placed on a torula yeast-based diet with or without 0.2 ppm Se, and after 5 weeks, they were inoculated withH. bakeriinfective third-stage larvae (L3s). Two weeks after inoculation, the mice were treated with an anthelmintic and then rested, reinoculated with L3s, and evaluated at various times after reinoculation. Analysis of gene expression in parasite-induced cysts and surrounding tissue isolated from the intestine of infected mice showed that the local-tissue Th2 response was decreased in Se-deficient mice compared to that in Se-adequate mice. In addition, adult worms recovered from Se-deficient mice had higher ATP levels than worms from Se-adequate mice, indicating greater metabolic activity in the face of a suboptimal Se-dependent local immune response. Notably, the process of worm expulsion was restored within 2 to 4 days after feeding a Se-adequate diet to Se-deficient mice. Expulsion was associated with an increased local expression of Th2-associated genes in the small intestine, intestinal glutathione peroxidase activity, secreted Relm-β protein, anti-H. bakeriIgG1 production, and reduced worm fecundity and ATP-dependent metabolic activity.
Oxford-Style Debates in a Microbiology Course for Majors: A Method for Delivering Content and Engaging Critical Thinking Skills
Authors: Boucaud Dwayne W. , Nabel Michael , Eggers Christian H.
Published: May 2013

Developing scientific expertise in the classroom involves promoting higher-order cognitive skills as well as content mastery. Effective use of constructivism can facilitate these outcomes. However this is often difficult to accomplish when delivery of content is paramount. Utilizing many of the tenets of constructivist pedagogy, we have designed an Oxford-style debate assignment to be used in an introductory microbiology course. Two teams of students were assigned a debatable topic within microbiology. Over a five-week period students completed an informative web page consisting of three parts: background on the topic, data-based positions for each side of the argument, and a data-based persuasive argument to support their assigned position. This was followed by an in-class presentation and debate. Analysis of student performance on knowledge-based questions shows that students retain debate-derived content acquired primarily outside of lectures significantly better than content delivered during a normal lecture. Importantly, students who performed poorly on the lecture-derived questions did as well on debate-derived questions as other students. Students also performed well on questions requiring higher-order cognitive skills and in synthesizing data-driven arguments in support of a position during the debate. Student perceptions of their knowledge-base in areas covered by the debate and their skills in using scientific databases and analyzing primary literature showed a significant increase in pre- and postassignment comparisons. Our data demonstrate that an Oxford-style debate can be used effectively to deliver relevant content, increase higher-order cognitive skills, and increase self-efficacy in science-specific skills, all contributing to developing expertise in the field.
Using Student-Produced Time-Lapse Plant Movies to communicate concepts in Plant Biology
Authors: Harrison-Pitaniello Marcia
Published: May 2013

Why do students think plants are “boring”? One factor may be that they do not see plant movement in real (i.e., their) time. This attitude may negatively impact their understanding of plant biology. Time-lapse movies of plants allow students to see the sophistication of movements involved in both organ development and orientation. The objective of this project was to develop simple methods to capture image sequences for lab analysis and for converting into movies. The technology for making time-lapse movies is now easily attainable and fairly inexpensive, allowing its use for skill levels from grade school through college undergraduates. Presented are example time-lapse movie exercises from both an undergraduate plant physiology course and outreach activities. The time-lapse plant exercises are adaptable to explore numerous topics that incorporate science standards core concepts, competencies, and disciplinary practices as well as to integrate higher order thinking skills and build skills in hypothesis development and communicating results to various audiences.
How Much Is Too Much Assessment? Insight into Assessment-Driven Student Learning Gains in Large-Scale Undergraduate Microbiology Courses
Authors: Wang Jack T. H. , Schembri Mark A. , Hall Roy A.
Published: May 2013

Designing and implementing assessment tasks in large-scale undergraduate science courses is a labor-intensive process subject to increasing scrutiny from students and quality assurance authorities alike. Recent pedagogical research has provided conceptual frameworks for teaching introductory undergraduate microbiology, but has yet to define best-practice assessment guidelines. This study assessed the applicability of Biggs’ theory of constructive alignment in designing consistent learning objectives, activities, and assessment items that aligned with the American Society for Microbiology’s concept-based microbiology curriculum in MICR2000, an introductory microbiology course offered at the University of Queensland, Australia. By improving the internal consistency in assessment criteria and increasing the number of assessment items explicitly aligned to the course learning objectives, the teaching team was able to efficiently provide adequate feedback on numerous assessment tasks throughout the semester, which contributed to improved student performance and learning gains. When comparing the constructively aligned 2011 offering of MICR2000 with its 2010 counterpart, students obtained higher marks in both coursework assignments and examinations as the semester progressed. Students also valued the additional feedback provided, as student rankings for course feedback provision increased in 2011 and assessment and feedback was identified as a key strength of MICR2000. By designing MICR2000 using constructive alignment and iterative assessment tasks that followed a common set of learning outcomes, the teaching team was able to effectively deliver detailed and timely feedback in a large introductory microbiology course. This study serves as a case study for how constructive alignment can be integrated into modern teaching practices for large-scale courses.
PILOTing Undergraduate Students to Hands-On Teaching and Research Skills
Authors: Borgon Robert A. , Verity Nicole , Teter Ken
Published: May 2013

Undergraduate research can make a positive impact on science education. Unfortunately, the one student-one mentor paradigm of undergraduate research generates a wide range of variability in the student’s experience and further limits its availability to a select few students. In contrast, a single faculty member can offer multiple undergraduate teaching positions that provide a consistent experience for the student. We attempted to combine the undergraduate research and teaching experiences in an internship practicum called Peer Instruction and Laboratory Occupational Training (PILOT). Students enrolled in PILOT served as teaching assistants for the upper division Quantitative Biological Methods (QBM) laboratory course. In addition, PILOT students worked on an independent lab project that provided them with hands-on training and supported the QBM course. The development of presentation and teaching skills was also emphasized in PILOT. These activities were designed to improve student communication skills, lab skills, and knowledge of molecular biology content. Here, we describe the PILOT curriculum and report the results of an anonymous assessment survey administered to 75 students who had completed PILOT in the previous five semesters. Our data indicate that PILOT provides an effective format to expand undergraduate opportunities for research and teaching experiences.
A Poster-Session Review to Reinforce Course Concepts and Improve Scientific Communication Skills
Authors: Stanton Julie Dangremond
Published: May 2013

A poster-session review is a novel learning activity designed to help students master material, monitor understanding, and practice communicating scientific information. For this strategy, each student is asked to become an expert on a randomly assigned topic from the semester. They create small posters summarizing the most important concepts from their topic and predict likely exam questions from this material. During lecture or lab, students present their work in a poster session and spend time viewing other students’ work. Prior to a comprehensive final exam, undergraduate genetics students participated in a poster-session review and were surveyed about the perceived benefits. They self-reported that the activity helped them understand a genetics topic, prepare for the final exam, and improve their scientific communication skills. A poster-session review can be incorporated into any undergraduate biology course to help achieve these goals.
Observing Fluorescent Probes in Living Cells using a Low-Cost LED Flashlight Retrofitted to a Common Vintage Light Microscope
Authors: Babbitt G. A. , Hanzlik C. A. , Busse K. N.
Published: May 2013

While the application of molecular biological techniques based upon fluorescent probes has rapidly expanded over recent decades, the equipment cost of fluorescent microscopy has largely prevented its adoption in the college and high school classroom. We offer a simple solution to this problem by describing in detail how to build with simple tools, a fluorescent microscope using a common brand of colored LED flashlights and second-hand components of vintage Nikon microscopes. This extremely low cost solution is qualitatively compared to an expensive modern Zeiss system.
Biosafety Guidelines for Handling Microorganisms in the Teaching Laboratory: Development and Rationale
Authors: Emmert Elizabeth A. B. ,   the ASM Task Committee on Laboratory Biosafety
Published: May 2013

The safe handling of microorganisms in the teaching laboratory is a top priority. However, in the absence of a standard set of biosafety guidelines tailored to the teaching laboratory, individual educators and institutions have been left to develop their own plans. This has resulted in a lack of consistency, and differing levels of biosafety practices across institutions. Influenced by the lack of clear guidelines and a recent outbreak of
Salmonella
infections that was traced back to teaching laboratory exposures, the Education Board of the American Society for Microbiology charged a task force to develop a uniform set of biosafety guidelines for working with microorganisms in the teaching laboratory. These guidelines represent best practices for safely handling microbes, based on the safety requirements found in the Centers for Disease Control and Prevention’s (CDC’s) Biosafety in Microbiological and Biomedical Laboratories (BMBL). Guidelines for safely handling microbes at both biosafety level 1 (BSL1) and biosafety level 2 (BSL2) were developed. The guidelines are brief by design for ease of use and are accompanied by an extensive appendix containing explanatory notes, sample documents, and additional resources. These guidelines provide educators with a clear and consistent way to safely work with microorganisms in the teaching laboratory.
Why a ‘Systems Approach to Microbiology’ Might Not Be the Best ApproachReview of:	Microbiology: A Systems Approach,	3rd ed.;	CowanMarjorie Kelly; (	2012).	McGraw-Hill,	New York, NY.	786 pages.
Authors: McDonald Ann H.
Published: May 2013

Review of:
Microbiology: A Systems Approach, 3rd ed.;
Marjorie Kelly Cowan; (2012). McGraw-Hill, New York, NY. 786 pages.
Grow Plants the Organic Way: Give Them the Soil Microbes They CraveReview of:	Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web, revised ed.;	LowenfelsJeff and	LewisWayne; (	2010).	Timber Press Inc.,	Portland, OR.	220 pages.
Authors: Mixter Phil
Published: May 2013

Review of:
Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web, revised ed.;
Jeff Lowenfels and Wayne Lewis; (2010). Timber Press Inc., Portland, OR. 220 pages.
Eine 2-Parameter-Gleichung zur Beschreibung von Phasengleichgewichten in partiell mischbaren Systemen
Authors: Feix Gunter , Bittrich Hans-Joachim , Lempe Dieter
Published: May 2013

Ausgehend von der Konzeption lokaler Molenbrüche, wird für die freie molare Excess-Energie eine Gleichung mit zwei adjustierbaren Parametern entwickelt, die es gestattet, Phasengleichgewichte in mischbaren binären und polynären Systemen zu beschreiben. Darüber hinaus ist es möglich, die Parameter der binären Untersysteme aus charakteristischen, experimentell leicht zugänglichen Daten zu berechnen.
Ophthalmic surgical training following modernising medical careers: regional variation in experience across the UK
Authors: Rodrigues Ian AS , Symes Richard J , Turner Stephen , Sinha Arti , Bowler Gordon , Chan Wai H
Published: May 2013

Objectives

To evaluate surgical experience among current doctors appointed into ophthalmology training posts since the introduction of the Modernising Medical Careers programme. Additionally, to identify regional variations in surgical experience and training programme delivery.

Design

A cross-sectional survey.

Setting

The UK's four largest deaneries (Schools of Ophthalmology).

Participants

Trainee ophthalmologists, all having completed three or more years of training, who were appointed to the new ophthalmic specialty training programme.

Primary and secondary outcome measures

The mean annual surgical rate for each deanery in phacoemulsification cataract extractions and experience in other common elective and emergency surgical operations. Second, to calculate the mean timetabled clinical activity.

Results

The responses of 40 doctors were analysed, with a response rate of 83%. Overall, the phacoemulsification rate was 73.52±29.24 operations/year. This was significantly higher in the South Thames Deanery (99.69±26.16, p=0.0005) and significantly lower in the North Western Deanery (48.08±19.72, p=0.0008). The annual mean complex cataract rate was 5.21±4.38. Only 40% were confident in dealing with the most common complication of cataract surgery (vitreous loss). The mean trabeculectomy (surgery for glaucoma) rate was 0.47±1.16 and for squint surgery it was 3.54±2.82 operations/year. Regarding the common ocular trauma surgery, 42.5% had not sutured a corneal laceration and 60% a globe rupture. 50% thought the training programme would adequately prepare them surgically. The timetabled clinical activity was highest in the South Thames Deanery (48.17 h/week) and lowest in the North Western Deanery (40.82 h/week) due to variations in the European Working Time Directive implementation and on-call commitments.

Conclusions

Significant regional variations in surgical training experience exist between UK deaneries, particularly with respect to cataract surgery, and they appear to be correlated to timetabled activity. Experience and confidence levels in managing complex cataract surgery and complications were low and experience with previously commonly performed elective and emergency operations was minimal. Although doctors from all the regions surveyed were very likely to achieve the minimum cataract extractions required for specialist training completion, we have identified shortcomings of the current training programme that need attention.
TRAINING SUPPORT VECTOR MACHINES USING FRANK–WOLFE OPTIMIZATION METHODS
Authors: FRANDI EMANUELE , ÑANCULEF RICARDO , GASPARO MARIA GRAZIA , LODI STEFANO , SARTORI CLAUDIO
Published: May 2013

Training a support vector machine (SVM) requires the solution of a quadratic programming problem (QP) whose computational complexity becomes prohibitively expensive for large scale datasets. Traditional optimization methods cannot be directly applied in these cases, mainly due to memory restrictions. By adopting a slightly different objective function and under mild conditions on the kernel used within the model, efficient algorithms to train SVMs have been devised under the name of core vector machines (CVMs). This framework exploits the equivalence of the resulting learning problem with the task of building a minimal enclosing ball (MEB) problem in a feature space, where data is implicitly embedded by a kernel function. In this paper, we improve on the CVM approach by proposing two novel methods to build SVMs based on the Frank–Wolfe algorithm, recently revisited as a fast method to approximate the solution of a MEB problem. In contrast to CVMs, our algorithms do not require to compute the solutions of a sequence of increasingly complex QPs and are defined by using only analytic optimization steps. Experiments on a large collection of datasets show that our methods scale better than CVMs in most cases, sometimes at the price of a slightly lower accuracy. As CVMs, the proposed methods can be easily extended to machine learning problems other than binary classification. However, effective classifiers are also obtained using kernels which do not satisfy the condition required by CVMs, and thus our methods can be used for a wider set of problems.
PLANAR SYMMETRY IN f(T) GRAVITY
Authors: RODRIGUES MANUEL E. , HOUNDJO M. J. S. , MOMENI D. , MYRZAKULOV R.
Published: May 2013

Exact solutions for planar Weitzenboch geometries in generalized teleparallel gravity with torsion are presented. The model predicted the existence of Moller, Kottler–Whittaker and planar de-Sitter geometries for different forms of action.
HIGH ENERGY PARTICLE COLLISIONS NEAR THE BIFURCATION SURFACE
Authors: ZASLAVSKII OLEG B.
Published: May 2013

We consider generic nonextremal stationary dirty black holes. It is shown that in the vicinity of any bifurcation surface the energy of collision of two particles in the center of mass frame can grow unbound. This is a generic property that, in particular, includes collisions near the inner black hole horizon analyzed earlier by different methods. The similar results are also valid for cosmological horizons. The case of the de Sitter metric is discussed.
Minimum time-dependent travel times with contraction hierarchies
Authors: Batz G. Veit , Geisberger Robert , Sanders Peter , Vetter Christian
Published: May 2013

Time-dependent road networks are represented as weighted graphs, where the weight of an edge depends on the time one passes through that edge. This way, we can model periodic congestions during rush hour and similar effects. In this work we deal with the special case where edge weights are time-dependent travel times. Namely, we consider two problems in this setting: Earliest arrival queries ask for a minimum travel time route for a start and a destination depending on a given departure time. Travel time profile queries ask for the travel time profile for a start, a destination, and an interval of possible departure times. For an instance representing the German road network, for example, we can answer earliest arrival queries in less than 1.5ms. For travel time profile queries, which are much harder to answer, we need less than 40ms if the interval of possible departure times has a width of 24 hours. For inexact travel time profiles with an allowed error of about 1% this even reduces to 3.2ms. The underlying hierarchical representations of the road network, which are variants of a time-dependent contraction hierarchy (TCH), need less than 1GiB of space and can be generated in about 30 minutes. As far as we know, TCHs are currently the only method being able to answer travel time profile queries efficiently. Altogether, with TCHs, web servers with massive request traffic are able to provide fast time-dependent earliest arrival route planning and computation of travel time profiles.
An FPGA-Based Accelerator for Frequent Itemset Mining
Authors: Zhang Yan , Zhang Fan , Jin Zheming , Bakos Jason D.
Published: May 2013

In this article we describe a Field Programmable Gate Array (FPGA)-based coprocessor architecture for Frequent Itemset Mining (FIM). FIM is a common data mining task used to find frequently occurring subsets amongst a database of sets. FIM is a nonnumerical, data intensive computation and is used in machine learning and computational biology. FIM is particularly expensive---in terms of execution time and memory---when performed on large and/or sparse databases or when applied using a low appearance frequency threshold. Because of this, the development of increasingly efficient FIM algorithms and their mapping to parallel architectures is an active field. Previous attempts to accelerate FIM using FPGAs have relied on performance-limiting strategies such as iterative database loading and runtime logic unit reconfiguration. In this article, we present a novel architecture to implement Eclat, a well-known FIM algorithm. Unlike previous efforts, our technique does not impose limits on the maximum set size as a function of available FPGA logic resources and our design scales well to multiple FPGAs. In addition to a novel hardware design, we also present a corresponding compression scheme for intermediate results that are stored in on-chip memory. On a four-FPGA board, experimental results show up to 68X speedup compared to a highly optimized software implementation.
Quipu
Authors: Meeuws Roel , Ostadzadeh S. Arash , Galuzzi Carlo , Sima Vlad Mihai , Nane Razvan , Bertels Koen
Published: May 2013

There has been a steady increase in the utilization of heterogeneous architectures to tackle the growing need for computing performance and low-power systems. The execution of computation-intensive functions on specialized hardware enables to achieve substantial speedups and power savings. However, with a large legacy code base and software engineering experts, it is not at all obvious how to easily utilize these new architectures. As a result, there is a need for comprehensive tool support to bridge the knowledge gap of many engineers as well as to retarget legacy code. In this article, we present the
Quipu
modeling approach, which consists of a set of tools and a modeling methodology that can generate hardware estimation models, which provide valuable information for developers. This information helps to focus their efforts, to partition their application, and to select the right heterogeneous components. We present
Quipu
’s capability to generate domain-specific models, that are up to several times more accurate within their particular domain (error: 4.6%) as compared to domain-agnostic models (error: 23%). Finally, we show how
Quipu
can generate models for a new toolchain and platform within a few days.