bluuebunny/crossref_metadata_2025 huggingface dataset:
Manipulating phonological boundaries using distributional cues
Authors: Schreiber Eric , Onishi Kristine H. , Clayards Meghan
Published: May 2013

This study investigates the role of phonetic variability in category formation. The category boundary between /n/ and /m/ was manipulated in English-speaking adults. In Experiment 1 (n = 24), categories were indicated by lexical (novel word-object pairings) and distributional (within-category variability, category mean) information. During pre- and post-tests, listeners categorized stimuli from a 10-step re-synthesized continuum from “nado” to “mado.” During training participants heard a bimodal distribution of tokens with one mode spanning 7 steps (wide) and one spanning 3 (narrow). For half the participants the wide category was “nado” and for the other half it was “mado.” During training, tokens from each category were paired with different objects (socks or balls). A repeated-measures ANOVA showed that after training, categorization shifted toward the wide distribution [F(1,22) = 10.259,p < 0.01] and more so for ambiguous steps [F(9,198) = 5.283, p < 0.001]. In Experiment 2 (n = 12), auditory information was identical to experiment 1, but lexical information about the categories was removed (all training tokens referred to the same object). Listeners again shifted categorization toward the wide distribution [F(1,10) = 7.686, p < 0.05], indicating that distributional information alone was sufficient to change categorization behavior.
A preliminary ultrasound study of Nepali lingual articulations
Authors: Kochetov Alexei , Pouplier Marianne , Truong Sarah
Published: May 2013

Previous descriptive and phonetic works on Nepali provided conflicting accounts of place contrasts in coronal consonants. Specifically, apical stops were characterized as either retroflex or alveolar, while laminal affricates were described as either alveolar or palatal. Some of these works used static palatography, which shows the contact between the tongue and the palate, but provides no information about the tongue shape for a given consonant or its dynamic properties. In this study we used ultrasound to image tongue shapes for various Nepali lingual consonants produced by a single native speaker of Brahmin dialect. The results showed that the speaker’s apical stops were produced with a substantially raised tongue front and retracted tongue tip, as would be expected of retroflex articulations. Laminal affricates had the tongue shape similar to dental stops, yet with a somewhat retracted tongue tip, indicative of the alveolar constriction. Apicals that differed in laryngeal features (voiceless, voiced, aspirated, breathy) did not show systematic differences in the tongue shape, except for the voiced stop, which was somewhat less retracted. While limited to the single speaker, the results confirm and extend some previous observations about Nepali coronals as showing a 3-way place contrast among dentals, alveolars, and retroflexes.
Efficient Bayesian multi-source localization using a graphics processing unit
Authors: Dosso Stan E. , Dettmer Jan
Published: May 2013

This paper presents a highly efficient approach to matched-field localization of an unknown number of ocean acoustic sources employing a graphics processing unit (GPU) for massively parallel computations. A Bayesian formulation is developed in which the number, locations, and complex spectra (amplitudes and phases) of multiple sources, as well as noise variance at each frequency, are considered unknown random variables constrained by acoustic data and prior information. The number of sources is determined during an initial burn-in stage by minimizing the Bayesian information criterion using an efficient birth/death scheme. Marginal posterior probability distributions for source locations are then computed using Gibbs sampling. Source and noise spectra are sampled implicitly by applying analytic maximum-likelihood solutions in terms of the source locations (explicit parameters). This greatly reduces the dimensionality of the inversion, but requires solving a very large number (order 105) of complex matrix inversions for each sample of the explicit parameters. These inversions can be solved in parallel on a GPU, increasing efficiency by a factor of ~100. Examples are given of localizing a large number of sources (up to 10) in near real time.
Efficient implementation of power-law attenuation of elastic waves in time-domain numerical simulations
Authors: Calvo David C. , Canepa Gaetano
Published: May 2013

Numerical simulation of wave propagation in the time domain is easily parallelizable on high performance computing systems due to the spatially local nature of the governing equations. The disadvantage of working in the time domain arises when lossy media must be modeled which generally gives rise to convolution-type loss terms in the governing time-domain equations. Computation of these convolutions usually requires the storage of several solution fields at thousands of previous time steps. This requirement can be memory prohibitive in three-dimensions. In this talk we present a recursive convolution approach to computing lossy (power-law) elastic wave propagation that is an extension of the one-way, one-dimensional acoustic wave equation work done by Liebler [Liebler et al., J. Acoust. Soc. Am. 116 (2004)] in order to handle multiple dimensions and shear waves. Convolutions are computed recursively by first using a nonlinear least-squares technique to fit the kernel of the convolution with a series of decaying exponentials. We demonstrate how graphical processing units (GPUs) can be used to obtain speed-up factors as high as 35 on a test computation of time-domain scattering from a highly resonant but lossy elastic cylinder. [Work sponsored by the Office of Naval Research.]
What can we learn from simulated acoustic environments?
Authors: Seeber Bernhard U.
Published: May 2013

Psychoacoustic research has often used headphones to reproduce sound stimuli. Recently, the spatial dimension has regained attention in basic research and the talk will make a case for the importance of binaural hearing when assessing sound quality. Technological advances made it possible to accurately reproduce real and artificial sound stimuli with high spatial fidelity for their assessment. The Simulated Open Field Environment (SOFE) is a laboratory setup to reproduce sounds from multiple loudspeakers in an anechoic chamber. The free-field presentation allows participants to interact with sound stimuli in a natural way using head turns and movements - important when working with participants inexperienced with laboratory procedures. In connection with room simulation software the SOFE can also create acoustic scenes with multiple sources and sound reflections—thereby increasing the realism. I will give an overview of recent findings gained with the SOFE and their relation to evaluating sound quality.
Evaluation of contact pressure in human vocal folds during phonation using high-speed videoendoscopy, electroglottography, and magnetic resonance imaging
Authors: Li Zhe , Bakhshaee Hani , Helou Leah , Mongeau Luc , Kost Karen , Rosen Clark , Verdolini Katherine
Published: May 2013

Mechanical stresses on the vocal folds surface during high pitch or amplitude phonation have been postulated to cause vocal fold damage. Models for the quantitative estimate of the contact pressure may be valuable for prevention and treatment. The objective of this study was to non-invasively estimate the contact pressure for different phonation types, amplitudes, and pitch in human subjects using concurrent high-speed videoendoscopy and eletroglottography. The edge velocities before and after contact were estimated from the analysis of consecutive digital images. Instantaneous contact areas were determined from electroglottography along with magnetic resonance image (MRI). The contact pressure was assessed using the impulse momentum form of Newton’s second law. Quantitative verifications using silicone models were made. Investigations were then carried out in quantitative human subjects to compare contact pressures for three different voice types, pitches, and loudnesses. Contact pressures for breathy, normal, and pressed voice were obtained for fifteen female subjects. The results were verified through comparisons with values measured directly using a probe microphone. The proposed methods appear to be robust and accurate for contact pressure estimation.
Phenobarbital Indirectly Activates the Constitutive Active Androstane Receptor (CAR) by Inhibition of Epidermal Growth Factor Receptor Signaling
Authors: Mutoh Shingo , Sobhany Mack , Moore Rick , Perera Lalith , Pedersen Lee , Sueyoshi Tatsuya , Negishi Masahiko
Published: May 2013

The epidermal growth factor receptor is an unexpected target of the barbiturate phenobarbital.
Making Microbes Multicellular
Authors: VanHook Annalisa M.
Published: May 2013

Two kinases independently sense reduced respiration to initiate biofilm formation in
Bacillus
subtilis
.
Selection and Recombinant Phenotyping of a Novel CMX001 and Cidofovir Resistance Mutation in Human Cytomegalovirus
Authors: James Scott H. , Price Nathan B. , Hartline Caroll B. , Lanier E. Randall , Prichard Mark N.
Published: May 2013

CMX001 is an orally available lipid acyclic nucleotide phosphonate that delivers high intracellular levels of cidofovir (CDV)-diphosphate and exhibits enhanced
in vitro
antiviral activity against a wide range of double-stranded DNA viruses, including cytomegalovirus (CMV). Mutations in the DNA polymerase of CMV that impart resistance to CDV also render the virus resistant to CMX001. Here, we report a novel resistance mutation that arose under the selective pressure of CMX001. The wild-type CMV strain AD169 was propagated in human foreskin fibroblasts under increasing concentrations of CMX001 over 10 months, and the resulting strain (named CMX001
R
) was less susceptible to CDV and CMX001 in a plaque reduction assay. Genotypic analysis of virus strain CMX001
R
via conventional sequencing of the genes encoding the CMV DNA polymerase (
UL54
) and UL97 kinase (
UL97
) demonstrated one mutation that changed the wild-type aspartate to glutamate at position 542 in
UL54
. A recombinant virus with this novel D542E mutation was generated via bacterial artificial chromosome-mediated marker transfer experiments. Subsequent phenotypic resistance analysis of the D542E mutant demonstrated reductions in susceptibility of greater than 10-fold to CMX001 and CDV, but no resistance to foscarnet (FOS) or ganciclovir (GCV). Analysis of replicative fitness showed that both strain CMX001
R
and the D542E mutant viruses demonstrated a smaller plaque phenotype and slower replication kinetics than their respective parent viruses. These data describe the first resistance mutation generated under the selective pressure of CMX001 and suggest that CMX001 may have a unique resistance profile associated with reduced viral replication and maintenance of sensitivity to FOS and GCV.
Phosphatidylinositol 4-Kinase III Beta Is Essential for Replication of Human Rhinovirus and Its Inhibition Causes a Lethal Phenotype
In Vivo
Authors: Spickler Catherine , Lippens Julie , Laberge Marie-Kristine , Desmeules Sophie , Bellavance Édith , Garneau Michel , Guo Tim , Hucke Oliver , Leyssen Pieter , Neyts Johan , Vaillancourt Fréderic H. , Décor Anne , O'Meara Jeff , Franti Michael , Gauthier Annick
Published: May 2013

Human rhinovirus (HRV) is the predominant cause of the common cold, but more importantly, infection may have serious repercussions in asthmatics and chronic obstructive pulmonary disorder (COPD) patients. A cell-based antiviral screen against HRV was performed with a subset of our proprietary compound collection, and an aminothiazole series with pan-HRV species and enteroviral activity was identified. The series was found to act at the level of replication in the HRV infectious cycle.
In vitro
selection and sequencing of aminothiazole series-resistant HRV variants revealed a single-nucleotide mutation leading to the amino acid change I42V in the essential HRV 3A protein. This same mutation has been previously implicated in resistance to enviroxime, a former clinical-stage antipicornavirus agent. Enviroxime-like compounds have recently been shown to target the lipid kinase phosphatidylinositol 4-kinase III beta (PI4KIIIβ). A good correlation between PI4KIIIβ activity and HRV antiviral potency was found when analyzing the data over 80 compounds of the aminothiazole series, covering a 750-fold potency range. The mechanism of action through PI4KIIIβ inhibition was further demonstrated by small interfering RNA (siRNA) knockdown of PI4KB, which reduced HRV replication and also increased the potency of the PI4KIIIβ inhibitors. Inhibitors from two different structural classes with promising pharmacokinetic profiles and with very good selectivity for PI4KIIIβ were used to dissociate compound-related toxicity from target-related toxicity. Mortality was seen in all dosing groups of mice treated with either compound, therefore suggesting that short-term inhibition of PI4KIIIβ is deleterious.
Determination of Voriconazole Serum Concentration by Bioassay, a Valid Method for Therapeutic Drug Monitoring for Clinical Laboratories
Authors: Cendejas-Bueno Emilio , Cuenca-Estrella Manuel , Gomez-Lopez Alicia
Published: May 2013

We describe here a simple, fast, and reliable bioassay method for therapeutic drug monitoring of voriconazole. Fifty-eight clinical and external quality control samples were evaluated with this microbiological assay, and results were compared with those obtained with a previously validated chromatographic method. A good correlation between both assays was observed. This particular microbiological method was demonstrated to be simple and offers enough precision and accuracy to perform voriconazole therapeutic drug monitoring in laboratories without specialized equipment.
Transition Metal–α-Amino Acid Complexes with Antibiotic Activity against Mycobacterium spp
Authors: Karpin George W. , Merola Joseph S. , Falkinham Joseph O.
Published: May 2013

Synthetic iridium-, rhodium-, and ruthenium-amino acid complexes with hydrophobic
l
-amino acids have antibiotic activity against
Mycobacterium
spp., including
Mycobacterium bovis
BCG and the rapidly growing species
Mycobacterium abscessus
and
Mycobacterium chelonae
. Concentrations of transition metal-amino acid complexes demonstrating hemolysis or cytotoxicity were 10- to 25-fold higher than were the MICs.
Cytomegalovirus UL97 Kinase Catalytic Domain Mutations That Confer Multidrug Resistance
Authors: Chou Sunwen , Ercolani Ronald J. , Marousek Gail , Bowlin Terry L.
Published: May 2013

Human cytomegalovirus UL97 kinase mutations that commonly confer ganciclovir resistance cluster in different parts of the gene than those conferring resistance to maribavir, an experimental UL97 kinase inhibitor. The drug resistance, growth, and autophosphorylation phenotypes of several unusual UL97 mutations in the kinase catalytic domain were characterized. Mutations V466G and P521L, described in clinical specimens from ganciclovir-treated subjects, conferred a UL97 kinase knockout phenotype with no autophosphorylation, a severe growth defect, and high-level ganciclovir, cyclopropavir, and maribavir resistance, similar to mutations at the catalytic lysine residue K355. Mutations F342S and V356G, observed after propagation under cyclopropavirin vitro, showed much less growth attenuation and moderate- to high-level resistance to all three drugs while maintaining UL97 autophosphorylation competence and normal cytopathic effect in cell culture, a novel phenotype. F342S is located in the ATP-binding P-loop and is homologous to a c-Abl kinase mutation conferring resistance to imatinib. UL97 mutants with relatively preserved growth fitness and multidrug resistance are of greater concern in antiviral therapy than the severely growth-impaired UL97 knockout mutants. Current diagnostic genotyping assays are unlikely to detect F342S and V356G, and the frequency of their appearance in clinical specimens remains undefined.
Randomized Trial of the Virologic Response during up to Two Years of Entecavir-Adefovir Combination Therapy in Multiple-Drug-Refractory Chronic Hepatitis B Virus Patients
Authors: Lim Young-Suk , Lee Ji-Young , Lee Danbi , Shim Ju Hyun , Lee Han Chu , Lee Yung Sang , Suh Dong Jin
Published: May 2013

A 1-year trial with entecavir plus adefovir resulted in a rate of virological response (VR) higher than that seen with lamivudine plus adefovir in multiple-drug-refractory chronic hepatitis B (CHB) patients. This extension study enrolled 89 of 90 patients who completed a 52-week randomized trial comparing treatment with entecavir plus adefovir (EA) to treatment with lamivudine plus adefovir (LA). At the baseline of the original study, all patients had lamivudine-resistant hepatitis B virus (HBV) and serum HBV DNA > 2,000 IU/ml despite prior lamivudine plus adefovir therapy. Of the 89 enrolled patients, 45 initially randomized to receive entecavir plus adefovir and the other 44 randomized to receive lamivudine plus adefovir received entecavir plus adefovir for an additional 52 weeks (EA-EA and LA-EA, respectively). The proportions of patients with a VR (serum HBV DNA < 60 IU/ml) gradually increased in both groups and were comparable at week 104 (42.2% in the EA-EA group and 34.1% in the LA-EA group;P= 0.51). The mean reductions in serum HBV DNA from baseline in the two groups were similar (−2.8 log10IU/ml and −2.8 log10IU/ml, respectively;P= 0.87). At week 104, the number of patients who retained the preexisting HBV mutants resistant to adefovir or entecavir had decreased from 8 to 2 in the EA-EA group and from 15 to 6 in the LA-EA group (P= 0.27). Both study groups had favorable safety profiles. In conclusion, up to 104 weeks of entecavir plus adefovir treatment was associated with a progressive VR, a decrease of levels of preexisting drug-resistant mutants, and no selection for additional resistance mutants of HBV in multiple-drug-refractory CHB patients. (This study has been registered at ClinicalTrials.gov under registration no. NCT01023217.)
Discovery of a Sexual Cycle in Aspergillus lentulus, a Close Relative of A. fumigatus
Authors: Swilaiman Sameira S. , O'Gorman Céline M. , Balajee S. Arunmozhi , Dyer Paul S.
Published: May 2013

Aspergillus lentuluswas described in 2005 as a new species within theA. fumigatussensu lato complex. It is an opportunistic human pathogen causing invasive aspergillosis with high mortality rates, and it has been isolated from clinical and environmental sources. The species is morphologically nearly identical toA. fumigatussensu stricto, and this similarity has resulted in their frequent misidentification. Comparative studies show thatA. lentulushas some distinguishing growth features and decreasedin vitrosusceptibility to several antifungal agents, including amphotericin B and caspofungin. Similar to the once-presumed-asexualA. fumigatus, it has only been known to reproduce mitotically. However, we now show thatA. lentulushas a heterothallic sexual breeding system. A PCR-based mating-type diagnostic detected isolates of either theMAT1-1orMAT1-2genotype, and examination of 26 worldwide clinical and environmental isolates revealed similar ratios of the two mating types (38% versus 62%, respectively).MAT1-1andMAT1-2idiomorph regions were analyzed, revealing the presence of characteristic alpha and high-mobility-group (HMG) domain genes, together with other more unusual features such as aMAT1-2-4gene. We then demonstrated thatA. lentuluspossesses a functional sexual cycle with mature cleistothecia, containing heat-resistant ascospores, being produced after 3 weeks of incubation. Recombination was confirmed using molecular markers. However, isolates ofA. lentulusfailed to cross with highly fertile strains ofA. fumigatus, demonstrating reproductive isolation between these sibling species. The discovery of theA. lentulussexual stage has significant implications for the management of drug resistance and control of invasive aspergillosis associated with this emerging fungal pathogen.
Trypanosoma brucei Tb927.2.6100 Is an Essential Protein Associated with Kinetoplast DNA
Authors: Beck Kirsten , Acestor Nathalie , Schulfer Anjelique , Anupama Atashi , Carnes Jason , Panigrahi Aswini K. , Stuart Ken
Published: May 2013

The mitochondrial DNA of trypanosomatid protozoa consists of a complex, intercatenated network of tens of maxicircles and thousands of minicircles. This structure, called kinetoplast DNA (kDNA), requires numerous proteins and multiprotein complexes for replication, segregation, and transcription. In this study, we used a proteomic approach to identify proteins that are associated with the kDNA network. We identified a novel protein encoded by Tb927.2.6100 that was present in a fraction enriched for kDNA and colocalized the protein with kDNA by fluorescence microscopy. RNA interference (RNAi) knockdown of its expression resulted in a growth defect and changes in the proportion of kinetoplasts and nuclei in the cell population. RNAi also resulted in shrinkage and loss of the kinetoplasts, loss of maxicircle and minicircle components of kDNA at similar rates, and (perhaps secondarily) loss of edited and pre-edited mRNA. These results indicate that the Tb927.2.6100 protein is essential for the maintenance of kDNA.
Engaging Students in Authentic Microbiology Research in an Introductory Biology Laboratory Course is Correlated with Gains in Student Understanding of the Nature of Authentic Research and Critical Thinking
Authors: Gasper Brittany J. , Gardner Stephanie M.
Published: May 2013

Recent recommendations for biology education highlight the role of authentic research experiences early in undergraduate education as a means of increasing the number and quality of biology majors. These experiences will inform students on the nature of science, increase their confidence in doing science, as well as foster critical thinking skills, an area that has been lacking despite it being one of the desired outcomes at undergraduate institutions and with future employers. With these things in mind, we have developed an introductory biology laboratory course where students design and execute an authentic microbiology research project. Students in this course are assimilated into the community of researchers by engaging in scholarly activities such as participating in inquiry, reading scientific literature, and communicating findings in written and oral formats. After three iterations of a semester-long laboratory course, we found that students who took the course showed a significant increase in their understanding of the nature of authentic research and their level of critical thinking skills.
Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools
Authors: Ng Wenfa
Published: May 2013

Ever since the first observation of “animalcules” under a microscope, and the subsequent discovery of microorganisms of myriad size, shape, pigmentation and motility modes, classification in aid of microbial identification is key to understanding inter-relationships between diverse microbes. Combining universal applicability with robustness, 16S rRNA sequencing is the gold standard for microbial typing; however, recent developments in clinical diagnostics have called attention to a shift towards PCR-independent instrumentation and methods given PCR’s requirement for expensive and complex sample preparation. Using ribosomal proteins as biomarkers for evolutionary relatedness, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) - originally developed for the soft ionization of proteins and peptides in proteomics studies - has been successfully applied to identifying bacteria, archaea, fungi and viruses to the species, and, on occasions, sub-species level. Though experimentally proven and increasingly adopted in the clinic, the relatively low-cost (on a per sample basis) and rapid MALDI-TOF MS microbial identification technique, along with its theoretical principles and methodology, is a conspicuous absentee in contemporary microbiology curricula. Motivated by a desire to close the curriculum gap, this article describes a discovery-based activity for teaching microbial identification - using MALDI-TOF MS in combination with open-source genomics and proteomics search tools – while providing tips on mass spectra interpretation and activity implementation for lowering the barrier for classroom adoption. Infused with inquiry-based learning concepts guiding students in identifying microbes from environmental water samples with unknown species diversity, the activity spurs students’ learning by igniting their spirit of inquiry, which leads to better mastery of concepts; a significant departure from conventional laboratory exercises that, in verifying known theory or results, lack the ability to excite students or impart skills for seeking answers to their own questions. Suitable as part of a laboratory sequence complementing bioinformatics, analytical chemistry or life sciences courses, the activity’s modular nature also affords creative content adjustments for catering to differing curricula needs and learning styles. Nor is the exercise restricted to water samples, other samples (with appropriate modifications in inoculation protocols) such as vegetable leaves are also interesting microcosms for performing microbial censuses. Taken together, from sample collection to cultivation and microbial typing, students engage in an integrated exercise designed to impart conceptual knowledge and practical skills – while unlocking the joy of learning and discovery – by answering a research question with unknown answers: what are the microorganisms present in an environmental water sample?
Examining an Online Microbiology Game as an Effective Tool for Teaching the Scientific Process
Authors: Bowling Kristi G. , Klisch Yvonne , Wang Shu , Beier Margaret
Published: May 2013

This study investigates the effectiveness of the online Flash game
Disease Defenders
in producing knowledge gains for concepts related to the scientific process.
Disease Defenders
was specifically designed to model how the scientific process is central to a variety of disciplines and science careers. An additional question relates to the game’s ability to shift attitudes toward science. Middle school classes from grades six to eight were assigned to the experimental group (n = 489) or control group (n = 367) and asked to participate in a three-session intervention. The sessions involved completing a pretest, a game play session, and taking a posttest. Students in the experimental group played
Disease Defenders
while students in the control group played an alternative science game. Results showed a significant increase in mean science knowledge scores for all grades in the experimental group, with sixth grade and seventh grade students gaining more knowledge than eighth grade students. Additionally, results showed a significant positive change in science attitudes only among sixth graders, who also rated their satisfaction with the game more favorably than students in higher grades. No differences in mean test scores were found between genders for science knowledge or science attitudes, suggesting that the game is equally effective for males and females.
The Bad Bugs Book Club: Science, Literacy, and Engagement
Authors: Verran Joanna
Published: May 2013

The Bad Bugs Bookclub was launched in 2009. It comprises scientists and non-scientists. The aim of the Bookclub is to read and discuss novels where infectious disease forms part of the plot, in order to enhance learning about microbiology. The focus of the discussion is on appreciation of the novel, its scientific (microbiologic) accuracy and relevance to contemporary microbiology. There are several potential audiences for the Bad Bugs Bookclub, for example students in a classroom setting, or in a more social environment, and/or the general public. Meeting reports and reading guides have been posted on a dedicated website. For education purposes, additional project work for assessment is suggested for students reading each novel. Bookclub meetings may be held on particular dates in the microbiologic calendar, coupled with additional public engagement activities and student participation. The approach has significant flexibility in terms of intended audience, assessment and extension work, and provides a refreshing and stimulating alternative means for talking about microbiology.
Using Interactive Animations to Enhance Teaching, Learning, and Retention of Respiration Pathway Concepts in Face-to-Face and Online High School, Undergraduate, and Continuing Education Learning Environments
Authors: Rice Sederick C.
Published: May 2013

One major tool set teachers/instructors can use is online interactive animations, which presents content in a way that helps pique students' interest and differentiates instructional content. The Virtual Cell Animation Collections (VCAC), developed from the Molecular and Cellular Biology Learning Center, has developed a series of online interactive animations that provide teacher/instructors and students with immersive learning tools for studying and understanding respiration processes. These virtual tools work as powerful instructional devices to help explain and reinforce concepts of metabolic pathways that would normally be taught traditionally using static textbook pages or by neumonic flashcards. High school, undergraduate, and continuing education students of today learn and retain knowledge differently than their predecessors. Now teachers face new challenges and must engage and assess students, within a small window during classroom instruction, but also have the skills to provide useful content in distance learning environments. Educators have to keep up with changing trends in education as a result of technological advances, higher student/teacher ratios, and the influence of social media on education. It is critical for teachers/instructors to be able to present content that not only keeps students interested but also helps bridge learning gaps. VCAC provides high school, undergraduate, and continuing education biology or life science teachers/instructors with classroom strategies and tools for introducing respiration content through free open source online resources. VCAC content supports the development of more inquiry-based classroom and distance-learning environments that can be facilitated by teachers/instructors, which helps improve retention of important respiration subject content and problem-based learning skills for students.
An Undergraduate Laboratory Activity Demonstrating Bacteriophage Specificity
Authors: Allen Mary E. , Gyure Ruth A.
Published: May 2013

Bacteriophage are among the most diverse and numerous microbes inhabiting our planet. Yet many laboratory activities fail to engage students in meaningful exploration of their diversity, unique characteristics, and abundance. In this curriculum activity students use a standard plaque assay to enumerate bacteriophage particles from a natural sample and use the scientific method to address questions about host specificity and diversity. A raw primary sewage sample is enriched for bacteriophage using hosts in the family Enterobacteriaceae. Students hypothesize about host specificity and use quantitative data (serial dilution and plaque assay) to test their hypotheses. Combined class data also help them answer questions about phage diversity. The exercise was field tested with a class of 47 students using pre- and posttests. For all learning outcomes posttest scores were higher than pretest scores at or belowp= 0.01. Average individualized learning gain (G) was also calculated for each learning outcome. Students’ use of scientific language in reference to bacteriophage and host interaction significantly improved (p= 0.002; G = 0.50). Improved means of expression helped students construct better hypotheses on phage host specificity (G = 0.31,p= 0.01) and to explain the plaque assay method (G = 0.33,p= 0.002). At the end of the exercise students also demonstrated improved knowledge and understanding of phage specificity as related to phage therapy in humans (p< 0.001; G = 51).
Using Primary Literature to Teach Science Literacy to Introductory Biology Students
Authors: Krontiris-Litowitz Johanna
Published: May 2013

Undergraduate students struggle to read the scientific literature and educators have suggested that this may reflect deficiencies in their science literacy skills. In this two-year study we develop and test a strategy for using the scientific literature to teach science literacy skills to novice life science majors. The first year of the project served as a preliminary investigation in which we evaluated student science literacy skills, created a set of science literacy learning objectives aligned with Bloom’s taxonomy, and developed a set of homework assignments that used peer-reviewed articles to teach science literacy. In the second year of the project the effectiveness of the assignments and the learning objectives were evaluated. Summative student learning was evaluated in the second year on a final exam. The mean score was 83.5% (±20.3%) and there were significant learning gains (
p
< 0.05) in seven of nine of science literacy skills. Project data indicated that even though students achieved course-targeted lower-order science literacy objectives, many were deficient in higher-order literacy skills. Results of this project suggest that building scientific literacy is a continuing process which begins in first-year science courses with a set of fundamental skills that can serve the progressive development of literacy skills throughout the undergraduate curriculum.
Using PCR to Target Misconceptions about Gene Expression
Authors: Wright Leslie K. , Newman Dina L.
Published: May 2013

We present a PCR-based laboratory exercise that can be used with first- or second-year biology students to help overcome common misconceptions about gene expression. Biology students typically do not have a clear understanding of the difference between genes (DNA) and gene expression (mRNA/protein) and often believe that genes exist in an organism or cell only when they are expressed. This laboratory exercise allows students to carry out a PCR-based experiment designed to challenge their misunderstanding of the difference between genes and gene expression. Students first transform
E. coli
with an inducible GFP gene containing plasmid and observe induced and un-induced colonies. The following exercise creates cognitive dissonance when actual PCR results contradict their initial (incorrect) predictions of the presence of the GFP gene in transformed cells. Field testing of this laboratory exercise resulted in learning gains on both knowledge and application questions on concepts related to genes and gene expression.
Genomics Gets PersonalReview of:	My Beautiful Genome: Exposing Our Genetic Future, One Quirk at a Time;	FrankLone; (	2011).	Oneworld Publications,	Oxford, England.	313 pages.
Authors: Scheifele Lisa Z.
Published: May 2013

Review of:
My Beautiful Genome: Exposing Our Genetic Future, One Quirk at a Time;
Lone Frank; (2011). Oneworld Publications, Oxford, England. 313 pages.
Engaging EpidemicsReview of:	Spillover: Animal Infections and the Next Human Pandemic;	QuammenDavid; (	2012).	W.W. Norton and Co.,	New York, NY.	592 pages.
Authors: Fass Marion Field
Published: May 2013

Review of:
Spillover: Animal Infections and the Next Human Pandemic;
David Quammen; (2012). W.W. Norton and Co., New York, NY. 592 pages.
Sick from Freedom:
An Unusual Perspective on the Civil War and ReconstructionReview of:	Sick from Freedom: African-American Illness and Suffering during the Civil War and Reconstruction;	DownsJim; (	2012).	Oxford University Press,	Oxford, England.	280 pages.
Authors: Elder Elisabeth Davis
Published: May 2013

Review of:
Sick from Freedom: African-American Illness and Suffering during the Civil War and Reconstruction;
Jim Downs; (2012). Oxford University Press, Oxford, England. 280 pages.
A CHARACTERIZATION OF THE CATENOID AND HELICOID
Authors: RIVEROS CARLOS M. C. , CORRO ARMANDO M. V.
Published: May 2013

In this paper we show that a connected non-planar minimal surface whose asymptotic lines have the same geodesic curvature up to sign is a catenoid. As an application of this result we show that a connected non-planar minimal surface whose lines of curvature have the same geodesic curvature up to sign is a helicoid. Moreover, we show that the coordinates curves of the associate minimal surfaces to catenoid have the same geodesic curvature up to sign.
A REMARK ON THE DETERMINANT OF QUASI-ALTERNATING LINKS
Authors: QAZAQZEH K. , QUBLAN B. , JARADAT A.
Published: May 2013

We show that the crossing number of any link that is known to be quasi-alternating is less than or equal to its determinant. Based on this, we conjecture that the crossing number of any quasi-alternating link is less than or equal to its determinant. Thus if this conjecture is true, then it gives a new property of quasi-alternating links and easy obstruction to a link being quasi-alternating.
EFFICIENT LAPLACE INVERSION, WIENER-HOPF FACTORIZATION AND PRICING LOOKBACKS
Authors: BOYARCHENKO SVETLANA , LEVENDORSKIĬ SERGEI
Published: May 2013

We construct fast and accurate methods for (a) approximate Laplace inversion, (b) approximate calculation of the Wiener-Hopf factors for wide classes of Lévy processes with exponentially decaying Lévy densities, and (c) approximate pricing of lookback options. In all cases, we use appropriate conformal change-of-variable techniques, which allow us to apply the simplified trapezoid rule with a small number of terms (the changes of variables in the outer and inner integrals and in the formulas for the Wiener-Hopf factors must be compatible in a certain sense). The efficiency of the method stems from the properties of functions analytic in a strip (these properties were explicitly used in finance by Feng and Linetsky 2008). The same technique is applicable to the calculation of the pdfs of supremum and infimum processes, and to the calculation of the prices and sensitivities of options with lookback and barrier features.
A hybrid dynamic programming approach to the biobjective binary knapsack problem
Authors: Delort Charles , Spanjaard Olivier
Published: May 2013

This article is devoted to a study of the impact of using bound sets in biobjective dynamic programming. This notion, introduced by Villareal and Karwan [1981], has been independently revisited by Ehrgott and Gandibleux [2007], as well as by Sourd and Spanjaard [2008]. The idea behind it is very general and can, therefore, be adapted to a wide range of biobjective combinatorial problems. We focus here on the biobjective binary knapsack problem. We show that using bound sets to perform a hybrid dynamic programming procedure embedded in a two-phase method [Ulungu and Teghem 1995] yields numerical results that outperform previous dynamic programming approaches to the problem, both in execution times and memory requirements.
Dynamic graph clustering combining modularity and smoothness
Authors: Görke Robert , Maillard Pascal , Schumm Andrea , Staudt Christian , Wagner Dorothea
Published: May 2013

Maximizing the quality index
modularity
has become one of the primary methods for identifying the clustering structure within a graph. Since many contemporary networks are not static but evolve over time, traditional static approaches can be inappropriate for specific tasks. In this work, we pioneer the NP-hard problem of online dynamic modularity maximization. We develop scalable dynamizations of the currently fastest and the most widespread static heuristics and engineer a heuristic dynamization of an optimal static algorithm. Our algorithms efficiently maintain a
modularity
-based clustering of a graph for which dynamic changes arrive as a stream. For our quickest heuristic we prove a tight bound on its number of operations. In an experimental evaluation on both a real-world dynamic network and on dynamic clustered random graphs, we show that the dynamic maintenance of a clustering of a changing graph yields higher
modularity
than recomputation, guarantees much smoother clustering dynamics, and requires much lower runtimes. We conclude with giving sound recommendations for the choice of an algorithm.
ReShape
Authors: Neely Christopher E. , Brebner Gordon , Shang Weijia
Published: May 2013

The latest FPGA devices provide the headroom to implement large-scale and complex systems. A key requirement is the integration of modules from diverse sources to promote modular design and reuse. A contrary factor is that using dynamic partial reconfiguration typically requires low-level planning of the system implementation. In this article, we introduce ReShape: a high-level approach for designing reconfigurable systems by interconnecting modules, which gives a “plug and play” look and feel, is supported by tools that carry out implementation functions, and is carried through to support system reconfiguration during operation. The emphasis is on the inter-module connections and abstracting the communication patterns that are typical between modules: for example, the streaming of data, or the reading and writing of data to and from memory modules. The details of wiring and signaling are hidden from view, via metadata associated with individual modules. This setting allows system reconfiguration at the module level, both by supporting type checking of replacement modules and by managing the overall system implementation, via metadata associated with its FPGA floorplan. The methodology and tools have been implemented in a prototype targeted to a domain-specific setting---high-speed networking---and have been validated on real telecommunications design projects.
Radical Chemoradiotherapy for Urethral Squamous Cell Carcinoma: Two Case Reports and a Review of the Literature
Authors: Coop H. , Pettit L. , Boon C. , Ramachandra P.
Published: May 2013

Primary urethral squamous cell carcinoma is rare. Its management is particularly challenging owing to the paucity of evidence from randomised trials to inform practice. We report two male and female cases of squamous cell carcinoma of the urethra, which were treated with concomitant cisplatin and radiotherapy. These cases add to the body of case reports that have shown benefit for concomitant chemoradiotherapy in urethral squamous cell carcinoma. They also illustrate that single agent chemotherapy, namely, cisplatin, may be used successfully with limited toxicities.
Discrimination between Alzheimer's Disease and Mild Cognitive Impairment Using SOM and PSO-SVM
Authors: Yang Shih-Ting , Lee Jiann-Der , Chang Tzyh-Chyang , Huang Chung-Hsien , Wang Jiun-Jie , Hsu Wen-Chuin , Chan Hsiao-Lung , Wai Yau-Yau , Li Kuan-Yi
Published: May 2013

In this study, an MRI-based classification framework was proposed to distinguish the patients with AD and MCI from normal participants by using multiple features and different classifiers. First, we extracted features (volume and shape) from MRI data by using a series of image processing steps. Subsequently, we applied principal component analysis (PCA) to convert a set of features of possibly correlated variables into a smaller set of values of linearly uncorrelated variables, decreasing the dimensions of feature space. Finally, we developed a novel data mining framework in combination with support vector machine (SVM) and particle swarm optimization (PSO) for the AD/MCI classification. In order to compare the hybrid method with traditional classifier, two kinds of classifiers, that is, SVM and a self-organizing map (SOM), were trained for patient classification. With the proposed framework, the classification accuracy is improved up to 82.35% and 77.78% in patients with AD and MCI. The result achieved up to 94.12% and 88.89% in AD and MCI by combining the volumetric features and shape features and using PCA. The present results suggest that novel multivariate methods of pattern matching reach a clinically relevant accuracy for the a priori prediction of the progression from MCI to AD.
Integration of HIV Care with Primary Health Care Services: Effect on Patient Satisfaction and Stigma in Rural Kenya
Authors: Odeny Thomas A. , Penner Jeremy , Lewis-Kulzer Jayne , Leslie Hannah H. , Shade Starley B. , Adero Walter , Kioko Jackson , Cohen Craig R. , Bukusi Elizabeth A.
Published: May 2013

HIV departments within Kenyan health facilities are usually better staffed and equipped than departments offering non-HIV services. Integration of HIV services into primary care may address this issue of skewed resource allocation. Between 2008 and 2010, we piloted a system of integrating HIV services into primary care in rural Kenya. Before integration, we conducted a survey among returning adults ≥18-year old attending the HIV clinic. We then integrated HIV and primary care services. Three and twelve months after integration, we administered the same questionnaires to a sample of returning adults attending the integrated clinic. Changes in patient responses were assessed using truncated linear regression and logistic regression. At 12 months after integration, respondents were more likely to be satisfied with reception services (adjusted odds ratio, aOR 2.71, 95% CI 1.32–5.56), HIV education (aOR 3.28, 95% CI 1.92–6.83), and wait time (aOR 1.97 95% CI 1.03–3.76). Men's comfort with receiving care at an integrated clinic did not change (aOR = 0.46 95% CI 0.06–3.86). Women were more likely to express discomfort after integration (aOR 3.37 95% CI 1.33–8.52). Integration of HIV services into primary care services was associated with significant increases in patient satisfaction in certain domains, with no negative effect on satisfaction.
Diabetic Muscle Infarction: A Rare Cause of Acute Limb Pain in Dialysis Patients
Authors: De Vlieger G. , Bammens B. , Claus F. , Vos R. , Claes K.
Published: May 2013

Diabetic muscle infarction is a rare microangiopathic complication occurring in patients with advanced diabetes mellitus. Diabetic patients with chronic kidney disease stage Vd are prone to develop this complication. The presenting symptom is a localized painful swelling of the affected limb. Symptoms usually resolve spontaneously during the following weeks, but frequent relapse can occur and in some cases swelling may lead to compartment syndrome. Biochemical blood analyses show an elevated C-reactive protein, but creatine kinase is often normal. Diagnosis can be made on clinical presentation and imaging, with magnetic resonance imaging as the gold standard. Histology is often not contributive. Treatment consists of rest, analgesics, rigorous glycemic control and low-dose aspirin. Severe cases of compartment syndrome require fasciotomy. In the current paper, we present two diabetic patients with cystic fibrosis, who are treated with automated peritoneal dialysis and suffered from episodic lower limb infarction. We subsequently review 48 episodes of diabetic muscle infarction previously reported in the literature in patients with end-stage renal disease.
New Multiple Solution to the Boussinesq Equation and the Burgers-Like Equation
Authors: Bulut Hasan , Tuz Münevver , Akturk Tolga
Published: May 2013

By considering an improved tanh function method, we found some exact solutions of Boussinesq and Burgers-like equations. The main idea of this method is to take full advantage of the Riccati equation which has more new solutions. We found some exact solutions of the Boussinesq equation and the Burgers-like equation.