bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of two channel selection criteria for noise suppression in cochlear implants
Authors: Hazrati Oldooz , Loizou Philipos C.
Published: March 2013

The performance of current channel selection criteria used in cochlear implant (CI) devices (e.g., maximum selection criterion used in ACE) degrades significantly in the presence of noise. In noisy backgrounds, coding strategies that select the “right” channels for stimulation could potentially produce substantial improvements in intelligibility. In this study, the performance of two alternative channel selection criteria is assessed in terms of intelligibility and subjective quality with CI users in noise. The performance is compared against that of the maximum selection scheme employed in the ACE strategy (comparison is also made with the CIS strategy). Sentences were presented to seven CI users in speech weighted noise (−5, 0, and 5 dB SNR). Both channel selection criteria were implemented under ideal conditions where a priori knowledge of the target and masker was assumed. This was done to assess the full potential benefit of selecting the “right” channels for stimulation in noisy backgrounds. Substantial intelligibility improvement relative to the CI users' daily strategy (i.e., ACE or CIS) was achieved with the two different channel selection criteria under all noisy conditions considered. No significant difference in subjective quality of noisy speech processed by the two channel selection criteria was observed.
Pulse compression in a time variant system with application to ultrasonic vibrometry
Authors: Martin J. S. , Rogers P. H. , Gray M. D.
Published: March 2013

Pulse compression is normally applied only to time-invariant systems, as the variation of a system's properties during its interrogation violates assumptions of the compression process. However, there is an exact solution to the pulse-compression problem when the time variance satisfies two criteria, which are the same as those required for the operation of an ultrasonic vibrometer in the context of a tissue elastography system. One is that the variations be very small in comparison with the wavelength of the interrogating ultrasound. The other is that the bandwidth of the variations be within one Nyquist band as sampled by the periodic interrogation signal. The solution to this problem involves a step-wise interpolation of the static pulse-compression transfer function in the frequency domain. This technique, in conjunction with the selection of an appropriate interrogation signal, offers significant advantages in measurement time or measurement resolution for an ultrasonic vibrometer limited by additive noise at the receiver. The characteristics of optimal interrogation signals for this technique are the signal's crest factor, spectral energy distribution, and phasing. These relate to the intended compression pulse, the noise, and the static response of the system. The technique has been demonstrated analytically, experimentally, and with numerical models.
Relationships between unoccupied classroom acoustical conditions and elementary student achievement measured in eastern Nebraska
Authors: Ronsse Lauren M. , Wang Lily M.
Published: March 2013

Building standards recommend maximum background noise levels (BNL) and reverberation times (RT) for unoccupied classrooms. However, existing research does not show a consistent correlation between these parameters and student achievement. Through in situ testing, this research seeks to determine what acoustical conditions should be attained in elementary schools for students to meet educational goals. Acoustical measurements were conducted in a Nebraska public school system and correlated to achievement scores from students in the surveyed classrooms. Unoccupied BNLs and RTs were gathered in 34 third and 33 fifth-grade classrooms. Additionally, binaural room impulse response measurements were gathered in a subset of the classrooms. The results suggest that student reading and language subject areas may be negatively impacted by higher unoccupied BNLs; to meet the upper half of NE state targets, these levels should be less than 45 dBA. However, the percentage of students receiving free or reduced price lunches is more strongly correlated to achievement than BNLs, and the negative correlations between noise and achievement are not significant when controlling for this demographic variable. One statistically significant relationship that remained when controlling for demographics was that classrooms with lower distortion of frequency-smoothed magnitude values generally had students with higher language scores.
Ultrasonic attenuation and speed of sound of cornstarch suspensions
Authors: Johnson Benjamin L. , Holland Mark R. , Miller James G. , Katz Jonathan I.
Published: March 2013

The goal of this study is to contribute to the physics underlying the material properties of suspensions that exhibit shear thickening through the ultrasonic characterization of suspensions of cornstarch in a density-matched solution. Ultrasonic measurements at frequencies in the range of 4 to 8 MHz of the speed of sound and the frequency-dependent attenuation properties are reported for concentrations of cornstarch in a density-matched aqueous (cesium chloride brine) suspension, ranging up to 40% cornstarch. The speed of sound is found to range from 1483 ± 10 m/s in pure brine to 1765 ± 9 m/s in the 40% cornstarch suspension. The bulk modulus of a granule of cornstarch is inferred to be 1.2(± 0.1) × 1010 Pa. The attenuation coefficient at 5 MHz increases from essentially zero in brine to 12.0 ± 1.2 dB/cm at 40% cornstarch.
Development of a glottal area index that integrates glottal gap size and open quotient
Authors: Chen Gang , Kreiman Jody , Gerratt Bruce R. , Neubauer Juergen , Shue Yen-Liang , Alwan Abeer
Published: March 2013

Because voice signals result from vocal fold vibration, perceptually meaningful vibratory measures should quantify those aspects of vibration that correspond to differences in voice quality. In this study, glottal area waveforms were extracted from high-speed videoendoscopy of the vocal folds. Principal component analysis was applied to these waveforms to investigate the factors that vary with voice quality. Results showed that the first principal component derived from tokens without glottal gaps was significantly (p < 0.01) associated with the open quotient (OQ). The alternating-current (AC) measure had a significant effect (p < 0.01) on the first principal component among tokens exhibiting glottal gaps. A measure AC/OQ, defined as the ratio of AC to OQ, was proposed to combine both amplitude and temporal characteristics of the glottal area waveform for both complete and incomplete glottal closures. Analyses of “glide” phonations in which quality varied continuously from breathy to pressed showed that the AC/OQ measure was able to characterize the corresponding continuum of glottal area waveform variation, regardless of the presence or absence of glottal gaps.
A wave finite element analysis of the passive cochlea
Authors: Elliott Stephen J. , Ni Guangjian , Mace Brian R. , Lineton Ben
Published: March 2013

Current models of the cochlea can be characterized as being either based on the assumed propagation of a single slow wave, which provides good insight, or involve the solution of a numerical model, such as in the finite element method, which allows the incorporation of more detailed anatomical features. In this paper it is shown how the wave finite element method can be used to decompose the results of a finite element calculation in terms of wave components, which allows the insight of the wave approach to be brought to bear on more complicated numerical models. In order to illustrate the method, a simple box model is considered, of a passive, locally reacting, basilar membrane interacting via three-dimensional fluid coupling. An analytic formulation of the dispersion equation is used initially to illustrate the types of wave one would expect in such a model. The wave finite element is then used to calculate the wavenumbers of all the waves in the finite element model. It is shown that only a single wave type dominates the response until this peaks at the best place in the cochlea, where an evanescent, higher order fluid wave can make a significant contribution.
Interaural correlation discrimination from diffuse field reference correlations
Authors: Walther Andreas , Faller Christof
Published: March 2013

Just noticeable differences in interaural correlation (ρ-jnds) from diffuse sound field reference correlations are obtained. In a three-interval, three-alternative forced-choice procedure, ρ-jnds are measured for positive and negative deviations from nine narrowband reference conditions. Stimuli are 1 equivalent rectangular bandwidth wide noise bursts with center frequencies between 165 and 1500 Hz. The frequency dependent reference correlation (ρref) is determined by the simulated interaural correlation under ideal diffuse sound field conditions. Results show that the interaural correlation at threshold for deviation toward the positive correlation range follows the reference curve in a nonlinear fashion. For deviation toward the negative correlation range the interaural correlation at threshold is further afar the reference curve and does not markedly resemble its trend. The results indicate that the previously found asymmetry for correlation discrimination from uncorrelated broadband stimuli to the positive and negative correlation range becomes less pronounced for narrowband stimuli. For positive deviation, the highest jnds are found for the region where the reference curve occupies the global minimum in ρref; despite that, the interaural correlation at threshold for positive deviation exhibits its lowest value at that point.
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote
Authors: Schönknecht Gerald , Chen Wei-Hua , Ternes Chad M. , Barbier Guillaume G. , Shrestha Roshan P. , Stanke Mario , Bräutigam Andrea , Baker Brett J. , Banfield Jillian F. , Garavito R. Michael , Carr Kevin , Wilkerson Curtis , Rensing Stefan A. , Gagneul David , Dickenson Nicholas E. , Oesterhelt Christine , Lercher Martin J. , Weber Andreas P. M.
Published: March 2013

Hot, Toxic Eukaryote

Unusually, the single-celled eukaryote red alga,
Galdieria sulphuraria
, can thrive in hot, acidic springs. This organism is endowed with extraordinary metabolic talents and can consume a variety of strange carbohydrates, as well as turn on photosynthesis when the food runs out.

Schönknecht
et al.

(p.
1207
; see the Perspective by
Rocha
) discerned from phylogenetic analysis of its genome that during its evolution,
G. sulphuraria
appears to have commandeered at least 75 bacterial and archaeal genes by horizontal gene transfer and then applied gene expansion to boost its metabolic repertoire.
With a Little Help from Prokaryotes
Authors: Rocha Eduardo P. C.
Published: March 2013

Red algae can adapt to extreme conditions through horizontal gene transfer from free-living prokaryotic extremophiles.

[Also see Report by

Schönknecht
et al.

]
Business as Usual—or Not?
2052
A Global Forecast for the Next Forty Years

by Jorgen Randers

Chelsea Green, White River Junction, VT, 2012. 414 pp. $34.95. ISBN 9781603584678. Paper, $24.95. ISBN 9781603584210.
Authors: Horn Robert E.
Published: March 2013

Tapping his own work on sustainable futures and predictions from a range of other researchers and thinkers, Randers sketches the world that he believes we will most likely find ourselves in 40 years on.
Guilty by Association
Authors: Joshi Nikhil S. , Jacks Tyler
Published: March 2013

Fingerprinting regulatory T cells in tumors reveals that they are specific for organ-expressed antigens.

[Also see Report by

Malchow
et al.

]
A Sea Change for U.S. Oceanography
Authors: Kintisch Eli
Published: March 2013

Marine scientists are confronting declining budgets and a shrinking research fleet as torrents of data from new technologies remake their field.
The New Generation of Sea Scientist
Authors: Kintisch Eli
Published: March 2013

Time at sea is no longer a mandatory part of oceanographic education.
Ahoy, Telepresence
Authors: Kintisch Eli
Published: March 2013

One way oceanographers are coping with dwindling ship time is by using "telepresence" video technology to connect landlocked scientists with colleagues at sea.
Europe's Science Superwoman Struggles to Get Off the Ground
Authors: Kupferschmidt Kai
Published: March 2013

The first chief science adviser for the European Commission's president speaks her mind and some call her "inspiring," but can she influence policy?
Performance of the GenoType MTBDR
plus
Assay Directly on Sputum Specimens from Brazilian Patients with Tuberculosis Treatment Failure or Relapse
Authors: Maschmann Raquel de Abreu , Sá Spies Fernanda , Nunes Luciana de Souza , Ribeiro Andrezza Wolowski , Machado Taís Raquel Marcon , Zaha Arnaldo , Rossetti Maria Lucia Rosa
Published: March 2013

Rapid identification of drug resistance in clinical isolates of
Mycobacterium tuberculosis
is important in determining treatment for tuberculosis. The aim of this work was evaluate the performance of the GenoType MDRTB
plus
assay directly on sputum of patients who had treatment failure or relapse in a routine outpatient setting in southern Brazil.
Electronic Nose Technology for Detection of Invasive Pulmonary Aspergillosis in Prolonged Chemotherapy-Induced Neutropenia: a Proof-of-Principle Study
Authors: de Heer Koen , van der Schee Marc P. , Zwinderman Koos , van den Berk Inge A. H. , Visser Caroline Elisabeth , van Oers Rien , Sterk Peter J.
Published: March 2013

Although the high mortality rate of pulmonary invasive aspergillosis (IA) in patients with prolonged chemotherapy-induced neutropenia (PCIN) can be reduced by timely diagnosis, a diagnostic test that reliably detects IA at an early stage is lacking. We hypothesized that an electronic nose (eNose) could fulfill this need. An eNose can discriminate various lung diseases through the analysis of exhaled volatile organic compounds (VOCs). An eNose is cheap and noninvasive and yields results within minutes. In a single-center prospective cohort study, we included patients who were treated with chemotherapy expected to result in PCIN. Based on standardized indications, a full diagnostic workup was performed to confirm invasive aspergillosis or to rule it out. Patients with no aspergillosis were considered controls, and patients with probable or proven aspergillosis were considered index cases. Exhaled breath was examined with a Cyranose 320 (Smith Detections, Pasadena, CA). The resulting data were analyzed using principal component reduction. The primary endpoint was cross-validated diagnostic accuracy, defined as the percentage of patients correctly classified using the leave-one-out method. Accuracy was validated by 100,000 random classifications. We included 46 subjects who underwent 16 diagnostic workups, resulting in 6 cases and 5 controls. The cross-validated accuracy of the eNose in diagnosing IA was 90.9% (
P
= 0.022; sensitivity, 100%; specificity, 83.3%). Receiver operating characteristic analysis showed an area under the curve of 0.93. These preliminary data indicate that PCIN patients with IA have a distinct exhaled VOC profile that can be detected with eNose technology. The diagnostic accuracy of the eNose for invasive aspergillosis warrants validation.
Detection of Avian Retroviruses in Vaccines by Amplification on DF-1 Cells with Immunostaining and Fluorescent Product-Enhanced Reverse Transcriptase Endpoint Methods
Authors: Birmingham Cheryl L. , Dupont Dominique , Riou Patrice , Armanet Corinne , Edamura Kerrie Nichol , Martinho Briolange , Serres Aurelie , Jacouton Severine , Detrez Valerie , McNeil Bryan , Schreiber Martha , Gaillac David , Bonnevay Thierry , Gisonni-Lex Lucy , Mallet Laurent
Published: March 2013

In order to ensure the safety of vaccines produced on avian cells, rigorous testing for the absence of avian retroviruses must be performed. Current methods used to detect avian retroviruses often exhibit a high invalid-test/false-positive rate, rely on hard-to-secure reagents, and/or have readouts that are difficult to standardize. Herein, we describe the development and validation of two consistent and sensitive methods for the detection of avian retroviruses in vaccines: viral amplification on DF-1 cells followed by immunostaining for the detection of avian leukosis virus (ALV) and viral amplification on DF-1 cells followed by fluorescent product-enhanced reverse transcriptase (F-PERT) for the detection of all avian retroviruses. Both assays share an infectivity stage on DF-1 cells followed by a different endpoint readout depending on the retrovirus to be detected. Validation studies demonstrated a limit of detection of one 50% cell culture infectious dose (CCID
50
)/ml for retrovirus in a 30-ml test inoculum volume for both methods, which was as sensitive as a classical method used in the vaccine industry, namely, viral amplification on primary chicken embryo fibroblasts followed by the complement fixation test for avian leukosis virus (COFAL). Furthermore, viral amplification on DF-1 cells followed by either immunostaining or F-PERT demonstrated a sensitivity that exceeds the regulatory requirements for detection of ALV strains. A head-to-head comparison of the two endpoint methods showed that viral amplification on DF-1 cells followed by F-PERT is a suitable method to be used as a stand-alone test to ensure that vaccine preparations are free from infectious avian retroviruses.
Use of G-Protein-Coupled and -Uncoupled CCR5 Receptors by CCR5 Inhibitor-Resistant and -Sensitive Human Immunodeficiency Virus Type 1 Variants
Authors: Berro Reem , Yasmeen Anila , Abrol Ravinder , Trzaskowski Bartosz , Abi-Habib Sarya , Grunbeck Amy , Lascano Danny , Goddard William A. , Klasse Per Johan , Sakmar Thomas P. , Moore John P.
Published: March 2013

Small-molecule CCR5 inhibitors such as vicriviroc (VVC) and maraviroc (MVC) are allosteric modulators that impair HIV-1 entry by stabilizing a CCR5 conformation that the virus recognizes inefficiently. Viruses resistant to these compounds are able to bind the inhibitor-CCR5 complex while also interacting with the free coreceptor. CCR5 also interacts intracellularly with G proteins, as part of its signal transduction functions, and this process alters its conformation. Here we investigated whether the action of VVC against inhibitor-sensitive and -resistant viruses is affected by whether or not CCR5 is coupled to G proteins such as Gα
i
. Treating CD4
+
T cells with pertussis toxin to uncouple the Gα
i
subunit from CCR5 increased the potency of VVC against the sensitive viruses and revealed that VVC-resistant viruses use the inhibitor-bound form of Gα
i
-coupled CCR5 more efficiently than they use uncoupled CCR5. Supportive evidence was obtained by expressing a signaling-deficient CCR5 mutant with an impaired ability to bind to G proteins, as well as two constitutively active mutants that activate G proteins in the absence of external stimuli. The implication of these various studies is that the association of intracellular domains of CCR5 with the signaling machinery affects the conformation of the external and transmembrane domains and how they interact with small-molecule inhibitors of HIV-1 entry.
Characterization of Virus-Encoded RNA Interference Suppressors in Caenorhabditis elegans
Authors: Guo Xunyang , Lu Rui
Published: March 2013

In fungi, plants, and invertebrates, antiviral RNA interference (RNAi) directed by virus-derived small interfering RNAs (siRNAs) represents a major antiviral defense that the invading viruses have to overcome in order to establish infection. As a counterdefense mechanism, viruses of these hosts produce diverse classes of proteins capable of suppressing the biogenesis and/or function of viral siRNAs. This RNA-directed viral immunity (RDVI) in the nematode
Caenorhabditis elegans
is known to exhibit some unique features. Currently, little is known about viral suppression of RNAi in
C. elegans
. Here, we show that ectopic expression of the B2 protein encoded by Flock House virus (FHV) suppresses RNAi induced by either long double-stranded RNA (dsRNA) or an FHV-based replicon and facilitates the natural infection of
C. elegans
by Orsay virus but is not active against RNA silencing mediated by microRNAs. We report the development of an assay for the identification of viral suppressor of RNAi (VSR) in
C. elegans
based on the suppression of a viral replicon-triggered RDVI by ectopic expression of candidate proteins. No VSR activity was detected for either of the two Orsay viral proteins proposed previously as VSRs. We detected, among the known heterologous VSRs, VSR activity for B2 of Nodamura virus but not for 2b of tomato aspermy virus, p29 of fungus-infecting hypovirus, or p19 of tomato bushy stunt virus. We further show that, unlike that in plants and insects, FHV B2 suppresses worm RDVI mainly by interfering with the function of virus-derived primary siRNAs.
Human Papillomaviruses Modulate MicroRNA 145 Expression To Directly Control Genome Amplification
Authors: Gunasekharan Vignesh , Laimins Laimonis A.
Published: March 2013

Human papillomaviruses (HPVs) modulate expression of host microRNAs. Our deep-sequencing analysis of organotypic raft cultures identified microRNA 145 (miR-145) as a differentiation-dependent microRNA that has functionally active target sequences in the HPV-31 E1 and E2 open reading frames. Overexpression of miR-145 in HPV-positive cells resulted in reduced genome amplification and late gene expression, along with decreased levels of cellular transcription factor KLF-4. Our studies show that HPV modulates miR-145 expression to control its own life cycle.
Structure of Schmallenberg Orthobunyavirus Nucleoprotein Suggests a Novel Mechanism of Genome Encapsidation
Authors: Dong Haohao , Li Ping , Elliott Richard M. , Dong Changjiang
Published: March 2013

Schmallenberg virus (SBV), a newly emerged orthobunyavirus (family
Bunyaviridae
), has spread rapidly across Europe and has caused congenital abnormalities in the offspring of cattle, sheep, and goats. Like other orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that encodes four structural and two nonstructural proteins. The nucleoprotein (N) encapsidates the three viral genomic RNA segments and plays a crucial role in viral RNA transcription and replication. Here we report the crystal structure of the bacterially expressed SBV nucleoprotein to a 3.06-Å resolution. The protomer is composed of two domains (N-terminal and C-terminal domains) with flexible N-terminal and C-terminal arms. The N protein has a novel fold and forms a central positively charged cleft for genomic RNA binding. The nucleoprotein purified under native conditions forms a tetramer, while the nucleoprotein obtained following denaturation and refolding forms a hexamer. Our structural and functional analyses demonstrate that both N-terminal and C-terminal arms are involved in N-N interaction and oligomerization and play an essential role in viral RNA synthesis, suggesting a novel mechanism for viral RNA encapsidation and transcription.
Characterization of a New World Monopartite Begomovirus Causing Leaf Curl Disease of Tomato in Ecuador and Peru Reveals a New Direction in Geminivirus Evolution
Authors: Melgarejo Tomas A. , Kon Tatsuya , Rojas Maria R. , Paz-Carrasco Lenin , Zerbini F. Murilo , Gilbertson Robert L.
Published: March 2013

All characterized whitefly-transmitted geminiviruses (begomoviruses) with origins in the New World (NW) have bipartite genomes composed of a DNA-A and DNA-B component. Recently, an NW begomovirus lacking a DNA-B component was associated with tomato leaf curl disease (ToLCD) in Peru, and it was named Tomato leaf deformation virus (ToLDeV). Here, we show that isolates of ToLDeV associated with ToLCD in Ecuador and Peru have a single, genetically diverse genomic DNA that is most closely related to DNA-A components of NW bipartite begomoviruses. Agroinoculation of multimeric clones of the genomic DNA of three ToLDeV genotypes (two variants and a strain) resulted in the development of tomato leaf curl symptoms indistinguishable from those of ToLCD in Ecuador and Peru. Biological properties of these ToLDeV genotypes were similar to those of Old World (OW) monopartite tomato-infecting begomoviruses, including lack of sap transmissibility, phloem limitation, a resistance phenotype in tomato germplasm with the
Ty-1
gene, and functional properties of the V1 (capsid protein) and C4 genes. Differences in symptom phenotypes induced by the ToLDeV genotypes in tomato and
Nicotiana benthamiana
plants were associated with a highly divergent left intergenic region and C4 gene. Together, these results establish that ToLDeV is an emergent NW monopartite begomovirus that is causing ToLCD in Ecuador and Peru. This is the first report of an indigenous NW monopartite begomovirus, and evidence is presented that it emerged from the DNA-A component of a NW bipartite progenitor via convergent evolution and recombination.
A Cluster of Virus-Encoded MicroRNAs Accelerates Acute Systemic Epstein-Barr Virus Infection but Does Not Significantly Enhance Virus-Induced Oncogenesis
In Vivo
Authors: Wahl Angela , Linnstaedt Sarah D. , Esoda Caitlin , Krisko John F. , Martinez-Torres Francisco , Delecluse Henri-Jacques , Cullen Bryan R. , Garcia J. Victor
Published: March 2013

Over 90% of the adult human population is chronically infected with the Epstein-Barr virus (EBV), an oncogenic herpesvirus. EBV primarily infects naive human B cells and persists latently in memory B cells. Most individuals experience an asymptomatic infection that is effectively controlled by the adaptive immune response. However, EBV-associated lymphomas can develop in immunocompromised individuals. These tumors typically express all nine EBV latent proteins (latency III). Latency III is also associated with the expression of three precursor microRNAs (miRNAs) located within the EBV BHRF1 gene locus. The role of these BHRF1 miRNAs was unclear until recent
in vitro
studies demonstrated that they cooperate to enhance virus-induced B cell transformation and decrease the antigenic load of virus-infected cells, indicating that the BHRF1 miRNA cluster may serve as a novel therapeutic target for the treatment of latency III EBV-associated malignancies. However, to date, it is not known if BHRF1 miRNAs enhance virus-induced oncogenesis and/or immune evasion of EBV
in vivo
. To understand the
in vivo
contribution of the BHRF1 miRNA cluster to EBV infection and EBV-associated tumorigenesis, we monitored EBV infection and assessed tumor formation in humanized mice exposed to wild-type virus and a viral mutant (Δ123) that lacks all three BHRF1 miRNAs. Our results demonstrate that while the BHRF1 miRNAs facilitate the development of acute systemic EBV infection, they do not enhance the overall oncogenic potential of EBV
in vivo
.
Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA
Authors: Kempf Brian J. , Kelly Michelle M. , Springer Courtney L. , Peersen Olve B. , Barton David J.
Published: March 2013

Picornaviruses have 3′ polyadenylated RNA genomes, but the mechanisms by which these genomes are polyadenylated during viral replication remain obscure. Based on prior studies, we proposed a model wherein the poliovirus RNA-dependent RNA polymerase (3D
pol
) uses a reiterative transcription mechanism while replicating the poly(A) and poly(U) portions of viral RNA templates. To further test this model, we examined whether mutations in 3D
pol
influenced the polyadenylation of virion RNA. We identified nine alanine substitution mutations in 3D
pol
that resulted in shorter or longer 3′ poly(A) tails in virion RNA. These mutations could disrupt structural features of 3D
pol
required for the recruitment of a cellular poly(A) polymerase; however, the structural orientation of these residues suggests a direct role of 3D
pol
in the polyadenylation of RNA genomes. Reaction mixtures containing purified 3D
pol
and a template RNA with a defined poly(U) sequence provided data consistent with a template-dependent reiterative transcription mechanism for polyadenylation. The phylogenetically conserved structural features of 3D
pol
involved in the polyadenylation of virion RNA include a thumb domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysine and arginine residues that interact with the phosphates of both the RNA template and product strands.
Human MicroRNA hsa-miR-296-5p Suppresses Enterovirus 71 Replication by Targeting the Viral Genome
Authors: Zheng Zhenhua , Ke Xianliang , Wang Meng , He Siyi , Li Qian , Zheng Caishang , Zhang Zhenfeng , Liu Yan , Wang Hanzhong
Published: March 2013

Enterovirus 71 (EV71) has emerged as a major cause of neurological disease following the near eradication of poliovirus. Accumulating evidence suggests that mammalian microRNAs (miRNAs), a class of noncoding RNAs of 18 to 23 nucleotides (nt) with important regulatory roles in many cellular processes, participate in host antiviral defenses. However, the roles of miRNAs in EV71 infection and pathogenesis are still unclear. Here, hsa-miR-296-5p expression was significantly increased in EV71-infected human cells. As determined by virus titration, quantitative real-time PCR (qRT-PCR), and Western blotting, overexpression of hsa-miR-296-5p inhibited, while inhibition of endogenous hsa-miR-296-5p facilitated, EV71 infection. Additionally, two potential hsa-miR-296-5p targets (nt 2115 to 2135 and nt 2896 to 2920) located in the EV71 genome (strain BrCr) were bioinformatically predicted and validated by luciferase reporter assays and Western blotting. Genomic alignment of various EV71 strains revealed synonymous mutations in hsa-miR-296-5p target sequences. Furthermore, the introduction of synonymous mutations into the EV71 BrCr genome by site-directed mutagenesis impaired the viral inhibitory effects of hsa-miR-296-5p and facilitated mutant virus infection. Meanwhile, compensatory mutations in corresponding hsa-miR-296-5p target sequences of the EV71 HeN strain (GenBank accession number
JN256064
) restored the inhibitory effects of the miRNA. These results indicate that hsa-miR-296-5p inhibits EV71 replication by targeting the viral genome. Our findings support the notion that cellular miRNAs can inhibit virus infection and that the virus mutates to escape suppression by cellular miRNAs.
Venezuelan Equine Encephalitis Replicon Particles Can Induce Rapid Protection against Foot-and-Mouth Disease Virus
Authors: Diaz-San Segundo Fayna , Dias Camila C. A. , Moraes Mauro P. , Weiss Marcelo , Perez-Martin Eva , Owens Gary , Custer Max , Kamrud Kurt , de los Santos Teresa , Grubman Marvin J.
Published: March 2013

We have previously shown that delivery of the porcine type I interferon gene (poIFN-α/β) with a replication-defective human adenovirus vector (adenovirus 5 [Ad5]) can sterilely protect swine challenged with foot-and-mouth disease virus (FMDV) 1 day later. However, the need of relatively high doses of Ad5 limits the applicability of such a control strategy in the livestock industry. Venezuelan equine encephalitis virus (VEE) empty replicon particles (VRPs) can induce rapid protection of mice against either homologous or, in some cases, heterologous virus challenge. As an alternative approach to induce rapid protection against FMDV, we have examined the ability of VRPs containing either the gene for green fluorescent protein (VRP-GFP) or poIFN-α (VRP-poIFN-α) to block FMDV replicationin vitroandin vivo. Pretreatment of swine or bovine cell lines with either VRP significantly inhibited subsequent infection with FMDV as early as 6 h after treatment and for at least 120 h posttreatment. Furthermore, mice pretreated with either 107or 108infectious units of VRP-GFP and challenged with a lethal dose of FMDV 24 h later were protected from death. Protection was induced as early as 6 h after treatment and lasted for at least 48 h and correlated with induction of an antiviral response and production of IFN-α. By 6 h after treatment several genes were upregulated, and the number of genes and the level of induction increased at 24 h. Finally, we demonstrated that the chemokine IP-10, which is induced by IFN-α and VRP-GFP, is directly involved in protection against FMDV.
Non-syndromic multiple supernumerary teeth: report of a case with 13 supplemental teeth
Authors: Ansari Afroz Alam , Malhotra Seema , Pandey Ramesh Kumar , Bharti Kusum
Published: March 2013

The presence of supernumerary teeth (STs) may give rise to a variety of clinical problems. These include failure of a tooth to erupt, delayed eruption, ectopic eruption, diastema, rotation of adjacent teeth, displacement of teeth and crowding. This case describes a 14-year-old male patient who presented with the complaint of pain in the left mandibular posterior region. Intraoral examination revealed the presence of carious retained deciduous second molar in this region. An orthopantomogram was advised which ‘initially’ revealed 11 STs, positioned in all four quadrants in posterior regions. Two more STs were detected in the following investigations totalling 13. Dental literature rarely reports presence of STs in such a large number. The objective of this case is to report detection of STs, radiographic examination, extraction of the retained deciduous molars and STs in the mandible to facilitate eruption of mandibular premolars.
Selective decontamination of the digestive tract and selective oropharyngeal decontamination in intensive care unit patients: a cost-effectiveness analysis
Authors: Oostdijk Evelien A N , de Wit G A , Bakker Marina , de Smet Anne Marie G A , Bonten M J M
Published: March 2013

Objective

To determine costs and effects of selective digestive tract decontamination (SDD) and selective oropharyngeal decontamination (SOD) as compared with standard care (ie, no SDD/SOD (SC)) from a healthcare perspective in Dutch Intensive Care Units (ICUs).

Design

A post hoc analysis of a previously performed cluster-randomised trial (NEJM2009;360:20).

Setting

13 Dutch ICUs.

Participants

Patients with ICU-stay of >48 h that received SDD (n=2045), SOD (n=1904) or SC (n=1990).

Interventions

SDD or SOD.

Primary and secondary outcome measures

Effects were based on hospital survival, expressed as crude Life Years Gained (cLYG). The incremental cost-effectiveness ratio (ICER) was calculated, with corresponding cost acceptability curves. Sensitivity analyses were performed for discount rates, costs of SDD, SOD and mechanical ventilation.

Results

Total costs per patient were €41 941 for SC (95% CI €40 184 to €43 698), €40 433 for SOD (95% CI €38 838 to €42 029) and €41 183 for SOD (95% CI €39 408 to €42 958). SOD and SDD resulted in crude LYG of +0.04 and +0.25, respectively, as compared with SC, implying that both SDD and SOD are dominant (ie, cheaper and more beneficial) over SC. In cost-effectiveness acceptability curves probabilities for cost-effectiveness, compared with standard care, ranged from 89% to 93% for SOD and from 63% to 72% for SDD, for acceptable costs for 1 LYG ranging from €0 to €20 000. Sensitivity analysis for mechanical ventilation and discount rates did not change interpretation. Yet, if costs of the topical component of SDD and SOD would increase 40-fold to €400/day and €40/day (maximum values based on free market prices in 2012), the estimated ICER as compared with SC for SDD would be €21 590 per LYG. SOD would remain cost-saving.

Conclusions

SDD and SOD were both effective and cost-saving in Dutch ICUs.
Medical students' subjective ratings of stress levels and awareness of student support services about mental health
Authors: Walter Garry , Soh Nerissa Li-Wey , Norgren Jaconelli Sanna , Lampe Lisa , Malhi Gin S , Hunt Glenn
Published: March 2013

Purpose

To descriptively assess medical students' concerns for their mental and emotional state, perceived need to conceal mental problems, perceived level of support at university, knowledge and use of student support services, and experience of stresses of daily life.

Study design

From March to September 2011, medical students at an Australian university were invited to complete an anonymous online survey.

Results

475 responses were received. Students rated study and examinations (48.9%), financial concerns (38.1%), isolation (19.4%) and relationship concerns (19.2%) as very or extremely stressful issues. Knowledge of available support services was high, with 90.8% indicating they were aware of the university's medical centre. Treatment rates were modest (31.7%). Students' concerns about their mental state were generally low, but one in five strongly felt they needed to conceal their emotional problems.

Conclusions

Despite widespread awareness of appropriate support services, a large proportion of students felt they needed to conceal mental and emotional problems. Overall treatment rates for students who were greatly concerned about their mental and emotional state appeared modest, and, although comparable with those of similarly aged community populations, may reflect undertreatment. It would be appropriate for universities to address stressors identified by students. Strategies for encouraging distressed students to obtain appropriate assessment and treatment should also be explored. Those students who do seek healthcare are most likely to see a primary care physician, suggesting an important screening role for these health professionals.
ON OSCILLATORS IN PHYLLOSILICATE EXCITABLE AUTOMATA
Authors: ADAMATZKY ANDREW
Published: March 2013

Phyllosilicate is a sheet of silicate tetrahedra bound by basal oxygens. A phyllosilicate excitable automaton is a regular network of finite state machines, which mimics structure of a silicate sheet. A node of the silicate sheet is an automaton, which takes resting, excited and refractory states, and updates its state in discrete time depending on a sum of excited states of its three (silicon automata) or six (oxygen automata) closest neighbors. Oscillator is a localized compact configuration of nonquiescent states which undergoes finite growth and modification but returns to its original state in a finite number of steps. We show that phyllosilicate excitable automata exhibit waves and oscillating localizations (oscillators) dynamics. Basic types of oscillators are classified and characterized.
HARMONIC FUNCTIONS AND THE SPECTRUM OF THE LAPLACIAN ON THE SIERPINSKI CARPET
Authors: BEGUÉ MATTHEW , KALLONIATIS TRISTAN , STRICHARTZ ROBERT S.
Published: March 2013

Kusuoka and Zhou have defined the Laplacian on the Sierpinski carpet using average values of functions on small cells and the graph structure of cell adjacency. We have implemented an algorithm that uses their method to approximate solutions to boundary value problems. As a result we have a wealth of data concerning harmonic functions with prescribed boundary values, and eigenfunctions of the Laplacian with either Neumann or Dirichlet boundary conditions. We will present some of this data and discuss some ideas for defining normal derivatives on the boundary of the carpet.
ADAPTIVE TRIGONOMETRIC HERMITE WAVELET FINITE ELEMENT METHOD FOR STRUCTURAL ANALYSIS
Authors: HE WEN-YU , REN WEI-XIN
Published: March 2013

Owing to its good approximation characteristics of trigonometric functions and the multi-resolution local characteristics of wavelet, the trigonometric Hermite wavelet function is used as the element interpolation function. The corresponding trigonometric wavelet beam element is formulated based on the principle of minimum potential energy. As the order of wavelet can be enhanced easily and the multi-resolution can be achieved by the multi-scale of wavelet, the hierarchical and multi-resolution trigonometric wavelet beam element methods are proposed for the adaptive analysis. Numerical examples have demonstrated that the aforementioned two methods are effective in improving the computational accuracy. The trigonometric wavelet finite element method (WFEM) proposed herein provides an alternative approach for improving the computational accuracy, which can be tailored for the problem considered.
COMMUNITY STRUCTURE DETECTION IN THE EVOLUTION OF THE UNITED STATES AIRPORT NETWORK
Authors: GEGOV EMIL , POSTORINO M. NADIA , ATHERTON MARK , GOBET FERNAND
Published: March 2013

This paper investigates community structure in the US Airport Network as it evolved from 1990 to 2010 by looking at six bi-monthly intervals in 1990, 2000 and 2010, using data obtained from the Bureau of Transportation Statistics of the US Department of Transport. The data contained monthly records of origin–destination pairs of domestic airports and the number of passengers carried. The topological properties and the volume of people traveling are both studied in detail, revealing high heterogeneity in space and time. A recently developed community structure detection method, accounting for the spatial nature of these networks, is applied and reveals a picture of the communities within. The patterns of communities plotted for each bi-monthly interval reveal some interesting seasonal variations of passenger flows and airport clusters that do not occupy a single US region. The long-term evolution of the network between those years is explored and found to have consistently improved its stability. The more recent structure of the network (2010) is compared with migration patterns among the four US macro-regions (West, Midwest, Northeast and South) in order to identify possible relationships and the results highlight a clear overlap between US domestic air travel and migration.
DEPENDENCE OF ORGANIC/INORGANIC PHOTOVOLTAIC DEVICE PERFORMANCE ON PRECURSOR'S CONCENTRATION USED FOR ELECTROSPUN TiO2 NANOFIBERS
Authors: TANVEER MUHAMMAD , HABIB AMIR , KHAN MUHAMMAD BILAL
Published: March 2013

Electrospun TiO2 nanofibers were synthesized by optimizing various electrospinning conditions. The effect of the precursor's concentration present in sol used for electrospinning was studied for the performance of hybrid photovoltaic devices. The synthesized nanofibers were characterized by XRD and UV-Vis absorption spectroscopy and morphology of the fibers were investigated by FE-SEM. The surface of fibers was modified, and these modified fibers were applied to P3HT/ TiO2 / N719 composite nanofibers photovoltaic devices. The device performance was investigated by analysis of the incident photon to current conversion efficiency and a J– V characteristic under 1. 5G illuminations, which show that efficiency of the devices, can be improved from 0.13% to 0.83% by introducing TiO2 nanofibers synthesized by optimum precursor's concentration.
Genetic and Phenotypic Characteristics of Baker's Yeast: Relevance to Baking
Authors: Randez-Gil Francisca , Córcoles-Sáez Isaac , Prieto José A.
Published: March 2013

Yeasts rarely encounter ideal physiological conditions during their industrial life span; therefore, their ability to adapt to changing conditions determines their usefulness and applicability. This is especially true for baking strains of Saccharomyces cerevisiae. The success of this yeast in the ancient art of bread making is based on its capacity to rapidly transform carbohydrates into CO2 rather than its unusual resistance to environmental stresses. Moreover, baker's yeast must exhibit efficient respiratory metabolism during yeast manufacturing, which determines biomass yield. However, optimal growth conditions often have negative consequences in other commercially important aspects, such as fermentative power or stress tolerance. This article reviews the genetic and physiological characteristics of baking yeast strains, emphasizing the activation of regulatory mechanisms in response to carbon source and stress signaling and their importance in defining targets for strain selection and improvement.
Impacts of Preharvest Factors During Kernel Development on Rice Quality and Functionality
Authors: Siebenmorgen Terry J. , Grigg Brandon C. , Lanning Sarah B.
Published: March 2013

Rice quality and functionality are characterized in many ways, depending largely on the industry segment using the rice. These characteristics include appearance, milling, and cooking parameters. Recently, variable quality of rice grown in the United States has been reported, but the cause was not well documented. Agronomic impacts include planting time, irrigation and fertility, cultivar selection, and harvest conditions. However, recent research suggests that ambient air temperature, specifically elevated nighttime air temperature (NTAT) during grain filling, dramatically affects the variability of rice milling quality, in terms of milled- and head-rice yields; appearance, in terms of chalkiness; and functional characteristics, including viscosity profiles, gelatinization temperatures, and proximate concentrations. Future research is needed to develop cultivars that are resistant to stress resulting from elevated NTAT during the critical period of grain filling, and, for the near term, to develop altered production management practices that mitigate elevated-temperature stress.
A New Generation of Food-Borne Pathogen Detection Based on Ribosomal RNA
Authors: Livezey Kristin , Kaplan Shannon , Wisniewski Michele , Becker Michael M.
Published: March 2013

Listeria and Salmonella detection assays for food and environmental surfaces that target ribosomal RNA (rRNA) have been developed. The large number of rRNA molecules in bacteria enabled the development of molecular assays that use enrichment times as short as 12 hours for Salmonella and 24 hours for Listeria. These assays run on a fully automated molecular pathogen detection system, which provides walk-away capability and produces 300 assay results in eight hours.
Cold stress and the cold pressor test
Authors: Silverthorn Dee U. , Michael Joel
Published: March 2013

Temperature and other environmental stressors are known to affect blood pressure and heart rate. In this activity, students perform the cold pressor test, demonstrating increased blood pressure during a 1- to 2-min immersion of one hand in ice water. The cold pressor test is used clinically to evaluate autonomic and left ventricular function. This activity is easily adapted to an inquiry format that asks students to go to the scientific literature to learn about the test and then design a protocol for carrying out the test in classmates. The data collected are ideal for teaching graphical presentation of data and statistical analysis.
Combination of didactic lectures and review sessions in endocrinology leads to improvement in student performance as measured by assessments
Authors: Qureshi Ayisha , Cozine Cassy , Rizvi Farwa
Published: March 2013

There can be no single best way of learning, and each teaching mode has its own merits and demerits. Didactic lectures in and of themselves are insufficient, whereas a problem-based tutorial alone can be as ineffective. This study was conducted to determine if a problem-based review after didactic lectures would lead to better student performance. To compare performance, the same student group was taught three units of endocrinology (growth hormone, thyroid hormone, and diabetes). Students were divided into the following three groups: diabetes didactic lectures only, growth hormone didactic lectures plus review, and thyroid hormone didactic lectures plus review. All three topics were covered in the didactic lectures, but only growth hormone and thyroid hormone topics were covered in the review session. At the end of the course, all students were given formative assessments in the form of multiple-choice questions. A highly significant increase ( P < 0.000) in the percentage of correct responses on the questions covering growth hormone (mean: 0.838, SD: 0.158) and thyroid hormone (mean: 0.686, SD: 0.232) compared with diabetes (mean: 0.478, SD: 0.259) was observed. In conclusion, this study provides further evidence that the combination of didactic lectures and an active review session leads to an improvement in student performance.